diff --git a/nipype/algorithms/tests/test_auto_ACompCor.py b/nipype/algorithms/tests/test_auto_ACompCor.py index 5c44844cf9..a266d57ddb 100644 --- a/nipype/algorithms/tests/test_auto_ACompCor.py +++ b/nipype/algorithms/tests/test_auto_ACompCor.py @@ -9,7 +9,8 @@ def test_ACompCor_inputs(): header_prefix=dict(), high_pass_cutoff=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ignore_initial_volumes=dict(usedefault=True, diff --git a/nipype/algorithms/tests/test_auto_AddCSVRow.py b/nipype/algorithms/tests/test_auto_AddCSVRow.py index f38319040b..31cc6f7a09 100644 --- a/nipype/algorithms/tests/test_auto_AddCSVRow.py +++ b/nipype/algorithms/tests/test_auto_AddCSVRow.py @@ -6,7 +6,8 @@ def test_AddCSVRow_inputs(): input_map = dict(_outputs=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_ArtifactDetect.py b/nipype/algorithms/tests/test_auto_ArtifactDetect.py index 054bc1da99..196d297847 100644 --- a/nipype/algorithms/tests/test_auto_ArtifactDetect.py +++ b/nipype/algorithms/tests/test_auto_ArtifactDetect.py @@ -8,7 +8,8 @@ def test_ArtifactDetect_inputs(): ), global_threshold=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), intersect_mask=dict(), diff --git a/nipype/algorithms/tests/test_auto_CalculateMedian.py b/nipype/algorithms/tests/test_auto_CalculateMedian.py index 88888d5bbe..77784f1bc9 100644 --- a/nipype/algorithms/tests/test_auto_CalculateMedian.py +++ b/nipype/algorithms/tests/test_auto_CalculateMedian.py @@ -4,7 +4,8 @@ def test_CalculateMedian_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(), diff --git a/nipype/algorithms/tests/test_auto_ComputeDVARS.py b/nipype/algorithms/tests/test_auto_ComputeDVARS.py index 7c59f851d1..81aa16dde4 100644 --- a/nipype/algorithms/tests/test_auto_ComputeDVARS.py +++ b/nipype/algorithms/tests/test_auto_ComputeDVARS.py @@ -10,7 +10,8 @@ def test_ComputeDVARS_inputs(): ), figsize=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py index 61f64de033..e6cda0e7d7 100644 --- a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py +++ b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py @@ -4,7 +4,8 @@ def test_ComputeMeshWarp_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), metric=dict(usedefault=True, diff --git a/nipype/algorithms/tests/test_auto_CreateNifti.py b/nipype/algorithms/tests/test_auto_CreateNifti.py index 3e365b8894..0d74e283fe 100644 --- a/nipype/algorithms/tests/test_auto_CreateNifti.py +++ b/nipype/algorithms/tests/test_auto_CreateNifti.py @@ -9,7 +9,8 @@ def test_CreateNifti_inputs(): ), header_file=dict(mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ) diff --git a/nipype/algorithms/tests/test_auto_Distance.py b/nipype/algorithms/tests/test_auto_Distance.py index 5cf8c425c8..713221c14a 100644 --- a/nipype/algorithms/tests/test_auto_Distance.py +++ b/nipype/algorithms/tests/test_auto_Distance.py @@ -4,7 +4,8 @@ def test_Distance_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mask_volume=dict(), diff --git a/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py b/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py index e230992eec..cb56b470a4 100644 --- a/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py +++ b/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py @@ -8,7 +8,8 @@ def test_FramewiseDisplacement_inputs(): ), figsize=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py index 764d821bc6..726b3bec5b 100644 --- a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py +++ b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py @@ -4,7 +4,8 @@ def test_FuzzyOverlap_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_ref=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_Gunzip.py b/nipype/algorithms/tests/test_auto_Gunzip.py index 6b06654f1d..43f74364c5 100644 --- a/nipype/algorithms/tests/test_auto_Gunzip.py +++ b/nipype/algorithms/tests/test_auto_Gunzip.py @@ -4,7 +4,8 @@ def test_Gunzip_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_ICC.py b/nipype/algorithms/tests/test_auto_ICC.py index da3110fd76..ec2a37baa6 100644 --- a/nipype/algorithms/tests/test_auto_ICC.py +++ b/nipype/algorithms/tests/test_auto_ICC.py @@ -4,7 +4,8 @@ def test_ICC_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mask=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py index 3c6077922b..c19a4a7506 100644 --- a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py +++ b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py @@ -5,7 +5,8 @@ def test_MeshWarpMaths_inputs(): input_map = dict(float_trait=dict(), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_surf=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_ModifyAffine.py b/nipype/algorithms/tests/test_auto_ModifyAffine.py index c7b4b25d0c..a9c7fe1b49 100644 --- a/nipype/algorithms/tests/test_auto_ModifyAffine.py +++ b/nipype/algorithms/tests/test_auto_ModifyAffine.py @@ -4,7 +4,8 @@ def test_ModifyAffine_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), transformation_matrix=dict(usedefault=True, diff --git a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py index 7b12363ee8..6d3fe0c879 100644 --- a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py +++ b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py @@ -4,7 +4,8 @@ def test_NonSteadyStateDetector_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_P2PDistance.py b/nipype/algorithms/tests/test_auto_P2PDistance.py index 59c749da30..a1ddcd56c0 100644 --- a/nipype/algorithms/tests/test_auto_P2PDistance.py +++ b/nipype/algorithms/tests/test_auto_P2PDistance.py @@ -4,7 +4,8 @@ def test_P2PDistance_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), metric=dict(usedefault=True, diff --git a/nipype/algorithms/tests/test_auto_PickAtlas.py b/nipype/algorithms/tests/test_auto_PickAtlas.py index 990b71e289..11b84f8e8a 100644 --- a/nipype/algorithms/tests/test_auto_PickAtlas.py +++ b/nipype/algorithms/tests/test_auto_PickAtlas.py @@ -10,7 +10,8 @@ def test_PickAtlas_inputs(): ), hemi=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), labels=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_Similarity.py b/nipype/algorithms/tests/test_auto_Similarity.py index 4dce363864..6b90321975 100644 --- a/nipype/algorithms/tests/test_auto_Similarity.py +++ b/nipype/algorithms/tests/test_auto_Similarity.py @@ -4,7 +4,8 @@ def test_Similarity_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mask1=dict(), diff --git a/nipype/algorithms/tests/test_auto_SimpleThreshold.py b/nipype/algorithms/tests/test_auto_SimpleThreshold.py index 0031f4bb7f..8d4993425e 100644 --- a/nipype/algorithms/tests/test_auto_SimpleThreshold.py +++ b/nipype/algorithms/tests/test_auto_SimpleThreshold.py @@ -4,7 +4,8 @@ def test_SimpleThreshold_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), threshold=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_SpecifyModel.py b/nipype/algorithms/tests/test_auto_SpecifyModel.py index 33d5435b5f..11af243c11 100644 --- a/nipype/algorithms/tests/test_auto_SpecifyModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifyModel.py @@ -12,7 +12,8 @@ def test_SpecifyModel_inputs(): ), high_pass_filter_cutoff=dict(mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_units=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_SpecifySPMModel.py b/nipype/algorithms/tests/test_auto_SpecifySPMModel.py index 7a33ac63c4..bea8ee473e 100644 --- a/nipype/algorithms/tests/test_auto_SpecifySPMModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifySPMModel.py @@ -14,7 +14,8 @@ def test_SpecifySPMModel_inputs(): ), high_pass_filter_cutoff=dict(mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_units=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py index 4caf1c1033..c8e07a292b 100644 --- a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py @@ -12,7 +12,8 @@ def test_SpecifySparseModel_inputs(): ), high_pass_filter_cutoff=dict(mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_units=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py index 95581bb111..169dcf6d80 100644 --- a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py +++ b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py @@ -6,7 +6,8 @@ def test_StimulusCorrelation_inputs(): input_map = dict(concatenated_design=dict(mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), intensity_values=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_TCompCor.py b/nipype/algorithms/tests/test_auto_TCompCor.py index b39c946d9d..8f9585f26b 100644 --- a/nipype/algorithms/tests/test_auto_TCompCor.py +++ b/nipype/algorithms/tests/test_auto_TCompCor.py @@ -9,7 +9,8 @@ def test_TCompCor_inputs(): header_prefix=dict(), high_pass_cutoff=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ignore_initial_volumes=dict(usedefault=True, diff --git a/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py b/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py index d6e38722fe..14e20fd36a 100644 --- a/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py +++ b/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py @@ -4,7 +4,8 @@ def test_TVTKBaseInterface_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ) diff --git a/nipype/algorithms/tests/test_auto_WarpPoints.py b/nipype/algorithms/tests/test_auto_WarpPoints.py index ab59d22cff..d866214fec 100644 --- a/nipype/algorithms/tests/test_auto_WarpPoints.py +++ b/nipype/algorithms/tests/test_auto_WarpPoints.py @@ -4,7 +4,8 @@ def test_WarpPoints_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), interp=dict(mandatory=True, diff --git a/nipype/interfaces/afni/tests/test_auto_ABoverlap.py b/nipype/interfaces/afni/tests/test_auto_ABoverlap.py index 9c2d2f0cc3..9baf98d246 100644 --- a/nipype/interfaces/afni/tests/test_auto_ABoverlap.py +++ b/nipype/interfaces/afni/tests/test_auto_ABoverlap.py @@ -9,7 +9,8 @@ def test_ABoverlap_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file_a=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py index 2a8f66de41..0f670fa2f4 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py @@ -9,7 +9,8 @@ def test_AFNICommand_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), num_threads=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py b/nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py index 6d848cedd0..8ab19a670a 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py @@ -9,7 +9,8 @@ def test_AFNICommandBase_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), terminal_output=dict(deprecated='1.0.0', diff --git a/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py b/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py index bab1a3e829..664237b4d7 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py @@ -9,7 +9,8 @@ def test_AFNIPythonCommand_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), num_threads=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py index 63bdebab28..e01cc9dd28 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py @@ -11,7 +11,8 @@ def test_AFNItoNIFTI_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py b/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py index b18e056d75..adf8750b1c 100644 --- a/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py +++ b/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py @@ -22,7 +22,8 @@ def test_AlignEpiAnatPy_inputs(): ), epi_strip=dict(argstr='-epi_strip %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-epi %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Allineate.py b/nipype/interfaces/afni/tests/test_auto_Allineate.py index 5c4a916228..b8b79df004 100644 --- a/nipype/interfaces/afni/tests/test_auto_Allineate.py +++ b/nipype/interfaces/afni/tests/test_auto_Allineate.py @@ -33,7 +33,8 @@ def test_Allineate_inputs(): ), fine_blur=dict(argstr='-fineblur %f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-source %s', diff --git a/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py b/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py index 90f70ecfa4..cc87a813b3 100644 --- a/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py +++ b/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py @@ -12,7 +12,8 @@ def test_AutoTLRC_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-input %s', diff --git a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py index 54964487a8..dab38ec832 100644 --- a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py @@ -11,7 +11,8 @@ def test_AutoTcorrelate_inputs(): ), eta2=dict(argstr='-eta2', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Autobox.py b/nipype/interfaces/afni/tests/test_auto_Autobox.py index 83fd613606..968bcf5839 100644 --- a/nipype/interfaces/afni/tests/test_auto_Autobox.py +++ b/nipype/interfaces/afni/tests/test_auto_Autobox.py @@ -9,7 +9,8 @@ def test_Autobox_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-input %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Automask.py b/nipype/interfaces/afni/tests/test_auto_Automask.py index a31cc87cd9..afc4c7dad5 100644 --- a/nipype/interfaces/afni/tests/test_auto_Automask.py +++ b/nipype/interfaces/afni/tests/test_auto_Automask.py @@ -19,7 +19,8 @@ def test_Automask_inputs(): ), erode=dict(argstr='-erode %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Axialize.py b/nipype/interfaces/afni/tests/test_auto_Axialize.py index 93869e283e..2b8f1a76be 100644 --- a/nipype/interfaces/afni/tests/test_auto_Axialize.py +++ b/nipype/interfaces/afni/tests/test_auto_Axialize.py @@ -15,7 +15,8 @@ def test_Axialize_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Bandpass.py b/nipype/interfaces/afni/tests/test_auto_Bandpass.py index 5f5cffcabe..289c5abe4f 100644 --- a/nipype/interfaces/afni/tests/test_auto_Bandpass.py +++ b/nipype/interfaces/afni/tests/test_auto_Bandpass.py @@ -19,7 +19,8 @@ def test_Bandpass_inputs(): mandatory=True, position=-3, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py index 43338e43d9..1311e237cf 100644 --- a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py +++ b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py @@ -16,7 +16,8 @@ def test_BlurInMask_inputs(): fwhm=dict(argstr='-FWHM %f', mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-input %s', diff --git a/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py b/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py index 7ebd52778a..5b5c2a34b9 100644 --- a/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py +++ b/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py @@ -17,7 +17,8 @@ def test_BlurToFWHM_inputs(): ), fwhmxy=dict(argstr='-FWHMxy %f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-input %s', diff --git a/nipype/interfaces/afni/tests/test_auto_BrickStat.py b/nipype/interfaces/afni/tests/test_auto_BrickStat.py index f1ccb2fe55..55abae4c6d 100644 --- a/nipype/interfaces/afni/tests/test_auto_BrickStat.py +++ b/nipype/interfaces/afni/tests/test_auto_BrickStat.py @@ -9,7 +9,8 @@ def test_BrickStat_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Bucket.py b/nipype/interfaces/afni/tests/test_auto_Bucket.py index 879e91f02f..63ebbc6d5c 100644 --- a/nipype/interfaces/afni/tests/test_auto_Bucket.py +++ b/nipype/interfaces/afni/tests/test_auto_Bucket.py @@ -9,7 +9,8 @@ def test_Bucket_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Calc.py b/nipype/interfaces/afni/tests/test_auto_Calc.py index d352adb704..09fd99c753 100644 --- a/nipype/interfaces/afni/tests/test_auto_Calc.py +++ b/nipype/interfaces/afni/tests/test_auto_Calc.py @@ -13,7 +13,8 @@ def test_Calc_inputs(): mandatory=True, position=3, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file_a=dict(argstr='-a %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Cat.py b/nipype/interfaces/afni/tests/test_auto_Cat.py index e4beca3454..857c9ade60 100644 --- a/nipype/interfaces/afni/tests/test_auto_Cat.py +++ b/nipype/interfaces/afni/tests/test_auto_Cat.py @@ -9,7 +9,8 @@ def test_Cat_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_CatMatvec.py b/nipype/interfaces/afni/tests/test_auto_CatMatvec.py index 3782a3a37d..e94fa12df3 100644 --- a/nipype/interfaces/afni/tests/test_auto_CatMatvec.py +++ b/nipype/interfaces/afni/tests/test_auto_CatMatvec.py @@ -13,7 +13,8 @@ def test_CatMatvec_inputs(): descr='Output matrix in augmented form (last row is 0 0 0 1)This option does not work with -MATRIX or -ONELINE', xor=['matrix', 'oneline'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_CenterMass.py b/nipype/interfaces/afni/tests/test_auto_CenterMass.py index c64c4e8b36..34d6d5ec2f 100644 --- a/nipype/interfaces/afni/tests/test_auto_CenterMass.py +++ b/nipype/interfaces/afni/tests/test_auto_CenterMass.py @@ -21,7 +21,8 @@ def test_CenterMass_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_ClipLevel.py b/nipype/interfaces/afni/tests/test_auto_ClipLevel.py index 0843c0e67e..815d8530ce 100644 --- a/nipype/interfaces/afni/tests/test_auto_ClipLevel.py +++ b/nipype/interfaces/afni/tests/test_auto_ClipLevel.py @@ -17,7 +17,8 @@ def test_ClipLevel_inputs(): position=3, xor='doall', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Copy.py b/nipype/interfaces/afni/tests/test_auto_Copy.py index 046f9d87c2..0917a0628e 100644 --- a/nipype/interfaces/afni/tests/test_auto_Copy.py +++ b/nipype/interfaces/afni/tests/test_auto_Copy.py @@ -9,7 +9,8 @@ def test_Copy_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Deconvolve.py b/nipype/interfaces/afni/tests/test_auto_Deconvolve.py index 5c8878b5ed..972b9a0128 100644 --- a/nipype/interfaces/afni/tests/test_auto_Deconvolve.py +++ b/nipype/interfaces/afni/tests/test_auto_Deconvolve.py @@ -41,7 +41,8 @@ def test_Deconvolve_inputs(): ), goforit=dict(argstr='-GOFORIT %i', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='-input %s', diff --git a/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py b/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py index d820239d6b..a9b41f29ad 100644 --- a/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py +++ b/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py @@ -13,7 +13,8 @@ def test_DegreeCentrality_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Despike.py b/nipype/interfaces/afni/tests/test_auto_Despike.py index 268d76b55a..21891fb546 100644 --- a/nipype/interfaces/afni/tests/test_auto_Despike.py +++ b/nipype/interfaces/afni/tests/test_auto_Despike.py @@ -9,7 +9,8 @@ def test_Despike_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Detrend.py b/nipype/interfaces/afni/tests/test_auto_Detrend.py index d3f81979a4..16a1d1fd77 100644 --- a/nipype/interfaces/afni/tests/test_auto_Detrend.py +++ b/nipype/interfaces/afni/tests/test_auto_Detrend.py @@ -9,7 +9,8 @@ def test_Detrend_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Dot.py b/nipype/interfaces/afni/tests/test_auto_Dot.py index a9c5941da5..9042c7a8f7 100644 --- a/nipype/interfaces/afni/tests/test_auto_Dot.py +++ b/nipype/interfaces/afni/tests/test_auto_Dot.py @@ -25,7 +25,8 @@ def test_Dot_inputs(): ), full=dict(argstr='-full', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='%s ...', diff --git a/nipype/interfaces/afni/tests/test_auto_ECM.py b/nipype/interfaces/afni/tests/test_auto_ECM.py index 3d38246a2b..4c923ea494 100644 --- a/nipype/interfaces/afni/tests/test_auto_ECM.py +++ b/nipype/interfaces/afni/tests/test_auto_ECM.py @@ -19,7 +19,8 @@ def test_ECM_inputs(): ), full=dict(argstr='-full', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Edge3.py b/nipype/interfaces/afni/tests/test_auto_Edge3.py index 108ce31912..7889b82551 100644 --- a/nipype/interfaces/afni/tests/test_auto_Edge3.py +++ b/nipype/interfaces/afni/tests/test_auto_Edge3.py @@ -17,7 +17,8 @@ def test_Edge3_inputs(): gscale=dict(argstr='-gscale', xor=['fscale', 'nscale', 'scale_floats'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-input %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Eval.py b/nipype/interfaces/afni/tests/test_auto_Eval.py index 5673adc4b9..d317f48627 100644 --- a/nipype/interfaces/afni/tests/test_auto_Eval.py +++ b/nipype/interfaces/afni/tests/test_auto_Eval.py @@ -13,7 +13,8 @@ def test_Eval_inputs(): mandatory=True, position=3, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file_a=dict(argstr='-a %s', diff --git a/nipype/interfaces/afni/tests/test_auto_FWHMx.py b/nipype/interfaces/afni/tests/test_auto_FWHMx.py index 97f2359535..669ea278e8 100644 --- a/nipype/interfaces/afni/tests/test_auto_FWHMx.py +++ b/nipype/interfaces/afni/tests/test_auto_FWHMx.py @@ -32,7 +32,8 @@ def test_FWHMx_inputs(): geom=dict(argstr='-geom', xor=['arith'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-input %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Fim.py b/nipype/interfaces/afni/tests/test_auto_Fim.py index c70714089f..e9a60c1d3e 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fim.py +++ b/nipype/interfaces/afni/tests/test_auto_Fim.py @@ -16,7 +16,8 @@ def test_Fim_inputs(): mandatory=True, position=2, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-input %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Fourier.py b/nipype/interfaces/afni/tests/test_auto_Fourier.py index ddd22c65bd..02cb81bccc 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fourier.py +++ b/nipype/interfaces/afni/tests/test_auto_Fourier.py @@ -12,7 +12,8 @@ def test_Fourier_inputs(): highpass=dict(argstr='-highpass %f', mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_GCOR.py b/nipype/interfaces/afni/tests/test_auto_GCOR.py index 9f307dda34..b4f2679556 100644 --- a/nipype/interfaces/afni/tests/test_auto_GCOR.py +++ b/nipype/interfaces/afni/tests/test_auto_GCOR.py @@ -9,7 +9,8 @@ def test_GCOR_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-input %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Hist.py b/nipype/interfaces/afni/tests/test_auto_Hist.py index b7cebb027b..64952d334e 100644 --- a/nipype/interfaces/afni/tests/test_auto_Hist.py +++ b/nipype/interfaces/afni/tests/test_auto_Hist.py @@ -11,7 +11,8 @@ def test_Hist_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-input %s', diff --git a/nipype/interfaces/afni/tests/test_auto_LFCD.py b/nipype/interfaces/afni/tests/test_auto_LFCD.py index a1beef49c8..7cacf5f728 100644 --- a/nipype/interfaces/afni/tests/test_auto_LFCD.py +++ b/nipype/interfaces/afni/tests/test_auto_LFCD.py @@ -13,7 +13,8 @@ def test_LFCD_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_MaskTool.py b/nipype/interfaces/afni/tests/test_auto_MaskTool.py index 9c0e4289fd..775b34adab 100644 --- a/nipype/interfaces/afni/tests/test_auto_MaskTool.py +++ b/nipype/interfaces/afni/tests/test_auto_MaskTool.py @@ -25,7 +25,8 @@ def test_MaskTool_inputs(): ), frac=dict(argstr='-frac %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-input %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Maskave.py b/nipype/interfaces/afni/tests/test_auto_Maskave.py index 080eb2db26..ef7ef9f983 100644 --- a/nipype/interfaces/afni/tests/test_auto_Maskave.py +++ b/nipype/interfaces/afni/tests/test_auto_Maskave.py @@ -9,7 +9,8 @@ def test_Maskave_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Means.py b/nipype/interfaces/afni/tests/test_auto_Means.py index 90420861c5..b1ab57c9b9 100644 --- a/nipype/interfaces/afni/tests/test_auto_Means.py +++ b/nipype/interfaces/afni/tests/test_auto_Means.py @@ -13,7 +13,8 @@ def test_Means_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file_a=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Merge.py b/nipype/interfaces/afni/tests/test_auto_Merge.py index cef21f818f..efb4a8f301 100644 --- a/nipype/interfaces/afni/tests/test_auto_Merge.py +++ b/nipype/interfaces/afni/tests/test_auto_Merge.py @@ -14,7 +14,8 @@ def test_Merge_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Notes.py b/nipype/interfaces/afni/tests/test_auto_Notes.py index c36ccabb08..1724c1c7a5 100644 --- a/nipype/interfaces/afni/tests/test_auto_Notes.py +++ b/nipype/interfaces/afni/tests/test_auto_Notes.py @@ -16,7 +16,8 @@ def test_Notes_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_NwarpApply.py b/nipype/interfaces/afni/tests/test_auto_NwarpApply.py index bf9cba8a2f..1df8eb30ea 100644 --- a/nipype/interfaces/afni/tests/test_auto_NwarpApply.py +++ b/nipype/interfaces/afni/tests/test_auto_NwarpApply.py @@ -11,7 +11,8 @@ def test_NwarpApply_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-source %s', diff --git a/nipype/interfaces/afni/tests/test_auto_NwarpCat.py b/nipype/interfaces/afni/tests/test_auto_NwarpCat.py index 6e5077e645..fcfae528cf 100644 --- a/nipype/interfaces/afni/tests/test_auto_NwarpCat.py +++ b/nipype/interfaces/afni/tests/test_auto_NwarpCat.py @@ -11,7 +11,8 @@ def test_NwarpCat_inputs(): ), expad=dict(argstr='-expad %d', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py b/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py index 3d5e8cf9bf..ae62f3924a 100644 --- a/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py +++ b/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py @@ -17,7 +17,8 @@ def test_OneDToolPy_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-infile %s', diff --git a/nipype/interfaces/afni/tests/test_auto_OutlierCount.py b/nipype/interfaces/afni/tests/test_auto_OutlierCount.py index 8658ad5bba..7d8b28ab65 100644 --- a/nipype/interfaces/afni/tests/test_auto_OutlierCount.py +++ b/nipype/interfaces/afni/tests/test_auto_OutlierCount.py @@ -20,7 +20,8 @@ def test_OutlierCount_inputs(): fraction=dict(argstr='-fraction', usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_QualityIndex.py b/nipype/interfaces/afni/tests/test_auto_QualityIndex.py index a0af353f63..09a3855b92 100644 --- a/nipype/interfaces/afni/tests/test_auto_QualityIndex.py +++ b/nipype/interfaces/afni/tests/test_auto_QualityIndex.py @@ -19,7 +19,8 @@ def test_QualityIndex_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Qwarp.py b/nipype/interfaces/afni/tests/test_auto_Qwarp.py index 55015e0fbe..8a40687a10 100644 --- a/nipype/interfaces/afni/tests/test_auto_Qwarp.py +++ b/nipype/interfaces/afni/tests/test_auto_Qwarp.py @@ -49,7 +49,8 @@ def test_Qwarp_inputs(): hel=dict(argstr='-hel', xor=['nmi', 'mi', 'lpc', 'lpa', 'pear'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-source %s', diff --git a/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py b/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py index eed8b3b3e4..b0c4f00c74 100644 --- a/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py +++ b/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py @@ -15,7 +15,8 @@ def test_QwarpPlusMinus_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), minpatch=dict(argstr='-minpatch %d', diff --git a/nipype/interfaces/afni/tests/test_auto_ROIStats.py b/nipype/interfaces/afni/tests/test_auto_ROIStats.py index cdb6c8c570..2b720fb0c6 100644 --- a/nipype/interfaces/afni/tests/test_auto_ROIStats.py +++ b/nipype/interfaces/afni/tests/test_auto_ROIStats.py @@ -9,7 +9,8 @@ def test_ROIStats_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Refit.py b/nipype/interfaces/afni/tests/test_auto_Refit.py index 63ab824617..81b72ea2cb 100644 --- a/nipype/interfaces/afni/tests/test_auto_Refit.py +++ b/nipype/interfaces/afni/tests/test_auto_Refit.py @@ -21,7 +21,8 @@ def test_Refit_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Remlfit.py b/nipype/interfaces/afni/tests/test_auto_Remlfit.py index 37566fd66d..3511414f11 100644 --- a/nipype/interfaces/afni/tests/test_auto_Remlfit.py +++ b/nipype/interfaces/afni/tests/test_auto_Remlfit.py @@ -34,7 +34,8 @@ def test_Remlfit_inputs(): ), gltsym=dict(argstr='-gltsym "%s" %s...', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='-input "%s"', diff --git a/nipype/interfaces/afni/tests/test_auto_Resample.py b/nipype/interfaces/afni/tests/test_auto_Resample.py index 34227627db..21215f56f1 100644 --- a/nipype/interfaces/afni/tests/test_auto_Resample.py +++ b/nipype/interfaces/afni/tests/test_auto_Resample.py @@ -9,7 +9,8 @@ def test_Resample_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-inset %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Retroicor.py b/nipype/interfaces/afni/tests/test_auto_Retroicor.py index 142bf0f42d..57b23f6a18 100644 --- a/nipype/interfaces/afni/tests/test_auto_Retroicor.py +++ b/nipype/interfaces/afni/tests/test_auto_Retroicor.py @@ -16,7 +16,8 @@ def test_Retroicor_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_SVMTest.py b/nipype/interfaces/afni/tests/test_auto_SVMTest.py index 4a7c892d2b..dbda1b28c5 100644 --- a/nipype/interfaces/afni/tests/test_auto_SVMTest.py +++ b/nipype/interfaces/afni/tests/test_auto_SVMTest.py @@ -11,7 +11,8 @@ def test_SVMTest_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-testvol %s', diff --git a/nipype/interfaces/afni/tests/test_auto_SVMTrain.py b/nipype/interfaces/afni/tests/test_auto_SVMTrain.py index 17515f7cda..a0ba4dba42 100644 --- a/nipype/interfaces/afni/tests/test_auto_SVMTrain.py +++ b/nipype/interfaces/afni/tests/test_auto_SVMTrain.py @@ -16,7 +16,8 @@ def test_SVMTrain_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-trainvol %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Seg.py b/nipype/interfaces/afni/tests/test_auto_Seg.py index 5d57b5b7b5..1069121f79 100644 --- a/nipype/interfaces/afni/tests/test_auto_Seg.py +++ b/nipype/interfaces/afni/tests/test_auto_Seg.py @@ -19,7 +19,8 @@ def test_Seg_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-anat %s', diff --git a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py index e31d29f62f..97277301c3 100644 --- a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py +++ b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py @@ -9,7 +9,8 @@ def test_SkullStrip_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-input %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Synthesize.py b/nipype/interfaces/afni/tests/test_auto_Synthesize.py index a24137ed3a..bd95eca3a5 100644 --- a/nipype/interfaces/afni/tests/test_auto_Synthesize.py +++ b/nipype/interfaces/afni/tests/test_auto_Synthesize.py @@ -19,7 +19,8 @@ def test_Synthesize_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), matrix=dict(argstr='-matrix %s', diff --git a/nipype/interfaces/afni/tests/test_auto_TCat.py b/nipype/interfaces/afni/tests/test_auto_TCat.py index 9b1c61c496..597ead13cb 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCat.py +++ b/nipype/interfaces/afni/tests/test_auto_TCat.py @@ -9,7 +9,8 @@ def test_TCat_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr=' %s', diff --git a/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py b/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py index da3b0fb383..58fc2108e3 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py +++ b/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py @@ -9,7 +9,8 @@ def test_TCatSubBrick_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='%s%s ...', diff --git a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py index d15485235e..a57d8a6a10 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py @@ -9,7 +9,8 @@ def test_TCorr1D_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ktaub=dict(argstr=' -ktaub', diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py index 78accd3bb8..17f5e4ff19 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py @@ -42,7 +42,8 @@ def test_TCorrMap_inputs(): suffix='_hist', ), histogram_bin_numbers=dict(), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-input %s', diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py index 2debe70369..8857a2affe 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py @@ -9,7 +9,8 @@ def test_TCorrelate_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), num_threads=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_TNorm.py b/nipype/interfaces/afni/tests/test_auto_TNorm.py index e47a91340a..fbb11ec746 100644 --- a/nipype/interfaces/afni/tests/test_auto_TNorm.py +++ b/nipype/interfaces/afni/tests/test_auto_TNorm.py @@ -11,7 +11,8 @@ def test_TNorm_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_TShift.py b/nipype/interfaces/afni/tests/test_auto_TShift.py index a2cf3847bb..ee7663bbd6 100644 --- a/nipype/interfaces/afni/tests/test_auto_TShift.py +++ b/nipype/interfaces/afni/tests/test_auto_TShift.py @@ -11,7 +11,8 @@ def test_TShift_inputs(): ), ignore=dict(argstr='-ignore %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_TStat.py b/nipype/interfaces/afni/tests/test_auto_TStat.py index 7d5a87645f..2315d81512 100644 --- a/nipype/interfaces/afni/tests/test_auto_TStat.py +++ b/nipype/interfaces/afni/tests/test_auto_TStat.py @@ -9,7 +9,8 @@ def test_TStat_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_To3D.py b/nipype/interfaces/afni/tests/test_auto_To3D.py index 3124ad083c..5f39148167 100644 --- a/nipype/interfaces/afni/tests/test_auto_To3D.py +++ b/nipype/interfaces/afni/tests/test_auto_To3D.py @@ -17,7 +17,8 @@ def test_To3D_inputs(): ), funcparams=dict(argstr='-time:zt %s alt+z2', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_folder=dict(argstr='%s/*.dcm', diff --git a/nipype/interfaces/afni/tests/test_auto_Undump.py b/nipype/interfaces/afni/tests/test_auto_Undump.py index aaab0427a2..b5f1041b60 100644 --- a/nipype/interfaces/afni/tests/test_auto_Undump.py +++ b/nipype/interfaces/afni/tests/test_auto_Undump.py @@ -19,7 +19,8 @@ def test_Undump_inputs(): ), head_only=dict(argstr='-head_only', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-master %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Unifize.py b/nipype/interfaces/afni/tests/test_auto_Unifize.py index e5be64e70d..e9f5095619 100644 --- a/nipype/interfaces/afni/tests/test_auto_Unifize.py +++ b/nipype/interfaces/afni/tests/test_auto_Unifize.py @@ -15,7 +15,8 @@ def test_Unifize_inputs(): ), gm=dict(argstr='-GM', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-input %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Volreg.py b/nipype/interfaces/afni/tests/test_auto_Volreg.py index 25f8942b98..a8aa8a8832 100644 --- a/nipype/interfaces/afni/tests/test_auto_Volreg.py +++ b/nipype/interfaces/afni/tests/test_auto_Volreg.py @@ -14,7 +14,8 @@ def test_Volreg_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Warp.py b/nipype/interfaces/afni/tests/test_auto_Warp.py index d37ed85676..ef2d23d460 100644 --- a/nipype/interfaces/afni/tests/test_auto_Warp.py +++ b/nipype/interfaces/afni/tests/test_auto_Warp.py @@ -13,7 +13,8 @@ def test_Warp_inputs(): ), gridset=dict(argstr='-gridset %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py index 244b5049ce..70cb544bc5 100644 --- a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py +++ b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py @@ -9,7 +9,8 @@ def test_ZCutUp_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Zcat.py b/nipype/interfaces/afni/tests/test_auto_Zcat.py index 7b625bb5f5..6de330b5ae 100644 --- a/nipype/interfaces/afni/tests/test_auto_Zcat.py +++ b/nipype/interfaces/afni/tests/test_auto_Zcat.py @@ -14,7 +14,8 @@ def test_Zcat_inputs(): fscale=dict(argstr='-fscale', xor=['nscale'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_Zeropad.py b/nipype/interfaces/afni/tests/test_auto_Zeropad.py index dfb5ac0981..5a23c1a46d 100644 --- a/nipype/interfaces/afni/tests/test_auto_Zeropad.py +++ b/nipype/interfaces/afni/tests/test_auto_Zeropad.py @@ -36,7 +36,8 @@ def test_Zeropad_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='%s', diff --git a/nipype/interfaces/ants/registration.py b/nipype/interfaces/ants/registration.py index 785205952f..a5fd0e63da 100644 --- a/nipype/interfaces/ants/registration.py +++ b/nipype/interfaces/ants/registration.py @@ -1303,7 +1303,7 @@ class MeasureImageSimilarity(ANTSCommand): >>> sim.inputs.fixed_image_mask = 'mask.nii' >>> sim.inputs.moving_image_mask = 'mask.nii.gz' >>> sim.cmdline - u'MeasureImageSimilarity --dimensionality 3 --masks ["mask.nii","mask.nii.gz"] \ + 'MeasureImageSimilarity --dimensionality 3 --masks ["mask.nii","mask.nii.gz"] \ --metric MI["T1.nii","resting.nii",1.0,5,Regular,1.0]' """ _cmd = 'MeasureImageSimilarity' diff --git a/nipype/interfaces/ants/segmentation.py b/nipype/interfaces/ants/segmentation.py index 05125cbd69..6c594b5e24 100644 --- a/nipype/interfaces/ants/segmentation.py +++ b/nipype/interfaces/ants/segmentation.py @@ -13,9 +13,8 @@ import os from ...external.due import BibTeX -from ...utils.filemanip import split_filename, copyfile -from ..base import (TraitedSpec, File, traits, InputMultiPath, OutputMultiPath, isdefined, - _exists_in_path) +from ...utils.filemanip import split_filename, copyfile, which +from ..base import TraitedSpec, File, traits, InputMultiPath, OutputMultiPath, isdefined from .base import ANTSCommand, ANTSCommandInputSpec @@ -724,7 +723,7 @@ def _run_interface(self, runtime, correct_return_codes=(0,)): if ants_path is None: # Check for antsRegistration, which is under bin/ (the $ANTSPATH) instead of # checking for antsBrainExtraction.sh which is under script/ - _, cmd_path = _exists_in_path('antsRegistration', runtime.environ) + cmd_path = which('antsRegistration', env=runtime.environ) if not cmd_path: raise RuntimeError( 'The environment variable $ANTSPATH is not defined in host "%s", ' @@ -1326,7 +1325,7 @@ class KellyKapowski(ANTSCommand): >>> kk.inputs.number_integration_points = 10 >>> kk.inputs.thickness_prior_estimate = 10 >>> kk.cmdline - u'KellyKapowski --convergence "[45,0.0,10]" \ + 'KellyKapowski --convergence "[45,0.0,10]" \ --output "[segmentation0_cortical_thickness.nii.gz,segmentation0_warped_white_matter.nii.gz]" \ --image-dimensionality 3 --gradient-step 0.025000 --number-of-integration-points 10 \ --segmentation-image "[segmentation0.nii.gz,2,3]" --smoothing-variance 1.000000 \ diff --git a/nipype/interfaces/ants/tests/test_auto_ANTS.py b/nipype/interfaces/ants/tests/test_auto_ANTS.py index 50386d2704..682d070ee2 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTS.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTS.py @@ -21,7 +21,8 @@ def test_ANTS_inputs(): ), gradient_step_length=dict(requires=['transformation_model'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), metric=dict(mandatory=True, diff --git a/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py b/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py index e3a410fcb4..c58eeefc67 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py @@ -9,7 +9,8 @@ def test_ANTSCommand_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), num_threads=dict(nohash=True, diff --git a/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py b/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py index 1b5652a4ce..fcdc519aad 100644 --- a/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py +++ b/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py @@ -17,7 +17,8 @@ def test_AffineInitializer_inputs(): mandatory=True, position=1, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), local_search=dict(argstr='%d', diff --git a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py index 1ea0db9a82..09d95a4205 100644 --- a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py @@ -31,7 +31,8 @@ def test_AntsJointFusion_inputs(): exclusion_image_label=dict(argstr='-e %s', requires=['exclusion_image'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mask_image=dict(argstr='-x %s', diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py index f7451edde1..b159e6ee1d 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py @@ -16,7 +16,8 @@ def test_ApplyTransforms_inputs(): ), float=dict(argstr='--float %d', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_image=dict(argstr='--input %s', diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py index e36cad94bb..b9f3f63d54 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py @@ -11,7 +11,8 @@ def test_ApplyTransformsToPoints_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_file=dict(argstr='--input %s', diff --git a/nipype/interfaces/ants/tests/test_auto_Atropos.py b/nipype/interfaces/ants/tests/test_auto_Atropos.py index ff405ad1af..9cb7d36844 100644 --- a/nipype/interfaces/ants/tests/test_auto_Atropos.py +++ b/nipype/interfaces/ants/tests/test_auto_Atropos.py @@ -16,7 +16,8 @@ def test_Atropos_inputs(): ), icm_use_synchronous_update=dict(argstr='%s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), initialization=dict(argstr='%s', diff --git a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py index af33926d93..52ff9679ee 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py @@ -14,7 +14,8 @@ def test_AverageAffineTransform_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), num_threads=dict(nohash=True, diff --git a/nipype/interfaces/ants/tests/test_auto_AverageImages.py b/nipype/interfaces/ants/tests/test_auto_AverageImages.py index 4504f30469..4c49eb27c0 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageImages.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageImages.py @@ -13,7 +13,8 @@ def test_AverageImages_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), images=dict(argstr='%s', diff --git a/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py b/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py index 7576c36f27..3f1ade4bc3 100644 --- a/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py +++ b/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py @@ -26,7 +26,8 @@ def test_BrainExtraction_inputs(): ), extraction_registration_mask=dict(argstr='-f %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), image_suffix=dict(argstr='-s %s', diff --git a/nipype/interfaces/ants/tests/test_auto_ComposeMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_ComposeMultiTransform.py index 5f020e7dbb..c9465f6a8e 100644 --- a/nipype/interfaces/ants/tests/test_auto_ComposeMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_ComposeMultiTransform.py @@ -13,7 +13,8 @@ def test_ComposeMultiTransform_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), num_threads=dict(nohash=True, diff --git a/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py b/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py index 083e5d0d7b..2afe734522 100644 --- a/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py +++ b/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py @@ -23,7 +23,8 @@ def test_ConvertScalarImageToRGB_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_image=dict(argstr='%s', diff --git a/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py b/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py index 4216eb047d..8ad0203370 100644 --- a/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py @@ -29,7 +29,8 @@ def test_CorticalThickness_inputs(): ), extraction_registration_mask=dict(argstr='-f %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), image_suffix=dict(argstr='-s %s', diff --git a/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py b/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py index b5531137aa..561853e79b 100644 --- a/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py +++ b/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py @@ -16,7 +16,8 @@ def test_CreateJacobianDeterminantImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), imageDimension=dict(argstr='%d', diff --git a/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py b/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py index 14d8456fe1..38f24644a9 100644 --- a/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py +++ b/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py @@ -15,7 +15,8 @@ def test_CreateTiledMosaic_inputs(): ), flip_slice=dict(argstr='-f %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_image=dict(argstr='-i %s', diff --git a/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py b/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py index 5ba205137c..7d120a2f2e 100644 --- a/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py +++ b/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py @@ -12,7 +12,8 @@ def test_DenoiseImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_image=dict(argstr='-i %s', diff --git a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py index b714d2c8a5..c58c8abf20 100644 --- a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py +++ b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py @@ -17,7 +17,8 @@ def test_GenWarpFields_inputs(): ), force_proceed=dict(argstr='-f 1', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_image=dict(argstr='-i %s', diff --git a/nipype/interfaces/ants/tests/test_auto_JointFusion.py b/nipype/interfaces/ants/tests/test_auto_JointFusion.py index 5f1dcb5256..796c7a7e13 100644 --- a/nipype/interfaces/ants/tests/test_auto_JointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_JointFusion.py @@ -26,7 +26,8 @@ def test_JointFusion_inputs(): ), exclusion_region=dict(argstr='-x %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), method=dict(argstr='-m %s', diff --git a/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py b/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py index 99936119bd..e94cd44b1d 100644 --- a/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py +++ b/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py @@ -28,7 +28,8 @@ def test_KellyKapowski_inputs(): ), gray_matter_prob_image=dict(argstr='--gray-matter-probability-image "%s"', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), max_invert_displacement_field_iters=dict(argstr='--maximum-number-of-invert-displacement-field-iterations %d', diff --git a/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py b/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py index 8a19b6fb64..83b6b37d83 100644 --- a/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py @@ -12,7 +12,8 @@ def test_LaplacianThickness_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_gm=dict(argstr='%s', diff --git a/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py b/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py index 76787b1b87..fbed924b24 100644 --- a/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py +++ b/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py @@ -16,7 +16,8 @@ def test_MeasureImageSimilarity_inputs(): ), fixed_image_mask=dict(argstr='%s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), metric=dict(argstr='%s', diff --git a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py index bc14b1f0c2..5057cb4ddf 100644 --- a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py +++ b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py @@ -18,7 +18,8 @@ def test_MultiplyImages_inputs(): mandatory=True, position=1, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), num_threads=dict(nohash=True, diff --git a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py index 72331ffb6b..044b16ce50 100644 --- a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py +++ b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py @@ -23,7 +23,8 @@ def test_N4BiasFieldCorrection_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_image=dict(argstr='--input-image %s', diff --git a/nipype/interfaces/ants/tests/test_auto_Registration.py b/nipype/interfaces/ants/tests/test_auto_Registration.py index 0d71636425..ea9bc02e79 100644 --- a/nipype/interfaces/ants/tests/test_auto_Registration.py +++ b/nipype/interfaces/ants/tests/test_auto_Registration.py @@ -32,7 +32,8 @@ def test_Registration_inputs(): ), float=dict(argstr='--float %d', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), initial_moving_transform=dict(argstr='%s', diff --git a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py index 602ec83d27..9678152ba4 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py @@ -13,7 +13,8 @@ def test_WarpImageMultiTransform_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_image=dict(argstr='%s', diff --git a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py index 7f0d6b13f2..f7f310b5f8 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py @@ -13,7 +13,8 @@ def test_WarpTimeSeriesImageMultiTransform_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_image=dict(argstr='%s', diff --git a/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py b/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py index d13cc2296e..05e12b9a00 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py +++ b/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py @@ -26,7 +26,8 @@ def test_antsBrainExtraction_inputs(): ), extraction_registration_mask=dict(argstr='-f %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), image_suffix=dict(argstr='-s %s', diff --git a/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py b/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py index d5a891049e..0e7a7ca4ba 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py @@ -29,7 +29,8 @@ def test_antsCorticalThickness_inputs(): ), extraction_registration_mask=dict(argstr='-f %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), image_suffix=dict(argstr='-s %s', diff --git a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py index 678231b004..7dfd0f6539 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py +++ b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py @@ -17,7 +17,8 @@ def test_antsIntroduction_inputs(): ), force_proceed=dict(argstr='-f 1', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_image=dict(argstr='-i %s', diff --git a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py index 73c5499239..9b5005e840 100644 --- a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py +++ b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py @@ -17,7 +17,8 @@ def test_buildtemplateparallel_inputs(): ), gradient_step_size=dict(argstr='-g %f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='%s', diff --git a/nipype/interfaces/base/__init__.py b/nipype/interfaces/base/__init__.py new file mode 100644 index 0000000000..ee0f10fd7a --- /dev/null +++ b/nipype/interfaces/base/__init__.py @@ -0,0 +1,31 @@ +# -*- 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: +""" +Nipype base interfaces +---------------------- + +This module defines the API of all nipype interfaces. + +""" +from .core import ( + Interface, BaseInterface, SimpleInterface, + CommandLine, StdOutCommandLine, + MpiCommandLine, SEMLikeCommandLine, PackageInfo +) + +from .specs import ( + BaseTraitedSpec, TraitedSpec, DynamicTraitedSpec, + BaseInterfaceInputSpec, CommandLineInputSpec, + StdOutCommandLineInputSpec +) + +from .traits_extension import ( + traits, Undefined, TraitDictObject, TraitListObject, TraitError, isdefined, + File, Directory, Str, DictStrStr, has_metadata, ImageFile, + MultiPath, OutputMultiPath, InputMultiPath) + +from .support import ( + Bunch, InterfaceResult, load_template, + NipypeInterfaceError +) diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base/core.py similarity index 56% rename from nipype/interfaces/base.py rename to nipype/interfaces/base/core.py index 91e6c6bc8c..f6f9ba655a 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base/core.py @@ -2,52 +2,58 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: """ -Package contains interfaces for using existing functionality in other packages +Nipype interfaces core +...................... -Exaples FSL, matlab/SPM , afni -Requires Packages to be installed +Defines the ``Interface`` API and the body of the +most basic interfaces. +The I/O specifications corresponding to these base +interfaces are found in the ``specs`` module. + """ from __future__ import print_function, division, unicode_literals, absolute_import -import gc -from builtins import range, object, open, str, bytes +from builtins import object, open, str, bytes +import gc from copy import deepcopy -import datetime from datetime import datetime as dt import errno -import locale import os import re import platform -from string import Template import select import subprocess as sp import sys from textwrap import wrap -from warnings import warn import simplejson as json from dateutil.parser import parse as parseutc -from packaging.version import Version -import collections - -from .. import config, logging, LooseVersion, __version__ -from ..utils.provenance import write_provenance -from ..utils.misc import is_container, trim, str2bool -from ..utils.filemanip import (md5, hash_infile, FileNotFoundError, hash_timestamp, - split_filename, to_str, read_stream) -from .traits_extension import ( - traits, Undefined, TraitDictObject, TraitListObject, TraitError, isdefined, - File, Directory, DictStrStr, has_metadata, ImageFile) -from ..external.due import due + +from ... import config, logging, LooseVersion +from ...utils.provenance import write_provenance +from ...utils.misc import trim, str2bool +from ...utils.filemanip import ( + FileNotFoundError, split_filename, read_stream, which, + get_dependencies, canonicalize_env as _canonicalize_env) + +from ...external.due import due + +from .traits_extension import traits, isdefined, TraitError +from .specs import ( + BaseInterfaceInputSpec, CommandLineInputSpec, + StdOutCommandLineInputSpec, MpiCommandLineInputSpec +) +from .support import ( + Bunch, Stream, InterfaceResult, NipypeInterfaceError +) + from future import standard_library standard_library.install_aliases() -nipype_version = Version(__version__) + iflogger = logging.getLogger('interface') -FLOAT_FORMAT = '{:.10f}'.format PY35 = sys.version_info >= (3, 5) PY3 = sys.version_info[0] > 2 VALID_TERMINAL_OUTPUT = ['stream', 'allatonce', 'file', 'file_split', @@ -55,610 +61,6 @@ __docformat__ = 'restructuredtext' -class Str(traits.Unicode): - """Replacement for the default traits.Str based in bytes""" - - -traits.Str = Str - - -class NipypeInterfaceError(Exception): - """Custom error for interfaces""" - - def __init__(self, value): - self.value = value - - def __str__(self): - return '{}'.format(self.value) - - -def _exists_in_path(cmd, environ): - """ - Based on a code snippet from - http://orip.org/2009/08/python-checking-if-executable-exists-in.html - """ - - if 'PATH' in environ: - input_environ = environ.get("PATH") - else: - input_environ = os.environ.get("PATH", "") - extensions = os.environ.get("PATHEXT", "").split(os.pathsep) - for directory in input_environ.split(os.pathsep): - base = os.path.join(directory, cmd) - options = [base] + [(base + ext) for ext in extensions] - for filename in options: - if os.path.exists(filename): - return True, filename - return False, None - - -def load_template(name): - """Load a template from the script_templates directory - - Parameters - ---------- - name : str - The name of the file to load - - Returns - ------- - template : string.Template - - """ - full_fname = os.path.join(os.path.dirname(__file__), - 'script_templates', name) - template_file = open(full_fname) - template = Template(template_file.read()) - template_file.close() - return template - - -class Bunch(object): - """Dictionary-like class that provides attribute-style access to it's items. - - A `Bunch` is a simple container that stores it's items as class - attributes. Internally all items are stored in a dictionary and - the class exposes several of the dictionary methods. - - Examples - -------- - >>> from nipype.interfaces.base import Bunch - >>> inputs = Bunch(infile='subj.nii', fwhm=6.0, register_to_mean=True) - >>> inputs - Bunch(fwhm=6.0, infile='subj.nii', register_to_mean=True) - >>> inputs.register_to_mean = False - >>> inputs - Bunch(fwhm=6.0, infile='subj.nii', register_to_mean=False) - - - Notes - ----- - The Bunch pattern came from the Python Cookbook: - - .. [1] A. Martelli, D. Hudgeon, "Collecting a Bunch of Named - Items", Python Cookbook, 2nd Ed, Chapter 4.18, 2005. - - """ - - def __init__(self, *args, **kwargs): - self.__dict__.update(*args, **kwargs) - - def update(self, *args, **kwargs): - """update existing attribute, or create new attribute - - Note: update is very much like HasTraits.set""" - self.__dict__.update(*args, **kwargs) - - def items(self): - """iterates over bunch attributes as key, value pairs""" - return list(self.__dict__.items()) - - def iteritems(self): - """iterates over bunch attributes as key, value pairs""" - warn('iteritems is deprecated, use items instead') - return list(self.items()) - - def get(self, *args): - """Support dictionary get() functionality - """ - return self.__dict__.get(*args) - - def set(self, **kwargs): - """Support dictionary get() functionality - """ - return self.__dict__.update(**kwargs) - - def dictcopy(self): - """returns a deep copy of existing Bunch as a dictionary""" - return deepcopy(self.__dict__) - - def __repr__(self): - """representation of the sorted Bunch as a string - - Currently, this string representation of the `inputs` Bunch of - interfaces is hashed to determine if the process' dirty-bit - needs setting or not. Till that mechanism changes, only alter - this after careful consideration. - """ - outstr = ['Bunch('] - first = True - for k, v in sorted(self.items()): - if not first: - outstr.append(', ') - if isinstance(v, dict): - pairs = [] - for key, value in sorted(v.items()): - pairs.append("'%s': %s" % (key, value)) - v = '{' + ', '.join(pairs) + '}' - outstr.append('%s=%s' % (k, v)) - else: - outstr.append('%s=%r' % (k, v)) - first = False - outstr.append(')') - return ''.join(outstr) - - def _hash_infile(self, adict, key): - # Inject file hashes into adict[key] - stuff = adict[key] - if not is_container(stuff): - stuff = [stuff] - file_list = [] - for afile in stuff: - if os.path.isfile(afile): - md5obj = md5() - with open(afile, 'rb') as fp: - while True: - data = fp.read(8192) - if not data: - break - md5obj.update(data) - md5hex = md5obj.hexdigest() - else: - md5hex = None - file_list.append((afile, md5hex)) - return file_list - - def _get_bunch_hash(self): - """Return a dictionary of our items with hashes for each file. - - Searches through dictionary items and if an item is a file, it - calculates the md5 hash of the file contents and stores the - file name and hash value as the new key value. - - However, the overall bunch hash is calculated only on the hash - value of a file. The path and name of the file are not used in - the overall hash calculation. - - Returns - ------- - dict_withhash : dict - Copy of our dictionary with the new file hashes included - with each file. - hashvalue : str - The md5 hash value of the `dict_withhash` - - """ - - infile_list = [] - for key, val in list(self.items()): - if is_container(val): - # XXX - SG this probably doesn't catch numpy arrays - # containing embedded file names either. - if isinstance(val, dict): - # XXX - SG should traverse dicts, but ignoring for now - item = None - else: - if len(val) == 0: - raise AttributeError('%s attribute is empty' % key) - item = val[0] - else: - item = val - try: - if isinstance(item, str) and os.path.isfile(item): - infile_list.append(key) - except TypeError: - # `item` is not a file or string. - continue - dict_withhash = self.dictcopy() - dict_nofilename = self.dictcopy() - for item in infile_list: - dict_withhash[item] = self._hash_infile(dict_withhash, item) - dict_nofilename[item] = [val[1] for val in dict_withhash[item]] - # Sort the items of the dictionary, before hashing the string - # representation so we get a predictable order of the - # dictionary. - sorted_dict = to_str(sorted(dict_nofilename.items())) - return dict_withhash, md5(sorted_dict.encode()).hexdigest() - - def __pretty__(self, p, cycle): - """Support for the pretty module - - pretty is included in ipython.externals for ipython > 0.10""" - if cycle: - p.text('Bunch(...)') - else: - p.begin_group(6, 'Bunch(') - first = True - for k, v in sorted(self.items()): - if not first: - p.text(',') - p.breakable() - p.text(k + '=') - p.pretty(v) - first = False - p.end_group(6, ')') - - -class InterfaceResult(object): - """Object that contains the results of running a particular Interface. - - Attributes - ---------- - version : version of this Interface result object (a readonly property) - interface : class type - A copy of the `Interface` class that was run to generate this result. - inputs : a traits free representation of the inputs - outputs : Bunch - An `Interface` specific Bunch that contains all possible files - that are generated by the interface. The `outputs` are used - as the `inputs` to another node when interfaces are used in - the pipeline. - runtime : Bunch - - Contains attributes that describe the runtime environment when - the `Interface` was run. Contains the attributes: - - * cmdline : The command line string that was executed - * cwd : The directory the ``cmdline`` was executed in. - * stdout : The output of running the ``cmdline``. - * stderr : Any error messages output from running ``cmdline``. - * returncode : The code returned from running the ``cmdline``. - - """ - - def __init__(self, interface, runtime, inputs=None, outputs=None, - provenance=None): - self._version = 2.0 - self.interface = interface - self.runtime = runtime - self.inputs = inputs - self.outputs = outputs - self.provenance = provenance - - @property - def version(self): - return self._version - - -class BaseTraitedSpec(traits.HasTraits): - """Provide a few methods necessary to support nipype interface api - - The inputs attribute of interfaces call certain methods that are not - available in traits.HasTraits. These are provided here. - - new metadata: - - * usedefault : set this to True if the default value of the trait should be - used. Unless this is set, the attributes are set to traits.Undefined - - new attribute: - - * get_hashval : returns a tuple containing the state of the trait as a dict - and hashvalue corresponding to dict. - - XXX Reconsider this in the long run, but it seems like the best - solution to move forward on the refactoring. - """ - package_version = nipype_version - - def __init__(self, **kwargs): - """ Initialize handlers and inputs""" - # NOTE: In python 2.6, object.__init__ no longer accepts input - # arguments. HasTraits does not define an __init__ and - # therefore these args were being ignored. - # super(TraitedSpec, self).__init__(*args, **kwargs) - super(BaseTraitedSpec, self).__init__(**kwargs) - traits.push_exception_handler(reraise_exceptions=True) - undefined_traits = {} - for trait in self.copyable_trait_names(): - if not self.traits()[trait].usedefault: - undefined_traits[trait] = Undefined - self.trait_set(trait_change_notify=False, **undefined_traits) - self._generate_handlers() - self.trait_set(**kwargs) - - def items(self): - """ Name, trait generator for user modifiable traits - """ - for name in sorted(self.copyable_trait_names()): - yield name, self.traits()[name] - - def __repr__(self): - """ Return a well-formatted representation of the traits """ - outstr = [] - for name, value in sorted(self.trait_get().items()): - outstr.append('%s = %s' % (name, value)) - return '\n{}\n'.format('\n'.join(outstr)) - - def _generate_handlers(self): - """Find all traits with the 'xor' metadata and attach an event - handler to them. - """ - has_xor = dict(xor=lambda t: t is not None) - xors = self.trait_names(**has_xor) - for elem in xors: - self.on_trait_change(self._xor_warn, elem) - has_deprecation = dict(deprecated=lambda t: t is not None) - deprecated = self.trait_names(**has_deprecation) - for elem in deprecated: - self.on_trait_change(self._deprecated_warn, elem) - - def _xor_warn(self, obj, name, old, new): - """ Generates warnings for xor traits - """ - if isdefined(new): - trait_spec = self.traits()[name] - # for each xor, set to default_value - for trait_name in trait_spec.xor: - if trait_name == name: - # skip ourself - continue - if isdefined(getattr(self, trait_name)): - self.trait_set(trait_change_notify=False, - **{'%s' % name: Undefined}) - msg = ('Input "%s" is mutually exclusive with input "%s", ' - 'which is already set') % (name, trait_name) - raise IOError(msg) - - def _requires_warn(self, obj, name, old, new): - """Part of the xor behavior - """ - if isdefined(new): - trait_spec = self.traits()[name] - msg = None - for trait_name in trait_spec.requires: - if not isdefined(getattr(self, trait_name)): - if not msg: - msg = 'Input %s requires inputs: %s' \ - % (name, ', '.join(trait_spec.requires)) - if msg: # only one requires warning at a time. - warn(msg) - - def _deprecated_warn(self, obj, name, old, new): - """Checks if a user assigns a value to a deprecated trait - """ - if isdefined(new): - trait_spec = self.traits()[name] - msg1 = ('Input %s in interface %s is deprecated.' % - (name, - self.__class__.__name__.split('InputSpec')[0])) - msg2 = ('Will be removed or raise an error as of release %s' - % trait_spec.deprecated) - if trait_spec.new_name: - if trait_spec.new_name not in self.copyable_trait_names(): - raise TraitError(msg1 + ' Replacement trait %s not found' % - trait_spec.new_name) - msg3 = 'It has been replaced by %s.' % trait_spec.new_name - else: - msg3 = '' - msg = ' '.join((msg1, msg2, msg3)) - if Version(str(trait_spec.deprecated)) < self.package_version: - raise TraitError(msg) - else: - if trait_spec.new_name: - msg += 'Unsetting old value %s; setting new value %s.' % ( - name, trait_spec.new_name) - warn(msg) - if trait_spec.new_name: - self.trait_set(trait_change_notify=False, - **{'%s' % name: Undefined, - '%s' % trait_spec.new_name: new}) - - def _hash_infile(self, adict, key): - """ Inject file hashes into adict[key]""" - stuff = adict[key] - if not is_container(stuff): - stuff = [stuff] - file_list = [] - for afile in stuff: - if is_container(afile): - hashlist = self._hash_infile({'infiles': afile}, 'infiles') - hash = [val[1] for val in hashlist] - else: - if config.get('execution', - 'hash_method').lower() == 'timestamp': - hash = hash_timestamp(afile) - elif config.get('execution', - 'hash_method').lower() == 'content': - hash = hash_infile(afile) - else: - raise Exception("Unknown hash method: %s" % - config.get('execution', 'hash_method')) - file_list.append((afile, hash)) - return file_list - - def get(self, **kwargs): - """ Returns traited class as a dict - - Augments the trait get function to return a dictionary without - notification handles - """ - out = super(BaseTraitedSpec, self).get(**kwargs) - out = self._clean_container(out, Undefined) - return out - - def get_traitsfree(self, **kwargs): - """ Returns traited class as a dict - - Augments the trait get function to return a dictionary without - any traits. The dictionary does not contain any attributes that - were Undefined - """ - out = super(BaseTraitedSpec, self).get(**kwargs) - out = self._clean_container(out, skipundefined=True) - return out - - def _clean_container(self, object, undefinedval=None, skipundefined=False): - """Convert a traited obejct into a pure python representation. - """ - if isinstance(object, TraitDictObject) or isinstance(object, dict): - out = {} - for key, val in list(object.items()): - if isdefined(val): - out[key] = self._clean_container(val, undefinedval) - else: - if not skipundefined: - out[key] = undefinedval - elif (isinstance(object, TraitListObject) or - isinstance(object, list) or isinstance(object, tuple)): - out = [] - for val in object: - if isdefined(val): - out.append(self._clean_container(val, undefinedval)) - else: - if not skipundefined: - out.append(undefinedval) - else: - out.append(None) - if isinstance(object, tuple): - out = tuple(out) - else: - if isdefined(object): - out = object - else: - if not skipundefined: - out = undefinedval - return out - - def has_metadata(self, name, metadata, value=None, recursive=True): - """ - Return has_metadata for the requested trait name in this - interface - """ - return has_metadata(self.trait(name).trait_type, metadata, value, - recursive) - - def get_hashval(self, hash_method=None): - """Return a dictionary of our items with hashes for each file. - - Searches through dictionary items and if an item is a file, it - calculates the md5 hash of the file contents and stores the - file name and hash value as the new key value. - - However, the overall bunch hash is calculated only on the hash - value of a file. The path and name of the file are not used in - the overall hash calculation. - - Returns - ------- - dict_withhash : dict - Copy of our dictionary with the new file hashes included - with each file. - hashvalue : str - The md5 hash value of the traited spec - - """ - - dict_withhash = [] - dict_nofilename = [] - for name, val in sorted(self.get().items()): - if not isdefined(val) or self.has_metadata(name, "nohash", True): - # skip undefined traits and traits with nohash=True - continue - - hash_files = (not self.has_metadata(name, "hash_files", False) and not - self.has_metadata(name, "name_source")) - dict_nofilename.append((name, - self._get_sorteddict(val, hash_method=hash_method, - hash_files=hash_files))) - dict_withhash.append((name, - self._get_sorteddict(val, True, hash_method=hash_method, - hash_files=hash_files))) - return dict_withhash, md5(to_str(dict_nofilename).encode()).hexdigest() - - def _get_sorteddict(self, objekt, dictwithhash=False, hash_method=None, - hash_files=True): - if isinstance(objekt, dict): - out = [] - for key, val in sorted(objekt.items()): - if isdefined(val): - out.append((key, - self._get_sorteddict(val, dictwithhash, - hash_method=hash_method, - hash_files=hash_files))) - elif isinstance(objekt, (list, tuple)): - out = [] - for val in objekt: - if isdefined(val): - out.append(self._get_sorteddict(val, dictwithhash, - hash_method=hash_method, - hash_files=hash_files)) - if isinstance(objekt, tuple): - out = tuple(out) - else: - if isdefined(objekt): - if (hash_files and isinstance(objekt, (str, bytes)) and - os.path.isfile(objekt)): - if hash_method is None: - hash_method = config.get('execution', 'hash_method') - - if hash_method.lower() == 'timestamp': - hash = hash_timestamp(objekt) - elif hash_method.lower() == 'content': - hash = hash_infile(objekt) - else: - raise Exception("Unknown hash method: %s" % hash_method) - if dictwithhash: - out = (objekt, hash) - else: - out = hash - elif isinstance(objekt, float): - out = FLOAT_FORMAT(objekt) - else: - out = objekt - return out - - -class DynamicTraitedSpec(BaseTraitedSpec): - """ A subclass to handle dynamic traits - - This class is a workaround for add_traits and clone_traits not - functioning well together. - """ - - def __deepcopy__(self, memo): - """ bug in deepcopy for HasTraits results in weird cloning behavior for - added traits - """ - id_self = id(self) - if id_self in memo: - return memo[id_self] - dup_dict = deepcopy(self.get(), memo) - # access all keys - for key in self.copyable_trait_names(): - if key in self.__dict__.keys(): - _ = getattr(self, key) - # clone once - dup = self.clone_traits(memo=memo) - for key in self.copyable_trait_names(): - try: - _ = getattr(dup, key) - except: - pass - # clone twice - dup = self.clone_traits(memo=memo) - dup.trait_set(**dup_dict) - return dup - - -class TraitedSpec(BaseTraitedSpec): - """ Create a subclass with strict traits. - - This is used in 90% of the cases. - """ - _ = traits.Disallow - - class Interface(object): """This is an abstract definition for Interface objects. @@ -731,12 +133,6 @@ def _get_filecopy_info(self): raise NotImplementedError -class BaseInterfaceInputSpec(TraitedSpec): - ignore_exception = traits.Bool(False, usedefault=True, nohash=True, - desc='Print an error message instead of throwing an exception ' - 'in case the interface fails to run') - - class BaseInterface(Interface): """Implements common interface functionality. @@ -1045,7 +441,7 @@ def run(self, **inputs): results : an InterfaceResult object containing a copy of the instance that was executed, provenance information and, if successful, results """ - from ..utils.profiler import ResourceMonitor + from ...utils.profiler import ResourceMonitor enable_rm = config.resource_monitor and self.resource_monitor force_raise = not getattr(self.inputs, 'ignore_exception', False) @@ -1229,6 +625,7 @@ class SimpleInterface(BaseInterface): .. testsetup:: + >>> from .specs import TraitedSpec >>> tmp = getfixture('tmpdir') >>> old = tmp.chdir() # changing to a temporary directory @@ -1271,87 +668,6 @@ def _list_outputs(self): return self._results -class Stream(object): - """Function to capture stdout and stderr streams with timestamps - - stackoverflow.com/questions/4984549/merge-and-sync-stdout-and-stderr/5188359 - """ - - def __init__(self, name, impl): - self._name = name - self._impl = impl - self._buf = '' - self._rows = [] - self._lastidx = 0 - self.default_encoding = locale.getdefaultlocale()[1] or 'UTF-8' - - def fileno(self): - "Pass-through for file descriptor." - return self._impl.fileno() - - def read(self, drain=0): - "Read from the file descriptor. If 'drain' set, read until EOF." - while self._read(drain) is not None: - if not drain: - break - - def _read(self, drain): - "Read from the file descriptor" - fd = self.fileno() - buf = os.read(fd, 4096).decode(self.default_encoding) - if not buf and not self._buf: - return None - if '\n' not in buf: - if not drain: - self._buf += buf - return [] - - # prepend any data previously read, then split into lines and format - buf = self._buf + buf - if '\n' in buf: - tmp, rest = buf.rsplit('\n', 1) - else: - tmp = buf - rest = None - self._buf = rest - now = datetime.datetime.now().isoformat() - rows = tmp.split('\n') - self._rows += [(now, '%s %s:%s' % (self._name, now, r), r) - for r in rows] - for idx in range(self._lastidx, len(self._rows)): - iflogger.info(self._rows[idx][1]) - self._lastidx = len(self._rows) - - -def _canonicalize_env(env): - """Windows requires that environment be dicts with bytes as keys and values - This function converts any unicode entries for Windows only, returning the - dictionary untouched in other environments. - - Parameters - ---------- - env : dict - environment dictionary with unicode or bytes keys and values - - Returns - ------- - env : dict - Windows: environment dictionary with bytes keys and values - Other: untouched input ``env`` - """ - if os.name != 'nt': - return env - - out_env = {} - for key, val in env.items(): - if not isinstance(key, bytes): - key = key.encode('utf-8') - if not isinstance(val, bytes): - val = val.encode('utf-8') - out_env[key] = val - return out_env - - def run_command(runtime, output=None, timeout=0.01): """Run a command, read stdout and stderr, prefix with timestamp. @@ -1389,7 +705,9 @@ def run_command(runtime, output=None, timeout=0.01): shell=True, cwd=runtime.cwd, env=env, - close_fds=True) + close_fds=True, + ) + result = { 'stdout': [], 'stderr': [], @@ -1475,52 +793,6 @@ def _process(drain=0): return runtime -def get_dependencies(name, environ): - """Return library dependencies of a dynamically linked executable - - Uses otool on darwin, ldd on linux. Currently doesn't support windows. - - """ - cmd = None - if sys.platform == 'darwin': - cmd = 'otool -L `which {}`'.format - elif 'linux' in sys.platform: - cmd = 'ldd `which {}`'.format - - if cmd is None: - return 'Platform %s not supported' % sys.platform - - try: - proc = sp.Popen( - cmd(name), stdout=sp.PIPE, stderr=sp.PIPE, shell=True, - env=environ, close_fds=True) - o, _ = proc.communicate() - proc.terminate() - gc.collect() - except: - iflogger.warning( - 'Could not get linked libraries for "%s".', name) - return 'Failed collecting dependencies' - return o.rstrip() - - -class CommandLineInputSpec(BaseInterfaceInputSpec): - args = Str(argstr='%s', desc='Additional parameters to the command') - environ = DictStrStr(desc='Environment variables', usedefault=True, - nohash=True) - # This input does not have a "usedefault=True" so the set_default_terminal_output() - # method would work - terminal_output = traits.Enum('stream', 'allatonce', 'file', 'none', - deprecated='1.0.0', - desc=('Control terminal output: `stream` - ' - 'displays to terminal immediately (default), ' - '`allatonce` - waits till command is ' - 'finished to display output, `file` - ' - 'writes output to file, `none` - output' - ' is ignored'), - nohash=True) - - class CommandLine(BaseInterface): """Implements functionality to interact with command line programs class must be instantiated with a command argument @@ -1641,15 +913,17 @@ def raise_exception(self, runtime): def _get_environ(self): return getattr(self.inputs, 'environ', {}) - def version_from_command(self, flag='-v'): + def version_from_command(self, flag='-v', cmd=None): iflogger.warning('version_from_command member of CommandLine was ' 'Deprecated in nipype-1.0.0 and deleted in 1.1.0') - cmdname = self.cmd.split()[0] + if cmd is None: + cmd = self.cmd.split()[0] + env = dict(os.environ) - if _exists_in_path(cmdname, env): + if which(cmd, env=env): out_environ = self._get_environ() env.update(out_environ) - proc = sp.Popen(' '.join((cmdname, flag)), + proc = sp.Popen(' '.join((cmd, flag)), shell=True, env=env, stdout=sp.PIPE, @@ -1681,11 +955,13 @@ def _run_interface(self, runtime, correct_return_codes=(0,)): # which $cmd executable_name = self.cmd.split()[0] - exist_val, cmd_path = _exists_in_path(executable_name, - runtime.environ) - if not exist_val: - raise IOError("command '%s' could not be found on host %s" % - (self.cmd.split()[0], runtime.hostname)) + cmd_path = which(executable_name, env=runtime.environ) + + if cmd_path is None: + raise IOError( + 'No command "%s" found on host %s. Please check that the ' + 'corresponding package is installed.' % ( + executable_name, runtime.hostname)) runtime.command_path = cmd_path runtime.dependencies = (get_dependencies(executable_name, runtime.environ) @@ -1856,10 +1132,6 @@ def _parse_inputs(self, skip=None): return first_args + all_args + last_args -class StdOutCommandLineInputSpec(CommandLineInputSpec): - out_file = File(argstr="> %s", position=-1, genfile=True) - - class StdOutCommandLine(CommandLine): input_spec = StdOutCommandLineInputSpec @@ -1870,15 +1142,6 @@ def _gen_outfilename(self): raise NotImplementedError -class MpiCommandLineInputSpec(CommandLineInputSpec): - use_mpi = traits.Bool(False, - desc="Whether or not to run the command with mpiexec", - usedefault=True) - n_procs = traits.Int(desc="Num processors to specify to mpiexec. Do not " - "specify if this is managed externally (e.g. through " - "SGE)") - - class MpiCommandLine(CommandLine): """Implements functionality to interact with command line programs that can be run with MPI (i.e. using 'mpiexec'). @@ -1982,117 +1245,3 @@ def version(klass): @staticmethod def parse_version(raw_info): raise NotImplementedError - - -class MultiPath(traits.List): - """ Abstract class - shared functionality of input and output MultiPath - """ - - def validate(self, object, name, value): - - # want to treat range and other sequences (except str) as list - if not isinstance(value, (str, bytes)) and isinstance(value, collections.Sequence): - value = list(value) - - if not isdefined(value) or \ - (isinstance(value, list) and len(value) == 0): - return Undefined - - newvalue = value - - if not isinstance(value, list) \ - or (self.inner_traits() and - isinstance(self.inner_traits()[0].trait_type, - traits.List) and not - isinstance(self.inner_traits()[0].trait_type, - InputMultiPath) and - isinstance(value, list) and - value and not - isinstance(value[0], list)): - newvalue = [value] - value = super(MultiPath, self).validate(object, name, newvalue) - - if value: - return value - - self.error(object, name, value) - - -class OutputMultiPath(MultiPath): - """ Implements a user friendly traits that accepts one or more - paths to files or directories. This is the output version which - return a single string whenever possible (when it was set to a - single value or a list of length 1). Default value of this trait - is _Undefined. It does not accept empty lists. - - XXX This should only be used as a final resort. We should stick to - established Traits to the extent possible. - - XXX This needs to be vetted by somebody who understands traits - - >>> from nipype.interfaces.base import OutputMultiPath - >>> class A(TraitedSpec): - ... foo = OutputMultiPath(File(exists=False)) - >>> a = A() - >>> a.foo - - - >>> a.foo = '/software/temp/foo.txt' - >>> a.foo - '/software/temp/foo.txt' - - >>> a.foo = ['/software/temp/foo.txt'] - >>> a.foo - '/software/temp/foo.txt' - - >>> a.foo = ['/software/temp/foo.txt', '/software/temp/goo.txt'] - >>> a.foo - ['/software/temp/foo.txt', '/software/temp/goo.txt'] - - """ - - def get(self, object, name): - value = self.get_value(object, name) - if len(value) == 0: - return Undefined - elif len(value) == 1: - return value[0] - else: - return value - - def set(self, object, name, value): - self.set_value(object, name, value) - - -class InputMultiPath(MultiPath): - """ Implements a user friendly traits that accepts one or more - paths to files or directories. This is the input version which - always returns a list. Default value of this trait - is _Undefined. It does not accept empty lists. - - XXX This should only be used as a final resort. We should stick to - established Traits to the extent possible. - - XXX This needs to be vetted by somebody who understands traits - - >>> from nipype.interfaces.base import InputMultiPath - >>> class A(TraitedSpec): - ... foo = InputMultiPath(File(exists=False)) - >>> a = A() - >>> a.foo - - - >>> a.foo = '/software/temp/foo.txt' - >>> a.foo - ['/software/temp/foo.txt'] - - >>> a.foo = ['/software/temp/foo.txt'] - >>> a.foo - ['/software/temp/foo.txt'] - - >>> a.foo = ['/software/temp/foo.txt', '/software/temp/goo.txt'] - >>> a.foo - ['/software/temp/foo.txt', '/software/temp/goo.txt'] - - """ - pass diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py new file mode 100644 index 0000000000..f0d1184d85 --- /dev/null +++ b/nipype/interfaces/base/specs.py @@ -0,0 +1,396 @@ +# -*- 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: +""" + +Base I/O specifications for Nipype interfaces +............................................. + +Define the API for the I/O of interfaces + +""" +from __future__ import print_function, division, unicode_literals, absolute_import + +import os +from copy import deepcopy +from warnings import warn +from builtins import str, bytes +from packaging.version import Version + +from ...utils.misc import is_container +from ...utils.filemanip import md5, hash_infile, hash_timestamp, to_str +from .traits_extension import ( + traits, Undefined, isdefined, TraitError, TraitDictObject, TraitListObject, + has_metadata, +) + +from ... import config, __version__ + +FLOAT_FORMAT = '{:.10f}'.format +nipype_version = Version(__version__) + + +class BaseTraitedSpec(traits.HasTraits): + """ + Provide a few methods necessary to support nipype interface api + + The inputs attribute of interfaces call certain methods that are not + available in traits.HasTraits. These are provided here. + + new metadata: + + * usedefault : set this to True if the default value of the trait should be + used. Unless this is set, the attributes are set to traits.Undefined + + new attribute: + + * get_hashval : returns a tuple containing the state of the trait as a dict + and hashvalue corresponding to dict. + + XXX Reconsider this in the long run, but it seems like the best + solution to move forward on the refactoring. + """ + package_version = nipype_version + + def __init__(self, **kwargs): + """ Initialize handlers and inputs""" + # NOTE: In python 2.6, object.__init__ no longer accepts input + # arguments. HasTraits does not define an __init__ and + # therefore these args were being ignored. + # super(TraitedSpec, self).__init__(*args, **kwargs) + super(BaseTraitedSpec, self).__init__(**kwargs) + traits.push_exception_handler(reraise_exceptions=True) + undefined_traits = {} + for trait in self.copyable_trait_names(): + if not self.traits()[trait].usedefault: + undefined_traits[trait] = Undefined + self.trait_set(trait_change_notify=False, **undefined_traits) + self._generate_handlers() + self.trait_set(**kwargs) + + def items(self): + """ Name, trait generator for user modifiable traits + """ + for name in sorted(self.copyable_trait_names()): + yield name, self.traits()[name] + + def __repr__(self): + """ Return a well-formatted representation of the traits """ + outstr = [] + for name, value in sorted(self.trait_get().items()): + outstr.append('%s = %s' % (name, value)) + return '\n{}\n'.format('\n'.join(outstr)) + + def _generate_handlers(self): + """Find all traits with the 'xor' metadata and attach an event + handler to them. + """ + has_xor = dict(xor=lambda t: t is not None) + xors = self.trait_names(**has_xor) + for elem in xors: + self.on_trait_change(self._xor_warn, elem) + has_deprecation = dict(deprecated=lambda t: t is not None) + deprecated = self.trait_names(**has_deprecation) + for elem in deprecated: + self.on_trait_change(self._deprecated_warn, elem) + + def _xor_warn(self, obj, name, old, new): + """ Generates warnings for xor traits + """ + if isdefined(new): + trait_spec = self.traits()[name] + # for each xor, set to default_value + for trait_name in trait_spec.xor: + if trait_name == name: + # skip ourself + continue + if isdefined(getattr(self, trait_name)): + self.trait_set(trait_change_notify=False, + **{'%s' % name: Undefined}) + msg = ('Input "%s" is mutually exclusive with input "%s", ' + 'which is already set') % (name, trait_name) + raise IOError(msg) + + def _requires_warn(self, obj, name, old, new): + """Part of the xor behavior + """ + if isdefined(new): + trait_spec = self.traits()[name] + msg = None + for trait_name in trait_spec.requires: + if not isdefined(getattr(self, trait_name)): + if not msg: + msg = 'Input %s requires inputs: %s' \ + % (name, ', '.join(trait_spec.requires)) + if msg: # only one requires warning at a time. + warn(msg) + + def _deprecated_warn(self, obj, name, old, new): + """Checks if a user assigns a value to a deprecated trait + """ + if isdefined(new): + trait_spec = self.traits()[name] + msg1 = ('Input %s in interface %s is deprecated.' % + (name, + self.__class__.__name__.split('InputSpec')[0])) + msg2 = ('Will be removed or raise an error as of release %s' + % trait_spec.deprecated) + if trait_spec.new_name: + if trait_spec.new_name not in self.copyable_trait_names(): + raise TraitError(msg1 + ' Replacement trait %s not found' % + trait_spec.new_name) + msg3 = 'It has been replaced by %s.' % trait_spec.new_name + else: + msg3 = '' + msg = ' '.join((msg1, msg2, msg3)) + if Version(str(trait_spec.deprecated)) < self.package_version: + raise TraitError(msg) + else: + if trait_spec.new_name: + msg += 'Unsetting old value %s; setting new value %s.' % ( + name, trait_spec.new_name) + warn(msg) + if trait_spec.new_name: + self.trait_set(trait_change_notify=False, + **{'%s' % name: Undefined, + '%s' % trait_spec.new_name: new}) + + def _hash_infile(self, adict, key): + """ Inject file hashes into adict[key]""" + stuff = adict[key] + if not is_container(stuff): + stuff = [stuff] + file_list = [] + for afile in stuff: + if is_container(afile): + hashlist = self._hash_infile({'infiles': afile}, 'infiles') + hash = [val[1] for val in hashlist] + else: + if config.get('execution', + 'hash_method').lower() == 'timestamp': + hash = hash_timestamp(afile) + elif config.get('execution', + 'hash_method').lower() == 'content': + hash = hash_infile(afile) + else: + raise Exception("Unknown hash method: %s" % + config.get('execution', 'hash_method')) + file_list.append((afile, hash)) + return file_list + + def get(self, **kwargs): + """ Returns traited class as a dict + + Augments the trait get function to return a dictionary without + notification handles + """ + out = super(BaseTraitedSpec, self).get(**kwargs) + out = self._clean_container(out, Undefined) + return out + + def get_traitsfree(self, **kwargs): + """ Returns traited class as a dict + + Augments the trait get function to return a dictionary without + any traits. The dictionary does not contain any attributes that + were Undefined + """ + out = super(BaseTraitedSpec, self).get(**kwargs) + out = self._clean_container(out, skipundefined=True) + return out + + def _clean_container(self, objekt, undefinedval=None, skipundefined=False): + """Convert a traited obejct into a pure python representation. + """ + if isinstance(objekt, TraitDictObject) or isinstance(objekt, dict): + out = {} + for key, val in list(objekt.items()): + if isdefined(val): + out[key] = self._clean_container(val, undefinedval) + else: + if not skipundefined: + out[key] = undefinedval + elif (isinstance(objekt, TraitListObject) or + isinstance(objekt, list) or isinstance(objekt, tuple)): + out = [] + for val in objekt: + if isdefined(val): + out.append(self._clean_container(val, undefinedval)) + else: + if not skipundefined: + out.append(undefinedval) + else: + out.append(None) + if isinstance(objekt, tuple): + out = tuple(out) + else: + if isdefined(objekt): + out = objekt + else: + if not skipundefined: + out = undefinedval + return out + + def has_metadata(self, name, metadata, value=None, recursive=True): + """ + Return has_metadata for the requested trait name in this + interface + """ + return has_metadata(self.trait(name).trait_type, metadata, value, + recursive) + + def get_hashval(self, hash_method=None): + """Return a dictionary of our items with hashes for each file. + + Searches through dictionary items and if an item is a file, it + calculates the md5 hash of the file contents and stores the + file name and hash value as the new key value. + + However, the overall bunch hash is calculated only on the hash + value of a file. The path and name of the file are not used in + the overall hash calculation. + + Returns + ------- + list_withhash : dict + Copy of our dictionary with the new file hashes included + with each file. + hashvalue : str + The md5 hash value of the traited spec + + """ + + list_withhash = [] + list_nofilename = [] + for name, val in sorted(self.get().items()): + if not isdefined(val) or self.has_metadata(name, "nohash", True): + # skip undefined traits and traits with nohash=True + continue + + hash_files = (not self.has_metadata(name, "hash_files", False) and not + self.has_metadata(name, "name_source")) + list_nofilename.append((name, + self._get_sorteddict(val, hash_method=hash_method, + hash_files=hash_files))) + list_withhash.append((name, + self._get_sorteddict(val, True, hash_method=hash_method, + hash_files=hash_files))) + return list_withhash, md5(to_str(list_nofilename).encode()).hexdigest() + + def _get_sorteddict(self, objekt, dictwithhash=False, hash_method=None, + hash_files=True): + if isinstance(objekt, dict): + out = [] + for key, val in sorted(objekt.items()): + if isdefined(val): + out.append((key, + self._get_sorteddict(val, dictwithhash, + hash_method=hash_method, + hash_files=hash_files))) + elif isinstance(objekt, (list, tuple)): + out = [] + for val in objekt: + if isdefined(val): + out.append(self._get_sorteddict(val, dictwithhash, + hash_method=hash_method, + hash_files=hash_files)) + if isinstance(objekt, tuple): + out = tuple(out) + else: + if isdefined(objekt): + if (hash_files and isinstance(objekt, (str, bytes)) and + os.path.isfile(objekt)): + if hash_method is None: + hash_method = config.get('execution', 'hash_method') + + if hash_method.lower() == 'timestamp': + hash = hash_timestamp(objekt) + elif hash_method.lower() == 'content': + hash = hash_infile(objekt) + else: + raise Exception("Unknown hash method: %s" % hash_method) + if dictwithhash: + out = (objekt, hash) + else: + out = hash + elif isinstance(objekt, float): + out = FLOAT_FORMAT(objekt) + else: + out = objekt + return out + + +class TraitedSpec(BaseTraitedSpec): + """ Create a subclass with strict traits. + + This is used in 90% of the cases. + """ + _ = traits.Disallow + + +class BaseInterfaceInputSpec(TraitedSpec): + ignore_exception = traits.Bool(False, usedefault=True, nohash=True, deprecated='1.0.0', + desc='Print an error message instead of throwing an exception ' + 'in case the interface fails to run') + + +class DynamicTraitedSpec(BaseTraitedSpec): + """ A subclass to handle dynamic traits + + This class is a workaround for add_traits and clone_traits not + functioning well together. + """ + + def __deepcopy__(self, memo): + """ bug in deepcopy for HasTraits results in weird cloning behavior for + added traits + """ + id_self = id(self) + if id_self in memo: + return memo[id_self] + dup_dict = deepcopy(self.get(), memo) + # access all keys + for key in self.copyable_trait_names(): + if key in self.__dict__.keys(): + _ = getattr(self, key) + # clone once + dup = self.clone_traits(memo=memo) + for key in self.copyable_trait_names(): + try: + _ = getattr(dup, key) + except: + pass + # clone twice + dup = self.clone_traits(memo=memo) + dup.trait_set(**dup_dict) + return dup + + +class CommandLineInputSpec(BaseInterfaceInputSpec): + args = traits.Str(argstr='%s', desc='Additional parameters to the command') + environ = traits.DictStrStr(desc='Environment variables', usedefault=True, + nohash=True) + # This input does not have a "usedefault=True" so the set_default_terminal_output() + # method would work + terminal_output = traits.Enum('stream', 'allatonce', 'file', 'none', + deprecated='1.0.0', + desc=('Control terminal output: `stream` - ' + 'displays to terminal immediately (default), ' + '`allatonce` - waits till command is ' + 'finished to display output, `file` - ' + 'writes output to file, `none` - output' + ' is ignored'), + nohash=True) + + +class StdOutCommandLineInputSpec(CommandLineInputSpec): + out_file = traits.File(argstr="> %s", position=-1, genfile=True) + + +class MpiCommandLineInputSpec(CommandLineInputSpec): + use_mpi = traits.Bool(False, + desc="Whether or not to run the command with mpiexec", + usedefault=True) + n_procs = traits.Int(desc="Num processors to specify to mpiexec. Do not " + "specify if this is managed externally (e.g. through " + "SGE)") diff --git a/nipype/interfaces/base/support.py b/nipype/interfaces/base/support.py new file mode 100644 index 0000000000..f047cd120f --- /dev/null +++ b/nipype/interfaces/base/support.py @@ -0,0 +1,302 @@ +# -*- 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: +""" + +Miscellaneous tools to support Interface functionality +...................................................... + +""" +from __future__ import print_function, division, unicode_literals, absolute_import +from builtins import range, object, str + +import os +from copy import deepcopy + +import datetime +import locale + +from ... import logging +from ...utils.misc import is_container +from ...utils.filemanip import md5, to_str, hash_infile +iflogger = logging.getLogger('interface') + + +class NipypeInterfaceError(Exception): + """Custom error for interfaces""" + + def __init__(self, value): + self.value = value + + def __str__(self): + return '{}'.format(self.value) + + +class Bunch(object): + """Dictionary-like class that provides attribute-style access to it's items. + + A `Bunch` is a simple container that stores it's items as class + attributes. Internally all items are stored in a dictionary and + the class exposes several of the dictionary methods. + + Examples + -------- + >>> from nipype.interfaces.base import Bunch + >>> inputs = Bunch(infile='subj.nii', fwhm=6.0, register_to_mean=True) + >>> inputs + Bunch(fwhm=6.0, infile='subj.nii', register_to_mean=True) + >>> inputs.register_to_mean = False + >>> inputs + Bunch(fwhm=6.0, infile='subj.nii', register_to_mean=False) + + Notes + ----- + The Bunch pattern came from the Python Cookbook: + + .. [1] A. Martelli, D. Hudgeon, "Collecting a Bunch of Named + Items", Python Cookbook, 2nd Ed, Chapter 4.18, 2005. + + """ + + def __init__(self, *args, **kwargs): + self.__dict__.update(*args, **kwargs) + + def update(self, *args, **kwargs): + """update existing attribute, or create new attribute + + Note: update is very much like HasTraits.set""" + self.__dict__.update(*args, **kwargs) + + def items(self): + """iterates over bunch attributes as key, value pairs""" + return list(self.__dict__.items()) + + def iteritems(self): + """iterates over bunch attributes as key, value pairs""" + iflogger.warning('iteritems is deprecated, use items instead') + return list(self.items()) + + def get(self, *args): + """Support dictionary get() functionality + """ + return self.__dict__.get(*args) + + def set(self, **kwargs): + """Support dictionary get() functionality + """ + return self.__dict__.update(**kwargs) + + def dictcopy(self): + """returns a deep copy of existing Bunch as a dictionary""" + return deepcopy(self.__dict__) + + def __repr__(self): + """representation of the sorted Bunch as a string + + Currently, this string representation of the `inputs` Bunch of + interfaces is hashed to determine if the process' dirty-bit + needs setting or not. Till that mechanism changes, only alter + this after careful consideration. + """ + outstr = ['Bunch('] + first = True + for k, v in sorted(self.items()): + if not first: + outstr.append(', ') + if isinstance(v, dict): + pairs = [] + for key, value in sorted(v.items()): + pairs.append("'%s': %s" % (key, value)) + v = '{' + ', '.join(pairs) + '}' + outstr.append('%s=%s' % (k, v)) + else: + outstr.append('%s=%r' % (k, v)) + first = False + outstr.append(')') + return ''.join(outstr) + + def _get_bunch_hash(self): + """Return a dictionary of our items with hashes for each file. + + Searches through dictionary items and if an item is a file, it + calculates the md5 hash of the file contents and stores the + file name and hash value as the new key value. + + However, the overall bunch hash is calculated only on the hash + value of a file. The path and name of the file are not used in + the overall hash calculation. + + Returns + ------- + dict_withhash : dict + Copy of our dictionary with the new file hashes included + with each file. + hashvalue : str + The md5 hash value of the `dict_withhash` + + """ + + infile_list = [] + for key, val in list(self.items()): + if is_container(val): + # XXX - SG this probably doesn't catch numpy arrays + # containing embedded file names either. + if isinstance(val, dict): + # XXX - SG should traverse dicts, but ignoring for now + item = None + else: + if len(val) == 0: + raise AttributeError('%s attribute is empty' % key) + item = val[0] + else: + item = val + try: + if isinstance(item, str) and os.path.isfile(item): + infile_list.append(key) + except TypeError: + # `item` is not a file or string. + continue + dict_withhash = self.dictcopy() + dict_nofilename = self.dictcopy() + for item in infile_list: + dict_withhash[item] = _hash_bunch_dict(dict_withhash, item) + dict_nofilename[item] = [val[1] for val in dict_withhash[item]] + # Sort the items of the dictionary, before hashing the string + # representation so we get a predictable order of the + # dictionary. + sorted_dict = to_str(sorted(dict_nofilename.items())) + return dict_withhash, md5(sorted_dict.encode()).hexdigest() + + def __pretty__(self, p, cycle): + """Support for the pretty module + + pretty is included in ipython.externals for ipython > 0.10""" + if cycle: + p.text('Bunch(...)') + else: + p.begin_group(6, 'Bunch(') + first = True + for k, v in sorted(self.items()): + if not first: + p.text(',') + p.breakable() + p.text(k + '=') + p.pretty(v) + first = False + p.end_group(6, ')') + + +def _hash_bunch_dict(adict, key): + """Inject file hashes into adict[key]""" + stuff = adict[key] + if not is_container(stuff): + stuff = [stuff] + return [(afile, hash_infile(afile)) + for afile in stuff] + + +class InterfaceResult(object): + """Object that contains the results of running a particular Interface. + + Attributes + ---------- + version : version of this Interface result object (a readonly property) + interface : class type + A copy of the `Interface` class that was run to generate this result. + inputs : a traits free representation of the inputs + outputs : Bunch + An `Interface` specific Bunch that contains all possible files + that are generated by the interface. The `outputs` are used + as the `inputs` to another node when interfaces are used in + the pipeline. + runtime : Bunch + + Contains attributes that describe the runtime environment when + the `Interface` was run. Contains the attributes: + + * cmdline : The command line string that was executed + * cwd : The directory the ``cmdline`` was executed in. + * stdout : The output of running the ``cmdline``. + * stderr : Any error messages output from running ``cmdline``. + * returncode : The code returned from running the ``cmdline``. + + """ + + def __init__(self, interface, runtime, inputs=None, outputs=None, + provenance=None): + self._version = 2.0 + self.interface = interface + self.runtime = runtime + self.inputs = inputs + self.outputs = outputs + self.provenance = provenance + + @property + def version(self): + return self._version + + +class Stream(object): + """Function to capture stdout and stderr streams with timestamps + + stackoverflow.com/questions/4984549/merge-and-sync-stdout-and-stderr/5188359 + """ + + def __init__(self, name, impl): + self._name = name + self._impl = impl + self._buf = '' + self._rows = [] + self._lastidx = 0 + self.default_encoding = locale.getdefaultlocale()[1] or 'UTF-8' + + def fileno(self): + "Pass-through for file descriptor." + return self._impl.fileno() + + def read(self, drain=0): + "Read from the file descriptor. If 'drain' set, read until EOF." + while self._read(drain) is not None: + if not drain: + break + + def _read(self, drain): + "Read from the file descriptor" + fd = self.fileno() + buf = os.read(fd, 4096).decode(self.default_encoding) + if not buf and not self._buf: + return None + if '\n' not in buf: + if not drain: + self._buf += buf + return [] + + # prepend any data previously read, then split into lines and format + buf = self._buf + buf + if '\n' in buf: + tmp, rest = buf.rsplit('\n', 1) + else: + tmp = buf + rest = None + self._buf = rest + now = datetime.datetime.now().isoformat() + rows = tmp.split('\n') + self._rows += [(now, '%s %s:%s' % (self._name, now, r), r) + for r in rows] + for idx in range(self._lastidx, len(self._rows)): + iflogger.info(self._rows[idx][1]) + self._lastidx = len(self._rows) + + +def load_template(name): + """ + Deprecated stub for backwards compatibility, + please use nipype.interfaces.fsl.model.load_template + + """ + from ..fsl.model import load_template + iflogger.warning( + 'Deprecated in 1.0.0, and will be removed in 1.1.0, ' + 'please use nipype.interfaces.fsl.model.load_template instead.' + ) + return load_template(name) diff --git a/nipype/interfaces/base/tests/__init__.py b/nipype/interfaces/base/tests/__init__.py new file mode 100644 index 0000000000..40a96afc6f --- /dev/null +++ b/nipype/interfaces/base/tests/__init__.py @@ -0,0 +1 @@ +# -*- coding: utf-8 -*- diff --git a/nipype/interfaces/tests/test_auto_BaseInterface.py b/nipype/interfaces/base/tests/test_auto_BaseInterface.py similarity index 76% rename from nipype/interfaces/tests/test_auto_BaseInterface.py rename to nipype/interfaces/base/tests/test_auto_BaseInterface.py index 9c1f2cfaa6..33652036c7 100644 --- a/nipype/interfaces/tests/test_auto_BaseInterface.py +++ b/nipype/interfaces/base/tests/test_auto_BaseInterface.py @@ -1,10 +1,11 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..base import BaseInterface +from ..core import BaseInterface def test_BaseInterface_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_CommandLine.py b/nipype/interfaces/base/tests/test_auto_CommandLine.py similarity index 85% rename from nipype/interfaces/tests/test_auto_CommandLine.py rename to nipype/interfaces/base/tests/test_auto_CommandLine.py index c5904dda69..8154f73a3d 100644 --- a/nipype/interfaces/tests/test_auto_CommandLine.py +++ b/nipype/interfaces/base/tests/test_auto_CommandLine.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..base import CommandLine +from ..core import CommandLine def test_CommandLine_inputs(): @@ -9,7 +9,8 @@ def test_CommandLine_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), terminal_output=dict(deprecated='1.0.0', diff --git a/nipype/interfaces/tests/test_auto_MpiCommandLine.py b/nipype/interfaces/base/tests/test_auto_MpiCommandLine.py similarity index 86% rename from nipype/interfaces/tests/test_auto_MpiCommandLine.py rename to nipype/interfaces/base/tests/test_auto_MpiCommandLine.py index 3a5841e198..644de736ba 100644 --- a/nipype/interfaces/tests/test_auto_MpiCommandLine.py +++ b/nipype/interfaces/base/tests/test_auto_MpiCommandLine.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..base import MpiCommandLine +from ..core import MpiCommandLine def test_MpiCommandLine_inputs(): @@ -9,7 +9,8 @@ def test_MpiCommandLine_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), n_procs=dict(), diff --git a/nipype/interfaces/base/tests/test_auto_SEMLikeCommandLine.py b/nipype/interfaces/base/tests/test_auto_SEMLikeCommandLine.py new file mode 100644 index 0000000000..98ee386ee4 --- /dev/null +++ b/nipype/interfaces/base/tests/test_auto_SEMLikeCommandLine.py @@ -0,0 +1,25 @@ +# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT +from __future__ import unicode_literals +from ..core import SEMLikeCommandLine + + +def test_SEMLikeCommandLine_inputs(): + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(deprecated='1.0.0', + nohash=True, + usedefault=True, + ), + terminal_output=dict(deprecated='1.0.0', + nohash=True, + ), + ) + inputs = SEMLikeCommandLine.input_spec() + + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): + assert getattr(inputs.traits()[key], metakey) == value + diff --git a/nipype/interfaces/tests/test_auto_SimpleInterface.py b/nipype/interfaces/base/tests/test_auto_SimpleInterface.py similarity index 76% rename from nipype/interfaces/tests/test_auto_SimpleInterface.py rename to nipype/interfaces/base/tests/test_auto_SimpleInterface.py index b00d1f9a3c..6c19b125f2 100644 --- a/nipype/interfaces/tests/test_auto_SimpleInterface.py +++ b/nipype/interfaces/base/tests/test_auto_SimpleInterface.py @@ -1,10 +1,11 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..base import SimpleInterface +from ..core import SimpleInterface def test_SimpleInterface_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_StdOutCommandLine.py b/nipype/interfaces/base/tests/test_auto_StdOutCommandLine.py similarity index 86% rename from nipype/interfaces/tests/test_auto_StdOutCommandLine.py rename to nipype/interfaces/base/tests/test_auto_StdOutCommandLine.py index ad49a04abb..a876e1b61e 100644 --- a/nipype/interfaces/tests/test_auto_StdOutCommandLine.py +++ b/nipype/interfaces/base/tests/test_auto_StdOutCommandLine.py @@ -1,6 +1,6 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from __future__ import unicode_literals -from ..base import StdOutCommandLine +from ..core import StdOutCommandLine def test_StdOutCommandLine_inputs(): @@ -9,7 +9,8 @@ def test_StdOutCommandLine_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), out_file=dict(argstr='> %s', diff --git a/nipype/interfaces/base/tests/test_core.py b/nipype/interfaces/base/tests/test_core.py new file mode 100644 index 0000000000..1eb2cf4b42 --- /dev/null +++ b/nipype/interfaces/base/tests/test_core.py @@ -0,0 +1,473 @@ +# -*- 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: +from __future__ import print_function, unicode_literals +from future import standard_library +from builtins import open +import os +import simplejson as json + +import pytest + +from .... import config +from ....testing import example_data +from ... import base as nib + +standard_library.install_aliases() + + +def check_dict(ref_dict, tst_dict): + """Compare dictionaries of inputs and and those loaded from json files""" + def to_list(x): + if isinstance(x, tuple): + x = list(x) + + if isinstance(x, list): + for i, xel in enumerate(x): + x[i] = to_list(xel) + + return x + + failed_dict = {} + for key, value in list(ref_dict.items()): + newval = to_list(tst_dict[key]) + if newval != value: + failed_dict[key] = (value, newval) + return failed_dict + + +def test_Interface(): + assert nib.Interface.input_spec is None + assert nib.Interface.output_spec is None + with pytest.raises(NotImplementedError): + nib.Interface() + with pytest.raises(NotImplementedError): + nib.Interface.help() + with pytest.raises(NotImplementedError): + nib.Interface._inputs_help() + with pytest.raises(NotImplementedError): + nib.Interface._outputs_help() + with pytest.raises(NotImplementedError): + nib.Interface._outputs() + + class DerivedInterface(nib.Interface): + def __init__(self): + pass + + nif = DerivedInterface() + with pytest.raises(NotImplementedError): + nif.run() + with pytest.raises(NotImplementedError): + nif.aggregate_outputs() + with pytest.raises(NotImplementedError): + nif._list_outputs() + with pytest.raises(NotImplementedError): + nif._get_filecopy_info() + + +def test_BaseInterface(): + config.set('monitoring', 'enable', '0') + + assert nib.BaseInterface.help() is None + assert nib.BaseInterface._get_filecopy_info() == [] + + class InputSpec(nib.TraitedSpec): + foo = nib.traits.Int(desc='a random int') + goo = nib.traits.Int(desc='a random int', mandatory=True) + moo = nib.traits.Int(desc='a random int', mandatory=False) + hoo = nib.traits.Int(desc='a random int', usedefault=True) + zoo = nib.File(desc='a file', copyfile=False) + woo = nib.File(desc='a file', copyfile=True) + + class OutputSpec(nib.TraitedSpec): + foo = nib.traits.Int(desc='a random int') + + class DerivedInterface(nib.BaseInterface): + input_spec = InputSpec + resource_monitor = False + + assert DerivedInterface.help() is None + assert 'moo' in ''.join(DerivedInterface._inputs_help()) + assert DerivedInterface()._outputs() is None + assert DerivedInterface._get_filecopy_info()[0]['key'] == 'woo' + assert DerivedInterface._get_filecopy_info()[0]['copy'] + assert DerivedInterface._get_filecopy_info()[1]['key'] == 'zoo' + assert not DerivedInterface._get_filecopy_info()[1]['copy'] + assert DerivedInterface().inputs.foo == nib.Undefined + with pytest.raises(ValueError): + DerivedInterface()._check_mandatory_inputs() + assert DerivedInterface(goo=1)._check_mandatory_inputs() is None + with pytest.raises(ValueError): + DerivedInterface().run() + with pytest.raises(NotImplementedError): + DerivedInterface(goo=1).run() + + class DerivedInterface2(DerivedInterface): + output_spec = OutputSpec + + def _run_interface(self, runtime): + return runtime + + assert DerivedInterface2.help() is None + assert DerivedInterface2()._outputs().foo == nib.Undefined + with pytest.raises(NotImplementedError): + DerivedInterface2(goo=1).run() + + default_inpu_spec = nib.BaseInterface.input_spec + nib.BaseInterface.input_spec = None + with pytest.raises(Exception): + nib.BaseInterface() + nib.BaseInterface.input_spec = default_inpu_spec + + +def test_BaseInterface_load_save_inputs(tmpdir): + tmp_json = tmpdir.join('settings.json').strpath + + class InputSpec(nib.TraitedSpec): + input1 = nib.traits.Int() + input2 = nib.traits.Float() + input3 = nib.traits.Bool() + input4 = nib.traits.Str() + + class DerivedInterface(nib.BaseInterface): + input_spec = InputSpec + + def __init__(self, **inputs): + super(DerivedInterface, self).__init__(**inputs) + + inputs_dict = {'input1': 12, 'input3': True, + 'input4': 'some string'} + bif = DerivedInterface(**inputs_dict) + bif.save_inputs_to_json(tmp_json) + bif2 = DerivedInterface() + bif2.load_inputs_from_json(tmp_json) + assert bif2.inputs.get_traitsfree() == inputs_dict + + bif3 = DerivedInterface(from_file=tmp_json) + assert bif3.inputs.get_traitsfree() == inputs_dict + + inputs_dict2 = inputs_dict.copy() + inputs_dict2.update({'input4': 'some other string'}) + bif4 = DerivedInterface(from_file=tmp_json, input4=inputs_dict2['input4']) + assert bif4.inputs.get_traitsfree() == inputs_dict2 + + bif5 = DerivedInterface(input4=inputs_dict2['input4']) + bif5.load_inputs_from_json(tmp_json, overwrite=False) + assert bif5.inputs.get_traitsfree() == inputs_dict2 + + bif6 = DerivedInterface(input4=inputs_dict2['input4']) + bif6.load_inputs_from_json(tmp_json) + assert bif6.inputs.get_traitsfree() == inputs_dict + + # test get hashval in a complex interface + from nipype.interfaces.ants import Registration + settings = example_data(example_data('smri_ants_registration_settings.json')) + with open(settings) as setf: + data_dict = json.load(setf) + + tsthash = Registration() + tsthash.load_inputs_from_json(settings) + assert {} == check_dict(data_dict, tsthash.inputs.get_traitsfree()) + + tsthash2 = Registration(from_file=settings) + assert {} == check_dict(data_dict, tsthash2.inputs.get_traitsfree()) + + _, hashvalue = tsthash.inputs.get_hashval(hash_method='timestamp') + assert 'ec5755e07287e04a4b409e03b77a517c' == hashvalue + + +def test_input_version(): + class InputSpec(nib.TraitedSpec): + foo = nib.traits.Int(desc='a random int', min_ver='0.9') + + class DerivedInterface1(nib.BaseInterface): + input_spec = InputSpec + obj = DerivedInterface1() + obj._check_version_requirements(obj.inputs) + + config.set('execution', 'stop_on_unknown_version', True) + + with pytest.raises(Exception): + obj._check_version_requirements(obj.inputs) + + config.set_default_config() + + class InputSpec(nib.TraitedSpec): + foo = nib.traits.Int(desc='a random int', min_ver='0.9') + + class DerivedInterface1(nib.BaseInterface): + input_spec = InputSpec + _version = '0.8' + obj = DerivedInterface1() + obj.inputs.foo = 1 + with pytest.raises(Exception): + obj._check_version_requirements() + + class InputSpec(nib.TraitedSpec): + foo = nib.traits.Int(desc='a random int', min_ver='0.9') + + class DerivedInterface1(nib.BaseInterface): + input_spec = InputSpec + _version = '0.10' + obj = DerivedInterface1() + obj._check_version_requirements(obj.inputs) + + class InputSpec(nib.TraitedSpec): + foo = nib.traits.Int(desc='a random int', min_ver='0.9') + + class DerivedInterface1(nib.BaseInterface): + input_spec = InputSpec + _version = '0.9' + obj = DerivedInterface1() + obj.inputs.foo = 1 + obj._check_version_requirements(obj.inputs) + + class InputSpec(nib.TraitedSpec): + foo = nib.traits.Int(desc='a random int', max_ver='0.7') + + class DerivedInterface2(nib.BaseInterface): + input_spec = InputSpec + _version = '0.8' + obj = DerivedInterface2() + obj.inputs.foo = 1 + with pytest.raises(Exception): + obj._check_version_requirements() + + class InputSpec(nib.TraitedSpec): + foo = nib.traits.Int(desc='a random int', max_ver='0.9') + + class DerivedInterface1(nib.BaseInterface): + input_spec = InputSpec + _version = '0.9' + obj = DerivedInterface1() + obj.inputs.foo = 1 + obj._check_version_requirements(obj.inputs) + + +def test_output_version(): + class InputSpec(nib.TraitedSpec): + foo = nib.traits.Int(desc='a random int') + + class OutputSpec(nib.TraitedSpec): + foo = nib.traits.Int(desc='a random int', min_ver='0.9') + + class DerivedInterface1(nib.BaseInterface): + input_spec = InputSpec + output_spec = OutputSpec + _version = '0.10' + resource_monitor = False + + obj = DerivedInterface1() + assert obj._check_version_requirements(obj._outputs()) == [] + + class InputSpec(nib.TraitedSpec): + foo = nib.traits.Int(desc='a random int') + + class OutputSpec(nib.TraitedSpec): + foo = nib.traits.Int(desc='a random int', min_ver='0.11') + + class DerivedInterface1(nib.BaseInterface): + input_spec = InputSpec + output_spec = OutputSpec + _version = '0.10' + resource_monitor = False + + obj = DerivedInterface1() + assert obj._check_version_requirements(obj._outputs()) == ['foo'] + + class InputSpec(nib.TraitedSpec): + foo = nib.traits.Int(desc='a random int') + + class OutputSpec(nib.TraitedSpec): + foo = nib.traits.Int(desc='a random int', min_ver='0.11') + + class DerivedInterface1(nib.BaseInterface): + input_spec = InputSpec + output_spec = OutputSpec + _version = '0.10' + resource_monitor = False + + def _run_interface(self, runtime): + return runtime + + def _list_outputs(self): + return {'foo': 1} + obj = DerivedInterface1() + with pytest.raises(KeyError): + obj.run() + + +def test_Commandline(): + with pytest.raises(Exception): + nib.CommandLine() + ci = nib.CommandLine(command='which') + assert ci.cmd == 'which' + assert ci.inputs.args == nib.Undefined + ci2 = nib.CommandLine(command='which', args='ls') + assert ci2.cmdline == 'which ls' + ci3 = nib.CommandLine(command='echo') + ci3.resource_monitor = False + ci3.inputs.environ = {'MYENV': 'foo'} + res = ci3.run() + assert res.runtime.environ['MYENV'] == 'foo' + assert res.outputs is None + + class CommandLineInputSpec1(nib.CommandLineInputSpec): + foo = nib.Str(argstr='%s', desc='a str') + goo = nib.traits.Bool(argstr='-g', desc='a bool', position=0) + hoo = nib.traits.List(argstr='-l %s', desc='a list') + moo = nib.traits.List(argstr='-i %d...', desc='a repeated list', + position=-1) + noo = nib.traits.Int(argstr='-x %d', desc='an int') + roo = nib.traits.Str(desc='not on command line') + soo = nib.traits.Bool(argstr="-soo") + + nib.CommandLine.input_spec = CommandLineInputSpec1 + ci4 = nib.CommandLine(command='cmd') + ci4.inputs.foo = 'foo' + ci4.inputs.goo = True + ci4.inputs.hoo = ['a', 'b'] + ci4.inputs.moo = [1, 2, 3] + ci4.inputs.noo = 0 + ci4.inputs.roo = 'hello' + ci4.inputs.soo = False + cmd = ci4._parse_inputs() + assert cmd[0] == '-g' + assert cmd[-1] == '-i 1 -i 2 -i 3' + assert 'hello' not in ' '.join(cmd) + assert '-soo' not in ' '.join(cmd) + ci4.inputs.soo = True + cmd = ci4._parse_inputs() + assert '-soo' in ' '.join(cmd) + + class CommandLineInputSpec2(nib.CommandLineInputSpec): + foo = nib.File(argstr='%s', desc='a str', genfile=True) + nib.CommandLine.input_spec = CommandLineInputSpec2 + ci5 = nib.CommandLine(command='cmd') + with pytest.raises(NotImplementedError): + ci5._parse_inputs() + + class DerivedClass(nib.CommandLine): + input_spec = CommandLineInputSpec2 + + def _gen_filename(self, name): + return 'filename' + + ci6 = DerivedClass(command='cmd') + assert ci6._parse_inputs()[0] == 'filename' + nib.CommandLine.input_spec = nib.CommandLineInputSpec + + +def test_Commandline_environ(monkeypatch, tmpdir): + from nipype import config + config.set_default_config() + + tmpdir.chdir() + monkeypatch.setitem(os.environ, 'DISPLAY', ':1') + # Test environment + ci3 = nib.CommandLine(command='echo') + res = ci3.run() + assert res.runtime.environ['DISPLAY'] == ':1' + + # Test display_variable option + monkeypatch.delitem(os.environ, 'DISPLAY', raising=False) + config.set('execution', 'display_variable', ':3') + res = ci3.run() + assert 'DISPLAY' not in ci3.inputs.environ + assert 'DISPLAY' not in res.runtime.environ + + # If the interface has _redirect_x then yes, it should be set + ci3._redirect_x = True + res = ci3.run() + assert res.runtime.environ['DISPLAY'] == ':3' + + # Test overwrite + monkeypatch.setitem(os.environ, 'DISPLAY', ':1') + ci3.inputs.environ = {'DISPLAY': ':2'} + res = ci3.run() + assert res.runtime.environ['DISPLAY'] == ':2' + + +def test_CommandLine_output(tmpdir): + # Create one file + tmpdir.chdir() + file = tmpdir.join('foo.txt') + file.write('123456\n') + name = os.path.basename(file.strpath) + + ci = nib.CommandLine(command='ls -l') + ci.terminal_output = 'allatonce' + res = ci.run() + assert res.runtime.merged == '' + assert name in res.runtime.stdout + + # Check stdout is written + ci = nib.CommandLine(command='ls -l') + ci.terminal_output = 'file_stdout' + res = ci.run() + assert os.path.isfile('stdout.nipype') + assert name in res.runtime.stdout + tmpdir.join('stdout.nipype').remove(ignore_errors=True) + + # Check stderr is written + ci = nib.CommandLine(command='ls -l') + ci.terminal_output = 'file_stderr' + res = ci.run() + assert os.path.isfile('stderr.nipype') + tmpdir.join('stderr.nipype').remove(ignore_errors=True) + + # Check outputs are thrown away + ci = nib.CommandLine(command='ls -l') + ci.terminal_output = 'none' + res = ci.run() + assert res.runtime.stdout == '' and \ + res.runtime.stderr == '' and \ + res.runtime.merged == '' + + # Check that new interfaces are set to default 'stream' + ci = nib.CommandLine(command='ls -l') + res = ci.run() + assert ci.terminal_output == 'stream' + assert name in res.runtime.stdout and \ + res.runtime.stderr == '' + + # Check only one file is generated + ci = nib.CommandLine(command='ls -l') + ci.terminal_output = 'file' + res = ci.run() + assert os.path.isfile('output.nipype') + assert name in res.runtime.merged and \ + res.runtime.stdout == '' and \ + res.runtime.stderr == '' + tmpdir.join('output.nipype').remove(ignore_errors=True) + + # Check split files are generated + ci = nib.CommandLine(command='ls -l') + ci.terminal_output = 'file_split' + res = ci.run() + assert os.path.isfile('stdout.nipype') + assert os.path.isfile('stderr.nipype') + assert name in res.runtime.stdout + + +def test_global_CommandLine_output(tmpdir): + """Ensures CommandLine.set_default_terminal_output works""" + from nipype.interfaces.fsl import BET + + ci = nib.CommandLine(command='ls -l') + assert ci.terminal_output == 'stream' # default case + + ci = BET() + assert ci.terminal_output == 'stream' # default case + + nib.CommandLine.set_default_terminal_output('allatonce') + ci = nib.CommandLine(command='ls -l') + assert ci.terminal_output == 'allatonce' + + nib.CommandLine.set_default_terminal_output('file') + ci = nib.CommandLine(command='ls -l') + assert ci.terminal_output == 'file' + + # Check default affects derived interfaces + ci = BET() + assert ci.terminal_output == 'file' diff --git a/nipype/interfaces/tests/test_resource_monitor.py b/nipype/interfaces/base/tests/test_resource_monitor.py similarity index 93% rename from nipype/interfaces/tests/test_resource_monitor.py rename to nipype/interfaces/base/tests/test_resource_monitor.py index a8b2b41a9e..88e71921c4 100644 --- a/nipype/interfaces/tests/test_resource_monitor.py +++ b/nipype/interfaces/base/tests/test_resource_monitor.py @@ -11,10 +11,10 @@ import pytest # Import packages -from nipype import config -from nipype.utils.profiler import _use_resources -from nipype.interfaces.base import traits, CommandLine, CommandLineInputSpec -from nipype.interfaces import utility as niu +from .... import config +from ....utils.profiler import _use_resources +from ...base import traits, CommandLine, CommandLineInputSpec +from ... import utility as niu # Try to enable the resource monitor config.enable_resource_monitor() diff --git a/nipype/interfaces/base/tests/test_specs.py b/nipype/interfaces/base/tests/test_specs.py new file mode 100644 index 0000000000..168e021339 --- /dev/null +++ b/nipype/interfaces/base/tests/test_specs.py @@ -0,0 +1,317 @@ +# -*- 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: +from __future__ import print_function, unicode_literals +from future import standard_library +import os +import warnings + +import pytest + +from ....utils.filemanip import split_filename +from ... import base as nib +from ...base import traits, Undefined + +standard_library.install_aliases() + + +@pytest.fixture(scope="module") +def setup_file(request, tmpdir_factory): + tmp_dir = tmpdir_factory.mktemp('files') + tmp_infile = tmp_dir.join('foo.txt') + with tmp_infile.open('w') as fp: + fp.writelines(['123456789']) + + tmp_dir.chdir() + + return tmp_infile.strpath + + +def test_TraitedSpec(): + assert nib.TraitedSpec().get_hashval() + assert nib.TraitedSpec().__repr__() == '\n\n' + + class spec(nib.TraitedSpec): + foo = nib.traits.Int + goo = nib.traits.Float(usedefault=True) + + assert spec().foo == Undefined + assert spec().goo == 0.0 + specfunc = lambda x: spec(hoo=x) + with pytest.raises(nib.traits.TraitError): + specfunc(1) + infields = spec(foo=1) + hashval = ([('foo', 1), ('goo', '0.0000000000')], 'e89433b8c9141aa0fda2f8f4d662c047') + assert infields.get_hashval() == hashval + assert infields.__repr__() == '\nfoo = 1\ngoo = 0.0\n' + + +@pytest.mark.skip +def test_TraitedSpec_dynamic(): + from pickle import dumps, loads + a = nib.BaseTraitedSpec() + a.add_trait('foo', nib.traits.Int) + a.foo = 1 + assign_a = lambda: setattr(a, 'foo', 'a') + with pytest.raises(Exception): + assign_a + pkld_a = dumps(a) + unpkld_a = loads(pkld_a) + assign_a_again = lambda: setattr(unpkld_a, 'foo', 'a') + with pytest.raises(Exception): + assign_a_again + + +def test_TraitedSpec_logic(): + class spec3(nib.TraitedSpec): + _xor_inputs = ('foo', 'bar') + + foo = nib.traits.Int(xor=_xor_inputs, + desc='foo or bar, not both') + bar = nib.traits.Int(xor=_xor_inputs, + desc='bar or foo, not both') + kung = nib.traits.Float(requires=('foo',), + position=0, + desc='kung foo') + + class out3(nib.TraitedSpec): + output = nib.traits.Int + + class MyInterface(nib.BaseInterface): + input_spec = spec3 + output_spec = out3 + + myif = MyInterface() + # NOTE_dj, FAIL: I don't get a TypeError, only a UserWarning + # with pytest.raises(TypeError): + # setattr(myif.inputs, 'kung', 10.0) + myif.inputs.foo = 1 + assert myif.inputs.foo == 1 + set_bar = lambda: setattr(myif.inputs, 'bar', 1) + with pytest.raises(IOError): + set_bar() + assert myif.inputs.foo == 1 + myif.inputs.kung = 2 + assert myif.inputs.kung == 2.0 + + +def test_deprecation(): + with warnings.catch_warnings(record=True) as w: + warnings.filterwarnings('always', '', UserWarning) + + class DeprecationSpec1(nib.TraitedSpec): + foo = nib.traits.Int(deprecated='0.1') + spec_instance = DeprecationSpec1() + set_foo = lambda: setattr(spec_instance, 'foo', 1) + with pytest.raises(nib.TraitError): + set_foo() + assert len(w) == 0, 'no warnings, just errors' + + with warnings.catch_warnings(record=True) as w: + warnings.filterwarnings('always', '', UserWarning) + + class DeprecationSpec2(nib.TraitedSpec): + foo = nib.traits.Int(deprecated='100', new_name='bar') + spec_instance = DeprecationSpec2() + set_foo = lambda: setattr(spec_instance, 'foo', 1) + with pytest.raises(nib.TraitError): + set_foo() + assert len(w) == 0, 'no warnings, just errors' + + with warnings.catch_warnings(record=True) as w: + warnings.filterwarnings('always', '', UserWarning) + + class DeprecationSpec3(nib.TraitedSpec): + foo = nib.traits.Int(deprecated='1000', new_name='bar') + bar = nib.traits.Int() + spec_instance = DeprecationSpec3() + not_raised = True + try: + spec_instance.foo = 1 + except nib.TraitError: + not_raised = False + assert not_raised + assert len(w) == 1, 'deprecated warning 1 %s' % [w1.message for w1 in w] + + with warnings.catch_warnings(record=True) as w: + warnings.filterwarnings('always', '', UserWarning) + + class DeprecationSpec3(nib.TraitedSpec): + foo = nib.traits.Int(deprecated='1000', new_name='bar') + bar = nib.traits.Int() + spec_instance = DeprecationSpec3() + not_raised = True + try: + spec_instance.foo = 1 + except nib.TraitError: + not_raised = False + assert not_raised + assert spec_instance.foo == Undefined + assert spec_instance.bar == 1 + assert len(w) == 1, 'deprecated warning 2 %s' % [w1.message for w1 in w] + + +def test_namesource(setup_file): + tmp_infile = setup_file + tmpd, nme, ext = split_filename(tmp_infile) + + class spec2(nib.CommandLineInputSpec): + moo = nib.File(name_source=['doo'], hash_files=False, argstr="%s", + position=2) + doo = nib.File(exists=True, argstr="%s", position=1) + goo = traits.Int(argstr="%d", position=4) + poo = nib.File(name_source=['goo'], hash_files=False, argstr="%s", + position=3) + + class TestName(nib.CommandLine): + _cmd = "mycommand" + input_spec = spec2 + testobj = TestName() + testobj.inputs.doo = tmp_infile + testobj.inputs.goo = 99 + assert '%s_generated' % nme in testobj.cmdline + assert '%d_generated' % testobj.inputs.goo in testobj.cmdline + testobj.inputs.moo = "my_%s_template" + assert 'my_%s_template' % nme in testobj.cmdline + + +def test_chained_namesource(setup_file): + tmp_infile = setup_file + tmpd, nme, ext = split_filename(tmp_infile) + + class spec2(nib.CommandLineInputSpec): + doo = nib.File(exists=True, argstr="%s", position=1) + moo = nib.File(name_source=['doo'], hash_files=False, argstr="%s", + position=2, name_template='%s_mootpl') + poo = nib.File(name_source=['moo'], hash_files=False, + argstr="%s", position=3) + + class TestName(nib.CommandLine): + _cmd = "mycommand" + input_spec = spec2 + + testobj = TestName() + testobj.inputs.doo = tmp_infile + res = testobj.cmdline + assert '%s' % tmp_infile in res + assert '%s_mootpl ' % nme in res + assert '%s_mootpl_generated' % nme in res + + +def test_cycle_namesource1(setup_file): + tmp_infile = setup_file + tmpd, nme, ext = split_filename(tmp_infile) + + class spec3(nib.CommandLineInputSpec): + moo = nib.File(name_source=['doo'], hash_files=False, argstr="%s", + position=1, name_template='%s_mootpl') + poo = nib.File(name_source=['moo'], hash_files=False, + argstr="%s", position=2) + doo = nib.File(name_source=['poo'], hash_files=False, + argstr="%s", position=3) + + class TestCycle(nib.CommandLine): + _cmd = "mycommand" + input_spec = spec3 + + # Check that an exception is raised + to0 = TestCycle() + not_raised = True + try: + to0.cmdline + except nib.NipypeInterfaceError: + not_raised = False + assert not not_raised + + +def test_cycle_namesource2(setup_file): + tmp_infile = setup_file + tmpd, nme, ext = split_filename(tmp_infile) + + class spec3(nib.CommandLineInputSpec): + moo = nib.File(name_source=['doo'], hash_files=False, argstr="%s", + position=1, name_template='%s_mootpl') + poo = nib.File(name_source=['moo'], hash_files=False, + argstr="%s", position=2) + doo = nib.File(name_source=['poo'], hash_files=False, + argstr="%s", position=3) + + class TestCycle(nib.CommandLine): + _cmd = "mycommand" + input_spec = spec3 + + # Check that loop can be broken by setting one of the inputs + to1 = TestCycle() + to1.inputs.poo = tmp_infile + + not_raised = True + try: + res = to1.cmdline + except nib.NipypeInterfaceError: + not_raised = False + print(res) + + assert not_raised + assert '%s' % tmp_infile in res + assert '%s_generated' % nme in res + assert '%s_generated_mootpl' % nme in res + + +def test_TraitedSpec_withFile(setup_file): + tmp_infile = setup_file + tmpd, nme = os.path.split(tmp_infile) + assert os.path.exists(tmp_infile) + + class spec2(nib.TraitedSpec): + moo = nib.File(exists=True) + doo = nib.traits.List(nib.File(exists=True)) + infields = spec2(moo=tmp_infile, doo=[tmp_infile]) + hashval = infields.get_hashval(hash_method='content') + assert hashval[1] == 'a00e9ee24f5bfa9545a515b7a759886b' + + +def test_TraitedSpec_withNoFileHashing(setup_file): + tmp_infile = setup_file + tmpd, nme = os.path.split(tmp_infile) + assert os.path.exists(tmp_infile) + + class spec2(nib.TraitedSpec): + moo = nib.File(exists=True, hash_files=False) + doo = nib.traits.List(nib.File(exists=True)) + infields = spec2(moo=nme, doo=[tmp_infile]) + hashval = infields.get_hashval(hash_method='content') + assert hashval[1] == '8da4669ff5d72f670a46ea3e7a203215' + + class spec3(nib.TraitedSpec): + moo = nib.File(exists=True, name_source="doo") + doo = nib.traits.List(nib.File(exists=True)) + infields = spec3(moo=nme, doo=[tmp_infile]) + hashval1 = infields.get_hashval(hash_method='content') + + class spec4(nib.TraitedSpec): + moo = nib.File(exists=True) + doo = nib.traits.List(nib.File(exists=True)) + infields = spec4(moo=nme, doo=[tmp_infile]) + hashval2 = infields.get_hashval(hash_method='content') + assert hashval1[1] != hashval2[1] + + +def test_ImageFile(): + x = nib.BaseInterface().inputs + + # setup traits + x.add_trait('nifti', nib.ImageFile(types=['nifti1', 'dicom'])) + x.add_trait('anytype', nib.ImageFile()) + x.add_trait('newtype', nib.ImageFile(types=['nifti10'])) + x.add_trait('nocompress', nib.ImageFile(types=['mgh'], + allow_compressed=False)) + + with pytest.raises(nib.TraitError): + x.nifti = 'test.mgz' + x.nifti = 'test.nii' + x.anytype = 'test.xml' + with pytest.raises(AttributeError): + x.newtype = 'test.nii' + with pytest.raises(nib.TraitError): + x.nocompress = 'test.nii.gz' + x.nocompress = 'test.mgh' diff --git a/nipype/interfaces/base/tests/test_support.py b/nipype/interfaces/base/tests/test_support.py new file mode 100644 index 0000000000..733501f5fd --- /dev/null +++ b/nipype/interfaces/base/tests/test_support.py @@ -0,0 +1,66 @@ +# -*- 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: +from __future__ import print_function, unicode_literals +import os +import pytest +from builtins import open +from future import standard_library +from pkg_resources import resource_filename as pkgrf + +from ....utils.filemanip import md5 +from ... import base as nib + +standard_library.install_aliases() + + +@pytest.mark.parametrize("args", [ + {}, + {'a': 1, 'b': [2, 3]} +]) +def test_bunch(args): + b = nib.Bunch(**args) + assert b.__dict__ == args + + +def test_bunch_attribute(): + b = nib.Bunch(a=1, b=[2, 3], c=None) + assert b.a == 1 + assert b.b == [2, 3] + assert b.c is None + + +def test_bunch_repr(): + b = nib.Bunch(b=2, c=3, a=dict(n=1, m=2)) + assert repr(b) == "Bunch(a={'m': 2, 'n': 1}, b=2, c=3)" + + +def test_bunch_methods(): + b = nib.Bunch(a=2) + b.update(a=3) + newb = b.dictcopy() + assert b.a == 3 + assert b.get('a') == 3 + assert b.get('badkey', 'otherthing') == 'otherthing' + assert b != newb + assert type(dict()) == type(newb) + assert newb['a'] == 3 + + +def test_bunch_hash(): + # NOTE: Since the path to the json file is included in the Bunch, + # the hash will be unique to each machine. + json_pth = pkgrf( + 'nipype', os.path.join('testing', 'data', 'realign_json.json')) + + b = nib.Bunch(infile=json_pth, + otherthing='blue', + yat=True) + newbdict, bhash = b._get_bunch_hash() + assert bhash == 'ddcc7b4ec5675df8cf317a48bd1857fa' + # Make sure the hash stored in the json file for `infile` is correct. + jshash = md5() + with open(json_pth, 'r') as fp: + jshash.update(fp.read().encode('utf-8')) + assert newbdict['infile'][0][1] == jshash.hexdigest() + assert newbdict['yat'] is True diff --git a/nipype/interfaces/traits_extension.py b/nipype/interfaces/base/traits_extension.py similarity index 71% rename from nipype/interfaces/traits_extension.py rename to nipype/interfaces/base/traits_extension.py index 0e84c15bce..18bdd003c2 100644 --- a/nipype/interfaces/traits_extension.py +++ b/nipype/interfaces/base/traits_extension.py @@ -1,7 +1,11 @@ # -*- 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: -"""This module contains Trait classes that we've pulled from the +""" +Traits extension +................ + +This module contains Trait classes that we've pulled from the traits source and fixed due to various bugs. File and Directory are redefined as the release version had dependencies on TraitsUI, which we do not want Nipype to depend on. At least not yet. @@ -18,13 +22,12 @@ """ from __future__ import print_function, division, unicode_literals, absolute_import -from builtins import filter, object, str, bytes +from builtins import str, bytes import os +import collections # perform all external trait imports here -import traits -if traits.__version__ < '3.7.0': - raise ImportError('Traits version 3.7.0 or higher must be installed') +from traits import __version__ as traits_version import traits.api as traits from traits.trait_handlers import TraitDictObject, TraitListObject from traits.trait_errors import TraitError @@ -32,9 +35,23 @@ from traits.api import BaseUnicode from traits.api import Unicode +from future import standard_library + +if traits_version < '3.7.0': + raise ImportError('Traits version 3.7.0 or higher must be installed') + +standard_library.install_aliases() + +class Str(Unicode): + """Replacement for the default traits.Str based in bytes""" + + +# Monkeypatch Str and DictStrStr for Python 2 compatibility +traits.Str = Str DictStrStr = traits.Dict((bytes, str), (bytes, str)) -Str = Unicode +traits.DictStrStr = DictStrStr + class BaseFile(BaseUnicode): """ Defines a trait whose value must be the name of a file. @@ -227,16 +244,17 @@ def __init__(self, value='', auto_set=False, entries=0, # - uncompressed (tuple[0]) extension # - compressed (tuple[1]) extension img_fmt_types = { - 'nifti1': [('.nii', '.nii.gz'), - (('.hdr', '.img'), ('.hdr', '.img.gz'))], - 'mgh': [('.mgh', '.mgz'), ('.mgh', '.mgh.gz')], - 'nifti2': [('.nii', '.nii.gz')], - 'cifti2': [('.nii', '.nii.gz')], - 'gifti': [('.gii', '.gii.gz')], - 'dicom': [('.dcm', '.dcm'), ('.IMA', '.IMA'), ('.tar', '.tar.gz')], - 'nrrd': [('.nrrd', 'nrrd'), ('nhdr', 'nhdr')], - 'afni': [('.HEAD', '.HEAD'), ('.BRIK', '.BRIK')] - } + 'nifti1': [('.nii', '.nii.gz'), + (('.hdr', '.img'), ('.hdr', '.img.gz'))], + 'mgh': [('.mgh', '.mgz'), ('.mgh', '.mgh.gz')], + 'nifti2': [('.nii', '.nii.gz')], + 'cifti2': [('.nii', '.nii.gz')], + 'gifti': [('.gii', '.gii.gz')], + 'dicom': [('.dcm', '.dcm'), ('.IMA', '.IMA'), ('.tar', '.tar.gz')], + 'nrrd': [('.nrrd', 'nrrd'), ('nhdr', 'nhdr')], + 'afni': [('.HEAD', '.HEAD'), ('.BRIK', '.BRIK')] +} + class ImageFile(File): """ Defines a trait of specific neuroimaging files """ @@ -334,3 +352,117 @@ def has_metadata(trait, metadata, value=None, recursive=True): count += has_metadata(handler, metadata, recursive) return count > 0 + + +class MultiPath(traits.List): + """ Abstract class - shared functionality of input and output MultiPath + """ + + def validate(self, object, name, value): + + # want to treat range and other sequences (except str) as list + if not isinstance(value, (str, bytes)) and isinstance(value, collections.Sequence): + value = list(value) + + if not isdefined(value) or \ + (isinstance(value, list) and len(value) == 0): + return Undefined + + newvalue = value + + if not isinstance(value, list) \ + or (self.inner_traits() and + isinstance(self.inner_traits()[0].trait_type, + traits.List) and not + isinstance(self.inner_traits()[0].trait_type, + InputMultiPath) and + isinstance(value, list) and + value and not + isinstance(value[0], list)): + newvalue = [value] + value = super(MultiPath, self).validate(object, name, newvalue) + + if value: + return value + + self.error(object, name, value) + + +class OutputMultiPath(MultiPath): + """ Implements a user friendly traits that accepts one or more + paths to files or directories. This is the output version which + return a single string whenever possible (when it was set to a + single value or a list of length 1). Default value of this trait + is _Undefined. It does not accept empty lists. + + XXX This should only be used as a final resort. We should stick to + established Traits to the extent possible. + + XXX This needs to be vetted by somebody who understands traits + + >>> from nipype.interfaces.base import OutputMultiPath, TraitedSpec + >>> class A(TraitedSpec): + ... foo = OutputMultiPath(File(exists=False)) + >>> a = A() + >>> a.foo + + + >>> a.foo = '/software/temp/foo.txt' + >>> a.foo + '/software/temp/foo.txt' + + >>> a.foo = ['/software/temp/foo.txt'] + >>> a.foo + '/software/temp/foo.txt' + + >>> a.foo = ['/software/temp/foo.txt', '/software/temp/goo.txt'] + >>> a.foo + ['/software/temp/foo.txt', '/software/temp/goo.txt'] + + """ + + def get(self, object, name): + value = self.get_value(object, name) + if len(value) == 0: + return Undefined + elif len(value) == 1: + return value[0] + else: + return value + + def set(self, object, name, value): + self.set_value(object, name, value) + + +class InputMultiPath(MultiPath): + """ Implements a user friendly traits that accepts one or more + paths to files or directories. This is the input version which + always returns a list. Default value of this trait + is _Undefined. It does not accept empty lists. + + XXX This should only be used as a final resort. We should stick to + established Traits to the extent possible. + + XXX This needs to be vetted by somebody who understands traits + + >>> from nipype.interfaces.base import InputMultiPath, TraitedSpec + >>> class A(TraitedSpec): + ... foo = InputMultiPath(File(exists=False)) + >>> a = A() + >>> a.foo + + + >>> a.foo = '/software/temp/foo.txt' + >>> a.foo + ['/software/temp/foo.txt'] + + >>> a.foo = ['/software/temp/foo.txt'] + >>> a.foo + ['/software/temp/foo.txt'] + + >>> a.foo = ['/software/temp/foo.txt', '/software/temp/goo.txt'] + >>> a.foo + ['/software/temp/foo.txt', '/software/temp/goo.txt'] + + """ + pass diff --git a/nipype/interfaces/brainsuite/brainsuite.py b/nipype/interfaces/brainsuite/brainsuite.py index 21014f42ea..60141bcb00 100644 --- a/nipype/interfaces/brainsuite/brainsuite.py +++ b/nipype/interfaces/brainsuite/brainsuite.py @@ -5,7 +5,7 @@ import re as regex from ..base import TraitedSpec, CommandLineInputSpec, CommandLine, File, traits, isdefined -from ..traits_extension import str + """This script provides interfaces for BrainSuite command line tools. Please see brainsuite.org for more information. @@ -902,7 +902,7 @@ class SVRegInputSpec(CommandLineInputSpec): 'Cortical Surface Extraction Sequence' ) dataSinkDelay = traits.List( - str, argstr='%s', + traits.Str, argstr='%s', desc='Connect datasink out_file to dataSinkDelay to delay execution of SVReg ' 'until dataSink has finished sinking CSE outputs.' 'For use with parallel processing workflows including Brainsuites Cortical ' @@ -1087,7 +1087,7 @@ class BDPInputSpec(CommandLineInputSpec): 'bvec and .bval files can be used instead (see diffusionGradientFile and bValueFile). ' ) BVecBValPair = traits.List( - str, minlen=2, maxlen=2, mandatory=True, position=-1, xor=['bMatrixFile'], + traits.Str, minlen=2, maxlen=2, mandatory=True, position=-1, xor=['bMatrixFile'], argstr='--bvec %s --bval %s', desc='Must input a list containing first the BVector file, then the BValue file (both must be absolute paths)\n' 'Example: bdp.inputs.BVecBValPair = [\'/directory/subdir/prefix.dwi.bvec\', \'/directory/subdir/prefix.dwi.bval\'] ' @@ -1100,7 +1100,7 @@ class BDPInputSpec(CommandLineInputSpec): 'usually has an extension of .bvec ' ) dataSinkDelay = traits.List( - str, argstr='%s', + traits.Str, argstr='%s', desc='For use in parallel processing workflows including Brainsuite Cortical ' 'Surface Extraction sequence. Connect datasink out_file to dataSinkDelay ' 'to delay execution of BDP until dataSink has finished sinking outputs. ' diff --git a/nipype/interfaces/brainsuite/tests/test_auto_BDP.py b/nipype/interfaces/brainsuite/tests/test_auto_BDP.py index b9d7038198..8a3526360c 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_BDP.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_BDP.py @@ -68,7 +68,8 @@ def test_BDP_inputs(): ), ignoreMemory=dict(argstr='--ignore-memory', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputDiffusionData=dict(argstr='--nii %s', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py b/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py index 7102bed23e..8183daa886 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py @@ -31,7 +31,8 @@ def test_Bfc_inputs(): ), histogramType=dict(argstr='%s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputMRIFile=dict(argstr='-i %s', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Bse.py b/nipype/interfaces/brainsuite/tests/test_auto_Bse.py index 883c882aa1..d79dc8baa0 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Bse.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Bse.py @@ -21,7 +21,8 @@ def test_Bse_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputMRIFile=dict(argstr='-i %s', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py b/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py index 551bbb210b..ac78853d2b 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py @@ -12,7 +12,8 @@ def test_Cerebro_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputAtlasLabelFile=dict(argstr='--atlaslabels %s', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py b/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py index 909124518d..badbcd7738 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py @@ -14,7 +14,8 @@ def test_Cortex_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), includeAllSubcorticalAreas=dict(argstr='-a', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py b/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py index 4d02736074..b96d456fce 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py @@ -9,7 +9,8 @@ def test_Dewisp_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputMaskFile=dict(argstr='-i %s', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py b/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py index 4f76cad507..d9a1752fc7 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py @@ -12,7 +12,8 @@ def test_Dfs_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputShadingVolume=dict(argstr='-c %s', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py b/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py index 55ccba8ad1..3909149567 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py @@ -9,7 +9,8 @@ def test_Hemisplit_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputHemisphereLabelFile=dict(argstr='-l %s', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py b/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py index ee59e2e62f..d161e2e6c0 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py @@ -11,7 +11,8 @@ def test_Pialmesh_inputs(): ), exportPrefix=dict(argstr='--prefix %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputMaskFile=dict(argstr='-m %s', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py b/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py index c0d9dcdaf1..06695eab51 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py @@ -9,7 +9,8 @@ def test_Pvc_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputMRIFile=dict(argstr='-i %s', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_SVReg.py b/nipype/interfaces/brainsuite/tests/test_auto_SVReg.py index b270dc1d61..a5d7408cc6 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_SVReg.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_SVReg.py @@ -20,7 +20,8 @@ def test_SVReg_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), iterations=dict(argstr="'-H %d'", diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py b/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py index a902be5886..404ce27a25 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py @@ -15,7 +15,8 @@ def test_Scrubmask_inputs(): foregroundTrimThreshold=dict(argstr='-f %d', usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputMaskFile=dict(argstr='-i %s', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py b/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py index 5d75d4939c..254461d7eb 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py @@ -13,7 +13,8 @@ def test_Skullfinder_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputMRIFile=dict(argstr='-i %s', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Tca.py b/nipype/interfaces/brainsuite/tests/test_auto_Tca.py index 9301685533..ec25d193ba 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Tca.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Tca.py @@ -12,7 +12,8 @@ def test_Tca_inputs(): foregroundDelta=dict(argstr='--delta %d', usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputMaskFile=dict(argstr='-i %s', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py b/nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py index 7c055bd0c9..8956e36da5 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py @@ -9,7 +9,8 @@ def test_ThicknessPVC_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), subjectFilePrefix=dict(argstr='%s', diff --git a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py index e56eb84a99..953a2688ac 100644 --- a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py +++ b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py @@ -23,7 +23,8 @@ def test_AnalyzeHeader_inputs(): greylevels=dict(argstr='-gl %s', units='NA', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='< %s', diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py index c71c1371b3..422e6eceeb 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py @@ -9,7 +9,8 @@ def test_ComputeEigensystem_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='< %s', diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py index 311d9182b8..81afa66e5f 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py @@ -9,7 +9,8 @@ def test_ComputeFractionalAnisotropy_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='< %s', diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py index 09d5cbdc3e..9981b8d017 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py @@ -9,7 +9,8 @@ def test_ComputeMeanDiffusivity_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='< %s', diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py index da428ebe3f..c3a41aa877 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py @@ -9,7 +9,8 @@ def test_ComputeTensorTrace_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='< %s', diff --git a/nipype/interfaces/camino/tests/test_auto_Conmat.py b/nipype/interfaces/camino/tests/test_auto_Conmat.py index e447923f0b..b55c60be67 100644 --- a/nipype/interfaces/camino/tests/test_auto_Conmat.py +++ b/nipype/interfaces/camino/tests/test_auto_Conmat.py @@ -9,7 +9,8 @@ def test_Conmat_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-inputfile %s', diff --git a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py index bb5012e6c1..1de87ea032 100644 --- a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py +++ b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py @@ -13,7 +13,8 @@ def test_DT2NIfTI_inputs(): mandatory=True, position=3, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-inputfile %s', diff --git a/nipype/interfaces/camino/tests/test_auto_DTIFit.py b/nipype/interfaces/camino/tests/test_auto_DTIFit.py index d4907557dc..2210c1c41c 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/camino/tests/test_auto_DTIFit.py @@ -11,7 +11,8 @@ def test_DTIFit_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py index 2d6d73f6cc..77f8f701dd 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py @@ -17,7 +17,8 @@ def test_DTLUTGen_inputs(): position=1, units='NA', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inversion=dict(argstr='-inversion %d', diff --git a/nipype/interfaces/camino/tests/test_auto_DTMetric.py b/nipype/interfaces/camino/tests/test_auto_DTMetric.py index 191cf83ba1..ffb95b0e89 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTMetric.py +++ b/nipype/interfaces/camino/tests/test_auto_DTMetric.py @@ -14,7 +14,8 @@ def test_DTMetric_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', diff --git a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py index 5b37c42c6c..d3aaf0ec2e 100644 --- a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py +++ b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py @@ -29,7 +29,8 @@ def test_FSL2Scheme_inputs(): ), flipz=dict(argstr='-flipz', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), interleave=dict(argstr='-interleave', diff --git a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py index 88ee396011..bbb8690129 100644 --- a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py +++ b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py @@ -9,7 +9,8 @@ def test_Image2Voxel_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-4dimage %s', diff --git a/nipype/interfaces/camino/tests/test_auto_ImageStats.py b/nipype/interfaces/camino/tests/test_auto_ImageStats.py index 597683508a..be0425cd89 100644 --- a/nipype/interfaces/camino/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/camino/tests/test_auto_ImageStats.py @@ -9,7 +9,8 @@ def test_ImageStats_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='-images %s', diff --git a/nipype/interfaces/camino/tests/test_auto_LinRecon.py b/nipype/interfaces/camino/tests/test_auto_LinRecon.py index b0686a5bdf..193bf51422 100644 --- a/nipype/interfaces/camino/tests/test_auto_LinRecon.py +++ b/nipype/interfaces/camino/tests/test_auto_LinRecon.py @@ -11,7 +11,8 @@ def test_LinRecon_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/camino/tests/test_auto_MESD.py b/nipype/interfaces/camino/tests/test_auto_MESD.py index a3ee83b6b4..ccd2f94a0c 100644 --- a/nipype/interfaces/camino/tests/test_auto_MESD.py +++ b/nipype/interfaces/camino/tests/test_auto_MESD.py @@ -14,7 +14,8 @@ def test_MESD_inputs(): fastmesd=dict(argstr='-fastmesd', requires=['mepointset'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-inputfile %s', diff --git a/nipype/interfaces/camino/tests/test_auto_ModelFit.py b/nipype/interfaces/camino/tests/test_auto_ModelFit.py index 2ea5013e7b..bb88c3032b 100644 --- a/nipype/interfaces/camino/tests/test_auto_ModelFit.py +++ b/nipype/interfaces/camino/tests/test_auto_ModelFit.py @@ -19,7 +19,8 @@ def test_ModelFit_inputs(): ), fixedmodq=dict(argstr='-fixedmod %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-inputfile %s', diff --git a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py index ddd4acea8e..dd3c97bb5f 100644 --- a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py +++ b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py @@ -11,7 +11,8 @@ def test_NIfTIDT2Camino_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-inputfile %s', diff --git a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py index c55f63d155..db40520152 100644 --- a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py +++ b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py @@ -11,7 +11,8 @@ def test_PicoPDFs_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='< %s', diff --git a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py index f215857b99..ad2c4df2a5 100644 --- a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py @@ -25,7 +25,8 @@ def test_ProcStreamlines_inputs(): ), gzip=dict(argstr='-gzip', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-inputfile %s', diff --git a/nipype/interfaces/camino/tests/test_auto_QBallMX.py b/nipype/interfaces/camino/tests/test_auto_QBallMX.py index 473e8f8299..bcdf5ba627 100644 --- a/nipype/interfaces/camino/tests/test_auto_QBallMX.py +++ b/nipype/interfaces/camino/tests/test_auto_QBallMX.py @@ -12,7 +12,8 @@ def test_QBallMX_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), order=dict(argstr='-order %d', diff --git a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py index a0323eaf3e..3bb61363e1 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py @@ -14,7 +14,8 @@ def test_SFLUTGen_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-inputfile %s', diff --git a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py index adcdeaa946..2d2cbc6ba5 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py @@ -9,7 +9,8 @@ def test_SFPICOCalibData_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), info_file=dict(argstr='-infooutputfile %s', diff --git a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py index 2378fa4b82..00bb953015 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py @@ -12,7 +12,8 @@ def test_SFPeaks_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-inputfile %s', diff --git a/nipype/interfaces/camino/tests/test_auto_Shredder.py b/nipype/interfaces/camino/tests/test_auto_Shredder.py index 70f6e786e7..695c529d3c 100644 --- a/nipype/interfaces/camino/tests/test_auto_Shredder.py +++ b/nipype/interfaces/camino/tests/test_auto_Shredder.py @@ -13,7 +13,8 @@ def test_Shredder_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='< %s', diff --git a/nipype/interfaces/camino/tests/test_auto_Track.py b/nipype/interfaces/camino/tests/test_auto_Track.py index f10e7b4936..510a970f39 100644 --- a/nipype/interfaces/camino/tests/test_auto_Track.py +++ b/nipype/interfaces/camino/tests/test_auto_Track.py @@ -23,7 +23,8 @@ def test_Track_inputs(): ), gzip=dict(argstr='-gzip', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-inputfile %s', diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py index 361838512d..d422972863 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py @@ -23,7 +23,8 @@ def test_TrackBallStick_inputs(): ), gzip=dict(argstr='-gzip', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-inputfile %s', diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py index 36eedf11f5..9fd6c6caac 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py @@ -33,7 +33,8 @@ def test_TrackBayesDirac_inputs(): ), gzip=dict(argstr='-gzip', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-inputfile %s', diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py index 9da147ba7c..7d23187cd5 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py @@ -26,7 +26,8 @@ def test_TrackBedpostxDeter_inputs(): ), gzip=dict(argstr='-gzip', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-inputfile %s', diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py index 84a94870dd..37d2e719dd 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py @@ -26,7 +26,8 @@ def test_TrackBedpostxProba_inputs(): ), gzip=dict(argstr='-gzip', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-inputfile %s', diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py index 8449ae0301..6f340c75bf 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py @@ -28,7 +28,8 @@ def test_TrackBootstrap_inputs(): ), gzip=dict(argstr='-gzip', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-inputfile %s', diff --git a/nipype/interfaces/camino/tests/test_auto_TrackDT.py b/nipype/interfaces/camino/tests/test_auto_TrackDT.py index ef41e17b26..6e4e13fd67 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackDT.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackDT.py @@ -23,7 +23,8 @@ def test_TrackDT_inputs(): ), gzip=dict(argstr='-gzip', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-inputfile %s', diff --git a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py index c8e6eb1bfb..814aa7d597 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py @@ -23,7 +23,8 @@ def test_TrackPICo_inputs(): ), gzip=dict(argstr='-gzip', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-inputfile %s', diff --git a/nipype/interfaces/camino/tests/test_auto_TractShredder.py b/nipype/interfaces/camino/tests/test_auto_TractShredder.py index c81a1ed71a..9d53cd246f 100644 --- a/nipype/interfaces/camino/tests/test_auto_TractShredder.py +++ b/nipype/interfaces/camino/tests/test_auto_TractShredder.py @@ -13,7 +13,8 @@ def test_TractShredder_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='< %s', diff --git a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py index 4b21696c21..1f7d8483a3 100644 --- a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py @@ -11,7 +11,8 @@ def test_VtkStreamlines_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr=' < %s', diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py index 3d4d91e935..7c3049e98a 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py @@ -14,7 +14,8 @@ def test_Camino2Trackvis_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-i %s', diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py index 24d5aa8b19..4caa6e1ab9 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py @@ -12,7 +12,8 @@ def test_Trackvis2Camino_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-i %s', diff --git a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py index 6252ee9218..567de03ab3 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py @@ -6,7 +6,8 @@ def test_AverageNetworks_inputs(): input_map = dict(group_id=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(mandatory=True, diff --git a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py index ea97eaecd8..cf62691f3b 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py @@ -13,7 +13,8 @@ def test_CFFConverter_inputs(): gifti_surfaces=dict(), gpickled_networks=dict(), graphml_networks=dict(), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), license=dict(), diff --git a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py index 3126066243..42efb72dfd 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py @@ -4,7 +4,8 @@ def test_CreateNodes_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), out_filename=dict(usedefault=True, diff --git a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py index 18dd6c1ec6..2323461f35 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py @@ -4,7 +4,8 @@ def test_MergeCNetworks_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(mandatory=True, diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py index e031b8cae2..27f607c530 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py @@ -6,7 +6,8 @@ def test_NetworkBasedStatistic_inputs(): input_map = dict(edge_key=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_group1=dict(mandatory=True, diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py index 46c077af1b..a8ccc8dd06 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py @@ -6,7 +6,8 @@ def test_NetworkXMetrics_inputs(): input_map = dict(compute_clique_related_measures=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(mandatory=True, diff --git a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py index f62f98b51e..8de2e0bf9a 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py +++ b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py @@ -7,7 +7,8 @@ def test_Parcellate_inputs(): input_map = dict(dilation=dict(usedefault=True, ), freesurfer_dir=dict(), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), out_roi_file=dict(genfile=True, diff --git a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py index 41f99aa5bf..a1c65f4db6 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py +++ b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py @@ -10,7 +10,8 @@ def test_ROIGen_inputs(): ), freesurfer_dir=dict(requires=['use_freesurfer_LUT'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), out_dict_file=dict(genfile=True, diff --git a/nipype/interfaces/dcmstack.py b/nipype/interfaces/dcmstack.py index e9dab240f6..9e49f2b326 100644 --- a/nipype/interfaces/dcmstack.py +++ b/nipype/interfaces/dcmstack.py @@ -19,10 +19,12 @@ import nibabel as nb import imghdr -from .base import (TraitedSpec, DynamicTraitedSpec, - InputMultiPath, File, Directory, - traits, BaseInterface) -from .traits_extension import isdefined, Undefined +from .base import ( + TraitedSpec, DynamicTraitedSpec, + InputMultiPath, File, Directory, + traits, BaseInterface, + isdefined, Undefined +) from ..utils import NUMPY_MMAP diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py index c5d6a4f31b..569f1ac79f 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py @@ -20,7 +20,8 @@ def test_DTIRecon_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), image_orientation_vectors=dict(argstr='-iop %f', diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py index 91a188d420..db5c48c1c9 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py @@ -13,7 +13,8 @@ def test_DTITracker_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_data_prefix=dict(argstr='%s', diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py index a3797e5805..d85c9558de 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py @@ -15,7 +15,8 @@ def test_HARDIMat_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), image_info=dict(argstr='-info %s', diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py index 9b5b2e744d..f4d116561e 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py @@ -17,7 +17,8 @@ def test_ODFRecon_inputs(): ), filter=dict(argstr='-f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), image_orientation_vectors=dict(argstr='-iop %f', diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py index 42a965c2e8..931375abd1 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py @@ -17,7 +17,8 @@ def test_ODFTracker_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), image_orientation_vectors=dict(argstr='-iop %f', diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py index 6eb0ade6c2..7db4168340 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py @@ -9,7 +9,8 @@ def test_SplineFilter_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), output_file=dict(argstr='%s', diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py index 3a31031465..8a9a0d9201 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py @@ -9,7 +9,8 @@ def test_TrackMerge_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), output_file=dict(argstr='%s', diff --git a/nipype/interfaces/dipy/tests/test_auto_APMQball.py b/nipype/interfaces/dipy/tests/test_auto_APMQball.py index 934bc3efff..33a5a512c7 100644 --- a/nipype/interfaces/dipy/tests/test_auto_APMQball.py +++ b/nipype/interfaces/dipy/tests/test_auto_APMQball.py @@ -6,7 +6,8 @@ def test_APMQball_inputs(): input_map = dict(b0_thres=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_bval=dict(mandatory=True, diff --git a/nipype/interfaces/dipy/tests/test_auto_CSD.py b/nipype/interfaces/dipy/tests/test_auto_CSD.py index 658294df02..bed97a5660 100644 --- a/nipype/interfaces/dipy/tests/test_auto_CSD.py +++ b/nipype/interfaces/dipy/tests/test_auto_CSD.py @@ -6,7 +6,8 @@ def test_CSD_inputs(): input_map = dict(b0_thres=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_bval=dict(mandatory=True, diff --git a/nipype/interfaces/dipy/tests/test_auto_DTI.py b/nipype/interfaces/dipy/tests/test_auto_DTI.py index fddaeb3bcb..524072e1e5 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DTI.py +++ b/nipype/interfaces/dipy/tests/test_auto_DTI.py @@ -6,7 +6,8 @@ def test_DTI_inputs(): input_map = dict(b0_thres=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_bval=dict(mandatory=True, diff --git a/nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py b/nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py index 5b98c1353d..3807c48139 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py +++ b/nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py @@ -4,7 +4,8 @@ def test_DipyBaseInterface_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ) diff --git a/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py b/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py index 6bee2dde83..63fabe8f88 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py +++ b/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py @@ -6,7 +6,8 @@ def test_DipyDiffusionInterface_inputs(): input_map = dict(b0_thres=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_bval=dict(mandatory=True, diff --git a/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py b/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py index d03508c8ce..05f29f6dc3 100644 --- a/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py +++ b/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py @@ -10,7 +10,8 @@ def test_EstimateResponseSH_inputs(): ), fa_thresh=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_bval=dict(mandatory=True, diff --git a/nipype/interfaces/dipy/tests/test_auto_RESTORE.py b/nipype/interfaces/dipy/tests/test_auto_RESTORE.py index 5458d5bb98..61e48c856a 100644 --- a/nipype/interfaces/dipy/tests/test_auto_RESTORE.py +++ b/nipype/interfaces/dipy/tests/test_auto_RESTORE.py @@ -6,7 +6,8 @@ def test_RESTORE_inputs(): input_map = dict(b0_thres=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_bval=dict(mandatory=True, diff --git a/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py b/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py index a3d708fb71..546627441c 100644 --- a/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py +++ b/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py @@ -13,7 +13,8 @@ def test_SimulateMultiTensor_inputs(): diff_sf=dict(usedefault=True, ), gradients=dict(), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_bval=dict(), diff --git a/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py b/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py index 80ef4ecab4..09c03dafbc 100644 --- a/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py +++ b/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py @@ -7,7 +7,8 @@ def test_StreamlineTractography_inputs(): input_map = dict(gfa_thresh=dict(mandatory=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(mandatory=True, diff --git a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py index 02000714a1..cb807e7ef8 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py +++ b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py @@ -6,7 +6,8 @@ def test_TensorMode_inputs(): input_map = dict(b0_thres=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_bval=dict(mandatory=True, diff --git a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py index 8308be79e8..2a352d6e36 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py +++ b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py @@ -5,7 +5,8 @@ def test_TrackDensityMap_inputs(): input_map = dict(data_dims=dict(), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(mandatory=True, diff --git a/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py b/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py index 6c93d0b54b..2f53e07c77 100644 --- a/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py @@ -9,7 +9,8 @@ def test_AnalyzeWarp_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), num_threads=dict(argstr='-threads %01d', diff --git a/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py b/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py index b2bef41dc4..7b6913f96f 100644 --- a/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py @@ -9,7 +9,8 @@ def test_ApplyWarp_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), moving_image=dict(argstr='-in %s', diff --git a/nipype/interfaces/elastix/tests/test_auto_EditTransform.py b/nipype/interfaces/elastix/tests/test_auto_EditTransform.py index cd995b8aa2..58a7d72e01 100644 --- a/nipype/interfaces/elastix/tests/test_auto_EditTransform.py +++ b/nipype/interfaces/elastix/tests/test_auto_EditTransform.py @@ -4,7 +4,8 @@ def test_EditTransform_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), interpolation=dict(argstr='FinalBSplineInterpolationOrder', diff --git a/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py b/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py index 496f00962f..3853fe0e8c 100644 --- a/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py @@ -9,7 +9,8 @@ def test_PointsWarp_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), num_threads=dict(argstr='-threads %01d', diff --git a/nipype/interfaces/elastix/tests/test_auto_Registration.py b/nipype/interfaces/elastix/tests/test_auto_Registration.py index 15b0202fe0..bf4c322e54 100644 --- a/nipype/interfaces/elastix/tests/test_auto_Registration.py +++ b/nipype/interfaces/elastix/tests/test_auto_Registration.py @@ -14,7 +14,8 @@ def test_Registration_inputs(): ), fixed_mask=dict(argstr='-fMask %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), initial_transform=dict(argstr='-t0 %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py b/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py index 0e3b028d0f..c2d0989c6f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py @@ -11,7 +11,8 @@ def test_AddXFormToHeader_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py index e3222c5ecd..140efd6227 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py @@ -19,7 +19,8 @@ def test_Aparc2Aseg_inputs(): filled=dict(), hypo_wm=dict(argstr='--hypo-as-wm', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), label_wm=dict(argstr='--labelwm', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py b/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py index a4195aacf4..3ee51e0398 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py @@ -9,7 +9,8 @@ def test_Apas2Aseg_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='--i %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py index 2d59dc9ad5..cd10358bcf 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py @@ -9,7 +9,8 @@ def test_ApplyMask_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py index 1acd09f2df..a96bf413f5 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py @@ -18,7 +18,8 @@ def test_ApplyVolTransform_inputs(): mandatory=True, xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), interp=dict(argstr='--interp %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py index b40c661664..f0f1d8ba9d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py @@ -30,7 +30,8 @@ def test_Binarize_inputs(): ), frame_no=dict(argstr='--frame %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='--i %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py b/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py index d7ff3ceea6..00dc73eb06 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py @@ -13,7 +13,8 @@ def test_CALabel_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py b/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py index e9964201c6..bf4bdd612a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py @@ -15,7 +15,8 @@ def test_CANormalize_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py b/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py index 6bc82e630d..d50d9d8e6b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py @@ -13,7 +13,8 @@ def test_CARegister_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py b/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py index 305a98631a..d59e369b33 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py @@ -9,7 +9,8 @@ def test_CheckTalairachAlignment_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-xfm %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py index 2c49bcde29..ea3dc4b1bb 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py @@ -18,7 +18,8 @@ def test_Concatenate_inputs(): ), gmean=dict(argstr='--gmean %d', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='--i %s...', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py b/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py index 2357c8709b..8dd0b1cb9e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py @@ -9,7 +9,8 @@ def test_ConcatenateLTA_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_lta1=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py b/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py index 033dd191c3..1cdec290b2 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py @@ -17,7 +17,8 @@ def test_Contrast_inputs(): hemisphere=dict(argstr='--%s-only', mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), orig=dict(mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py b/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py index 403012522f..3c6d0d91a3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py @@ -14,7 +14,8 @@ def test_Curvature_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py b/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py index d269a87590..06385fc361 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py @@ -22,7 +22,8 @@ def test_CurvatureStats_inputs(): mandatory=True, position=-3, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), min_max=dict(argstr='-m', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py index b88f3ec1d1..f517b74200 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py @@ -15,7 +15,8 @@ def test_DICOMConvert_inputs(): usedefault=True, ), file_mapping=dict(), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ignore_single_slice=dict(requires=['dicom_info'], diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py index 2050442d47..f0aa686853 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py @@ -9,7 +9,8 @@ def test_EMRegister_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py b/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py index bfc5818d37..aa23199671 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py @@ -13,7 +13,8 @@ def test_EditWMwithAseg_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py b/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py index cd3d64524b..910e415852 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py @@ -9,7 +9,8 @@ def test_EulerNumber_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py index 41e9c2c264..439378afe4 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py @@ -9,7 +9,8 @@ def test_ExtractMainComponent_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py b/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py index d56a704619..bd9d6e0e0f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py @@ -9,7 +9,8 @@ def test_FSCommand_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py b/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py index ee89b8242f..d9a7a8c6f6 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py @@ -9,7 +9,8 @@ def test_FSCommandOpenMP_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), num_threads=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py b/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py index 45c1646355..6bbb0ed0d7 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py @@ -9,7 +9,8 @@ def test_FSScriptCommand_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py index a5b63f9b03..22280e25a9 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py @@ -10,7 +10,8 @@ def test_FitMSParams_inputs(): usedefault=True, ), flip_list=dict(), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py b/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py index 7739767eb1..2176d18d54 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py @@ -17,7 +17,8 @@ def test_FixTopology_inputs(): mandatory=True, position=-1, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_brain=dict(mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py b/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py index 3d713eeb63..f2d4e53fa6 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py @@ -9,7 +9,8 @@ def test_FuseSegmentations_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_norms=dict(argstr='-n %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py index e122d0dc75..7b81fee22b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py @@ -51,7 +51,8 @@ def test_GLMFit_inputs(): genfile=True, ), hemi=dict(), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='--y %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py index 35bd042ad6..f49055a47e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py @@ -9,7 +9,8 @@ def test_ImageInfo_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py b/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py index 270a10a460..fe6998874f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py @@ -9,7 +9,8 @@ def test_Jacobian_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_mappedsurf=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py index 1b82182f63..867e01e00d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py @@ -9,7 +9,8 @@ def test_LTAConvert_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_fsl=dict(argstr='--infsl %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py index a8fa6e56b4..beece1b6d3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py @@ -15,7 +15,8 @@ def test_Label2Annot_inputs(): hemisphere=dict(argstr='--hemi %s', mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_labels=dict(argstr='--l %s...', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py index 0b6a68ebf2..55ed8f026c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py @@ -13,7 +13,8 @@ def test_Label2Label_inputs(): hemisphere=dict(argstr='--hemi %s', mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), out_file=dict(argstr='--trglabel %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py index f80602f76b..25b680036e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py @@ -26,7 +26,8 @@ def test_Label2Vol_inputs(): identity=dict(argstr='--identity', xor=('reg_file', 'reg_header', 'identity'), ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), invert_mtx=dict(argstr='--invertmtx', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py b/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py index f10ba94ef6..1cd0eacc4d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py @@ -11,7 +11,8 @@ def test_MNIBiasCorrection_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='--i %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py b/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py index 70d4e2c89b..1f64be215d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py @@ -9,7 +9,8 @@ def test_MPRtoMNI305_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py index 906fadef0c..8b5bc1135d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py @@ -49,7 +49,8 @@ def test_MRIConvert_inputs(): ), fwhm=dict(argstr='--fwhm %f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_center=dict(argstr='--in_center %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py b/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py index 12800572d9..e04b306c69 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py @@ -21,7 +21,8 @@ def test_MRICoreg_inputs(): ), ftol=dict(argstr='--ftol %e', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), initial_rotation=dict(argstr='--rot %g %g %g', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py index e1c05fd17a..f45165af12 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py @@ -9,7 +9,8 @@ def test_MRIFill_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py index df7cfaa11f..9f333c2643 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py @@ -13,7 +13,8 @@ def test_MRIMarchingCubes_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py index 1e61184ec1..87dc5ce59f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py @@ -9,7 +9,8 @@ def test_MRIPretess_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_filled=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py index 21ea0de247..2e0d137668 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py @@ -21,7 +21,8 @@ def test_MRISPreproc_inputs(): hemi=dict(argstr='--hemi %s', mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), num_iters=dict(argstr='--niters %d', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py index 79cd8056d0..56860ed6d3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py @@ -22,7 +22,8 @@ def test_MRISPreprocReconAll_inputs(): hemi=dict(argstr='--hemi %s', mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), lh_surfreg_target=dict(requires=['surfreg_files'], diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py index 410d64b706..9829b19326 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py @@ -9,7 +9,8 @@ def test_MRITessellate_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py index 7298ab6b0c..9c70889d59 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py @@ -26,7 +26,8 @@ def test_MRIsCALabel_inputs(): mandatory=True, position=-4, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), label=dict(argstr='-l %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py index 280e9e5ce0..0844523ac8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py @@ -13,7 +13,8 @@ def test_MRIsCalc_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file1=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py index 6262f74dbb..8ac919ad65 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py @@ -9,7 +9,8 @@ def test_MRIsCombine_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='--combinesurfs %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py index a6c07208d7..5fda94dd63 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py @@ -15,7 +15,8 @@ def test_MRIsConvert_inputs(): ), functional_file=dict(argstr='-f %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py index 995135da03..e292a2b2c5 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py @@ -15,7 +15,8 @@ def test_MRIsExpand_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py index 2ebe152b0a..3a93d5f1e1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py @@ -9,7 +9,8 @@ def test_MRIsInflate_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py index 86898a7bdb..97321adec8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py @@ -11,7 +11,8 @@ def test_MS_LDA_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), images=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py index bc833d1d73..d0fec86806 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py @@ -9,7 +9,8 @@ def test_MakeAverageSubject_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), out_name=dict(argstr='--out %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py b/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py index f90e1ca7e8..ed5c9021ab 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py @@ -16,7 +16,8 @@ def test_MakeSurfaces_inputs(): mandatory=True, position=-1, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_T1=dict(argstr='-T1 %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py b/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py index efe7f34d9f..33319e77ed 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py @@ -12,7 +12,8 @@ def test_Normalize_inputs(): gradient=dict(argstr='-g %d', usedefault=False, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py index 147a020837..a1bb43f9c5 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py @@ -51,7 +51,8 @@ def test_OneSampleTTest_inputs(): genfile=True, ), hemi=dict(), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='--y %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Paint.py b/nipype/interfaces/freesurfer/tests/test_auto_Paint.py index a8e2c0c582..27d836b4f7 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Paint.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Paint.py @@ -11,7 +11,8 @@ def test_Paint_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_surf=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py b/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py index 4c51a0b2fb..57034c4367 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py @@ -19,7 +19,8 @@ def test_ParcellationStats_inputs(): mandatory=True, position=-2, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_annotation=dict(argstr='-a %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py index ba90aa1ff2..59c1d931d9 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py @@ -15,7 +15,8 @@ def test_ParseDICOMDir_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), sortbyrun=dict(argstr='--sortbyrun', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py index f823855333..b28d035254 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py @@ -40,7 +40,8 @@ def test_ReconAll_inputs(): hires=dict(argstr='-hires', min_ver='6.0.0', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mprage=dict(argstr='-mprage', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Register.py b/nipype/interfaces/freesurfer/tests/test_auto_Register.py index 8a2646faec..fca0812be4 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Register.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Register.py @@ -12,7 +12,8 @@ def test_Register_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_smoothwm=dict(copyfile=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py b/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py index 0fef6c54f1..452cbb0cea 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py @@ -9,7 +9,8 @@ def test_RegisterAVItoTalairach_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py b/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py index 098795dc64..7e8aa0a3a7 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py @@ -13,7 +13,8 @@ def test_RelabelHypointensities_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), lh_white=dict(copyfile=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py b/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py index cb49998f98..d3b9719662 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py @@ -9,7 +9,8 @@ def test_RemoveIntersection_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py b/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py index 210ebe74e0..ae697ecaab 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py @@ -9,7 +9,8 @@ def test_RemoveNeck_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py index 9b275c2718..eea61f7cbf 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py @@ -9,7 +9,8 @@ def test_Resample_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-i %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py index 5388029eac..48f121cd70 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py @@ -31,7 +31,8 @@ def test_RobustRegister_inputs(): ), high_iterations=dict(argstr='--highit %d', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_xfm_file=dict(argstr='--transform', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py b/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py index d9b852bb36..c4fa30271b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py @@ -17,7 +17,8 @@ def test_RobustTemplate_inputs(): ), fixed_timepoint=dict(argstr='--fixtp', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='--mov %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py index 74239f5db0..fd6440f10f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py @@ -32,7 +32,8 @@ def test_SampleToSurface_inputs(): ico_order=dict(argstr='--icoorder %d', requires=['target_subject'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), interp_method=dict(argstr='--interp %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py index fecdc0ddb1..1f329ac491 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py @@ -49,7 +49,8 @@ def test_SegStats_inputs(): gca_color_table=dict(argstr='--ctab-gca %s', xor=('color_table_file', 'default_color_table', 'gca_color_table'), ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='--i %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py index 8860857354..45f79b2259 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py @@ -51,7 +51,8 @@ def test_SegStatsReconAll_inputs(): gca_color_table=dict(argstr='--ctab-gca %s', xor=('color_table_file', 'default_color_table', 'gca_color_table'), ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='--i %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py b/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py index 80bfca6d6d..b6ad0b3891 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py @@ -10,7 +10,8 @@ def test_SegmentCC_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-aseg %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py b/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py index 03a9805404..5109680305 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py @@ -9,7 +9,8 @@ def test_SegmentWM_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py index 41ad8650c0..06035d71d0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py @@ -9,7 +9,8 @@ def test_Smooth_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='--i %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py index fdcc51f755..eb2d70bec1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py @@ -17,7 +17,8 @@ def test_SmoothTessellation_inputs(): ), gaussian_curvature_smoothing_steps=dict(argstr='%d', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py b/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py index 2ac074eef8..ca5dd22c17 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py @@ -9,7 +9,8 @@ def test_Sphere_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py b/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py index b16cb6154c..54b5aab351 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py @@ -19,7 +19,8 @@ def test_SphericalAverage_inputs(): mandatory=True, position=-4, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_average=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py index 276b1157a9..d97095b429 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py @@ -12,7 +12,8 @@ def test_Surface2VolTransform_inputs(): hemi=dict(argstr='--hemi %s', mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mkmask=dict(argstr='--mkmask', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py index e85ab3409a..a0a18ba287 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py @@ -18,7 +18,8 @@ def test_SurfaceSmooth_inputs(): hemi=dict(argstr='--hemi %s', mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='--sval %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py index c7b9a48d32..b0c4a7c482 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py @@ -26,7 +26,8 @@ def test_SurfaceSnapshots_inputs(): identity_reg=dict(argstr='-overlay-reg-identity', xor=['overlay_reg', 'identity_reg', 'mni152_reg'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), invert_overlay=dict(argstr='-invphaseflag 1', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py index a414aa7d62..fd3cb37931 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py @@ -12,7 +12,8 @@ def test_SurfaceTransform_inputs(): hemi=dict(argstr='--hemi %s', mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), out_file=dict(argstr='--tval %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py index 15f89133ee..6c96565317 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py @@ -16,7 +16,8 @@ def test_SynthesizeFLASH_inputs(): mandatory=True, position=3, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), out_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py b/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py index 37597e6973..f7f3136f77 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py @@ -11,7 +11,8 @@ def test_TalairachAVI_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='--i %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py b/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py index 7c37835898..63ff45a3fe 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py @@ -9,7 +9,8 @@ def test_TalairachQC_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), log_file=dict(argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py b/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py index d40c03d7d9..a4f018bd7e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py @@ -19,7 +19,8 @@ def test_Tkregister2_inputs(): fstarg=dict(argstr='--fstarg', xor=['target_image'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), invert_lta_in=dict(requires=['lta_in'], diff --git a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py index f2f442d267..991a0e895f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py @@ -15,7 +15,8 @@ def test_UnpackSDICOMDir_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), log_file=dict(argstr='-log %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py b/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py index f86e2dde7a..1eaed2521b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py @@ -12,7 +12,8 @@ def test_VolumeMask_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_aseg=dict(argstr='--aseg_name %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py b/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py index f7f465ffce..f1f7469161 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py @@ -12,7 +12,8 @@ def test_WatershedSkullStrip_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/fix.py b/nipype/interfaces/fsl/fix.py index 0775cf62c5..cd4aacfedb 100644 --- a/nipype/interfaces/fsl/fix.py +++ b/nipype/interfaces/fsl/fix.py @@ -64,21 +64,24 @@ OutputMultiPath, BaseInterface, BaseInterfaceInputSpec, - traits + traits, + Directory, + File, + isdefined ) -from ..traits_extension import Directory, File, isdefined import os class TrainingSetCreatorInputSpec(BaseInterfaceInputSpec): mel_icas_in = InputMultiPath(Directory(exists=True), copyfile=False, - desc='Melodic output directories', - argstr='%s', position=-1) + desc='Melodic output directories', + argstr='%s', position=-1) + class TrainingSetCreatorOutputSpec(TraitedSpec): mel_icas_out = OutputMultiPath(Directory(exists=True), copyfile=False, - desc='Hand labels for noise vs signal', - argstr='%s', position=-1) + desc='Hand labels for noise vs signal', + argstr='%s', position=-1) class TrainingSetCreator(BaseInterface): diff --git a/nipype/interfaces/fsl/model.py b/nipype/interfaces/fsl/model.py index 701ee757db..f130c01679 100644 --- a/nipype/interfaces/fsl/model.py +++ b/nipype/interfaces/fsl/model.py @@ -17,6 +17,7 @@ import os from glob import glob from shutil import rmtree +from string import Template import numpy as np from nibabel import load @@ -25,12 +26,13 @@ from ...utils.filemanip import list_to_filename, filename_to_list from ...utils.misc import human_order_sorted from ...external.due import BibTeX -from ..base import (load_template, File, traits, isdefined, +from ..base import (File, traits, isdefined, TraitedSpec, BaseInterface, Directory, InputMultiPath, OutputMultiPath, BaseInterfaceInputSpec) from .base import FSLCommand, FSLCommandInputSpec, Info + class Level1DesignInputSpec(BaseInterfaceInputSpec): interscan_interval = traits.Float(mandatory=True, desc='Interscan interval (in secs)') @@ -1860,7 +1862,7 @@ class DualRegression(FSLCommand): >>> dual_regression.inputs.n_perm = 10 >>> dual_regression.inputs.out_dir = "my_output_directory" >>> dual_regression.cmdline - u'dual_regression allFA.nii 0 -1 10 my_output_directory functional.nii functional2.nii functional3.nii' + 'dual_regression allFA.nii 0 -1 10 my_output_directory functional.nii functional2.nii functional3.nii' >>> dual_regression.run() # doctest: +SKIP """ @@ -2168,3 +2170,25 @@ def _list_outputs(self): self.inputs.out_vnscales_name) return outputs + + +def load_template(name): + """Load a template from the model_templates directory + + Parameters + ---------- + name : str + The name of the file to load + + Returns + ------- + template : string.Template + + """ + from pkg_resources import resource_filename as pkgrf + full_fname = pkgrf( + 'nipype', os.path.join('interfaces', 'fsl', 'model_templates', name)) + with open(full_fname) as template_file: + template = Template(template_file.read()) + + return template diff --git a/nipype/interfaces/script_templates/feat_contrast_element.tcl b/nipype/interfaces/fsl/model_templates/feat_contrast_element.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_contrast_element.tcl rename to nipype/interfaces/fsl/model_templates/feat_contrast_element.tcl diff --git a/nipype/interfaces/script_templates/feat_contrast_ftest_element.tcl b/nipype/interfaces/fsl/model_templates/feat_contrast_ftest_element.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_contrast_ftest_element.tcl rename to nipype/interfaces/fsl/model_templates/feat_contrast_ftest_element.tcl diff --git a/nipype/interfaces/script_templates/feat_contrast_header.tcl b/nipype/interfaces/fsl/model_templates/feat_contrast_header.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_contrast_header.tcl rename to nipype/interfaces/fsl/model_templates/feat_contrast_header.tcl diff --git a/nipype/interfaces/script_templates/feat_contrast_prolog.tcl b/nipype/interfaces/fsl/model_templates/feat_contrast_prolog.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_contrast_prolog.tcl rename to nipype/interfaces/fsl/model_templates/feat_contrast_prolog.tcl diff --git a/nipype/interfaces/script_templates/feat_contrastmask_element.tcl b/nipype/interfaces/fsl/model_templates/feat_contrastmask_element.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_contrastmask_element.tcl rename to nipype/interfaces/fsl/model_templates/feat_contrastmask_element.tcl diff --git a/nipype/interfaces/script_templates/feat_contrastmask_footer.tcl b/nipype/interfaces/fsl/model_templates/feat_contrastmask_footer.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_contrastmask_footer.tcl rename to nipype/interfaces/fsl/model_templates/feat_contrastmask_footer.tcl diff --git a/nipype/interfaces/script_templates/feat_contrastmask_header.tcl b/nipype/interfaces/fsl/model_templates/feat_contrastmask_header.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_contrastmask_header.tcl rename to nipype/interfaces/fsl/model_templates/feat_contrastmask_header.tcl diff --git a/nipype/interfaces/script_templates/feat_contrasts.tcl b/nipype/interfaces/fsl/model_templates/feat_contrasts.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_contrasts.tcl rename to nipype/interfaces/fsl/model_templates/feat_contrasts.tcl diff --git a/nipype/interfaces/script_templates/feat_ev_custom.tcl b/nipype/interfaces/fsl/model_templates/feat_ev_custom.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_ev_custom.tcl rename to nipype/interfaces/fsl/model_templates/feat_ev_custom.tcl diff --git a/nipype/interfaces/script_templates/feat_ev_gamma.tcl b/nipype/interfaces/fsl/model_templates/feat_ev_gamma.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_ev_gamma.tcl rename to nipype/interfaces/fsl/model_templates/feat_ev_gamma.tcl diff --git a/nipype/interfaces/script_templates/feat_ev_hrf.tcl b/nipype/interfaces/fsl/model_templates/feat_ev_hrf.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_ev_hrf.tcl rename to nipype/interfaces/fsl/model_templates/feat_ev_hrf.tcl diff --git a/nipype/interfaces/script_templates/feat_ev_none.tcl b/nipype/interfaces/fsl/model_templates/feat_ev_none.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_ev_none.tcl rename to nipype/interfaces/fsl/model_templates/feat_ev_none.tcl diff --git a/nipype/interfaces/script_templates/feat_ev_ortho.tcl b/nipype/interfaces/fsl/model_templates/feat_ev_ortho.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_ev_ortho.tcl rename to nipype/interfaces/fsl/model_templates/feat_ev_ortho.tcl diff --git a/nipype/interfaces/script_templates/feat_fe_copes.tcl b/nipype/interfaces/fsl/model_templates/feat_fe_copes.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_fe_copes.tcl rename to nipype/interfaces/fsl/model_templates/feat_fe_copes.tcl diff --git a/nipype/interfaces/script_templates/feat_fe_ev_element.tcl b/nipype/interfaces/fsl/model_templates/feat_fe_ev_element.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_fe_ev_element.tcl rename to nipype/interfaces/fsl/model_templates/feat_fe_ev_element.tcl diff --git a/nipype/interfaces/script_templates/feat_fe_ev_header.tcl b/nipype/interfaces/fsl/model_templates/feat_fe_ev_header.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_fe_ev_header.tcl rename to nipype/interfaces/fsl/model_templates/feat_fe_ev_header.tcl diff --git a/nipype/interfaces/script_templates/feat_fe_featdirs.tcl b/nipype/interfaces/fsl/model_templates/feat_fe_featdirs.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_fe_featdirs.tcl rename to nipype/interfaces/fsl/model_templates/feat_fe_featdirs.tcl diff --git a/nipype/interfaces/script_templates/feat_fe_footer.tcl b/nipype/interfaces/fsl/model_templates/feat_fe_footer.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_fe_footer.tcl rename to nipype/interfaces/fsl/model_templates/feat_fe_footer.tcl diff --git a/nipype/interfaces/script_templates/feat_fe_header.tcl b/nipype/interfaces/fsl/model_templates/feat_fe_header.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_fe_header.tcl rename to nipype/interfaces/fsl/model_templates/feat_fe_header.tcl diff --git a/nipype/interfaces/script_templates/feat_header.tcl b/nipype/interfaces/fsl/model_templates/feat_header.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_header.tcl rename to nipype/interfaces/fsl/model_templates/feat_header.tcl diff --git a/nipype/interfaces/script_templates/feat_header_l1.tcl b/nipype/interfaces/fsl/model_templates/feat_header_l1.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_header_l1.tcl rename to nipype/interfaces/fsl/model_templates/feat_header_l1.tcl diff --git a/nipype/interfaces/script_templates/feat_nongui.tcl b/nipype/interfaces/fsl/model_templates/feat_nongui.tcl similarity index 100% rename from nipype/interfaces/script_templates/feat_nongui.tcl rename to nipype/interfaces/fsl/model_templates/feat_nongui.tcl diff --git a/nipype/interfaces/script_templates/featreg_header.tcl b/nipype/interfaces/fsl/model_templates/featreg_header.tcl similarity index 100% rename from nipype/interfaces/script_templates/featreg_header.tcl rename to nipype/interfaces/fsl/model_templates/featreg_header.tcl diff --git a/nipype/interfaces/fsl/tests/test_auto_AR1Image.py b/nipype/interfaces/fsl/tests/test_auto_AR1Image.py index 31a901ef47..e21844346a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AR1Image.py +++ b/nipype/interfaces/fsl/tests/test_auto_AR1Image.py @@ -13,7 +13,8 @@ def test_AR1Image_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py b/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py index 91ce98c97c..dc5daa76c5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py +++ b/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py @@ -9,7 +9,8 @@ def test_AccuracyTester_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mel_icas=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py index 4df9cf40c5..f5bad0d6f2 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py @@ -9,7 +9,8 @@ def test_ApplyMask_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py index 837b00d06d..c60fc9f5de 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py @@ -14,7 +14,8 @@ def test_ApplyTOPUP_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='--imain=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py index fddbab5bea..7056d1d363 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py @@ -16,7 +16,8 @@ def test_ApplyWarp_inputs(): ), field_file=dict(argstr='--warp=%s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='--in=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py b/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py index 63f38443e4..9e8b4d0877 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py @@ -54,7 +54,8 @@ def test_ApplyXFM_inputs(): ), force_scaling=dict(argstr='-forcescaling', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-in %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_AvScale.py b/nipype/interfaces/fsl/tests/test_auto_AvScale.py index a95d7888ee..eb582cc783 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AvScale.py +++ b/nipype/interfaces/fsl/tests/test_auto_AvScale.py @@ -11,7 +11,8 @@ def test_AvScale_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mat_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_B0Calc.py b/nipype/interfaces/fsl/tests/test_auto_B0Calc.py index 99e661ab8e..a03dba1061 100644 --- a/nipype/interfaces/fsl/tests/test_auto_B0Calc.py +++ b/nipype/interfaces/fsl/tests/test_auto_B0Calc.py @@ -19,7 +19,8 @@ def test_B0Calc_inputs(): ), extendboundary=dict(argstr='--extendboundary=%0.2f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-i %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py index db2d5c808a..7e57bdea55 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py +++ b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py @@ -39,7 +39,8 @@ def test_BEDPOSTX5_inputs(): grad_dev=dict(), gradnonlin=dict(argstr='-g', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), logdir=dict(argstr='--logdir=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_BET.py b/nipype/interfaces/fsl/tests/test_auto_BET.py index 9e0bfb356e..a0ba58c88a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BET.py +++ b/nipype/interfaces/fsl/tests/test_auto_BET.py @@ -17,7 +17,8 @@ def test_BET_inputs(): functional=dict(argstr='-F', xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py index ddb06020cb..d4c8eed2f9 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py @@ -9,7 +9,8 @@ def test_BinaryMaths_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py index a4c3f164bb..2142994a08 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py +++ b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py @@ -9,7 +9,8 @@ def test_ChangeDataType_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_Classifier.py b/nipype/interfaces/fsl/tests/test_auto_Classifier.py index 31458e74fa..d9e8180f87 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Classifier.py +++ b/nipype/interfaces/fsl/tests/test_auto_Classifier.py @@ -10,7 +10,8 @@ def test_Classifier_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mel_ica=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_Cleaner.py b/nipype/interfaces/fsl/tests/test_auto_Cleaner.py index 6ec9fee3c1..08f40263b5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cleaner.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cleaner.py @@ -32,7 +32,8 @@ def test_Cleaner_inputs(): position=2, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), terminal_output=dict(deprecated='1.0.0', diff --git a/nipype/interfaces/fsl/tests/test_auto_Cluster.py b/nipype/interfaces/fsl/tests/test_auto_Cluster.py index f8d58401d5..8085989aad 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cluster.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cluster.py @@ -21,7 +21,8 @@ def test_Cluster_inputs(): fractional=dict(argstr='--fractional', usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='--in=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_Complex.py b/nipype/interfaces/fsl/tests/test_auto_Complex.py index 1876cbb343..0a2133bb6f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Complex.py +++ b/nipype/interfaces/fsl/tests/test_auto_Complex.py @@ -39,7 +39,8 @@ def test_Complex_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), imaginary_in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py index b5c71395c7..de4296e751 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py +++ b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py @@ -20,7 +20,8 @@ def test_ContrastMgr_inputs(): ), fcon_file=dict(argstr='-f %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), output_type=dict(), diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py b/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py index 14a2747b5b..4ea9b536f9 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py @@ -14,7 +14,8 @@ def test_ConvertWarp_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), jacobian_max=dict(argstr='--jmax=%f', diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py index 4531a6dc80..1dad2d7d63 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py @@ -19,7 +19,8 @@ def test_ConvertXFM_inputs(): requires=['in_file2'], xor=['invert_xfm', 'concat_xfm', 'fix_scale_skew'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py b/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py index 7ced6130ed..8374c8c93d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py +++ b/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py @@ -20,7 +20,8 @@ def test_CopyGeom_inputs(): ignore_dims=dict(argstr='-d', position='-1', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py index 2455d040c2..02e031519e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py @@ -29,7 +29,8 @@ def test_DTIFit_inputs(): ), gradnonlin=dict(argstr='--gradnonlin=%s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), little_bit=dict(argstr='--littlebit', diff --git a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py index 69c1218cf9..2b8be886a6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py @@ -9,7 +9,8 @@ def test_DilateImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py index 2bf5805a30..1b063503dc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py +++ b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py @@ -13,7 +13,8 @@ def test_DistanceMap_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='--in=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_DualRegression.py b/nipype/interfaces/fsl/tests/test_auto_DualRegression.py index 0552cf6837..894a3a3ad4 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DualRegression.py +++ b/nipype/interfaces/fsl/tests/test_auto_DualRegression.py @@ -23,7 +23,8 @@ def test_DualRegression_inputs(): mandatory=True, position=1, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py index 5c52237ba7..969ecfa86d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py @@ -27,7 +27,8 @@ def test_EPIDeWarp_inputs(): exfdw=dict(argstr='--exfdw %s', genfile=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mag_file=dict(argstr='--mag %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_Eddy.py b/nipype/interfaces/fsl/tests/test_auto_Eddy.py index c40deb16bf..df4155472d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Eddy.py +++ b/nipype/interfaces/fsl/tests/test_auto_Eddy.py @@ -25,7 +25,8 @@ def test_Eddy_inputs(): ), fwhm=dict(argstr='--fwhm=%s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_acqp=dict(argstr='--acqp=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py index 0f4da84475..57bf91ac79 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py +++ b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py @@ -9,7 +9,8 @@ def test_EddyCorrect_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_EpiReg.py b/nipype/interfaces/fsl/tests/test_auto_EpiReg.py index cf52ba99ee..65e8134a30 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EpiReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_EpiReg.py @@ -21,7 +21,8 @@ def test_EpiReg_inputs(): ), fmapmagbrain=dict(argstr='--fmapmagbrain=%s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), no_clean=dict(argstr='--noclean', diff --git a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py index 84ce60f014..015b97e59e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py @@ -9,7 +9,8 @@ def test_ErodeImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py index 158a059f71..8abad8a656 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py +++ b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py @@ -13,7 +13,8 @@ def test_ExtractROI_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_FAST.py b/nipype/interfaces/fsl/tests/test_auto_FAST.py index d1410d0fcd..a5e54b0882 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FAST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FAST.py @@ -16,7 +16,8 @@ def test_FAST_inputs(): ), hyper=dict(argstr='-H %.2f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), img_type=dict(argstr='-t %d', diff --git a/nipype/interfaces/fsl/tests/test_auto_FEAT.py b/nipype/interfaces/fsl/tests/test_auto_FEAT.py index 52d990891a..bb024b4c29 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEAT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEAT.py @@ -13,7 +13,8 @@ def test_FEAT_inputs(): mandatory=True, position=0, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), output_type=dict(), diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py index f644dbbdcb..9aa25a02d8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py @@ -19,7 +19,8 @@ def test_FEATModel_inputs(): mandatory=True, position=0, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), output_type=dict(), diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py index a0f5e09177..9a46bd77c7 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py @@ -6,7 +6,8 @@ def test_FEATRegister_inputs(): input_map = dict(feat_dirs=dict(mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), reg_dof=dict(usedefault=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_FIRST.py b/nipype/interfaces/fsl/tests/test_auto_FIRST.py index 630774e9fe..61f369a0f1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FIRST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FIRST.py @@ -15,7 +15,8 @@ def test_FIRST_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-i %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py index 69940790fd..6caf4d6d9a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py @@ -26,7 +26,8 @@ def test_FLAMEO_inputs(): ), fix_mean=dict(argstr='--fixmean', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), infer_outliers=dict(argstr='--inferoutliers', diff --git a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py index 04448f0e0c..bd13a2fd36 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py @@ -53,7 +53,8 @@ def test_FLIRT_inputs(): ), force_scaling=dict(argstr='-forcescaling', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-in %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py index 7e76ff0250..19536f0913 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py @@ -38,7 +38,8 @@ def test_FNIRT_inputs(): ), hessian_precision=dict(argstr='--numprec=%s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='--in=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py b/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py index d31001dd66..a88daabceb 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py @@ -9,7 +9,8 @@ def test_FSLCommand_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), output_type=dict(), diff --git a/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py b/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py index 25cf6ae30e..adabb09143 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py @@ -39,7 +39,8 @@ def test_FSLXCommand_inputs(): ), fudge=dict(argstr='--fudge=%d', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), logdir=dict(argstr='--logdir=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py index 628e992e53..f88ffd7b6f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py +++ b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py @@ -33,7 +33,8 @@ def test_FUGUE_inputs(): icorr_only=dict(argstr='--icorronly', requires=['unwarped_file'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='--in=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py b/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py index 49aaf919f4..69565fa7c8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py +++ b/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py @@ -9,7 +9,8 @@ def test_FeatureExtractor_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mel_ica=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py index 76829f1c2d..576b7ea3ee 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py +++ b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py @@ -23,7 +23,8 @@ def test_FilterRegressor_inputs(): position=4, xor=['filter_all'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-i %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py index 82f3ac3f5b..cb5b925f15 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py +++ b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py @@ -9,7 +9,8 @@ def test_FindTheBiggest_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_GLM.py b/nipype/interfaces/fsl/tests/test_auto_GLM.py index e612dec331..846e3f4854 100644 --- a/nipype/interfaces/fsl/tests/test_auto_GLM.py +++ b/nipype/interfaces/fsl/tests/test_auto_GLM.py @@ -23,7 +23,8 @@ def test_GLM_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-i %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py b/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py index b5e6af6c3c..3a04429b2c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py +++ b/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py @@ -24,7 +24,8 @@ def test_ICA_AROMA_inputs(): fnirt_warp_file=dict(argstr='-warp %s', xor=['feat_dir'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-i %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py index 48b01b8025..bbff7e8b42 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py @@ -9,7 +9,8 @@ def test_ImageMaths_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py index 28bd9d465b..2991a45c9b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py @@ -11,7 +11,8 @@ def test_ImageMeants_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-i %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py index ea0b8b5d7d..0a97eb2e21 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py @@ -9,7 +9,8 @@ def test_ImageStats_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py index 2f40af2fdd..0d96f46d4d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py @@ -12,7 +12,8 @@ def test_InvWarp_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inverse_warp=dict(argstr='--out=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py index e0f907222b..bc02253720 100644 --- a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py @@ -14,7 +14,8 @@ def test_IsotropicSmooth_inputs(): position=4, xor=['sigma'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_L2Model.py b/nipype/interfaces/fsl/tests/test_auto_L2Model.py index 81f74cc923..ef86a37e0e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_L2Model.py +++ b/nipype/interfaces/fsl/tests/test_auto_L2Model.py @@ -4,7 +4,8 @@ def test_L2Model_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), num_copes=dict(mandatory=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_Level1Design.py b/nipype/interfaces/fsl/tests/test_auto_Level1Design.py index f5fcfe4093..c15f8e055a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Level1Design.py +++ b/nipype/interfaces/fsl/tests/test_auto_Level1Design.py @@ -7,7 +7,8 @@ def test_Level1Design_inputs(): input_map = dict(bases=dict(mandatory=True, ), contrasts=dict(), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), interscan_interval=dict(mandatory=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py index d68b1f2606..07ecdc9094 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py @@ -15,7 +15,8 @@ def test_MCFLIRT_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-in %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py index eed0671d7a..5e009e701d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py +++ b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py @@ -27,7 +27,8 @@ def test_MELODIC_inputs(): ), epsilonS=dict(argstr='--epsS=%f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='-i %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py index 3365cbeb7b..447be7025e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py +++ b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py @@ -9,7 +9,8 @@ def test_MakeDyadicVectors_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mask=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py index ae15b6348f..224bc3ee75 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py @@ -9,7 +9,8 @@ def test_MathsCommand_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py index 808f49725a..536a44bccf 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py @@ -13,7 +13,8 @@ def test_MaxImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py b/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py index 7f90f7828f..09aec304d8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py @@ -13,7 +13,8 @@ def test_MaxnImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py index 378417e20e..c444c296ad 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py @@ -13,7 +13,8 @@ def test_MeanImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_MedianImage.py b/nipype/interfaces/fsl/tests/test_auto_MedianImage.py index 1e88316ee4..b398d50975 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MedianImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MedianImage.py @@ -13,7 +13,8 @@ def test_MedianImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_Merge.py b/nipype/interfaces/fsl/tests/test_auto_Merge.py index dfd92da57e..0638326c65 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Merge.py +++ b/nipype/interfaces/fsl/tests/test_auto_Merge.py @@ -13,7 +13,8 @@ def test_Merge_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_MinImage.py b/nipype/interfaces/fsl/tests/test_auto_MinImage.py index 97376366ff..f2216fb083 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MinImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MinImage.py @@ -13,7 +13,8 @@ def test_MinImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py b/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py index 346451e737..7921e1031c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py +++ b/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py @@ -11,7 +11,8 @@ def test_MotionOutliers_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-i %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py index 4416477970..4a67036b55 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py @@ -9,7 +9,8 @@ def test_MultiImageMaths_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py index 69ef20f16c..c0bd71f12a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py @@ -7,7 +7,8 @@ def test_MultipleRegressDesign_inputs(): input_map = dict(contrasts=dict(mandatory=True, ), groups=dict(), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), regressors=dict(mandatory=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_Overlay.py b/nipype/interfaces/fsl/tests/test_auto_Overlay.py index 240154c74e..91b09fdd7a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Overlay.py +++ b/nipype/interfaces/fsl/tests/test_auto_Overlay.py @@ -28,7 +28,8 @@ def test_Overlay_inputs(): position=5, xor=('auto_thresh_bg', 'full_bg_range', 'bg_thresh'), ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), out_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py index dc5aaec0b5..98b8d69889 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py +++ b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py @@ -15,7 +15,8 @@ def test_PRELUDE_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), label_file=dict(argstr='--labels=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py b/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py index 7d03bd778a..36fd550b23 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py @@ -13,7 +13,8 @@ def test_PercentileImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py index 7a792847cf..e910f7e173 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py @@ -9,7 +9,8 @@ def test_PlotMotionParams_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py index 473332c4b3..feaa9d8449 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py @@ -9,7 +9,8 @@ def test_PlotTimeSeries_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py index 451893ef41..409c8bfee6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py +++ b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py @@ -9,7 +9,8 @@ def test_PowerSpectrum_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py index 7569e6622e..b9bf8c1c94 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py +++ b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py @@ -14,7 +14,8 @@ def test_PrepareFieldmap_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_magnitude=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py index ccfd85691c..12352f4a38 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py @@ -24,7 +24,8 @@ def test_ProbTrackX_inputs(): ), fsamples=dict(mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inv_xfm=dict(argstr='--invxfm=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py index bbf42576a6..249bc87777 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py @@ -32,7 +32,8 @@ def test_ProbTrackX2_inputs(): ), fsamples=dict(mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inv_xfm=dict(argstr='--invxfm=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py b/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py index 66a4509386..37648d5a2b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py @@ -9,7 +9,8 @@ def test_ProjThresh_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_Randomise.py b/nipype/interfaces/fsl/tests/test_auto_Randomise.py index 8483b92017..bcf65a0419 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Randomise.py +++ b/nipype/interfaces/fsl/tests/test_auto_Randomise.py @@ -30,7 +30,8 @@ def test_Randomise_inputs(): ), fcon=dict(argstr='-f %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-i %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py index 1af9adf8eb..0062b7d489 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py +++ b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py @@ -9,7 +9,8 @@ def test_Reorient2Std_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py b/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py index 392611182b..6b547109e1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py +++ b/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py @@ -11,7 +11,8 @@ def test_RobustFOV_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-i %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_SMM.py b/nipype/interfaces/fsl/tests/test_auto_SMM.py index 53a4087ec7..f6ed7d4fd2 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SMM.py +++ b/nipype/interfaces/fsl/tests/test_auto_SMM.py @@ -9,7 +9,8 @@ def test_SMM_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mask=dict(argstr='--mask="%s"', diff --git a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py index b97ecbf28d..e3da09dadf 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py +++ b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py @@ -21,7 +21,8 @@ def test_SUSAN_inputs(): mandatory=True, position=3, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py index 3a013c2974..d7caee328e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py +++ b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py @@ -11,7 +11,8 @@ def test_SigLoss_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-i %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py index f3007825a4..99d0b7215b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py +++ b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py @@ -15,7 +15,8 @@ def test_SliceTimer_inputs(): ), global_shift=dict(argstr='--tglobal', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='--in=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_Slicer.py b/nipype/interfaces/fsl/tests/test_auto_Slicer.py index 224d9447ed..6108b5f702 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Slicer.py +++ b/nipype/interfaces/fsl/tests/test_auto_Slicer.py @@ -20,7 +20,8 @@ def test_Slicer_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), image_edges=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_Smooth.py b/nipype/interfaces/fsl/tests/test_auto_Smooth.py index 503282ea4a..d653e4d7cb 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Smooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_Smooth.py @@ -14,7 +14,8 @@ def test_Smooth_inputs(): position=1, xor=['sigma'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py index bcc090fed1..c98830c384 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py +++ b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py @@ -13,7 +13,8 @@ def test_SmoothEstimate_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mask_file=dict(argstr='--mask=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py index 0457a50c2e..be3772926f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py @@ -9,7 +9,8 @@ def test_SpatialFilter_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_Split.py b/nipype/interfaces/fsl/tests/test_auto_Split.py index a95770b9ee..efe176be46 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Split.py +++ b/nipype/interfaces/fsl/tests/test_auto_Split.py @@ -13,7 +13,8 @@ def test_Split_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_StdImage.py b/nipype/interfaces/fsl/tests/test_auto_StdImage.py index 88eea8a627..8675590d07 100644 --- a/nipype/interfaces/fsl/tests/test_auto_StdImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_StdImage.py @@ -13,7 +13,8 @@ def test_StdImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py index 710c3baa39..c225c37ab0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py +++ b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py @@ -9,7 +9,8 @@ def test_SwapDimensions_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py index 2f55bf893e..fd04dadcbc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py @@ -25,7 +25,8 @@ def test_TOPUP_inputs(): ), fwhm=dict(argstr='--fwhm=%f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='--imain=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py index 230ffcba78..4f5bb4d84e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py @@ -13,7 +13,8 @@ def test_TemporalFilter_inputs(): position=4, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_Threshold.py b/nipype/interfaces/fsl/tests/test_auto_Threshold.py index 8e284d67b0..923deff51d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Threshold.py +++ b/nipype/interfaces/fsl/tests/test_auto_Threshold.py @@ -11,7 +11,8 @@ def test_Threshold_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py index d578bdea8e..0c5634d731 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py +++ b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py @@ -15,7 +15,8 @@ def test_TractSkeleton_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-i %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_Training.py b/nipype/interfaces/fsl/tests/test_auto_Training.py index 6ea6042c80..5d4d965951 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Training.py +++ b/nipype/interfaces/fsl/tests/test_auto_Training.py @@ -9,7 +9,8 @@ def test_Training_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), loo=dict(argstr='-l', diff --git a/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py b/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py index abe2237832..370e89fdf4 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py +++ b/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py @@ -4,7 +4,8 @@ def test_TrainingSetCreator_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mel_icas_in=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py index 4132931d57..eb43d00aaf 100644 --- a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py @@ -9,7 +9,8 @@ def test_UnaryMaths_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_VecReg.py b/nipype/interfaces/fsl/tests/test_auto_VecReg.py index 48795b253a..2308c13b04 100644 --- a/nipype/interfaces/fsl/tests/test_auto_VecReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_VecReg.py @@ -11,7 +11,8 @@ def test_VecReg_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-i %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py b/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py index 738192f1b7..cc8f9f9ce8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py @@ -18,7 +18,8 @@ def test_WarpPoints_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_coords=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPointsFromStd.py b/nipype/interfaces/fsl/tests/test_auto_WarpPointsFromStd.py index dd7b200d84..0824beae24 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPointsFromStd.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPointsFromStd.py @@ -15,7 +15,8 @@ def test_WarpPointsFromStd_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), img_file=dict(argstr='-img %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py b/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py index 23605bfeaf..ac7f73031b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py @@ -15,7 +15,8 @@ def test_WarpPointsToStd_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), img_file=dict(argstr='-img %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py b/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py index b879eb0e07..2361a8f7e4 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py @@ -9,7 +9,8 @@ def test_WarpUtils_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='--in=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_XFibres5.py b/nipype/interfaces/fsl/tests/test_auto_XFibres5.py index 5359c49d8d..f84b0b9ae8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_XFibres5.py +++ b/nipype/interfaces/fsl/tests/test_auto_XFibres5.py @@ -41,7 +41,8 @@ def test_XFibres5_inputs(): ), gradnonlin=dict(argstr='--gradnonlin=%s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), logdir=dict(argstr='--logdir=%s', diff --git a/nipype/interfaces/minc/tests/test_auto_Average.py b/nipype/interfaces/minc/tests/test_auto_Average.py index c903c88cfc..b7adb07145 100644 --- a/nipype/interfaces/minc/tests/test_auto_Average.py +++ b/nipype/interfaces/minc/tests/test_auto_Average.py @@ -59,7 +59,8 @@ def test_Average_inputs(): format_unsigned=dict(argstr='-unsigned', xor=('format_filetype', 'format_byte', 'format_short', 'format_int', 'format_long', 'format_float', 'format_double', 'format_signed', 'format_unsigned'), ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_files=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_BBox.py b/nipype/interfaces/minc/tests/test_auto_BBox.py index e57492702c..b469e57184 100644 --- a/nipype/interfaces/minc/tests/test_auto_BBox.py +++ b/nipype/interfaces/minc/tests/test_auto_BBox.py @@ -15,7 +15,8 @@ def test_BBox_inputs(): ), format_mincreshape=dict(argstr='-mincreshape', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_file=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_Beast.py b/nipype/interfaces/minc/tests/test_auto_Beast.py index 642bd6f6ea..9b24d9cb0b 100644 --- a/nipype/interfaces/minc/tests/test_auto_Beast.py +++ b/nipype/interfaces/minc/tests/test_auto_Beast.py @@ -23,7 +23,8 @@ def test_Beast_inputs(): ), flip_images=dict(argstr='-flip', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_file=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_BestLinReg.py b/nipype/interfaces/minc/tests/test_auto_BestLinReg.py index f8d670a9da..8d9641db16 100644 --- a/nipype/interfaces/minc/tests/test_auto_BestLinReg.py +++ b/nipype/interfaces/minc/tests/test_auto_BestLinReg.py @@ -12,7 +12,8 @@ def test_BestLinReg_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), output_mnc=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_BigAverage.py b/nipype/interfaces/minc/tests/test_auto_BigAverage.py index ee21ea0e32..f0f4bd20f8 100644 --- a/nipype/interfaces/minc/tests/test_auto_BigAverage.py +++ b/nipype/interfaces/minc/tests/test_auto_BigAverage.py @@ -12,7 +12,8 @@ def test_BigAverage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_files=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_Blob.py b/nipype/interfaces/minc/tests/test_auto_Blob.py index 8ae597fdc5..a0f2d95d40 100644 --- a/nipype/interfaces/minc/tests/test_auto_Blob.py +++ b/nipype/interfaces/minc/tests/test_auto_Blob.py @@ -11,7 +11,8 @@ def test_Blob_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_file=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_Blur.py b/nipype/interfaces/minc/tests/test_auto_Blur.py index 95aeaef0af..e50f0f0b47 100644 --- a/nipype/interfaces/minc/tests/test_auto_Blur.py +++ b/nipype/interfaces/minc/tests/test_auto_Blur.py @@ -27,7 +27,8 @@ def test_Blur_inputs(): ), gradient=dict(argstr='-gradient', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_file=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_Calc.py b/nipype/interfaces/minc/tests/test_auto_Calc.py index 860b41a06a..1e690a1468 100644 --- a/nipype/interfaces/minc/tests/test_auto_Calc.py +++ b/nipype/interfaces/minc/tests/test_auto_Calc.py @@ -62,7 +62,8 @@ def test_Calc_inputs(): format_unsigned=dict(argstr='-unsigned', xor=('format_filetype', 'format_byte', 'format_short', 'format_int', 'format_long', 'format_float', 'format_double', 'format_signed', 'format_unsigned'), ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ignore_nan=dict(argstr='-ignore_nan', diff --git a/nipype/interfaces/minc/tests/test_auto_Convert.py b/nipype/interfaces/minc/tests/test_auto_Convert.py index 97ab313ffb..6df129aee4 100644 --- a/nipype/interfaces/minc/tests/test_auto_Convert.py +++ b/nipype/interfaces/minc/tests/test_auto_Convert.py @@ -17,7 +17,8 @@ def test_Convert_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_file=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_Copy.py b/nipype/interfaces/minc/tests/test_auto_Copy.py index 6923ee0639..73662e9b88 100644 --- a/nipype/interfaces/minc/tests/test_auto_Copy.py +++ b/nipype/interfaces/minc/tests/test_auto_Copy.py @@ -9,7 +9,8 @@ def test_Copy_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_file=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_Dump.py b/nipype/interfaces/minc/tests/test_auto_Dump.py index 7066fe56c7..2e9ab091b4 100644 --- a/nipype/interfaces/minc/tests/test_auto_Dump.py +++ b/nipype/interfaces/minc/tests/test_auto_Dump.py @@ -21,7 +21,8 @@ def test_Dump_inputs(): header_data=dict(argstr='-h', xor=('coordinate_data', 'header_data'), ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_file=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_Extract.py b/nipype/interfaces/minc/tests/test_auto_Extract.py index feb6f338cb..0df7132519 100644 --- a/nipype/interfaces/minc/tests/test_auto_Extract.py +++ b/nipype/interfaces/minc/tests/test_auto_Extract.py @@ -48,7 +48,8 @@ def test_Extract_inputs(): flip_z_positive=dict(argstr='+zdirection', xor=('flip_z_positive', 'flip_z_negative', 'flip_z_any'), ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), image_maximum=dict(argstr='-image_maximum %s', diff --git a/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py b/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py index 0e2720037a..e09dc43c73 100644 --- a/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py +++ b/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py @@ -14,7 +14,8 @@ def test_Gennlxfm_inputs(): ), ident=dict(argstr='-ident', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), like=dict(argstr='-like %s', diff --git a/nipype/interfaces/minc/tests/test_auto_Math.py b/nipype/interfaces/minc/tests/test_auto_Math.py index 60a289f391..33946b7e44 100644 --- a/nipype/interfaces/minc/tests/test_auto_Math.py +++ b/nipype/interfaces/minc/tests/test_auto_Math.py @@ -73,7 +73,8 @@ def test_Math_inputs(): format_unsigned=dict(argstr='-unsigned', xor=('format_filetype', 'format_byte', 'format_short', 'format_int', 'format_long', 'format_float', 'format_double', 'format_signed', 'format_unsigned'), ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ignore_nan=dict(argstr='-ignore_nan', diff --git a/nipype/interfaces/minc/tests/test_auto_NlpFit.py b/nipype/interfaces/minc/tests/test_auto_NlpFit.py index bfd7586dba..905c4b9080 100644 --- a/nipype/interfaces/minc/tests/test_auto_NlpFit.py +++ b/nipype/interfaces/minc/tests/test_auto_NlpFit.py @@ -15,7 +15,8 @@ def test_NlpFit_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), init_xfm=dict(argstr='-init_xfm %s', diff --git a/nipype/interfaces/minc/tests/test_auto_Norm.py b/nipype/interfaces/minc/tests/test_auto_Norm.py index 2d45f249af..ca19629e3a 100644 --- a/nipype/interfaces/minc/tests/test_auto_Norm.py +++ b/nipype/interfaces/minc/tests/test_auto_Norm.py @@ -17,7 +17,8 @@ def test_Norm_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_file=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_Pik.py b/nipype/interfaces/minc/tests/test_auto_Pik.py index 1a15c2bb01..1e0b92fb35 100644 --- a/nipype/interfaces/minc/tests/test_auto_Pik.py +++ b/nipype/interfaces/minc/tests/test_auto_Pik.py @@ -22,7 +22,8 @@ def test_Pik_inputs(): horizontal_triplanar_view=dict(argstr='--horizontal', xor=('vertical_triplanar_view', 'horizontal_triplanar_view'), ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), image_range=dict(argstr='--image_range %s %s', diff --git a/nipype/interfaces/minc/tests/test_auto_Resample.py b/nipype/interfaces/minc/tests/test_auto_Resample.py index 1ed905fadb..f11c11daf0 100644 --- a/nipype/interfaces/minc/tests/test_auto_Resample.py +++ b/nipype/interfaces/minc/tests/test_auto_Resample.py @@ -51,7 +51,8 @@ def test_Resample_inputs(): half_width_sinc_window=dict(argstr='-width %s', requires=['sinc_interpolation'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_file=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_Reshape.py b/nipype/interfaces/minc/tests/test_auto_Reshape.py index b55b2e896d..64f28362c9 100644 --- a/nipype/interfaces/minc/tests/test_auto_Reshape.py +++ b/nipype/interfaces/minc/tests/test_auto_Reshape.py @@ -12,7 +12,8 @@ def test_Reshape_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_file=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_ToEcat.py b/nipype/interfaces/minc/tests/test_auto_ToEcat.py index 236bc4d9a7..3b48a27654 100644 --- a/nipype/interfaces/minc/tests/test_auto_ToEcat.py +++ b/nipype/interfaces/minc/tests/test_auto_ToEcat.py @@ -17,7 +17,8 @@ def test_ToEcat_inputs(): ), ignore_ecat_subheader_variable=dict(argstr='-ignore_ecat_subheader_variable', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ignore_patient_variable=dict(argstr='-ignore_patient_variable', diff --git a/nipype/interfaces/minc/tests/test_auto_ToRaw.py b/nipype/interfaces/minc/tests/test_auto_ToRaw.py index d231faa8d6..02af1da373 100644 --- a/nipype/interfaces/minc/tests/test_auto_ToRaw.py +++ b/nipype/interfaces/minc/tests/test_auto_ToRaw.py @@ -9,7 +9,8 @@ def test_ToRaw_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_file=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_VolSymm.py b/nipype/interfaces/minc/tests/test_auto_VolSymm.py index f6a56d153a..88145f639d 100644 --- a/nipype/interfaces/minc/tests/test_auto_VolSymm.py +++ b/nipype/interfaces/minc/tests/test_auto_VolSymm.py @@ -18,7 +18,8 @@ def test_VolSymm_inputs(): ), fit_nonlinear=dict(argstr='-nonlinear', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_file=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_Volcentre.py b/nipype/interfaces/minc/tests/test_auto_Volcentre.py index c8793ff79a..7bf95a9c3d 100644 --- a/nipype/interfaces/minc/tests/test_auto_Volcentre.py +++ b/nipype/interfaces/minc/tests/test_auto_Volcentre.py @@ -16,7 +16,8 @@ def test_Volcentre_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_file=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_Voliso.py b/nipype/interfaces/minc/tests/test_auto_Voliso.py index 89edd67d00..76ad3283c8 100644 --- a/nipype/interfaces/minc/tests/test_auto_Voliso.py +++ b/nipype/interfaces/minc/tests/test_auto_Voliso.py @@ -14,7 +14,8 @@ def test_Voliso_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_file=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_Volpad.py b/nipype/interfaces/minc/tests/test_auto_Volpad.py index 96709fe710..6ac867639e 100644 --- a/nipype/interfaces/minc/tests/test_auto_Volpad.py +++ b/nipype/interfaces/minc/tests/test_auto_Volpad.py @@ -18,7 +18,8 @@ def test_Volpad_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_file=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_XfmAvg.py b/nipype/interfaces/minc/tests/test_auto_XfmAvg.py index db63ccda08..3d288aa1cd 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmAvg.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmAvg.py @@ -16,7 +16,8 @@ def test_XfmAvg_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ignore_linear=dict(argstr='-ignore_linear', diff --git a/nipype/interfaces/minc/tests/test_auto_XfmConcat.py b/nipype/interfaces/minc/tests/test_auto_XfmConcat.py index 3859b91538..4d3cdadb24 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmConcat.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmConcat.py @@ -12,7 +12,8 @@ def test_XfmConcat_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_files=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_XfmInvert.py b/nipype/interfaces/minc/tests/test_auto_XfmInvert.py index ee56dfb262..10f5e9ec6a 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmInvert.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmInvert.py @@ -12,7 +12,8 @@ def test_XfmInvert_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_file=dict(argstr='%s', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py index c82e9b867b..64349fa299 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py @@ -9,7 +9,8 @@ def test_JistBrainMgdmSegmentation_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inAdjust=dict(argstr='--inAdjust %s', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py index 7d45f19c81..113bc27c4d 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py @@ -9,7 +9,8 @@ def test_JistBrainMp2rageDuraEstimation_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inDistance=dict(argstr='--inDistance %f', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py index ac2f9cfbb2..624326b534 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py @@ -9,7 +9,8 @@ def test_JistBrainMp2rageSkullStripping_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inFilter=dict(argstr='--inFilter %s', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py index 281751d399..8fe4e3df73 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py @@ -9,7 +9,8 @@ def test_JistBrainPartialVolumeFilter_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inInput=dict(argstr='--inInput %s', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py b/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py index baa2a6c77e..238e2fd02e 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py @@ -9,7 +9,8 @@ def test_JistCortexSurfaceMeshInflation_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inLevelset=dict(argstr='--inLevelset %s', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py index 86b4732d95..769202018d 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py @@ -9,7 +9,8 @@ def test_JistIntensityMp2rageMasking_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inBackground=dict(argstr='--inBackground %s', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py index 307b905f92..0485ed2ad2 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py @@ -9,7 +9,8 @@ def test_JistLaminarProfileCalculator_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inIntensity=dict(argstr='--inIntensity %s', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py index fa1c272e34..21f94d42e9 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py @@ -9,7 +9,8 @@ def test_JistLaminarProfileGeometry_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inProfile=dict(argstr='--inProfile %s', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py index f140358400..6d9ad3493a 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py @@ -9,7 +9,8 @@ def test_JistLaminarProfileSampling_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inCortex=dict(argstr='--inCortex %s', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py index a369b28b2c..012fa2872b 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py @@ -9,7 +9,8 @@ def test_JistLaminarROIAveraging_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inIntensity=dict(argstr='--inIntensity %s', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py index 9f5971c25f..e80496ec47 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py @@ -9,7 +9,8 @@ def test_JistLaminarVolumetricLayering_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inInner=dict(argstr='--inInner %s', diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py index 032c318472..c273cbf378 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py @@ -9,7 +9,8 @@ def test_MedicAlgorithmImageCalculator_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inOperation=dict(argstr='--inOperation %s', diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py index d97d670b7a..dd97b91a1f 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py @@ -9,7 +9,8 @@ def test_MedicAlgorithmLesionToads_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inAtlas=dict(argstr='--inAtlas %s', diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py index dac7501343..e089749b4c 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py @@ -9,7 +9,8 @@ def test_MedicAlgorithmMipavReorient_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inInterpolation=dict(argstr='--inInterpolation %s', diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py index 279e53416f..42a161c44e 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py @@ -9,7 +9,8 @@ def test_MedicAlgorithmN3_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inAutomatic=dict(argstr='--inAutomatic %s', diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py index c7a3e1bfcc..6d2c379fcf 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py @@ -9,7 +9,8 @@ def test_MedicAlgorithmSPECTRE2010_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inApply=dict(argstr='--inApply %s', diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py index 9c21194793..c895cd75d5 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py @@ -9,7 +9,8 @@ def test_MedicAlgorithmThresholdToBinaryMask_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inLabel=dict(argstr='--inLabel %s', diff --git a/nipype/interfaces/mipav/tests/test_auto_RandomVol.py b/nipype/interfaces/mipav/tests/test_auto_RandomVol.py index 3e4c22b80e..b7e3c098f7 100644 --- a/nipype/interfaces/mipav/tests/test_auto_RandomVol.py +++ b/nipype/interfaces/mipav/tests/test_auto_RandomVol.py @@ -9,7 +9,8 @@ def test_RandomVol_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inField=dict(argstr='--inField %s', diff --git a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py index de29c86fde..4fb5dcee55 100644 --- a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py +++ b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py @@ -11,7 +11,8 @@ def test_WatershedBEM_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), overwrite=dict(argstr='--overwrite', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py index 5ab7b11f6b..ef66cfc691 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py @@ -20,7 +20,8 @@ def test_ConstrainedSphericalDeconvolution_inputs(): filter_file=dict(argstr='-filter %s', position=-2, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py index dddd1a7e95..54a028727e 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py @@ -13,7 +13,8 @@ def test_DWI2SphericalHarmonicsImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py index 28c678b671..051172702f 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py @@ -15,7 +15,8 @@ def test_DWI2Tensor_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ignore_slice_by_volume=dict(argstr='-ignoreslices %s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py index 87af9bcc7e..46f45243ee 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py @@ -29,7 +29,8 @@ def test_DiffusionTensorStreamlineTrack_inputs(): mandatory=True, position=-2, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py index 48fb914125..dfe29bbb7c 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py @@ -13,7 +13,8 @@ def test_Directions2Amplitude_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py index 70cdd1a691..874ad1ba0e 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py @@ -15,7 +15,8 @@ def test_Erode_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py index 07928dfe43..5d81dbecd6 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py @@ -15,7 +15,8 @@ def test_EstimateResponseForSH_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py b/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py index c6582da586..5c53341e8f 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py @@ -21,7 +21,8 @@ def test_FilterTracks_inputs(): units='mm', xor=['exclude_file', 'exclude_spec'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py index 68251c23c0..f0571ad997 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py @@ -17,7 +17,8 @@ def test_FindShPeaks_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py index cd14499969..8e4167167f 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py @@ -13,7 +13,8 @@ def test_GenerateDirections_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), niter=dict(argstr='-niter %s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py index c8ce15714c..bda204c9ad 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py @@ -17,7 +17,8 @@ def test_GenerateWhiteMatterMask_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py index 2028d9ebab..ed9071256e 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py @@ -19,7 +19,8 @@ def test_MRConvert_inputs(): position=2, sep=',', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py index 61d8920633..efb8b92249 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py @@ -12,7 +12,8 @@ def test_MRMultiply_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py index ee3be59eff..a685293371 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py @@ -15,7 +15,8 @@ def test_MRTransform_inputs(): flip_x=dict(argstr='-flipx', position=1, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py index 4f6784bd5c..4fe4d2952b 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py @@ -9,7 +9,8 @@ def test_MRTrixInfo_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py index 15ab6d4919..19a0e6f710 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py @@ -12,7 +12,8 @@ def test_MRTrixViewer_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py index b56c033abb..0b13574b78 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py @@ -12,7 +12,8 @@ def test_MedianFilter3D_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py index bfeaab595b..f3fcda4884 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py @@ -25,7 +25,8 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): units='mm', xor=['exclude_file', 'exclude_spec'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py index 05afc4dd17..a8ef768850 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py @@ -25,7 +25,8 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): units='mm', xor=['exclude_file', 'exclude_spec'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py index 192d0b8a6a..5e028c40ac 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py @@ -25,7 +25,8 @@ def test_StreamlineTrack_inputs(): units='mm', xor=['exclude_file', 'exclude_spec'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py index 22da9f1842..e4f32e21d2 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py @@ -12,7 +12,8 @@ def test_Tensor2ApparentDiffusion_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py index 70fb981fc9..07535aa125 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py @@ -12,7 +12,8 @@ def test_Tensor2FractionalAnisotropy_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py index 62bde41c8b..724c9cb534 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py @@ -12,7 +12,8 @@ def test_Tensor2Vector_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py index 6668810b72..124e87a0b2 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py @@ -14,7 +14,8 @@ def test_Threshold_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py index 5265fe1ba4..f1a2a08355 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py @@ -15,7 +15,8 @@ def test_Tracks2Prob_inputs(): fraction=dict(argstr='-fraction', position=3, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix/tracking.py b/nipype/interfaces/mrtrix/tracking.py index 5570a9b8d1..c013d7b04a 100644 --- a/nipype/interfaces/mrtrix/tracking.py +++ b/nipype/interfaces/mrtrix/tracking.py @@ -15,8 +15,10 @@ import os.path as op from ...utils.filemanip import split_filename -from ..base import CommandLineInputSpec, CommandLine, traits, TraitedSpec, File -from ..traits_extension import isdefined +from ..base import ( + CommandLineInputSpec, CommandLine, traits, TraitedSpec, File, + isdefined +) class FilterTracksInputSpec(CommandLineInputSpec): diff --git a/nipype/interfaces/mrtrix3/base.py b/nipype/interfaces/mrtrix3/base.py index a9890d9653..0d91c3d56d 100644 --- a/nipype/interfaces/mrtrix3/base.py +++ b/nipype/interfaces/mrtrix3/base.py @@ -14,8 +14,7 @@ from __future__ import print_function, division, unicode_literals, absolute_import from ... import logging -from ..traits_extension import isdefined -from ..base import (CommandLineInputSpec, CommandLine, traits, File) +from ..base import (CommandLineInputSpec, CommandLine, traits, File, isdefined) iflogger = logging.getLogger('interface') diff --git a/nipype/interfaces/mrtrix3/connectivity.py b/nipype/interfaces/mrtrix3/connectivity.py index caa510e6e1..3b79b16442 100644 --- a/nipype/interfaces/mrtrix3/connectivity.py +++ b/nipype/interfaces/mrtrix3/connectivity.py @@ -16,8 +16,7 @@ import os import os.path as op -from ..traits_extension import isdefined -from ..base import (CommandLineInputSpec, traits, TraitedSpec, File) +from ..base import (CommandLineInputSpec, traits, TraitedSpec, File, isdefined) from .base import MRTrix3Base diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py index 141325e25b..c097856ef3 100644 --- a/nipype/interfaces/mrtrix3/preprocess.py +++ b/nipype/interfaces/mrtrix3/preprocess.py @@ -15,9 +15,8 @@ import os.path as op -from ..traits_extension import isdefined from ..base import (CommandLineInputSpec, CommandLine, traits, TraitedSpec, - File) + File, isdefined) from .base import MRTrix3BaseInputSpec, MRTrix3Base diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py b/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py index fa2bc2f222..9918c9ae32 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py @@ -9,7 +9,8 @@ def test_ACTPrepareFSL_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py index 1056ecadcc..25b9716f80 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py @@ -15,7 +15,8 @@ def test_BrainMask_inputs(): ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_bval=dict(), diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py b/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py index 4f12e08cfc..fdac1f65fb 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py @@ -9,7 +9,8 @@ def test_BuildConnectome_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py b/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py index f9dac1b48e..0183045c56 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py @@ -19,7 +19,8 @@ def test_ComputeTDI_inputs(): ), fwhm_tck=dict(argstr='-fwhm_tck %f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py index f645703bba..88f2ba343e 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py @@ -15,7 +15,8 @@ def test_EstimateFOD_inputs(): ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_bval=dict(), diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py index 693e522b80..f61669d5c9 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py @@ -15,7 +15,8 @@ def test_FitTensor_inputs(): ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_bval=dict(), diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py index 2afa4e46da..dd6d1d6408 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py @@ -9,7 +9,8 @@ def test_Generate5tt_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_fast=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py index 91463a46fb..4594894ef1 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py @@ -9,7 +9,8 @@ def test_LabelConfig_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_config=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py index 44fc68a474..1d306b6a86 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py @@ -9,7 +9,8 @@ def test_MRTrix3Base_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), terminal_output=dict(deprecated='1.0.0', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py b/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py index 6f07bd8eab..30dac94dda 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py @@ -9,7 +9,8 @@ def test_Mesh2PVE_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py b/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py index fb5f86f8d4..b881dc7d1b 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py @@ -9,7 +9,8 @@ def test_ReplaceFSwithFIRST_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_config=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py index 4a4aeb153e..268786ea94 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py @@ -17,7 +17,8 @@ def test_ResponseSD_inputs(): ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_bval=dict(), diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py b/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py index 284235ca55..d5f88bc470 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py @@ -9,7 +9,8 @@ def test_TCK2VTK_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py b/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py index 0103efc7e1..d51f5fe53e 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py @@ -12,7 +12,8 @@ def test_TensorMetrics_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py index e1a684b8d9..6c715202b5 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py @@ -32,7 +32,8 @@ def test_Tractography_inputs(): ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_bval=dict(), diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py index 42f3d0c6fd..fd362ebee2 100644 --- a/nipype/interfaces/mrtrix3/utils.py +++ b/nipype/interfaces/mrtrix3/utils.py @@ -15,9 +15,8 @@ import os.path as op -from ..traits_extension import isdefined from ..base import (CommandLineInputSpec, CommandLine, traits, TraitedSpec, - File, InputMultiPath) + File, InputMultiPath, isdefined) from .base import MRTrix3BaseInputSpec, MRTrix3Base diff --git a/nipype/interfaces/niftyfit/base.py b/nipype/interfaces/niftyfit/base.py index a2f64fcd6b..58cbcaed45 100644 --- a/nipype/interfaces/niftyfit/base.py +++ b/nipype/interfaces/niftyfit/base.py @@ -19,16 +19,11 @@ """ import os -import warnings from ..base import CommandLine from ...utils.filemanip import split_filename -warn = warnings.warn -warnings.filterwarnings('always', category=UserWarning) - - class NiftyFitCommand(CommandLine): """ Base support interface for NiftyFit commands. diff --git a/nipype/interfaces/niftyfit/tests/test_asl.py b/nipype/interfaces/niftyfit/tests/test_asl.py index 7d0df3376a..f949e26b76 100644 --- a/nipype/interfaces/niftyfit/tests/test_asl.py +++ b/nipype/interfaces/niftyfit/tests/test_asl.py @@ -4,12 +4,14 @@ import pytest -from nipype.interfaces.niftyfit import FitAsl -from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path -from nipype.testing import example_data +from ....testing import example_data +from ...niftyreg import get_custom_path +from ..asl import FitAsl +from ...niftyreg.tests.test_regutils import no_nifty_tool -@pytest.mark.skipif(no_nifty_package(cmd='fit_asl'), + +@pytest.mark.skipif(no_nifty_tool(cmd='fit_asl'), reason="niftyfit is not installed") def test_fit_asl(): """ Testing FitAsl interface.""" diff --git a/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py b/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py index 41a3d6cc5a..6c0a773fa6 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py @@ -43,7 +43,8 @@ def test_DwiTool_inputs(): name_source=['source_file'], name_template='%s_famap.nii.gz', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ivim_flag=dict(argstr='-ivim', diff --git a/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py b/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py index d596f0f633..db865b495c 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py @@ -29,7 +29,8 @@ def test_FitAsl_inputs(): ), gm_ttt=dict(argstr='-gmTTT %f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ir_output=dict(argstr='-IRoutput %s', diff --git a/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py b/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py index 7ca90b7304..96e8fd736f 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py @@ -50,7 +50,8 @@ def test_FitDwi_inputs(): gn_flag=dict(argstr='-gn', xor=['wls_flag'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ivim_flag=dict(argstr='-ivim', diff --git a/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py b/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py index 3b628975f4..32d1cb7b03 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py @@ -29,7 +29,8 @@ def test_FitQt1_inputs(): gn_flag=dict(argstr='-gn', position=8, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ir_flag=dict(argstr='-IR', diff --git a/nipype/interfaces/niftyfit/tests/test_auto_NiftyFitCommand.py b/nipype/interfaces/niftyfit/tests/test_auto_NiftyFitCommand.py index 813a4f69b5..1365775b56 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_NiftyFitCommand.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_NiftyFitCommand.py @@ -9,7 +9,8 @@ def test_NiftyFitCommand_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), terminal_output=dict(deprecated='1.0.0', diff --git a/nipype/interfaces/niftyfit/tests/test_dwi.py b/nipype/interfaces/niftyfit/tests/test_dwi.py index aee809e9c5..5b7d0f7348 100644 --- a/nipype/interfaces/niftyfit/tests/test_dwi.py +++ b/nipype/interfaces/niftyfit/tests/test_dwi.py @@ -3,12 +3,14 @@ import pytest -from nipype.interfaces.niftyfit import FitDwi, DwiTool -from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path -from nipype.testing import example_data +from ....testing import example_data +from ...niftyreg import get_custom_path +from ..dwi import FitDwi, DwiTool +from ...niftyreg.tests.test_regutils import no_nifty_tool -@pytest.mark.skipif(no_nifty_package(cmd='fit_dwi'), + +@pytest.mark.skipif(no_nifty_tool(cmd='fit_dwi'), reason="niftyfit is not installed") def test_fit_dwi(): """ Testing FitDwi interface.""" @@ -56,7 +58,7 @@ def test_fit_dwi(): assert fit_dwi.cmdline == expected_cmd -@pytest.mark.skipif(no_nifty_package(cmd='dwi_tool'), +@pytest.mark.skipif(no_nifty_tool(cmd='dwi_tool'), reason="niftyfit is not installed") def test_dwi_tool(): """ Testing DwiTool interface.""" diff --git a/nipype/interfaces/niftyfit/tests/test_qt1.py b/nipype/interfaces/niftyfit/tests/test_qt1.py index 2d64a6cec5..e2e78ed37d 100644 --- a/nipype/interfaces/niftyfit/tests/test_qt1.py +++ b/nipype/interfaces/niftyfit/tests/test_qt1.py @@ -4,12 +4,13 @@ import pytest -from nipype.interfaces.niftyfit import FitQt1 -from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path -from nipype.testing import example_data +from ....testing import example_data +from ...niftyreg import get_custom_path +from ...niftyreg.tests.test_regutils import no_nifty_tool +from ..qt1 import FitQt1 -@pytest.mark.skipif(no_nifty_package(cmd='fit_qt1'), +@pytest.mark.skipif(no_nifty_tool(cmd='fit_qt1'), reason="niftyfit is not installed") def test_fit_qt1(): """ Testing FitQt1 interface.""" diff --git a/nipype/interfaces/niftyreg/__init__.py b/nipype/interfaces/niftyreg/__init__.py index 64cc60a0ab..04c066dcae 100644 --- a/nipype/interfaces/niftyreg/__init__.py +++ b/nipype/interfaces/niftyreg/__init__.py @@ -9,7 +9,7 @@ Top-level namespace for niftyreg. """ -from .base import no_nifty_package, get_custom_path +from .base import get_custom_path from .reg import RegAladin, RegF3D from .regutils import (RegResample, RegJacobian, RegAverage, RegTools, RegTransform, RegMeasure) diff --git a/nipype/interfaces/niftyreg/base.py b/nipype/interfaces/niftyreg/base.py index bb09d96923..47859c9ec9 100644 --- a/nipype/interfaces/niftyreg/base.py +++ b/nipype/interfaces/niftyreg/base.py @@ -22,28 +22,18 @@ from builtins import property, super from distutils.version import StrictVersion import os -import shutil -import subprocess -from warnings import warn +from ... import logging from ..base import CommandLine, CommandLineInputSpec, traits, Undefined from ...utils.filemanip import split_filename +iflogger = logging.getLogger('interface') + def get_custom_path(command, env_dir='NIFTYREGDIR'): return os.path.join(os.getenv(env_dir, ''), command) -def no_nifty_package(cmd='reg_f3d'): - try: - return shutil.which(cmd) is None - except AttributeError: # Python < 3.3 - return not any( - [os.path.isfile(os.path.join(path, cmd)) and - os.access(os.path.join(path, cmd), os.X_OK) - for path in os.environ["PATH"].split(os.pathsep)]) - - class NiftyRegCommandInputSpec(CommandLineInputSpec): """Input Spec for niftyreg interfaces.""" # Set the number of omp thread to use @@ -65,18 +55,18 @@ def __init__(self, required_version=None, **inputs): self.num_threads = 1 super(NiftyRegCommand, self).__init__(**inputs) self.required_version = required_version - _version = self.get_version() + _version = self.version_from_command() if _version: _version = _version.decode("utf-8") if self._min_version is not None and \ StrictVersion(_version) < StrictVersion(self._min_version): msg = 'A later version of Niftyreg is required (%s < %s)' - warn(msg % (_version, self._min_version)) + iflogger.warning(msg, _version, self._min_version) if required_version is not None: if StrictVersion(_version) != StrictVersion(required_version): msg = 'The version of NiftyReg differs from the required' msg += '(%s != %s)' - warn(msg % (_version, self.required_version)) + iflogger.warning(msg, _version, self.required_version) self.inputs.on_trait_change(self._omp_update, 'omp_core_val') self.inputs.on_trait_change(self._environ_update, 'environ') self._omp_update() @@ -102,7 +92,7 @@ def _environ_update(self): self.inputs.omp_core_val = Undefined def check_version(self): - _version = self.get_version() + _version = self.version_from_command() if not _version: raise Exception('Niftyreg not found') # Decoding to string: @@ -116,18 +106,12 @@ def check_version(self): err += '(%s != %s)' raise ValueError(err % (_version, self.required_version)) - def get_version(self): - if no_nifty_package(cmd=self.cmd): - return None - exec_cmd = ''.join((self.cmd, ' -v')) - return subprocess.check_output(exec_cmd, shell=True).strip() - @property def version(self): - return self.get_version() + return self.version_from_command() def exists(self): - return self.get_version() is not None + return self.version_from_command() is not None def _format_arg(self, name, spec, value): if name == 'omp_core_val': diff --git a/nipype/interfaces/niftyreg/reg.py b/nipype/interfaces/niftyreg/reg.py index fa4a1701ee..bbc49ee2f2 100644 --- a/nipype/interfaces/niftyreg/reg.py +++ b/nipype/interfaces/niftyreg/reg.py @@ -20,17 +20,12 @@ absolute_import) from builtins import staticmethod import os -import warnings from ..base import TraitedSpec, File, traits, isdefined from .base import get_custom_path, NiftyRegCommand, NiftyRegCommandInputSpec from ...utils.filemanip import split_filename -warn = warnings.warn -warnings.filterwarnings('always', category=UserWarning) - - class RegAladinInputSpec(NiftyRegCommandInputSpec): """ Input Spec for RegAladin. """ # Input reference file diff --git a/nipype/interfaces/niftyreg/regutils.py b/nipype/interfaces/niftyreg/regutils.py index 214ccc9a45..4bbb73c687 100644 --- a/nipype/interfaces/niftyreg/regutils.py +++ b/nipype/interfaces/niftyreg/regutils.py @@ -18,7 +18,6 @@ from __future__ import (print_function, division, unicode_literals, absolute_import) from builtins import len, open, property, super -import warnings import os from ..base import TraitedSpec, File, traits, isdefined @@ -26,10 +25,6 @@ from ...utils.filemanip import split_filename -warn = warnings.warn -warnings.filterwarnings('always', category=UserWarning) - - class RegResampleInputSpec(NiftyRegCommandInputSpec): """ Input Spec for RegResample. """ # Input reference file diff --git a/nipype/interfaces/niftyreg/tests/test_auto_NiftyRegCommand.py b/nipype/interfaces/niftyreg/tests/test_auto_NiftyRegCommand.py index f97733e5ca..ee4b020bd0 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_NiftyRegCommand.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_NiftyRegCommand.py @@ -9,7 +9,8 @@ def test_NiftyRegCommand_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), omp_core_val=dict(argstr='-omp %i', diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py b/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py index a39dad2d73..d177916034 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py @@ -30,7 +30,8 @@ def test_RegAladin_inputs(): ), i_val=dict(argstr='-pi %d', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_aff_file=dict(argstr='-inaff %s', diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py b/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py index 7da4788379..7898d68cd3 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py @@ -39,7 +39,8 @@ def test_RegAverage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), omp_core_val=dict(argstr='-omp %i', diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py b/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py index 906439f23d..ba4301e756 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py @@ -38,7 +38,8 @@ def test_RegF3D_inputs(): ), fupth_thr_val=dict(argstr='--fUpTh %f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), incpp_file=dict(argstr='-incpp %s', diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py b/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py index 8bcd86d85e..fd4d81b6a1 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py @@ -9,7 +9,8 @@ def test_RegJacobian_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), omp_core_val=dict(argstr='-omp %i', diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py b/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py index 957442a86b..11b1248e6d 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py @@ -12,7 +12,8 @@ def test_RegMeasure_inputs(): flo_file=dict(argstr='-flo %s', mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), measure_type=dict(argstr='-%s', diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py b/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py index 130c734b69..7efa3c5068 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py @@ -12,7 +12,8 @@ def test_RegResample_inputs(): flo_file=dict(argstr='-flo %s', mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inter_val=dict(argstr='-inter %d', diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py b/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py index 5485a92b4d..8b8c371638 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py @@ -19,7 +19,8 @@ def test_RegTools_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-in %s', diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py b/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py index 624f07d350..3730a8b42d 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py @@ -41,7 +41,8 @@ def test_RegTransform_inputs(): position=-2, xor=['def_input', 'disp_input', 'flow_input', 'comp_input', 'upd_s_form_input', 'inv_aff_input', 'inv_nrr_input', 'make_aff_input', 'aff_2_rig_input', 'flirt_2_nr_input'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inv_aff_input=dict(argstr='-invAff %s', diff --git a/nipype/interfaces/niftyreg/tests/test_reg.py b/nipype/interfaces/niftyreg/tests/test_reg.py index 9a3705fba7..eb5566f46f 100644 --- a/nipype/interfaces/niftyreg/tests/test_reg.py +++ b/nipype/interfaces/niftyreg/tests/test_reg.py @@ -4,13 +4,13 @@ import pytest -from nipype.interfaces.niftyreg import (no_nifty_package, get_custom_path, - RegAladin, RegF3D) -from nipype.testing import example_data +from ....testing import example_data +from .. import (get_custom_path, RegAladin, RegF3D) +from .test_regutils import no_nifty_tool @pytest.mark.skipif( - no_nifty_package(cmd='reg_aladin'), + no_nifty_tool(cmd='reg_aladin'), reason="niftyreg is not installed. reg_aladin not found.") def test_reg_aladin(): """ tests for reg_aladin interface""" @@ -48,7 +48,7 @@ def test_reg_aladin(): @pytest.mark.skipif( - no_nifty_package(cmd='reg_f3d'), + no_nifty_tool(cmd='reg_f3d'), reason="niftyreg is not installed. reg_f3d not found.") def test_reg_f3d(): """ tests for reg_f3d interface""" diff --git a/nipype/interfaces/niftyreg/tests/test_regutils.py b/nipype/interfaces/niftyreg/tests/test_regutils.py index 4a8cf18fbf..763cb2f443 100644 --- a/nipype/interfaces/niftyreg/tests/test_regutils.py +++ b/nipype/interfaces/niftyreg/tests/test_regutils.py @@ -1,17 +1,23 @@ # -*- 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: - -from nipype.interfaces.niftyreg import (no_nifty_package, get_custom_path, - RegAverage, RegResample, RegJacobian, - RegTools, RegMeasure, RegTransform) -from nipype.testing import example_data import os import pytest +from ....utils.filemanip import which +from ....testing import example_data +from .. import ( + get_custom_path, RegAverage, RegResample, RegJacobian, + RegTools, RegMeasure, RegTransform +) + + +def no_nifty_tool(cmd=None): + return which(cmd) is None + @pytest.mark.skipif( - no_nifty_package(cmd='reg_resample'), + no_nifty_tool(cmd='reg_resample'), reason="niftyreg is not installed. reg_resample not found.") def test_reg_resample_res(): """ tests for reg_resample interface """ @@ -68,7 +74,7 @@ def test_reg_resample_res(): @pytest.mark.skipif( - no_nifty_package(cmd='reg_jacobian'), + no_nifty_tool(cmd='reg_jacobian'), reason="niftyreg is not installed. reg_jacobian not found.") def test_reg_jacobian_jac(): """ Test interface for RegJacobian """ @@ -132,7 +138,7 @@ def test_reg_jacobian_jac(): @pytest.mark.skipif( - no_nifty_package(cmd='reg_tools'), + no_nifty_tool(cmd='reg_tools'), reason="niftyreg is not installed. reg_tools not found.") def test_reg_tools_mul(): """ tests for reg_tools interface """ @@ -175,7 +181,7 @@ def test_reg_tools_mul(): @pytest.mark.skipif( - no_nifty_package(cmd='reg_average'), + no_nifty_tool(cmd='reg_average'), reason="niftyreg is not installed. reg_average not found.") def test_reg_average(): """ tests for reg_average interface """ @@ -323,7 +329,7 @@ def test_reg_average(): @pytest.mark.skipif( - no_nifty_package(cmd='reg_transform'), + no_nifty_tool(cmd='reg_transform'), reason="niftyreg is not installed. reg_transform not found.") def test_reg_transform_def(): """ tests for reg_transform interface """ @@ -432,7 +438,7 @@ def test_reg_transform_def(): @pytest.mark.skipif( - no_nifty_package(cmd='reg_measure'), + no_nifty_tool(cmd='reg_measure'), reason="niftyreg is not installed. reg_measure not found.") def test_reg_measure(): """ tests for reg_measure interface """ diff --git a/nipype/interfaces/niftyseg/base.py b/nipype/interfaces/niftyseg/base.py index 8025349714..a84fb9eb62 100644 --- a/nipype/interfaces/niftyseg/base.py +++ b/nipype/interfaces/niftyseg/base.py @@ -18,14 +18,7 @@ """ from __future__ import print_function, division, unicode_literals, absolute_import -from ..niftyreg.base import no_nifty_package from ..niftyfit.base import NiftyFitCommand -import subprocess -import warnings - - -warn = warnings.warn -warnings.filterwarnings('always', category=UserWarning) class NiftySegCommand(NiftyFitCommand): @@ -39,9 +32,5 @@ def __init__(self, **inputs): super(NiftySegCommand, self).__init__(**inputs) def get_version(self): - if no_nifty_package(cmd=self.cmd): - return None - # exec_cmd = ''.join((self.cmd, ' --version')) - exec_cmd = 'seg_EM --version' - # Using seg_EM for version (E.G: seg_stats --version doesn't work) - return subprocess.check_output(exec_cmd, shell=True).strip('\n') + return super(NiftySegCommand, self).version_from_command( + cmd='seg_EM', flag='--version') diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py index 6962adcda5..5a4a5cd3f3 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py @@ -9,7 +9,8 @@ def test_BinaryMaths_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py index 1c1617d2ce..b8ea1f87f7 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py @@ -9,7 +9,8 @@ def test_BinaryMathsInteger_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py index a42f84f4f8..dce54af8dc 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py @@ -9,7 +9,8 @@ def test_BinaryStats_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py b/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py index 00aed5210e..201f15153a 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py @@ -9,7 +9,8 @@ def test_CalcTopNCC_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-target %s', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_EM.py b/nipype/interfaces/niftyseg/tests/test_auto_EM.py index 8e76cd7dd7..9790ad9757 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_EM.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_EM.py @@ -13,7 +13,8 @@ def test_EM_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-in %s', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py b/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py index 9688599c1d..a95651bf61 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py @@ -15,7 +15,8 @@ def test_FillLesions_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_dilation=dict(argstr='-dil %d', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py b/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py index bf1707db6b..3530644d7d 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py @@ -18,7 +18,8 @@ def test_LabelFusion_inputs(): ), file_to_seg=dict(mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-in %s', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py b/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py index b16795a3d9..67435c1def 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py @@ -9,7 +9,8 @@ def test_MathsCommand_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_Merge.py b/nipype/interfaces/niftyseg/tests/test_auto_Merge.py index 969b8f2d24..4d13929b23 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_Merge.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_Merge.py @@ -11,7 +11,8 @@ def test_Merge_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_NiftySegCommand.py b/nipype/interfaces/niftyseg/tests/test_auto_NiftySegCommand.py index 8847241f56..d7483fc228 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_NiftySegCommand.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_NiftySegCommand.py @@ -9,7 +9,8 @@ def test_NiftySegCommand_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), terminal_output=dict(deprecated='1.0.0', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py b/nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py new file mode 100644 index 0000000000..ba6ea5a40c --- /dev/null +++ b/nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py @@ -0,0 +1,61 @@ +# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT +from __future__ import unicode_literals +from ..patchmatch import PatchMatch + + +def test_PatchMatch_inputs(): + input_map = dict(args=dict(argstr='%s', + ), + cs_size=dict(argstr='-cs %i', + ), + database_file=dict(argstr='-db %s', + mandatory=True, + position=3, + ), + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(deprecated='1.0.0', + nohash=True, + usedefault=True, + ), + in_file=dict(argstr='-i %s', + mandatory=True, + position=1, + ), + it_num=dict(argstr='-it %i', + ), + mask_file=dict(argstr='-m %s', + mandatory=True, + position=2, + ), + match_num=dict(argstr='-match %i', + ), + out_file=dict(argstr='-o %s', + name_source=['in_file'], + name_template='%s_pm.nii.gz', + position=4, + ), + patch_size=dict(argstr='-size %i', + ), + pm_num=dict(argstr='-pm %i', + ), + terminal_output=dict(deprecated='1.0.0', + nohash=True, + ), + ) + inputs = PatchMatch.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_PatchMatch_outputs(): + output_map = dict(out_file=dict(), + ) + outputs = PatchMatch.output_spec() + + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py b/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py index 82daa127cd..6ca821c52f 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py @@ -9,7 +9,8 @@ def test_StatsCommand_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py b/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py index 108d74a072..702b3961d9 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py @@ -9,7 +9,8 @@ def test_TupleMaths_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py b/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py index c7a2fdaf56..c5144bbc65 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py @@ -9,7 +9,8 @@ def test_UnaryMaths_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py b/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py index fa5a17cfce..81bea6f18b 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py @@ -9,7 +9,8 @@ def test_UnaryStats_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/niftyseg/tests/test_em_interfaces.py b/nipype/interfaces/niftyseg/tests/test_em_interfaces.py index 810a782b63..b95d574357 100644 --- a/nipype/interfaces/niftyseg/tests/test_em_interfaces.py +++ b/nipype/interfaces/niftyseg/tests/test_em_interfaces.py @@ -3,12 +3,13 @@ import pytest -from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path -from nipype.interfaces.niftyseg import EM -from nipype.testing import example_data +from ....testing import example_data +from ...niftyreg import get_custom_path +from ...niftyreg.tests.test_regutils import no_nifty_tool +from .. import EM -@pytest.mark.skipif(no_nifty_package(cmd='seg_EM'), +@pytest.mark.skipif(no_nifty_tool(cmd='seg_EM'), reason="niftyseg is not installed") def test_seg_em(): diff --git a/nipype/interfaces/niftyseg/tests/test_label_fusion.py b/nipype/interfaces/niftyseg/tests/test_label_fusion.py index f34fc9149f..6f41086531 100644 --- a/nipype/interfaces/niftyseg/tests/test_label_fusion.py +++ b/nipype/interfaces/niftyseg/tests/test_label_fusion.py @@ -3,12 +3,13 @@ import pytest -from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path -from nipype.interfaces.niftyseg import LabelFusion, CalcTopNCC -from nipype.testing import example_data +from ....testing import example_data +from ...niftyreg import get_custom_path +from ...niftyreg.tests.test_regutils import no_nifty_tool +from .. import LabelFusion, CalcTopNCC -@pytest.mark.skipif(no_nifty_package(cmd='seg_LabFusion'), +@pytest.mark.skipif(no_nifty_tool(cmd='seg_LabFusion'), reason="niftyseg is not installed") def test_seg_lab_fusion(): """ Test interfaces for seg_labfusion""" @@ -90,7 +91,7 @@ def test_seg_lab_fusion(): assert mv_node.cmdline == expected_cmd -@pytest.mark.skipif(no_nifty_package(cmd='seg_CalcTopNCC'), +@pytest.mark.skipif(no_nifty_tool(cmd='seg_CalcTopNCC'), reason="niftyseg is not installed") def test_seg_calctopncc(): """ Test interfaces for seg_CalctoNCC""" diff --git a/nipype/interfaces/niftyseg/tests/test_lesions.py b/nipype/interfaces/niftyseg/tests/test_lesions.py index 55250bde92..aaca2df0ba 100644 --- a/nipype/interfaces/niftyseg/tests/test_lesions.py +++ b/nipype/interfaces/niftyseg/tests/test_lesions.py @@ -3,12 +3,13 @@ import pytest -from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path -from nipype.interfaces.niftyseg import FillLesions -from nipype.testing import example_data +from ....testing import example_data +from ...niftyreg import get_custom_path +from ...niftyreg.tests.test_regutils import no_nifty_tool +from .. import FillLesions -@pytest.mark.skipif(no_nifty_package(cmd='seg_FillLesions'), +@pytest.mark.skipif(no_nifty_tool(cmd='seg_FillLesions'), reason="niftyseg is not installed") def test_seg_filllesions(): diff --git a/nipype/interfaces/niftyseg/tests/test_maths.py b/nipype/interfaces/niftyseg/tests/test_maths.py index 307adb503d..38dc765f10 100644 --- a/nipype/interfaces/niftyseg/tests/test_maths.py +++ b/nipype/interfaces/niftyseg/tests/test_maths.py @@ -3,14 +3,15 @@ import pytest -from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path -from nipype.interfaces.niftyseg import (UnaryMaths, BinaryMaths, - BinaryMathsInteger, TupleMaths, - Merge) -from nipype.testing import example_data +from ....testing import example_data +from ...niftyreg import get_custom_path +from ...niftyreg.tests.test_regutils import no_nifty_tool +from .. import (UnaryMaths, BinaryMaths, + BinaryMathsInteger, TupleMaths, + Merge) -@pytest.mark.skipif(no_nifty_package(cmd='seg_maths'), +@pytest.mark.skipif(no_nifty_tool(cmd='seg_maths'), reason="niftyseg is not installed") def test_unary_maths(): @@ -39,7 +40,7 @@ def test_unary_maths(): assert unarym.cmdline == expected_cmd -@pytest.mark.skipif(no_nifty_package(cmd='seg_maths'), +@pytest.mark.skipif(no_nifty_tool(cmd='seg_maths'), reason="niftyseg is not installed") def test_binary_maths(): @@ -70,7 +71,7 @@ def test_binary_maths(): assert binarym.cmdline == expected_cmd -@pytest.mark.skipif(no_nifty_package(cmd='seg_maths'), +@pytest.mark.skipif(no_nifty_tool(cmd='seg_maths'), reason="niftyseg is not installed") def test_int_binary_maths(): @@ -100,7 +101,7 @@ def test_int_binary_maths(): assert ibinarym.cmdline == expected_cmd -@pytest.mark.skipif(no_nifty_package(cmd='seg_maths'), +@pytest.mark.skipif(no_nifty_tool(cmd='seg_maths'), reason="niftyseg is not installed") def test_tuple_maths(): @@ -134,7 +135,7 @@ def test_tuple_maths(): assert tuplem.cmdline == expected_cmd -@pytest.mark.skipif(no_nifty_package(cmd='seg_maths'), +@pytest.mark.skipif(no_nifty_tool(cmd='seg_maths'), reason="niftyseg is not installed") def test_merge(): diff --git a/nipype/interfaces/niftyseg/tests/test_patchmatch.py b/nipype/interfaces/niftyseg/tests/test_patchmatch.py index b88552fb0d..ae2500a7d2 100644 --- a/nipype/interfaces/niftyseg/tests/test_patchmatch.py +++ b/nipype/interfaces/niftyseg/tests/test_patchmatch.py @@ -3,12 +3,13 @@ import pytest -from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path -from nipype.interfaces.niftyseg import PatchMatch -from nipype.testing import example_data +from ....testing import example_data +from ...niftyreg import get_custom_path +from ...niftyreg.tests.test_regutils import no_nifty_tool +from .. import PatchMatch -@pytest.mark.skipif(no_nifty_package(cmd='seg_PatchMatch'), +@pytest.mark.skipif(no_nifty_tool(cmd='seg_PatchMatch'), reason="niftyseg is not installed") def test_seg_patchmatch(): diff --git a/nipype/interfaces/niftyseg/tests/test_stats.py b/nipype/interfaces/niftyseg/tests/test_stats.py index ae3cfbfc6e..cd0948d1ae 100644 --- a/nipype/interfaces/niftyseg/tests/test_stats.py +++ b/nipype/interfaces/niftyseg/tests/test_stats.py @@ -3,12 +3,13 @@ import pytest -from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path -from nipype.interfaces.niftyseg import UnaryStats, BinaryStats -from nipype.testing import example_data +from ....testing import example_data +from ...niftyreg import get_custom_path +from ...niftyreg.tests.test_regutils import no_nifty_tool +from .. import UnaryStats, BinaryStats -@pytest.mark.skipif(no_nifty_package(cmd='seg_stats'), +@pytest.mark.skipif(no_nifty_tool(cmd='seg_stats'), reason="niftyseg is not installed") def test_unary_stats(): """ Test for the seg_stats interfaces """ @@ -35,7 +36,7 @@ def test_unary_stats(): assert unarys.cmdline == expected_cmd -@pytest.mark.skipif(no_nifty_package(cmd='seg_stats'), +@pytest.mark.skipif(no_nifty_tool(cmd='seg_stats'), reason="niftyseg is not installed") def test_binary_stats(): """ Test for the seg_stats interfaces """ diff --git a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py index 915f2c85d2..401f2b0f62 100644 --- a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py +++ b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py @@ -6,7 +6,8 @@ def test_ComputeMask_inputs(): input_map = dict(M=dict(), cc=dict(), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), m=dict(), diff --git a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py index 7d44248cbc..78f6d02c03 100644 --- a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py @@ -14,7 +14,8 @@ def test_EstimateContrast_inputs(): ), dof=dict(mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mask=dict(), diff --git a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py index 5c3f881179..5aca7d345c 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py +++ b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py @@ -10,7 +10,8 @@ def test_FitGLM_inputs(): ), hrf_model=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mask=dict(), diff --git a/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py b/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py index 80902a7d0c..0360e53df0 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py +++ b/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py @@ -6,7 +6,8 @@ def test_FmriRealign4d_inputs(): input_map = dict(between_loops=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(mandatory=True, diff --git a/nipype/interfaces/nipy/tests/test_auto_Similarity.py b/nipype/interfaces/nipy/tests/test_auto_Similarity.py index f9c815fedb..d65cf36b02 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Similarity.py +++ b/nipype/interfaces/nipy/tests/test_auto_Similarity.py @@ -4,7 +4,8 @@ def test_Similarity_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mask1=dict(), diff --git a/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py b/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py index b4e495a434..358bd6efa8 100644 --- a/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py +++ b/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py @@ -4,7 +4,8 @@ def test_SpaceTimeRealigner_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(mandatory=True, diff --git a/nipype/interfaces/nipy/tests/test_auto_Trim.py b/nipype/interfaces/nipy/tests/test_auto_Trim.py index c1bc16e103..0d2ad9063b 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Trim.py +++ b/nipype/interfaces/nipy/tests/test_auto_Trim.py @@ -8,7 +8,8 @@ def test_Trim_inputs(): ), end_index=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(mandatory=True, diff --git a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py index 4d970500d2..159907b978 100644 --- a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py +++ b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py @@ -11,7 +11,8 @@ def test_CoherenceAnalyzer_inputs(): ), frequency_range=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_TS=dict(), diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py index 89184c9325..1c2f7ce2cb 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py @@ -9,7 +9,8 @@ def test_BRAINSPosteriorToContinuousClass_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputBasalGmVolume=dict(argstr='--inputBasalGmVolume %s', diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py index de6ae06a6f..1168288a8b 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py @@ -29,7 +29,8 @@ def test_BRAINSTalairach_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py index ab262fd36b..6638bd2e5e 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py @@ -13,7 +13,8 @@ def test_BRAINSTalairachMask_inputs(): ), hemisphereMode=dict(argstr='--hemisphereMode %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py b/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py index ca540e4afd..cfee35cd08 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py @@ -9,7 +9,8 @@ def test_GenerateEdgeMapImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputMRVolumes=dict(argstr='--inputMRVolumes %s...', diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py b/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py index 5eecfc9987..48c4aca838 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py @@ -9,7 +9,8 @@ def test_GeneratePurePlugMask_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputImageModalities=dict(argstr='--inputImageModalities %s...', diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py b/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py index 8e3ec9c0d4..ac921cb7f6 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py @@ -11,7 +11,8 @@ def test_HistogramMatchingFilter_inputs(): ), histogramAlgorithm=dict(argstr='--histogramAlgorithm %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputBinaryVolume=dict(argstr='--inputBinaryVolume %s', diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py b/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py index 9b9fd7c3f5..e9ddc61051 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py @@ -11,7 +11,8 @@ def test_SimilarityIndex_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputManualVolume=dict(argstr='--inputManualVolume %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py index 90e24fca24..0a7e27fee1 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py @@ -20,7 +20,8 @@ def test_DWIConvert_inputs(): gradientVectorFile=dict(argstr='--gradientVectorFile %s', hash_files=False, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputBValues=dict(argstr='--inputBValues %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py index c892799709..5b88f17a54 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py @@ -11,7 +11,8 @@ def test_compareTractInclusion_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), numberOfPoints=dict(argstr='--numberOfPoints %d', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py index a241bd583b..4cbbf0e4ea 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py @@ -11,7 +11,8 @@ def test_dtiaverage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputs=dict(argstr='--inputs %s...', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py index 4f8e64f4ac..80a0f78fe0 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py @@ -31,7 +31,8 @@ def test_dtiestim_inputs(): idwi=dict(argstr='--idwi %s', hash_files=False, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), method=dict(argstr='--method %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py index 6d0cd8674e..6090c81526 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py @@ -44,7 +44,8 @@ def test_dtiprocess_inputs(): ), hField=dict(argstr='--hField ', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), interpolation=dict(argstr='--interpolation %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py index 81a0de61db..ca4ceaa0fa 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py @@ -9,7 +9,8 @@ def test_extractNrrdVectorIndex_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py index 10f2fbf341..1caaeaac78 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py @@ -11,7 +11,8 @@ def test_gtractAnisotropyMap_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputTensorVolume=dict(argstr='--inputTensorVolume %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py index 25825aa2dd..574119212f 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py @@ -13,7 +13,8 @@ def test_gtractAverageBvalues_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py index 137dd8046b..e3c4f337b7 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py @@ -13,7 +13,8 @@ def test_gtractClipAnisotropy_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py index 494c13715d..a8aab5aedf 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py @@ -18,7 +18,8 @@ def test_gtractCoRegAnatomy_inputs(): gridSize=dict(argstr='--gridSize %s', sep=',', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputAnatomicalVolume=dict(argstr='--inputAnatomicalVolume %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py index 73b53789f9..276952f0f9 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py @@ -11,7 +11,8 @@ def test_gtractConcatDwi_inputs(): ), ignoreOrigins=dict(argstr='--ignoreOrigins ', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s...', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py index f37d8ffbc0..dfb9a73889 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py @@ -9,7 +9,8 @@ def test_gtractCopyImageOrientation_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py index 6de2f18e71..c367284ef3 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py @@ -17,7 +17,8 @@ def test_gtractCoregBvalues_inputs(): ), fixedVolumeIndex=dict(argstr='--fixedVolumeIndex %d', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), maximumStepSize=dict(argstr='--maximumStepSize %f', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py index ec54af48d1..f50f8c47aa 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py @@ -11,7 +11,8 @@ def test_gtractCostFastMarching_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputAnisotropyVolume=dict(argstr='--inputAnisotropyVolume %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py index f607ad4ccb..bd461a549b 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py @@ -9,7 +9,8 @@ def test_gtractCreateGuideFiber_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputFiber=dict(argstr='--inputFiber %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py index 22cae40fed..0e6676c0fc 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py @@ -11,7 +11,8 @@ def test_gtractFastMarchingTracking_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputAnisotropyVolume=dict(argstr='--inputAnisotropyVolume %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py index 39a22ed5aa..15b4876080 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py @@ -19,7 +19,8 @@ def test_gtractFiberTracking_inputs(): ), guidedCurvatureThreshold=dict(argstr='--guidedCurvatureThreshold %f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputAnisotropyVolume=dict(argstr='--inputAnisotropyVolume %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py index e126e4ca38..0ae9c227a8 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py @@ -9,7 +9,8 @@ def test_gtractImageConformity_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py index 81af4d6aa5..36363523d0 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py @@ -9,7 +9,8 @@ def test_gtractInvertBSplineTransform_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py index 4423309e60..4e7cdebdd3 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py @@ -13,7 +13,8 @@ def test_gtractInvertDisplacementField_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), numberOfThreads=dict(argstr='--numberOfThreads %d', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py index 966821830f..8cc8cc1e4b 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py @@ -9,7 +9,8 @@ def test_gtractInvertRigidTransform_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputTransform=dict(argstr='--inputTransform %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py index fec40fec57..4cc895fb06 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py @@ -9,7 +9,8 @@ def test_gtractResampleAnisotropy_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputAnatomicalVolume=dict(argstr='--inputAnatomicalVolume %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py index d7c808d474..c77c067c51 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py @@ -9,7 +9,8 @@ def test_gtractResampleB0_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputAnatomicalVolume=dict(argstr='--inputAnatomicalVolume %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py index 29718e9c74..5fd928f854 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py @@ -9,7 +9,8 @@ def test_gtractResampleCodeImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputCodeVolume=dict(argstr='--inputCodeVolume %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py index bdc33175f3..569320ba6f 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py @@ -11,7 +11,8 @@ def test_gtractResampleDWIInPlace_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), imageOutputSize=dict(argstr='--imageOutputSize %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py index b632a364e8..b3c4abc11a 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py @@ -9,7 +9,8 @@ def test_gtractResampleFibers_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputForwardDeformationFieldVolume=dict(argstr='--inputForwardDeformationFieldVolume %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py index 3024df0100..af662c076c 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py @@ -18,7 +18,8 @@ def test_gtractTensor_inputs(): ignoreIndex=dict(argstr='--ignoreIndex %s', sep=',', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py index 6ee2300ce9..8f074267fe 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py @@ -9,7 +9,8 @@ def test_gtractTransformToDisplacementField_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py index 07eb1805dc..8efcf5d131 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py @@ -9,7 +9,8 @@ def test_maxcurvature_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), image=dict(argstr='--image %s', 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 0ebf64b10d..0342389ba4 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py @@ -23,7 +23,8 @@ def test_UKFTractography_inputs(): ), fullTensorModel=dict(argstr='--fullTensorModel ', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), labels=dict(argstr='--labels %s', 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 875efafa57..8da03c52fc 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py @@ -20,7 +20,8 @@ def test_fiberprocess_inputs(): ), h_field=dict(argstr='--h_field %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), index_space=dict(argstr='--index_space ', 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 1722f7a45b..4d241dc205 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py @@ -11,7 +11,8 @@ def test_fiberstats_inputs(): ), fiber_file=dict(argstr='--fiber_file %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), terminal_output=dict(deprecated='1.0.0', 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 99ca1ab608..b1a503a711 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py @@ -13,7 +13,8 @@ def test_fibertrack_inputs(): ), force=dict(argstr='--force ', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_roi_file=dict(argstr='--input_roi_file %s', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py b/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py index c50c1d82ba..ca3669e020 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py @@ -9,7 +9,8 @@ def test_CannyEdge_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py index 51e7cc218d..366fd626ab 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py @@ -15,7 +15,8 @@ def test_CannySegmentationLevelSetImageFilter_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), initialModel=dict(argstr='--initialModel %s', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py index 2f4ef52fd5..ce2c59dff9 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py @@ -9,7 +9,8 @@ def test_DilateImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputMaskVolume=dict(argstr='--inputMaskVolume %s', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py index b72bc65156..1e95808c9f 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py @@ -9,7 +9,8 @@ def test_DilateMask_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputBinaryVolume=dict(argstr='--inputBinaryVolume %s', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py index 1783ee8f27..a9136fcbd5 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py @@ -9,7 +9,8 @@ def test_DistanceMaps_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputLabelVolume=dict(argstr='--inputLabelVolume %s', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py index ddc61cd418..7504cc311e 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py @@ -9,7 +9,8 @@ def test_DumpBinaryTrainingVectors_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputHeaderFilename=dict(argstr='--inputHeaderFilename %s', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py index 113c1e08ef..659c88471c 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py @@ -9,7 +9,8 @@ def test_ErodeImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputMaskVolume=dict(argstr='--inputMaskVolume %s', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py b/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py index 82ea9a31a8..e81e2cf9d9 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py @@ -9,7 +9,8 @@ def test_FlippedDifference_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputMaskVolume=dict(argstr='--inputMaskVolume %s', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py index 6672cd4212..234494c3f4 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py @@ -9,7 +9,8 @@ def test_GenerateBrainClippedImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputImg=dict(argstr='--inputImg %s', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py index dd275ef4d1..d073e15ab0 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py @@ -11,7 +11,8 @@ def test_GenerateSummedGradientImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume1=dict(argstr='--inputVolume1 %s', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py index d8fab4b6c7..f9fb21b9da 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py @@ -9,7 +9,8 @@ def test_GenerateTestImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py index 694868d7b0..63215e0b8a 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py @@ -11,7 +11,8 @@ def test_GradientAnisotropicDiffusionImageFilter_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py b/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py index 434148c9cc..6920812aae 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py @@ -13,7 +13,8 @@ def test_HammerAttributeCreator_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputCSFVolume=dict(argstr='--inputCSFVolume %s', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py index d920277b11..c23362562c 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py @@ -9,7 +9,8 @@ def test_NeighborhoodMean_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputMaskVolume=dict(argstr='--inputMaskVolume %s', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py index 1b8d035c3d..ff2cdd38af 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py @@ -9,7 +9,8 @@ def test_NeighborhoodMedian_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputMaskVolume=dict(argstr='--inputMaskVolume %s', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py b/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py index 6d45bec9ca..45c55236d0 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py @@ -9,7 +9,8 @@ def test_STAPLEAnalysis_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputDimension=dict(argstr='--inputDimension %d', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py index 5bbeaa4640..d351d8d56f 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py @@ -9,7 +9,8 @@ def test_TextureFromNoiseImageFilter_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputRadius=dict(argstr='--inputRadius %d', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py index c6ad265663..771fa52f03 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py @@ -11,7 +11,8 @@ def test_TextureMeasureFilter_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputMaskVolume=dict(argstr='--inputMaskVolume %s', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py index 6aa1430502..e237ca41db 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py @@ -11,7 +11,8 @@ def test_UnbiasedNonLocalMeans_inputs(): ), hp=dict(argstr='--hp %f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py b/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py index 64a33379eb..ed643de764 100644 --- a/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py +++ b/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py @@ -13,7 +13,8 @@ def test_scalartransform_inputs(): ), h_field=dict(argstr='--h_field ', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_image=dict(argstr='--input_image %s', diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py index 92d51611eb..3df134093f 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py @@ -27,7 +27,8 @@ def test_BRAINSDemonWarp_inputs(): ), histogramMatch=dict(argstr='--histogramMatch ', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), initializeWithDisplacementField=dict(argstr='--initializeWithDisplacementField %s', diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py index 9e4bacc88f..00248d9093 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py @@ -38,7 +38,8 @@ def test_BRAINSFit_inputs(): ), histogramMatch=dict(argstr='--histogramMatch ', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), initialTransform=dict(argstr='--initialTransform %s', diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py index bb2c107ace..a2444018e2 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py @@ -16,7 +16,8 @@ def test_BRAINSResample_inputs(): gridSpacing=dict(argstr='--gridSpacing %s', sep=',', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py index 61babea6f1..c394a6cee1 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py @@ -9,7 +9,8 @@ def test_BRAINSResize_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py index 9d6f296b95..928fa49e61 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py @@ -13,7 +13,8 @@ def test_BRAINSTransformFromFiducials_inputs(): ), fixedLandmarksFile=dict(argstr='--fixedLandmarksFile %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), movingLandmarks=dict(argstr='--movingLandmarks %s...', diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py index 3a4579cf44..1fd9c45b34 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -27,7 +27,8 @@ def test_VBRAINSDemonWarp_inputs(): ), histogramMatch=dict(argstr='--histogramMatch ', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), initializeWithDisplacementField=dict(argstr='--initializeWithDisplacementField %s', diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py index 4858822be0..d07166b086 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py @@ -34,7 +34,8 @@ def test_BRAINSABC_inputs(): gridSize=dict(argstr='--gridSize %s', sep=',', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), implicitOutputs=dict(argstr='--implicitOutputs %s...', diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py index ebf7cf95c8..865ce1fe93 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py @@ -41,7 +41,8 @@ def test_BRAINSConstellationDetector_inputs(): ), houghEyeDetectorMode=dict(argstr='--houghEyeDetectorMode %d', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputLandmarksEMSP=dict(argstr='--inputLandmarksEMSP %s', diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py index 3b6424a6fe..b3962fd835 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py @@ -18,7 +18,8 @@ def test_BRAINSCreateLabelMapFromProbabilityMaps_inputs(): foregroundPriors=dict(argstr='--foregroundPriors %s', sep=',', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inclusionThreshold=dict(argstr='--inclusionThreshold %f', diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py index 210194d608..5e8a6f99bd 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py @@ -21,7 +21,8 @@ def test_BRAINSCut_inputs(): ), histogramEqualization=dict(argstr='--histogramEqualization ', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), method=dict(argstr='--method %s', diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py index 943488a385..38035b7903 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py @@ -9,7 +9,8 @@ def test_BRAINSMultiSTAPLE_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputCompositeT1Volume=dict(argstr='--inputCompositeT1Volume %s', diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py index 1746f5802b..577f01aba6 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -15,7 +15,8 @@ def test_BRAINSROIAuto_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py index 61306ad365..f9c7d4a191 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py @@ -9,7 +9,8 @@ def test_BinaryMaskEditorBasedOnLandmarks_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputBinaryVolume=dict(argstr='--inputBinaryVolume %s', diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py index c74a10b53c..cd29a7fd82 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py @@ -13,7 +13,8 @@ def test_ESLR_inputs(): ), high=dict(argstr='--high %d', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/semtools/tests/test_auto_DWICompare.py b/nipype/interfaces/semtools/tests/test_auto_DWICompare.py index 559a455485..a9c60b1229 100644 --- a/nipype/interfaces/semtools/tests/test_auto_DWICompare.py +++ b/nipype/interfaces/semtools/tests/test_auto_DWICompare.py @@ -9,7 +9,8 @@ def test_DWICompare_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume1=dict(argstr='--inputVolume1 %s', diff --git a/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py b/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py index 6e63c9df4c..271085be8c 100644 --- a/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py +++ b/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py @@ -11,7 +11,8 @@ def test_DWISimpleCompare_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume1=dict(argstr='--inputVolume1 %s', diff --git a/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py b/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py index c88b636252..83d0194964 100644 --- a/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py +++ b/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py @@ -9,7 +9,8 @@ def test_GenerateCsfClippedFromClassifiedImage_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputCassifiedVolume=dict(argstr='--inputCassifiedVolume %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py index aced937722..5c5db3a206 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py @@ -14,7 +14,8 @@ def test_BRAINSAlignMSP_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py index a0b78adbbd..a6868c4e61 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py @@ -13,7 +13,8 @@ def test_BRAINSClipInferior_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py index de684005fc..80d8158e5e 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py @@ -11,7 +11,8 @@ def test_BRAINSConstellationModeler_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputTrainingList=dict(argstr='--inputTrainingList %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py index d7fc1f048b..59f4b66f60 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py @@ -11,7 +11,8 @@ def test_BRAINSEyeDetector_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py index 9edd6e2170..b1f25c5be1 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py @@ -9,7 +9,8 @@ def test_BRAINSInitializedControlPoints_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py index 49db60b207..edb4119b52 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py @@ -9,7 +9,8 @@ def test_BRAINSLandmarkInitializer_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputFixedLandmarkFilename=dict(argstr='--inputFixedLandmarkFilename %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py index f0b4b048a8..8d8bfdab55 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py @@ -9,7 +9,8 @@ def test_BRAINSLinearModelerEPCA_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputTrainingList=dict(argstr='--inputTrainingList %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py index 4cb1ca5a6a..0210db6299 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py @@ -9,7 +9,8 @@ def test_BRAINSLmkTransform_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputFixedLandmarks=dict(argstr='--inputFixedLandmarks %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py index 22175171aa..20b0a4467e 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py @@ -19,7 +19,8 @@ def test_BRAINSMush_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputFirstVolume=dict(argstr='--inputFirstVolume %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py index bec713100c..81d0f89d08 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py @@ -9,7 +9,8 @@ def test_BRAINSSnapShotWriter_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputBinaryVolumes=dict(argstr='--inputBinaryVolumes %s...', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py index cb66216d8d..789b1f4a42 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py @@ -12,7 +12,8 @@ def test_BRAINSTransformConvert_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputTransform=dict(argstr='--inputTransform %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py index 3c37fbc518..212b60c3d5 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py @@ -17,7 +17,8 @@ def test_BRAINSTrimForegroundInDirection_inputs(): ), headSizeLimit=dict(argstr='--headSizeLimit %f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py b/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py index 6b305e1d6e..42064ce399 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py @@ -9,7 +9,8 @@ def test_CleanUpOverlapLabels_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputBinaryVolumes=dict(argstr='--inputBinaryVolumes %s...', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py b/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py index 3394a960fc..9c0d44ea96 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py @@ -39,7 +39,8 @@ def test_FindCenterOfBrain_inputs(): ), headSizeLimit=dict(argstr='--headSizeLimit %f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), imageMask=dict(argstr='--imageMask %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py b/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py index f66d1a8448..2b0a376b28 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py @@ -9,7 +9,8 @@ def test_GenerateLabelMapFromProbabilityMap_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolumes=dict(argstr='--inputVolumes %s...', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py b/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py index 0dcc63ea40..7e0f0c7b7c 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py @@ -9,7 +9,8 @@ def test_ImageRegionPlotter_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputBinaryROIVolume=dict(argstr='--inputBinaryROIVolume %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py b/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py index c46f64b679..ee2f544417 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py @@ -9,7 +9,8 @@ def test_JointHistogram_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputMaskVolumeInXAxis=dict(argstr='--inputMaskVolumeInXAxis %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py b/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py index ccb9afc0c2..228dfe4234 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py @@ -9,7 +9,8 @@ def test_ShuffleVectorsModule_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVectorFileBaseName=dict(argstr='--inputVectorFileBaseName %s', 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 1d8976faca..3885c5ac5e 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 @@ -9,7 +9,8 @@ def test_fcsv_to_hdf5_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), landmarkGlobPattern=dict(argstr='--landmarkGlobPattern %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py b/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py index fe413744f3..aedcbb3e63 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py @@ -9,7 +9,8 @@ def test_insertMidACPCpoint_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputLandmarkFile=dict(argstr='--inputLandmarkFile %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py index cb2cf17a4e..ef1668861f 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py @@ -9,7 +9,8 @@ def test_landmarksConstellationAligner_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputLandmarksPaired=dict(argstr='--inputLandmarksPaired %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py index b5b4bede05..4bf7c61ab7 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py @@ -11,7 +11,8 @@ def test_landmarksConstellationWeights_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputTemplateModel=dict(argstr='--inputTemplateModel %s', diff --git a/nipype/interfaces/setup.py b/nipype/interfaces/setup.py deleted file mode 100644 index 4a15082b2b..0000000000 --- a/nipype/interfaces/setup.py +++ /dev/null @@ -1,41 +0,0 @@ -# -*- 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: -from __future__ import print_function, division, unicode_literals, absolute_import - - -def configuration(parent_package='', top_path=None): - from numpy.distutils.misc_util import Configuration - - config = Configuration('interfaces', parent_package, top_path) - - config.add_subpackage('afni') - config.add_subpackage('ants') - config.add_subpackage('camino') - config.add_subpackage('camino2trackvis') - config.add_subpackage('cmtk') - config.add_subpackage('diffusion_toolkit') - config.add_subpackage('dipy') - config.add_subpackage('elastix') - config.add_subpackage('freesurfer') - config.add_subpackage('fsl') - config.add_subpackage('minc') - config.add_subpackage('mipav') - config.add_subpackage('mne') - config.add_subpackage('mrtrix') - config.add_subpackage('mrtrix3') - config.add_subpackage('niftyfit') - config.add_subpackage('niftyreg') - config.add_subpackage('niftyseg') - config.add_subpackage('nipy') - config.add_subpackage('spm') - config.add_subpackage('slicer') - - config.add_data_dir('script_templates') - config.add_data_dir('tests') - - return config - -if __name__ == '__main__': - from numpy.distutils.core import setup - setup(**configuration(top_path='').todict()) diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py index a251b7f4d2..d3c499df21 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py @@ -9,7 +9,8 @@ def test_DTIexport_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputTensor=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py index 988f16ed0e..cd4ae462f4 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py @@ -9,7 +9,8 @@ def test_DTIimport_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputFile=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py index 8e8e429125..2a97030210 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py @@ -11,7 +11,8 @@ def test_DWIJointRicianLMMSEFilter_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py index f9a9d42b9e..e71ae3106a 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py @@ -13,7 +13,8 @@ def test_DWIRicianLMMSEFilter_inputs(): ), hrf=dict(argstr='--hrf %f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py index f280f0c2f2..938855c9cf 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py @@ -11,7 +11,8 @@ def test_DWIToDTIEstimation_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py index a24b164c04..80b9d9b745 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py @@ -11,7 +11,8 @@ def test_DiffusionTensorScalarMeasurements_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py index e73dffce9a..247cd2612a 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py @@ -9,7 +9,8 @@ def test_DiffusionWeightedVolumeMasking_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py index 1f143c23e2..423ef009be 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py @@ -26,7 +26,8 @@ def test_ResampleDTIVolume_inputs(): ), hfieldtype=dict(argstr='--hfieldtype %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), image_center=dict(argstr='--image_center %s', diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py index 1ea38d5eaf..2dc06051ca 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py @@ -18,7 +18,8 @@ def test_TractographyLabelMapSeeding_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputroi=dict(argstr='--inputroi %s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py index 29a2a157e6..6d4ab7458b 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py @@ -9,7 +9,8 @@ def test_AddScalarVolumes_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume1=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py index 66fbe0f2d9..5a0c99453a 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py @@ -16,7 +16,8 @@ def test_CastScalarVolume_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), terminal_output=dict(deprecated='1.0.0', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py index 2c8a3787e5..0fe407f1de 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py @@ -12,7 +12,8 @@ def test_CheckerBoardFilter_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume1=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py index 619404f9d2..7139b3f13a 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py @@ -11,7 +11,8 @@ def test_CurvatureAnisotropicDiffusion_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py index 9dc8f32ade..f41d25c28d 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py @@ -18,7 +18,8 @@ def test_ExtractSkeleton_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), numPoints=dict(argstr='--numPoints %d', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py index d07344f49f..0ef6a909ca 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py @@ -9,7 +9,8 @@ def test_GaussianBlurImageFilter_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py index 02df01486d..a041642006 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py @@ -11,7 +11,8 @@ def test_GradientAnisotropicDiffusion_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py index 0579552ba7..e42fe05e13 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py @@ -9,7 +9,8 @@ def test_GrayscaleFillHoleImageFilter_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py index 439c6f1fd4..6f1257ee41 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py @@ -9,7 +9,8 @@ def test_GrayscaleGrindPeakImageFilter_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py index 9ed4578c95..36223bd829 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py @@ -9,7 +9,8 @@ def test_HistogramMatching_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py index 0d19440bb9..2ba011470b 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py @@ -21,7 +21,8 @@ def test_ImageLabelCombine_inputs(): ), first_overwrites=dict(argstr='--first_overwrites ', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), terminal_output=dict(deprecated='1.0.0', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py index 13c1a90db6..77a20ffe64 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py @@ -19,7 +19,8 @@ def test_MaskScalarVolume_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), label=dict(argstr='--label %d', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py index 81dc33b3f6..d0409009ec 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py @@ -9,7 +9,8 @@ def test_MedianImageFilter_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py index ebd9d4397b..ed171521a8 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py @@ -9,7 +9,8 @@ def test_MultiplyScalarVolumes_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume1=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py index 78fe5894d7..8397f5f1c5 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py @@ -16,7 +16,8 @@ def test_N4ITKBiasFieldCorrection_inputs(): histogramsharpening=dict(argstr='--histogramsharpening %s', sep=',', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputimage=dict(argstr='--inputimage %s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py index da74efc236..23be2e6372 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py @@ -24,7 +24,8 @@ def test_ResampleScalarVectorDWIVolume_inputs(): ), hfieldtype=dict(argstr='--hfieldtype %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), image_center=dict(argstr='--image_center %s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py index 0bf3e2b9bf..b46b24dc6a 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py @@ -9,7 +9,8 @@ def test_SubtractScalarVolumes_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume1=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py index 86af5dd138..49c3a67455 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py @@ -16,7 +16,8 @@ def test_ThresholdScalarVolume_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), lower=dict(argstr='--lower %d', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py index 153d99b00b..fd98549305 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py @@ -13,7 +13,8 @@ def test_VotingBinaryHoleFillingImageFilter_inputs(): ), foreground=dict(argstr='--foreground %d', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', 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 8d27926410..7f25ed92cc 100644 --- a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py +++ b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py @@ -11,7 +11,8 @@ def test_DWIUnbiasedNonLocalMeansFilter_inputs(): ), hp=dict(argstr='--hp %f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py index d8d595659a..91f4b37591 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py @@ -19,7 +19,8 @@ def test_AffineRegistration_inputs(): ), histogrambins=dict(argstr='--histogrambins %d', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), initialtransform=dict(argstr='--initialtransform %s', diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py index 9cb4a89979..98be6fbe12 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py @@ -23,7 +23,8 @@ def test_BSplineDeformableRegistration_inputs(): ), histogrambins=dict(argstr='--histogrambins %d', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), initialtransform=dict(argstr='--initialtransform %s', diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py index a343222138..e984395aa4 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py @@ -12,7 +12,8 @@ def test_BSplineToDeformationField_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), refImage=dict(argstr='--refImage %s', diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py index 18b5332194..9b90f3dc9b 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py @@ -34,7 +34,8 @@ def test_ExpertAutomatedRegistration_inputs(): ), fixedLandmarks=dict(argstr='--fixedLandmarks %s...', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), initialization=dict(argstr='--initialization %s', diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py index 71578e46fc..c80b8b66fb 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py @@ -19,7 +19,8 @@ def test_LinearRegistration_inputs(): ), histogrambins=dict(argstr='--histogrambins %d', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), initialtransform=dict(argstr='--initialtransform %s', diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py index c1f13b775d..d1262047eb 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py @@ -16,7 +16,8 @@ def test_MultiResolutionAffineRegistration_inputs(): ), fixedImageROI=dict(argstr='--fixedImageROI %s', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), metricTolerance=dict(argstr='--metricTolerance %f', diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py index 6922ddc50e..9c5fcd5c1f 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py @@ -9,7 +9,8 @@ def test_OtsuThresholdImageFilter_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py index 0c03c09d24..72a68ca5b9 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py @@ -13,7 +13,8 @@ def test_OtsuThresholdSegmentation_inputs(): ), faceConnected=dict(argstr='--faceConnected ', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py index addb12fd77..34db34c00d 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py @@ -16,7 +16,8 @@ def test_ResampleScalarVolume_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), interpolation=dict(argstr='--interpolation %s', diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py index ce9d3c924e..a56ad3b98e 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py @@ -19,7 +19,8 @@ def test_RigidRegistration_inputs(): ), histogrambins=dict(argstr='--histogrambins %d', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), initialtransform=dict(argstr='--initialtransform %s', diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py index 217245624d..f4809280f9 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py @@ -20,7 +20,8 @@ def test_IntensityDifferenceMetric_inputs(): followupVolume=dict(argstr='%s', position=-2, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), outputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py index 2c417eb8ed..4dfbdc66dd 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py @@ -24,7 +24,8 @@ def test_PETStandardUptakeValueComputation_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), labelMap=dict(argstr='--labelMap %s', diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py index 316a02ab09..fe5c7895f4 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py @@ -13,7 +13,8 @@ def test_ACPCTransform_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), midline=dict(argstr='--midline %s...', diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py index 92d51611eb..3df134093f 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py @@ -27,7 +27,8 @@ def test_BRAINSDemonWarp_inputs(): ), histogramMatch=dict(argstr='--histogramMatch ', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), initializeWithDisplacementField=dict(argstr='--initializeWithDisplacementField %s', diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py index 93664a066d..943629d5cc 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py @@ -44,7 +44,8 @@ def test_BRAINSFit_inputs(): ), histogramMatch=dict(argstr='--histogramMatch ', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), initialTransform=dict(argstr='--initialTransform %s', diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py index bb2c107ace..a2444018e2 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py @@ -16,7 +16,8 @@ def test_BRAINSResample_inputs(): gridSpacing=dict(argstr='--gridSpacing %s', sep=',', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py index 4687ccad2b..81d4422012 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py @@ -11,7 +11,8 @@ def test_FiducialRegistration_inputs(): ), fixedLandmarks=dict(argstr='--fixedLandmarks %s...', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), movingLandmarks=dict(argstr='--movingLandmarks %s...', diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py index 3a4579cf44..1fd9c45b34 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -27,7 +27,8 @@ def test_VBRAINSDemonWarp_inputs(): ), histogramMatch=dict(argstr='--histogramMatch ', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), initializeWithDisplacementField=dict(argstr='--initializeWithDisplacementField %s', diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py index f1472982ef..5b8a66ba36 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -13,7 +13,8 @@ def test_BRAINSROIAuto_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='--inputVolume %s', diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py index 6b9c257eda..e09922f0b1 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py @@ -22,7 +22,8 @@ def test_EMSegmentCommandLine_inputs(): generateEmptyMRMLSceneAndQuit=dict(argstr='--generateEmptyMRMLSceneAndQuit %s', hash_files=False, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), intermediateResultsDirectory=dict(argstr='--intermediateResultsDirectory %s', diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py index 139390ff84..4bd8a64f94 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py @@ -13,7 +13,8 @@ def test_RobustStatisticsSegmenter_inputs(): ), expectedVolume=dict(argstr='--expectedVolume %f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), intensityHomogeneity=dict(argstr='--intensityHomogeneity %f', diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py index 5b09910378..03eba8a580 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py @@ -9,7 +9,8 @@ def test_SimpleRegionGrowingSegmentation_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py b/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py index 8442d7fcff..425541245c 100644 --- a/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py +++ b/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py @@ -9,7 +9,8 @@ def test_DicomToNrrdConverter_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputDicomDirectory=dict(argstr='--inputDicomDirectory %s', diff --git a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py index 32a69b3972..5e83f5f935 100644 --- a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py +++ b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py @@ -9,7 +9,8 @@ def test_EMSegmentTransformToNewFormat_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputMRMLFileName=dict(argstr='--inputMRMLFileName %s', diff --git a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py index ae71550fe4..2b2f1ad0ee 100644 --- a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py @@ -18,7 +18,8 @@ def test_GrayscaleModelMaker_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), name=dict(argstr='--name %s', diff --git a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py index d5b112ea25..ded9cbe0be 100644 --- a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py +++ b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py @@ -11,7 +11,8 @@ def test_LabelMapSmoothing_inputs(): ), gaussianSigma=dict(argstr='--gaussianSigma %f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py index 90068164e9..4ba0f98458 100644 --- a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py +++ b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py @@ -19,7 +19,8 @@ def test_MergeModels_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), terminal_output=dict(deprecated='1.0.0', diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py index 4cb225c708..c779eb3238 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py @@ -24,7 +24,8 @@ def test_ModelMaker_inputs(): ), generateAll=dict(argstr='--generateAll ', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), jointsmooth=dict(argstr='--jointsmooth ', diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py index 2c1c7778e7..a54ee1fea6 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py @@ -18,7 +18,8 @@ def test_ModelToLabelMap_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), surface=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py index 0f36b8172b..dd0a987239 100644 --- a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py +++ b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py @@ -9,7 +9,8 @@ def test_OrientScalarVolume_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inputVolume1=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py index ad4ecb6a05..48b75608c8 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py +++ b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py @@ -19,7 +19,8 @@ def test_ProbeVolumeWithModel_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), terminal_output=dict(deprecated='1.0.0', diff --git a/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py b/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py index 0645e5a6dc..369a25b77d 100644 --- a/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py +++ b/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py @@ -9,7 +9,8 @@ def test_SlicerCommandLine_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), terminal_output=dict(deprecated='1.0.0', diff --git a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py index c5064f2f59..dfcfe7744c 100644 --- a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py +++ b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py @@ -6,7 +6,8 @@ def test_Analyze2nii_inputs(): input_map = dict(analyze_file=dict(mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), matlab_cmd=dict(), @@ -26,7 +27,8 @@ def test_Analyze2nii_inputs(): def test_Analyze2nii_outputs(): - output_map = dict(ignore_exception=dict(nohash=True, + output_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), matlab_cmd=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py index 5847ad98fe..36f32cc0c2 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py @@ -7,7 +7,8 @@ def test_ApplyDeformations_inputs(): input_map = dict(deformation_field=dict(field='comp{1}.def', mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(field='fnames', diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py index 849c5580db..ffe254c824 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py @@ -12,7 +12,8 @@ def test_ApplyInverseDeformation_inputs(): deformation_field=dict(field='comp{1}.inv.comp{1}.def', xor=['deformation'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(field='fnames', diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py index 8100981604..b1fc483046 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py @@ -4,7 +4,8 @@ def test_ApplyTransform_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(copyfile=True, diff --git a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py index 04bae31f0d..46caa23009 100644 --- a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py +++ b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py @@ -4,7 +4,8 @@ def test_CalcCoregAffine_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), invmat=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_Coregister.py b/nipype/interfaces/spm/tests/test_auto_Coregister.py index 468ad7e3e3..3c1ab4b50c 100644 --- a/nipype/interfaces/spm/tests/test_auto_Coregister.py +++ b/nipype/interfaces/spm/tests/test_auto_Coregister.py @@ -11,7 +11,8 @@ def test_Coregister_inputs(): ), fwhm=dict(field='eoptions.fwhm', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), jobtype=dict(usedefault=True, diff --git a/nipype/interfaces/spm/tests/test_auto_CreateWarped.py b/nipype/interfaces/spm/tests/test_auto_CreateWarped.py index c1a8d34725..f188d42e9e 100644 --- a/nipype/interfaces/spm/tests/test_auto_CreateWarped.py +++ b/nipype/interfaces/spm/tests/test_auto_CreateWarped.py @@ -8,7 +8,8 @@ def test_CreateWarped_inputs(): field='crt_warped.flowfields', mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), image_files=dict(copyfile=False, diff --git a/nipype/interfaces/spm/tests/test_auto_DARTEL.py b/nipype/interfaces/spm/tests/test_auto_DARTEL.py index c7197a586f..345c2b0b8c 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTEL.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTEL.py @@ -4,7 +4,8 @@ def test_DARTEL_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), image_files=dict(copyfile=False, diff --git a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py index d3e7815756..1743a5d791 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py @@ -15,7 +15,8 @@ def test_DARTELNorm2MNI_inputs(): ), fwhm=dict(field='mni_norm.fwhm', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), matlab_cmd=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_DicomImport.py b/nipype/interfaces/spm/tests/test_auto_DicomImport.py index dff4b04d06..48abb3c646 100644 --- a/nipype/interfaces/spm/tests/test_auto_DicomImport.py +++ b/nipype/interfaces/spm/tests/test_auto_DicomImport.py @@ -10,7 +10,8 @@ def test_DicomImport_inputs(): icedims=dict(field='convopts.icedims', usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(field='data', diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py index 76d4a25bf5..de1ac9ca63 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py @@ -11,7 +11,8 @@ def test_EstimateContrast_inputs(): ), group_contrast=dict(xor=['use_derivs'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), matlab_cmd=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py index 703c97c6fc..b9636e44ed 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py @@ -8,7 +8,8 @@ def test_EstimateModel_inputs(): mandatory=True, ), flags=dict(), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), matlab_cmd=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py index eaa4272d8d..34de3b2efe 100644 --- a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py @@ -19,7 +19,8 @@ def test_FactorialDesign_inputs(): ), global_normalization=dict(field='globalm.glonorm', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), matlab_cmd=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_Level1Design.py b/nipype/interfaces/spm/tests/test_auto_Level1Design.py index 908672beb7..5d0a14f5c5 100644 --- a/nipype/interfaces/spm/tests/test_auto_Level1Design.py +++ b/nipype/interfaces/spm/tests/test_auto_Level1Design.py @@ -11,7 +11,8 @@ def test_Level1Design_inputs(): ), global_intensity_normalization=dict(field='global', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), interscan_interval=dict(field='timing.RT', diff --git a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py index 54ec275450..6c8a465865 100644 --- a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py @@ -19,7 +19,8 @@ def test_MultipleRegressionDesign_inputs(): ), global_normalization=dict(field='globalm.glonorm', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(field='des.mreg.scans', diff --git a/nipype/interfaces/spm/tests/test_auto_NewSegment.py b/nipype/interfaces/spm/tests/test_auto_NewSegment.py index 4c77c5d203..6a2b9e1334 100644 --- a/nipype/interfaces/spm/tests/test_auto_NewSegment.py +++ b/nipype/interfaces/spm/tests/test_auto_NewSegment.py @@ -12,7 +12,8 @@ def test_NewSegment_inputs(): ), channel_info=dict(field='channel', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), matlab_cmd=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize.py b/nipype/interfaces/spm/tests/test_auto_Normalize.py index f6cb425d6a..7aa7949a11 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize.py @@ -11,7 +11,8 @@ def test_Normalize_inputs(): apply_to_files=dict(copyfile=True, field='subj.resample', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), jobtype=dict(usedefault=True, diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize12.py b/nipype/interfaces/spm/tests/test_auto_Normalize12.py index 9d537e34b1..74bf60132a 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize12.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize12.py @@ -18,7 +18,8 @@ def test_Normalize12_inputs(): mandatory=True, xor=['image_to_align', 'tpm'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), image_to_align=dict(copyfile=True, diff --git a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py index 1148cbf9fa..323660a95d 100644 --- a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py @@ -19,7 +19,8 @@ def test_OneSampleTTestDesign_inputs(): ), global_normalization=dict(field='globalm.glonorm', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(field='des.t1.scans', diff --git a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py index f9cce92a37..d2ab89aed8 100644 --- a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py @@ -23,7 +23,8 @@ def test_PairedTTestDesign_inputs(): ), grand_mean_scaling=dict(field='des.pt.gmsca', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), matlab_cmd=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_Realign.py b/nipype/interfaces/spm/tests/test_auto_Realign.py index 6c54c4a945..ef1989bc19 100644 --- a/nipype/interfaces/spm/tests/test_auto_Realign.py +++ b/nipype/interfaces/spm/tests/test_auto_Realign.py @@ -6,7 +6,8 @@ def test_Realign_inputs(): input_map = dict(fwhm=dict(field='eoptions.fwhm', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(copyfile=True, diff --git a/nipype/interfaces/spm/tests/test_auto_Reslice.py b/nipype/interfaces/spm/tests/test_auto_Reslice.py index 4a433e5b3d..a2f10d727c 100644 --- a/nipype/interfaces/spm/tests/test_auto_Reslice.py +++ b/nipype/interfaces/spm/tests/test_auto_Reslice.py @@ -4,7 +4,8 @@ def test_Reslice_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(mandatory=True, diff --git a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py index 06e8f2e607..4bca83c6cf 100644 --- a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py +++ b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py @@ -6,7 +6,8 @@ def test_ResliceToReference_inputs(): input_map = dict(bounding_box=dict(field='comp{2}.idbbvox.bb', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(field='fnames', diff --git a/nipype/interfaces/spm/tests/test_auto_SPMCommand.py b/nipype/interfaces/spm/tests/test_auto_SPMCommand.py index ed841142dd..0f36f719d7 100644 --- a/nipype/interfaces/spm/tests/test_auto_SPMCommand.py +++ b/nipype/interfaces/spm/tests/test_auto_SPMCommand.py @@ -4,7 +4,8 @@ def test_SPMCommand_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), matlab_cmd=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_Segment.py b/nipype/interfaces/spm/tests/test_auto_Segment.py index 739a4e1ca9..b18f405de1 100644 --- a/nipype/interfaces/spm/tests/test_auto_Segment.py +++ b/nipype/interfaces/spm/tests/test_auto_Segment.py @@ -22,7 +22,8 @@ def test_Segment_inputs(): ), gm_output_type=dict(field='output.GM', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), mask_image=dict(field='opts.msk', diff --git a/nipype/interfaces/spm/tests/test_auto_SliceTiming.py b/nipype/interfaces/spm/tests/test_auto_SliceTiming.py index 739d0157a1..357096a402 100644 --- a/nipype/interfaces/spm/tests/test_auto_SliceTiming.py +++ b/nipype/interfaces/spm/tests/test_auto_SliceTiming.py @@ -4,7 +4,8 @@ def test_SliceTiming_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(copyfile=False, diff --git a/nipype/interfaces/spm/tests/test_auto_Smooth.py b/nipype/interfaces/spm/tests/test_auto_Smooth.py index 378f504328..3f0426abb0 100644 --- a/nipype/interfaces/spm/tests/test_auto_Smooth.py +++ b/nipype/interfaces/spm/tests/test_auto_Smooth.py @@ -8,7 +8,8 @@ def test_Smooth_inputs(): ), fwhm=dict(field='fwhm', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), implicit_masking=dict(field='im', diff --git a/nipype/interfaces/spm/tests/test_auto_Threshold.py b/nipype/interfaces/spm/tests/test_auto_Threshold.py index e30b163857..017b1c5325 100644 --- a/nipype/interfaces/spm/tests/test_auto_Threshold.py +++ b/nipype/interfaces/spm/tests/test_auto_Threshold.py @@ -16,7 +16,8 @@ def test_Threshold_inputs(): ), height_threshold_type=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), matlab_cmd=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py index d73cd4f98f..7cd496ce94 100644 --- a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py +++ b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py @@ -10,7 +10,8 @@ def test_ThresholdStatistics_inputs(): ), height_threshold=dict(mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), matlab_cmd=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py index cb19a35f62..f38f8023be 100644 --- a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py @@ -27,7 +27,8 @@ def test_TwoSampleTTestDesign_inputs(): group2_files=dict(field='des.t2.scans2', mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), matlab_cmd=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py index f02579b66c..d61f7c623f 100644 --- a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py +++ b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py @@ -56,7 +56,8 @@ def test_VBMSegment_inputs(): gm_normalized=dict(field='estwrite.output.GM.warped', usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_files=dict(copyfile=False, diff --git a/nipype/interfaces/tests/test_auto_Bru2.py b/nipype/interfaces/tests/test_auto_Bru2.py index 8d20215ed7..ec4151cc8f 100644 --- a/nipype/interfaces/tests/test_auto_Bru2.py +++ b/nipype/interfaces/tests/test_auto_Bru2.py @@ -15,7 +15,8 @@ def test_Bru2_inputs(): ), force_conversion=dict(argstr='-f', ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), input_dir=dict(argstr='%s', diff --git a/nipype/interfaces/tests/test_auto_C3dAffineTool.py b/nipype/interfaces/tests/test_auto_C3dAffineTool.py index 0aff320afe..3abbf26110 100644 --- a/nipype/interfaces/tests/test_auto_C3dAffineTool.py +++ b/nipype/interfaces/tests/test_auto_C3dAffineTool.py @@ -12,7 +12,8 @@ def test_C3dAffineTool_inputs(): fsl2ras=dict(argstr='-fsl2ras', position=4, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), itk_transform=dict(argstr='-oitk %s', diff --git a/nipype/interfaces/tests/test_auto_DataFinder.py b/nipype/interfaces/tests/test_auto_DataFinder.py index f402bdc53d..82b74b6017 100644 --- a/nipype/interfaces/tests/test_auto_DataFinder.py +++ b/nipype/interfaces/tests/test_auto_DataFinder.py @@ -4,7 +4,8 @@ def test_DataFinder_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ignore_regexes=dict(), diff --git a/nipype/interfaces/tests/test_auto_DataGrabber.py b/nipype/interfaces/tests/test_auto_DataGrabber.py index 5795ce969d..8d95bf9637 100644 --- a/nipype/interfaces/tests/test_auto_DataGrabber.py +++ b/nipype/interfaces/tests/test_auto_DataGrabber.py @@ -5,7 +5,8 @@ def test_DataGrabber_inputs(): input_map = dict(base_directory=dict(), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), raise_on_empty=dict(usedefault=True, diff --git a/nipype/interfaces/tests/test_auto_DataSink.py b/nipype/interfaces/tests/test_auto_DataSink.py index 0ea2b71a6d..7c739969a7 100644 --- a/nipype/interfaces/tests/test_auto_DataSink.py +++ b/nipype/interfaces/tests/test_auto_DataSink.py @@ -11,7 +11,8 @@ def test_DataSink_inputs(): container=dict(), creds_path=dict(), encrypt_bucket_keys=dict(), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), local_copy=dict(), diff --git a/nipype/interfaces/tests/test_auto_Dcm2nii.py b/nipype/interfaces/tests/test_auto_Dcm2nii.py index e5c16c79b5..20a29004cb 100644 --- a/nipype/interfaces/tests/test_auto_Dcm2nii.py +++ b/nipype/interfaces/tests/test_auto_Dcm2nii.py @@ -33,7 +33,8 @@ def test_Dcm2nii_inputs(): id_in_filename=dict(argstr='-i', usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), nii_output=dict(argstr='-n', diff --git a/nipype/interfaces/tests/test_auto_Dcm2niix.py b/nipype/interfaces/tests/test_auto_Dcm2niix.py index 9c92e888ac..3d496f3aba 100644 --- a/nipype/interfaces/tests/test_auto_Dcm2niix.py +++ b/nipype/interfaces/tests/test_auto_Dcm2niix.py @@ -21,7 +21,8 @@ def test_Dcm2niix_inputs(): has_private=dict(argstr='-t', usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), merge_imgs=dict(argstr='-m', diff --git a/nipype/interfaces/tests/test_auto_FreeSurferSource.py b/nipype/interfaces/tests/test_auto_FreeSurferSource.py index 1af0874410..a99ddb9d4f 100644 --- a/nipype/interfaces/tests/test_auto_FreeSurferSource.py +++ b/nipype/interfaces/tests/test_auto_FreeSurferSource.py @@ -6,7 +6,8 @@ def test_FreeSurferSource_inputs(): input_map = dict(hemi=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), subject_id=dict(mandatory=True, diff --git a/nipype/interfaces/tests/test_auto_IOBase.py b/nipype/interfaces/tests/test_auto_IOBase.py index 02e45692a9..d8db29919a 100644 --- a/nipype/interfaces/tests/test_auto_IOBase.py +++ b/nipype/interfaces/tests/test_auto_IOBase.py @@ -4,7 +4,8 @@ def test_IOBase_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_JSONFileGrabber.py b/nipype/interfaces/tests/test_auto_JSONFileGrabber.py index 3a93359459..d6458e1e8f 100644 --- a/nipype/interfaces/tests/test_auto_JSONFileGrabber.py +++ b/nipype/interfaces/tests/test_auto_JSONFileGrabber.py @@ -5,7 +5,8 @@ def test_JSONFileGrabber_inputs(): input_map = dict(defaults=dict(), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(), diff --git a/nipype/interfaces/tests/test_auto_JSONFileSink.py b/nipype/interfaces/tests/test_auto_JSONFileSink.py index 32b51c9dc5..1d569e76d4 100644 --- a/nipype/interfaces/tests/test_auto_JSONFileSink.py +++ b/nipype/interfaces/tests/test_auto_JSONFileSink.py @@ -6,7 +6,8 @@ def test_JSONFileSink_inputs(): input_map = dict(_outputs=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_dict=dict(usedefault=True, diff --git a/nipype/interfaces/tests/test_auto_MatlabCommand.py b/nipype/interfaces/tests/test_auto_MatlabCommand.py index c9ec84b23b..71a5587767 100644 --- a/nipype/interfaces/tests/test_auto_MatlabCommand.py +++ b/nipype/interfaces/tests/test_auto_MatlabCommand.py @@ -9,7 +9,8 @@ def test_MatlabCommand_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), logfile=dict(argstr='-logfile %s', diff --git a/nipype/interfaces/tests/test_auto_MeshFix.py b/nipype/interfaces/tests/test_auto_MeshFix.py index 9f40f04355..04c314e2e2 100644 --- a/nipype/interfaces/tests/test_auto_MeshFix.py +++ b/nipype/interfaces/tests/test_auto_MeshFix.py @@ -38,7 +38,8 @@ def test_MeshFix_inputs(): finetuning_substeps=dict(argstr='%d', requires=['finetuning_distance'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file1=dict(argstr='%s', diff --git a/nipype/interfaces/tests/test_auto_MySQLSink.py b/nipype/interfaces/tests/test_auto_MySQLSink.py index 1218d8fac0..80bf344e63 100644 --- a/nipype/interfaces/tests/test_auto_MySQLSink.py +++ b/nipype/interfaces/tests/test_auto_MySQLSink.py @@ -14,7 +14,8 @@ def test_MySQLSink_inputs(): usedefault=True, xor=['config'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), password=dict(), diff --git a/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py b/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py index 773e7e24a3..0846313121 100644 --- a/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py +++ b/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py @@ -4,7 +4,8 @@ def test_NiftiGeneratorBase_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_PETPVC.py b/nipype/interfaces/tests/test_auto_PETPVC.py index 4fadd5aa81..6dbac76fa2 100644 --- a/nipype/interfaces/tests/test_auto_PETPVC.py +++ b/nipype/interfaces/tests/test_auto_PETPVC.py @@ -23,7 +23,8 @@ def test_PETPVC_inputs(): fwhm_z=dict(argstr='-z %.4f', mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-i %s', diff --git a/nipype/interfaces/tests/test_auto_Quickshear.py b/nipype/interfaces/tests/test_auto_Quickshear.py index 0f6821d228..e2edaf37c6 100644 --- a/nipype/interfaces/tests/test_auto_Quickshear.py +++ b/nipype/interfaces/tests/test_auto_Quickshear.py @@ -12,7 +12,8 @@ def test_Quickshear_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='%s', diff --git a/nipype/interfaces/tests/test_auto_S3DataGrabber.py b/nipype/interfaces/tests/test_auto_S3DataGrabber.py index a3c918c465..d5a2536eb8 100644 --- a/nipype/interfaces/tests/test_auto_S3DataGrabber.py +++ b/nipype/interfaces/tests/test_auto_S3DataGrabber.py @@ -10,7 +10,8 @@ def test_S3DataGrabber_inputs(): ), bucket_path=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), local_directory=dict(), diff --git a/nipype/interfaces/tests/test_auto_SQLiteSink.py b/nipype/interfaces/tests/test_auto_SQLiteSink.py index 74c9caaa46..e7319e4d29 100644 --- a/nipype/interfaces/tests/test_auto_SQLiteSink.py +++ b/nipype/interfaces/tests/test_auto_SQLiteSink.py @@ -6,7 +6,8 @@ def test_SQLiteSink_inputs(): input_map = dict(database_file=dict(mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), table_name=dict(mandatory=True, diff --git a/nipype/interfaces/tests/test_auto_SSHDataGrabber.py b/nipype/interfaces/tests/test_auto_SSHDataGrabber.py index 99e71d1ffe..1c350203e6 100644 --- a/nipype/interfaces/tests/test_auto_SSHDataGrabber.py +++ b/nipype/interfaces/tests/test_auto_SSHDataGrabber.py @@ -10,7 +10,8 @@ def test_SSHDataGrabber_inputs(): ), hostname=dict(mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), password=dict(), diff --git a/nipype/interfaces/tests/test_auto_SelectFiles.py b/nipype/interfaces/tests/test_auto_SelectFiles.py index da119bfcf6..12ca6ac859 100644 --- a/nipype/interfaces/tests/test_auto_SelectFiles.py +++ b/nipype/interfaces/tests/test_auto_SelectFiles.py @@ -7,7 +7,8 @@ def test_SelectFiles_inputs(): input_map = dict(base_directory=dict(), force_lists=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), raise_on_empty=dict(usedefault=True, diff --git a/nipype/interfaces/tests/test_auto_SignalExtraction.py b/nipype/interfaces/tests/test_auto_SignalExtraction.py index 4f101450b0..6f314f2f11 100644 --- a/nipype/interfaces/tests/test_auto_SignalExtraction.py +++ b/nipype/interfaces/tests/test_auto_SignalExtraction.py @@ -8,7 +8,8 @@ def test_SignalExtraction_inputs(): ), detrend=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(mandatory=True, diff --git a/nipype/interfaces/tests/test_auto_SlicerCommandLine.py b/nipype/interfaces/tests/test_auto_SlicerCommandLine.py index 70827978cc..26a4700a0e 100644 --- a/nipype/interfaces/tests/test_auto_SlicerCommandLine.py +++ b/nipype/interfaces/tests/test_auto_SlicerCommandLine.py @@ -9,7 +9,8 @@ def test_SlicerCommandLine_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), module=dict(), diff --git a/nipype/interfaces/tests/test_auto_XNATSink.py b/nipype/interfaces/tests/test_auto_XNATSink.py index 286c8b2ca9..e4ce926c6e 100644 --- a/nipype/interfaces/tests/test_auto_XNATSink.py +++ b/nipype/interfaces/tests/test_auto_XNATSink.py @@ -14,7 +14,8 @@ def test_XNATSink_inputs(): ), experiment_id=dict(mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), project_id=dict(mandatory=True, diff --git a/nipype/interfaces/tests/test_auto_XNATSource.py b/nipype/interfaces/tests/test_auto_XNATSource.py index b399d143aa..afd02e6c9d 100644 --- a/nipype/interfaces/tests/test_auto_XNATSource.py +++ b/nipype/interfaces/tests/test_auto_XNATSource.py @@ -8,7 +8,8 @@ def test_XNATSource_inputs(): config=dict(mandatory=True, xor=['server'], ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), pwd=dict(), diff --git a/nipype/interfaces/tests/test_base.py b/nipype/interfaces/tests/test_base.py deleted file mode 100644 index 48a44ad6a4..0000000000 --- a/nipype/interfaces/tests/test_base.py +++ /dev/null @@ -1,790 +0,0 @@ -# -*- 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: -from __future__ import print_function, unicode_literals -from future import standard_library -from builtins import open, str -import os -import warnings -import simplejson as json - -import pytest -import traits.api as traits -from nipype.testing import example_data -import nipype.interfaces.base as nib -from nipype.utils.filemanip import split_filename -from nipype.interfaces.base import Undefined, config -standard_library.install_aliases() - - -@pytest.mark.parametrize("args", [ - {}, - {'a': 1, 'b': [2, 3]} -]) -def test_bunch(args): - b = nib.Bunch(**args) - assert b.__dict__ == args - - -def test_bunch_attribute(): - b = nib.Bunch(a=1, b=[2, 3], c=None) - assert b.a == 1 - assert b.b == [2, 3] - assert b.c is None - - -def test_bunch_repr(): - b = nib.Bunch(b=2, c=3, a=dict(n=1, m=2)) - assert repr(b) == "Bunch(a={'m': 2, 'n': 1}, b=2, c=3)" - - -def test_bunch_methods(): - b = nib.Bunch(a=2) - b.update(a=3) - newb = b.dictcopy() - assert b.a == 3 - assert b.get('a') == 3 - assert b.get('badkey', 'otherthing') == 'otherthing' - assert b != newb - assert type(dict()) == type(newb) - assert newb['a'] == 3 - - -def test_bunch_hash(): - # NOTE: Since the path to the json file is included in the Bunch, - # the hash will be unique to each machine. - pth = os.path.split(os.path.abspath(__file__))[0] - json_pth = os.path.join(pth, 'realign_json.json') - b = nib.Bunch(infile=json_pth, - otherthing='blue', - yat=True) - newbdict, bhash = b._get_bunch_hash() - assert bhash == 'ddcc7b4ec5675df8cf317a48bd1857fa' - # Make sure the hash stored in the json file for `infile` is correct. - jshash = nib.md5() - with open(json_pth, 'r') as fp: - jshash.update(fp.read().encode('utf-8')) - assert newbdict['infile'][0][1] == jshash.hexdigest() - assert newbdict['yat'] is True - - -@pytest.fixture(scope="module") -def setup_file(request, tmpdir_factory): - tmp_dir = tmpdir_factory.mktemp('files') - tmp_infile = tmp_dir.join('foo.txt') - with tmp_infile.open('w') as fp: - fp.writelines([u'123456789']) - - tmp_dir.chdir() - - return tmp_infile.strpath - - -def test_TraitedSpec(): - assert nib.TraitedSpec().get_hashval() - assert nib.TraitedSpec().__repr__() == '\n\n' - - class spec(nib.TraitedSpec): - foo = nib.traits.Int - goo = nib.traits.Float(usedefault=True) - - assert spec().foo == Undefined - assert spec().goo == 0.0 - specfunc = lambda x: spec(hoo=x) - with pytest.raises(nib.traits.TraitError): specfunc(1) - infields = spec(foo=1) - hashval = ([('foo', 1), ('goo', '0.0000000000')], 'e89433b8c9141aa0fda2f8f4d662c047') - assert infields.get_hashval() == hashval - assert infields.__repr__() == '\nfoo = 1\ngoo = 0.0\n' - - -@pytest.mark.skip -def test_TraitedSpec_dynamic(): - from pickle import dumps, loads - a = nib.BaseTraitedSpec() - a.add_trait('foo', nib.traits.Int) - a.foo = 1 - assign_a = lambda: setattr(a, 'foo', 'a') - with pytest.raises(Exception): assign_a - pkld_a = dumps(a) - unpkld_a = loads(pkld_a) - assign_a_again = lambda: setattr(unpkld_a, 'foo', 'a') - with pytest.raises(Exception): assign_a_again - - -def test_TraitedSpec_logic(): - class spec3(nib.TraitedSpec): - _xor_inputs = ('foo', 'bar') - - foo = nib.traits.Int(xor=_xor_inputs, - desc='foo or bar, not both') - bar = nib.traits.Int(xor=_xor_inputs, - desc='bar or foo, not both') - kung = nib.traits.Float(requires=('foo',), - position=0, - desc='kung foo') - - class out3(nib.TraitedSpec): - output = nib.traits.Int - - class MyInterface(nib.BaseInterface): - input_spec = spec3 - output_spec = out3 - - myif = MyInterface() - # NOTE_dj, FAIL: I don't get a TypeError, only a UserWarning - #with pytest.raises(TypeError): - # setattr(myif.inputs, 'kung', 10.0) - myif.inputs.foo = 1 - assert myif.inputs.foo == 1 - set_bar = lambda: setattr(myif.inputs, 'bar', 1) - with pytest.raises(IOError): set_bar() - assert myif.inputs.foo == 1 - myif.inputs.kung = 2 - assert myif.inputs.kung == 2.0 - - -def test_deprecation(): - with warnings.catch_warnings(record=True) as w: - warnings.filterwarnings('always', '', UserWarning) - - class DeprecationSpec1(nib.TraitedSpec): - foo = nib.traits.Int(deprecated='0.1') - spec_instance = DeprecationSpec1() - set_foo = lambda: setattr(spec_instance, 'foo', 1) - with pytest.raises(nib.TraitError): set_foo() - assert len(w) == 0, 'no warnings, just errors' - - - with warnings.catch_warnings(record=True) as w: - warnings.filterwarnings('always', '', UserWarning) - - class DeprecationSpec2(nib.TraitedSpec): - foo = nib.traits.Int(deprecated='100', new_name='bar') - spec_instance = DeprecationSpec2() - set_foo = lambda: setattr(spec_instance, 'foo', 1) - with pytest.raises(nib.TraitError): set_foo() - assert len(w) == 0, 'no warnings, just errors' - - with warnings.catch_warnings(record=True) as w: - warnings.filterwarnings('always', '', UserWarning) - - class DeprecationSpec3(nib.TraitedSpec): - foo = nib.traits.Int(deprecated='1000', new_name='bar') - bar = nib.traits.Int() - spec_instance = DeprecationSpec3() - not_raised = True - try: - spec_instance.foo = 1 - except nib.TraitError: - not_raised = False - assert not_raised - assert len(w) == 1, 'deprecated warning 1 %s' % [w1.message for w1 in w] - - with warnings.catch_warnings(record=True) as w: - warnings.filterwarnings('always', '', UserWarning) - - class DeprecationSpec3(nib.TraitedSpec): - foo = nib.traits.Int(deprecated='1000', new_name='bar') - bar = nib.traits.Int() - spec_instance = DeprecationSpec3() - not_raised = True - try: - spec_instance.foo = 1 - except nib.TraitError: - not_raised = False - assert not_raised - assert spec_instance.foo == Undefined - assert spec_instance.bar == 1 - assert len(w) == 1, 'deprecated warning 2 %s' % [w1.message for w1 in w] - - -def test_namesource(setup_file): - tmp_infile = setup_file - tmpd, nme, ext = split_filename(tmp_infile) - - class spec2(nib.CommandLineInputSpec): - moo = nib.File(name_source=['doo'], hash_files=False, argstr="%s", - position=2) - doo = nib.File(exists=True, argstr="%s", position=1) - goo = traits.Int(argstr="%d", position=4) - poo = nib.File(name_source=['goo'], hash_files=False, argstr="%s", - position=3) - - class TestName(nib.CommandLine): - _cmd = "mycommand" - input_spec = spec2 - testobj = TestName() - testobj.inputs.doo = tmp_infile - testobj.inputs.goo = 99 - assert '%s_generated' % nme in testobj.cmdline - assert '%d_generated' % testobj.inputs.goo in testobj.cmdline - testobj.inputs.moo = "my_%s_template" - assert 'my_%s_template' % nme in testobj.cmdline - - -def test_chained_namesource(setup_file): - tmp_infile = setup_file - tmpd, nme, ext = split_filename(tmp_infile) - - class spec2(nib.CommandLineInputSpec): - doo = nib.File(exists=True, argstr="%s", position=1) - moo = nib.File(name_source=['doo'], hash_files=False, argstr="%s", - position=2, name_template='%s_mootpl') - poo = nib.File(name_source=['moo'], hash_files=False, - argstr="%s", position=3) - - class TestName(nib.CommandLine): - _cmd = "mycommand" - input_spec = spec2 - - testobj = TestName() - testobj.inputs.doo = tmp_infile - res = testobj.cmdline - assert '%s' % tmp_infile in res - assert '%s_mootpl ' % nme in res - assert '%s_mootpl_generated' % nme in res - - -def test_cycle_namesource1(setup_file): - tmp_infile = setup_file - tmpd, nme, ext = split_filename(tmp_infile) - - class spec3(nib.CommandLineInputSpec): - moo = nib.File(name_source=['doo'], hash_files=False, argstr="%s", - position=1, name_template='%s_mootpl') - poo = nib.File(name_source=['moo'], hash_files=False, - argstr="%s", position=2) - doo = nib.File(name_source=['poo'], hash_files=False, - argstr="%s", position=3) - - class TestCycle(nib.CommandLine): - _cmd = "mycommand" - input_spec = spec3 - - # Check that an exception is raised - to0 = TestCycle() - not_raised = True - try: - to0.cmdline - except nib.NipypeInterfaceError: - not_raised = False - assert not not_raised - - -def test_cycle_namesource2(setup_file): - tmp_infile = setup_file - tmpd, nme, ext = split_filename(tmp_infile) - - class spec3(nib.CommandLineInputSpec): - moo = nib.File(name_source=['doo'], hash_files=False, argstr="%s", - position=1, name_template='%s_mootpl') - poo = nib.File(name_source=['moo'], hash_files=False, - argstr="%s", position=2) - doo = nib.File(name_source=['poo'], hash_files=False, - argstr="%s", position=3) - - class TestCycle(nib.CommandLine): - _cmd = "mycommand" - input_spec = spec3 - - # Check that loop can be broken by setting one of the inputs - to1 = TestCycle() - to1.inputs.poo = tmp_infile - - not_raised = True - try: - res = to1.cmdline - except nib.NipypeInterfaceError: - not_raised = False - print(res) - - assert not_raised - assert '%s' % tmp_infile in res - assert '%s_generated' % nme in res - assert '%s_generated_mootpl' % nme in res - - -def test_TraitedSpec_withFile(setup_file): - tmp_infile = setup_file - tmpd, nme = os.path.split(tmp_infile) - assert os.path.exists(tmp_infile) - - class spec2(nib.TraitedSpec): - moo = nib.File(exists=True) - doo = nib.traits.List(nib.File(exists=True)) - infields = spec2(moo=tmp_infile, doo=[tmp_infile]) - hashval = infields.get_hashval(hash_method='content') - assert hashval[1] == 'a00e9ee24f5bfa9545a515b7a759886b' - - -def test_TraitedSpec_withNoFileHashing(setup_file): - tmp_infile = setup_file - tmpd, nme = os.path.split(tmp_infile) - assert os.path.exists(tmp_infile) - - class spec2(nib.TraitedSpec): - moo = nib.File(exists=True, hash_files=False) - doo = nib.traits.List(nib.File(exists=True)) - infields = spec2(moo=nme, doo=[tmp_infile]) - hashval = infields.get_hashval(hash_method='content') - assert hashval[1] == '8da4669ff5d72f670a46ea3e7a203215' - - class spec3(nib.TraitedSpec): - moo = nib.File(exists=True, name_source="doo") - doo = nib.traits.List(nib.File(exists=True)) - infields = spec3(moo=nme, doo=[tmp_infile]) - hashval1 = infields.get_hashval(hash_method='content') - - class spec4(nib.TraitedSpec): - moo = nib.File(exists=True) - doo = nib.traits.List(nib.File(exists=True)) - infields = spec4(moo=nme, doo=[tmp_infile]) - hashval2 = infields.get_hashval(hash_method='content') - assert hashval1[1] != hashval2[1] - - -def test_Interface(): - assert nib.Interface.input_spec == None - assert nib.Interface.output_spec == None - with pytest.raises(NotImplementedError): nib.Interface() - with pytest.raises(NotImplementedError): nib.Interface.help() - with pytest.raises(NotImplementedError): nib.Interface._inputs_help() - with pytest.raises(NotImplementedError): nib.Interface._outputs_help() - with pytest.raises(NotImplementedError): nib.Interface._outputs() - - class DerivedInterface(nib.Interface): - def __init__(self): - pass - - nif = DerivedInterface() - with pytest.raises(NotImplementedError): nif.run() - with pytest.raises(NotImplementedError): nif.aggregate_outputs() - with pytest.raises(NotImplementedError): nif._list_outputs() - with pytest.raises(NotImplementedError): nif._get_filecopy_info() - - -def test_BaseInterface(): - assert nib.BaseInterface.help() == None - assert nib.BaseInterface._get_filecopy_info() == [] - - class InputSpec(nib.TraitedSpec): - foo = nib.traits.Int(desc='a random int') - goo = nib.traits.Int(desc='a random int', mandatory=True) - moo = nib.traits.Int(desc='a random int', mandatory=False) - hoo = nib.traits.Int(desc='a random int', usedefault=True) - zoo = nib.File(desc='a file', copyfile=False) - woo = nib.File(desc='a file', copyfile=True) - - class OutputSpec(nib.TraitedSpec): - foo = nib.traits.Int(desc='a random int') - - class DerivedInterface(nib.BaseInterface): - input_spec = InputSpec - - assert DerivedInterface.help() == None - assert 'moo' in ''.join(DerivedInterface._inputs_help()) - assert DerivedInterface()._outputs() == None - assert DerivedInterface._get_filecopy_info()[0]['key'] == 'woo' - assert DerivedInterface._get_filecopy_info()[0]['copy'] - assert DerivedInterface._get_filecopy_info()[1]['key'] == 'zoo' - assert not DerivedInterface._get_filecopy_info()[1]['copy'] - assert DerivedInterface().inputs.foo == Undefined - with pytest.raises(ValueError): DerivedInterface()._check_mandatory_inputs() - assert DerivedInterface(goo=1)._check_mandatory_inputs() == None - with pytest.raises(ValueError): DerivedInterface().run() - with pytest.raises(NotImplementedError): DerivedInterface(goo=1).run() - - class DerivedInterface2(DerivedInterface): - output_spec = OutputSpec - - def _run_interface(self, runtime): - return runtime - - assert DerivedInterface2.help() == None - assert DerivedInterface2()._outputs().foo == Undefined - with pytest.raises(NotImplementedError): DerivedInterface2(goo=1).run() - - default_inpu_spec = nib.BaseInterface.input_spec - nib.BaseInterface.input_spec = None - with pytest.raises(Exception): nib.BaseInterface() - nib.BaseInterface.input_spec = default_inpu_spec - - -def test_BaseInterface_load_save_inputs(tmpdir): - tmp_json = tmpdir.join('settings.json').strpath - - class InputSpec(nib.TraitedSpec): - input1 = nib.traits.Int() - input2 = nib.traits.Float() - input3 = nib.traits.Bool() - input4 = nib.traits.Str() - - class DerivedInterface(nib.BaseInterface): - input_spec = InputSpec - - def __init__(self, **inputs): - super(DerivedInterface, self).__init__(**inputs) - - inputs_dict = {'input1': 12, 'input3': True, - 'input4': 'some string'} - bif = DerivedInterface(**inputs_dict) - bif.save_inputs_to_json(tmp_json) - bif2 = DerivedInterface() - bif2.load_inputs_from_json(tmp_json) - assert bif2.inputs.get_traitsfree() == inputs_dict - - bif3 = DerivedInterface(from_file=tmp_json) - assert bif3.inputs.get_traitsfree() == inputs_dict - - inputs_dict2 = inputs_dict.copy() - inputs_dict2.update({'input4': 'some other string'}) - bif4 = DerivedInterface(from_file=tmp_json, input4=inputs_dict2['input4']) - assert bif4.inputs.get_traitsfree() == inputs_dict2 - - bif5 = DerivedInterface(input4=inputs_dict2['input4']) - bif5.load_inputs_from_json(tmp_json, overwrite=False) - assert bif5.inputs.get_traitsfree() == inputs_dict2 - - bif6 = DerivedInterface(input4=inputs_dict2['input4']) - bif6.load_inputs_from_json(tmp_json) - assert bif6.inputs.get_traitsfree() == inputs_dict - - # test get hashval in a complex interface - from nipype.interfaces.ants import Registration - settings = example_data(example_data('smri_ants_registration_settings.json')) - with open(settings) as setf: - data_dict = json.load(setf) - - tsthash = Registration() - tsthash.load_inputs_from_json(settings) - assert {} == check_dict(data_dict, tsthash.inputs.get_traitsfree()) - - tsthash2 = Registration(from_file=settings) - assert {} == check_dict(data_dict, tsthash2.inputs.get_traitsfree()) - - _, hashvalue = tsthash.inputs.get_hashval(hash_method='timestamp') - assert 'ec5755e07287e04a4b409e03b77a517c' == hashvalue - - -def test_input_version(): - class InputSpec(nib.TraitedSpec): - foo = nib.traits.Int(desc='a random int', min_ver='0.9') - - class DerivedInterface1(nib.BaseInterface): - input_spec = InputSpec - obj = DerivedInterface1() - obj._check_version_requirements(obj.inputs) - - config.set('execution', 'stop_on_unknown_version', True) - - with pytest.raises(Exception): obj._check_version_requirements(obj.inputs) - - config.set_default_config() - - class InputSpec(nib.TraitedSpec): - foo = nib.traits.Int(desc='a random int', min_ver='0.9') - - class DerivedInterface1(nib.BaseInterface): - input_spec = InputSpec - _version = '0.8' - obj = DerivedInterface1() - obj.inputs.foo = 1 - with pytest.raises(Exception): obj._check_version_requirements() - - class InputSpec(nib.TraitedSpec): - foo = nib.traits.Int(desc='a random int', min_ver='0.9') - - class DerivedInterface1(nib.BaseInterface): - input_spec = InputSpec - _version = '0.10' - obj = DerivedInterface1() - obj._check_version_requirements(obj.inputs) - - class InputSpec(nib.TraitedSpec): - foo = nib.traits.Int(desc='a random int', min_ver='0.9') - - class DerivedInterface1(nib.BaseInterface): - input_spec = InputSpec - _version = '0.9' - obj = DerivedInterface1() - obj.inputs.foo = 1 - not_raised = True - obj._check_version_requirements(obj.inputs) - - class InputSpec(nib.TraitedSpec): - foo = nib.traits.Int(desc='a random int', max_ver='0.7') - - class DerivedInterface2(nib.BaseInterface): - input_spec = InputSpec - _version = '0.8' - obj = DerivedInterface2() - obj.inputs.foo = 1 - with pytest.raises(Exception): obj._check_version_requirements() - - class InputSpec(nib.TraitedSpec): - foo = nib.traits.Int(desc='a random int', max_ver='0.9') - - class DerivedInterface1(nib.BaseInterface): - input_spec = InputSpec - _version = '0.9' - obj = DerivedInterface1() - obj.inputs.foo = 1 - not_raised = True - obj._check_version_requirements(obj.inputs) - - -def test_output_version(): - class InputSpec(nib.TraitedSpec): - foo = nib.traits.Int(desc='a random int') - - class OutputSpec(nib.TraitedSpec): - foo = nib.traits.Int(desc='a random int', min_ver='0.9') - - class DerivedInterface1(nib.BaseInterface): - input_spec = InputSpec - output_spec = OutputSpec - _version = '0.10' - obj = DerivedInterface1() - assert obj._check_version_requirements(obj._outputs()) == [] - - class InputSpec(nib.TraitedSpec): - foo = nib.traits.Int(desc='a random int') - - class OutputSpec(nib.TraitedSpec): - foo = nib.traits.Int(desc='a random int', min_ver='0.11') - - class DerivedInterface1(nib.BaseInterface): - input_spec = InputSpec - output_spec = OutputSpec - _version = '0.10' - obj = DerivedInterface1() - assert obj._check_version_requirements(obj._outputs()) == ['foo'] - - class InputSpec(nib.TraitedSpec): - foo = nib.traits.Int(desc='a random int') - - class OutputSpec(nib.TraitedSpec): - foo = nib.traits.Int(desc='a random int', min_ver='0.11') - - class DerivedInterface1(nib.BaseInterface): - input_spec = InputSpec - output_spec = OutputSpec - _version = '0.10' - - def _run_interface(self, runtime): - return runtime - - def _list_outputs(self): - return {'foo': 1} - obj = DerivedInterface1() - with pytest.raises(KeyError): obj.run() - - -def test_Commandline(): - with pytest.raises(Exception): nib.CommandLine() - ci = nib.CommandLine(command='which') - assert ci.cmd == 'which' - assert ci.inputs.args == Undefined - ci2 = nib.CommandLine(command='which', args='ls') - assert ci2.cmdline == 'which ls' - ci3 = nib.CommandLine(command='echo') - ci3.inputs.environ = {'MYENV': 'foo'} - res = ci3.run() - assert res.runtime.environ['MYENV'] == 'foo' - assert res.outputs == None - - class CommandLineInputSpec1(nib.CommandLineInputSpec): - foo = nib.Str(argstr='%s', desc='a str') - goo = nib.traits.Bool(argstr='-g', desc='a bool', position=0) - hoo = nib.traits.List(argstr='-l %s', desc='a list') - moo = nib.traits.List(argstr='-i %d...', desc='a repeated list', - position=-1) - noo = nib.traits.Int(argstr='-x %d', desc='an int') - roo = nib.traits.Str(desc='not on command line') - soo = nib.traits.Bool(argstr="-soo") - nib.CommandLine.input_spec = CommandLineInputSpec1 - ci4 = nib.CommandLine(command='cmd') - ci4.inputs.foo = 'foo' - ci4.inputs.goo = True - ci4.inputs.hoo = ['a', 'b'] - ci4.inputs.moo = [1, 2, 3] - ci4.inputs.noo = 0 - ci4.inputs.roo = 'hello' - ci4.inputs.soo = False - cmd = ci4._parse_inputs() - assert cmd[0] == '-g' - assert cmd[-1] == '-i 1 -i 2 -i 3' - assert 'hello' not in ' '.join(cmd) - assert '-soo' not in ' '.join(cmd) - ci4.inputs.soo = True - cmd = ci4._parse_inputs() - assert '-soo' in ' '.join(cmd) - - class CommandLineInputSpec2(nib.CommandLineInputSpec): - foo = nib.File(argstr='%s', desc='a str', genfile=True) - nib.CommandLine.input_spec = CommandLineInputSpec2 - ci5 = nib.CommandLine(command='cmd') - with pytest.raises(NotImplementedError): ci5._parse_inputs() - - class DerivedClass(nib.CommandLine): - input_spec = CommandLineInputSpec2 - - def _gen_filename(self, name): - return 'filename' - - ci6 = DerivedClass(command='cmd') - assert ci6._parse_inputs()[0] == 'filename' - nib.CommandLine.input_spec = nib.CommandLineInputSpec - - -def test_Commandline_environ(monkeypatch, tmpdir): - from nipype import config - config.set_default_config() - - tmpdir.chdir() - monkeypatch.setitem(os.environ, 'DISPLAY', ':1') - # Test environment - ci3 = nib.CommandLine(command='echo') - res = ci3.run() - assert res.runtime.environ['DISPLAY'] == ':1' - - # Test display_variable option - monkeypatch.delitem(os.environ, 'DISPLAY', raising=False) - config.set('execution', 'display_variable', ':3') - res = ci3.run() - assert not 'DISPLAY' in ci3.inputs.environ - assert not 'DISPLAY' in res.runtime.environ - - # If the interface has _redirect_x then yes, it should be set - ci3._redirect_x = True - res = ci3.run() - assert res.runtime.environ['DISPLAY'] == ':3' - - # Test overwrite - monkeypatch.setitem(os.environ, 'DISPLAY', ':1') - ci3.inputs.environ = {'DISPLAY': ':2'} - res = ci3.run() - assert res.runtime.environ['DISPLAY'] == ':2' - - -def test_CommandLine_output(tmpdir): - # Create one file - tmpdir.chdir() - file = tmpdir.join('foo.txt') - file.write('123456\n') - name = os.path.basename(file.strpath) - - ci = nib.CommandLine(command='ls -l') - ci.terminal_output = 'allatonce' - res = ci.run() - assert res.runtime.merged == '' - assert name in res.runtime.stdout - - # Check stdout is written - ci = nib.CommandLine(command='ls -l') - ci.terminal_output = 'file_stdout' - res = ci.run() - assert os.path.isfile('stdout.nipype') - assert name in res.runtime.stdout - tmpdir.join('stdout.nipype').remove(ignore_errors=True) - - # Check stderr is written - ci = nib.CommandLine(command='ls -l') - ci.terminal_output = 'file_stderr' - res = ci.run() - assert os.path.isfile('stderr.nipype') - tmpdir.join('stderr.nipype').remove(ignore_errors=True) - - # Check outputs are thrown away - ci = nib.CommandLine(command='ls -l') - ci.terminal_output = 'none' - res = ci.run() - assert res.runtime.stdout == '' and \ - res.runtime.stderr == '' and \ - res.runtime.merged == '' - - # Check that new interfaces are set to default 'stream' - ci = nib.CommandLine(command='ls -l') - res = ci.run() - assert ci.terminal_output == 'stream' - assert name in res.runtime.stdout and \ - res.runtime.stderr == '' - - # Check only one file is generated - ci = nib.CommandLine(command='ls -l') - ci.terminal_output = 'file' - res = ci.run() - assert os.path.isfile('output.nipype') - assert name in res.runtime.merged and \ - res.runtime.stdout == '' and \ - res.runtime.stderr == '' - tmpdir.join('output.nipype').remove(ignore_errors=True) - - # Check split files are generated - ci = nib.CommandLine(command='ls -l') - ci.terminal_output = 'file_split' - res = ci.run() - assert os.path.isfile('stdout.nipype') - assert os.path.isfile('stderr.nipype') - assert name in res.runtime.stdout - - -def test_global_CommandLine_output(tmpdir): - """Ensures CommandLine.set_default_terminal_output works""" - from nipype.interfaces.fsl import BET - - ci = nib.CommandLine(command='ls -l') - assert ci.terminal_output == 'stream' # default case - - ci = BET() - assert ci.terminal_output == 'stream' # default case - - nib.CommandLine.set_default_terminal_output('allatonce') - ci = nib.CommandLine(command='ls -l') - assert ci.terminal_output == 'allatonce' - - nib.CommandLine.set_default_terminal_output('file') - ci = nib.CommandLine(command='ls -l') - assert ci.terminal_output == 'file' - - # Check default affects derived interfaces - ci = BET() - assert ci.terminal_output == 'file' - - -def check_dict(ref_dict, tst_dict): - """Compare dictionaries of inputs and and those loaded from json files""" - def to_list(x): - if isinstance(x, tuple): - x = list(x) - - if isinstance(x, list): - for i, xel in enumerate(x): - x[i] = to_list(xel) - - return x - - failed_dict = {} - for key, value in list(ref_dict.items()): - newval = to_list(tst_dict[key]) - if newval != value: - failed_dict[key] = (value, newval) - return failed_dict - -def test_ImageFile(): - x = nib.BaseInterface().inputs - - # setup traits - x.add_trait('nifti', nib.ImageFile(types=['nifti1', 'dicom'])) - x.add_trait('anytype', nib.ImageFile()) - x.add_trait('newtype', nib.ImageFile(types=['nifti10'])) - x.add_trait('nocompress', nib.ImageFile(types=['mgh'], - allow_compressed=False)) - - with pytest.raises(nib.TraitError): x.nifti = 'test.mgz' - x.nifti = 'test.nii' - x.anytype = 'test.xml' - with pytest.raises(AttributeError): x.newtype = 'test.nii' - with pytest.raises(nib.TraitError): x.nocompress = 'test.nii.gz' - x.nocompress = 'test.mgh' diff --git a/nipype/interfaces/utility/tests/test_auto_AssertEqual.py b/nipype/interfaces/utility/tests/test_auto_AssertEqual.py index 739725a417..0b561d9702 100644 --- a/nipype/interfaces/utility/tests/test_auto_AssertEqual.py +++ b/nipype/interfaces/utility/tests/test_auto_AssertEqual.py @@ -4,7 +4,8 @@ def test_AssertEqual_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), volume1=dict(mandatory=True, diff --git a/nipype/interfaces/utility/tests/test_auto_Function.py b/nipype/interfaces/utility/tests/test_auto_Function.py index 649d626a5f..1831728c04 100644 --- a/nipype/interfaces/utility/tests/test_auto_Function.py +++ b/nipype/interfaces/utility/tests/test_auto_Function.py @@ -6,7 +6,8 @@ def test_Function_inputs(): input_map = dict(function_str=dict(mandatory=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), ) diff --git a/nipype/interfaces/utility/tests/test_auto_Merge.py b/nipype/interfaces/utility/tests/test_auto_Merge.py index f98e70892b..07f5b60962 100644 --- a/nipype/interfaces/utility/tests/test_auto_Merge.py +++ b/nipype/interfaces/utility/tests/test_auto_Merge.py @@ -6,7 +6,8 @@ def test_Merge_inputs(): input_map = dict(axis=dict(usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), no_flatten=dict(usedefault=True, diff --git a/nipype/interfaces/utility/tests/test_auto_Select.py b/nipype/interfaces/utility/tests/test_auto_Select.py index 3c67785702..7889366b76 100644 --- a/nipype/interfaces/utility/tests/test_auto_Select.py +++ b/nipype/interfaces/utility/tests/test_auto_Select.py @@ -4,7 +4,8 @@ def test_Select_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), index=dict(mandatory=True, diff --git a/nipype/interfaces/utility/tests/test_auto_Split.py b/nipype/interfaces/utility/tests/test_auto_Split.py index 663ff65b13..a0e02af267 100644 --- a/nipype/interfaces/utility/tests/test_auto_Split.py +++ b/nipype/interfaces/utility/tests/test_auto_Split.py @@ -4,7 +4,8 @@ def test_Split_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), inlist=dict(mandatory=True, diff --git a/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py b/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py index 805c5f0921..83bd21b7bf 100644 --- a/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py +++ b/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py @@ -12,7 +12,8 @@ def test_Vnifti2Image_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-in %s', diff --git a/nipype/interfaces/vista/tests/test_auto_VtoMat.py b/nipype/interfaces/vista/tests/test_auto_VtoMat.py index 2e5345d80f..e9e198e90b 100644 --- a/nipype/interfaces/vista/tests/test_auto_VtoMat.py +++ b/nipype/interfaces/vista/tests/test_auto_VtoMat.py @@ -9,7 +9,8 @@ def test_VtoMat_inputs(): environ=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + ignore_exception=dict(deprecated='1.0.0', + nohash=True, usedefault=True, ), in_file=dict(argstr='-in %s', diff --git a/nipype/pipeline/engine/nodes.py b/nipype/pipeline/engine/nodes.py index 36d3ba1b40..5b972a7692 100644 --- a/nipype/pipeline/engine/nodes.py +++ b/nipype/pipeline/engine/nodes.py @@ -42,10 +42,10 @@ copyfiles, fnames_presuffix, loadpkl, split_filename, load_json, savepkl, write_rst_header, write_rst_dict, - write_rst_list, to_str) + write_rst_list, to_str, md5) from ...interfaces.base import (traits, InputMultiPath, CommandLine, Undefined, TraitedSpec, DynamicTraitedSpec, - Bunch, InterfaceResult, md5, Interface, + Bunch, InterfaceResult, Interface, TraitDictObject, TraitListObject, isdefined) from .utils import (generate_expanded_graph, modify_paths, export_graph, make_output_dir, write_workflow_prov, diff --git a/nipype/pipeline/engine/workflows.py b/nipype/pipeline/engine/workflows.py index 7e0a69d2a1..d58424fcd5 100644 --- a/nipype/pipeline/engine/workflows.py +++ b/nipype/pipeline/engine/workflows.py @@ -41,10 +41,10 @@ from ...utils.functions import (getsource, create_function_from_source) from ...interfaces.base import (traits, InputMultiPath, CommandLine, Undefined, TraitedSpec, DynamicTraitedSpec, - Bunch, InterfaceResult, md5, Interface, + Bunch, InterfaceResult, Interface, TraitDictObject, TraitListObject, isdefined) -from ...utils.filemanip import (save_json, FileNotFoundError, +from ...utils.filemanip import (save_json, FileNotFoundError, md5, filename_to_list, list_to_filename, copyfiles, fnames_presuffix, loadpkl, split_filename, load_json, savepkl, diff --git a/nipype/pipeline/plugins/ipythonx.py b/nipype/pipeline/plugins/ipythonx.py index 8cb3c4190a..d76cdfeb98 100644 --- a/nipype/pipeline/plugins/ipythonx.py +++ b/nipype/pipeline/plugins/ipythonx.py @@ -8,7 +8,7 @@ import sys from future.utils import raise_from -from ...interfaces.base import LooseVersion +from ... import LooseVersion from .base import (DistributedPluginBase, logger, report_crash) IPython_not_loaded = False @@ -20,8 +20,6 @@ IPython_not_loaded = True - - class IPythonXPlugin(DistributedPluginBase): """Execute workflow with ipython """ diff --git a/nipype/pipeline/plugins/tests/test_callback.py b/nipype/pipeline/plugins/tests/test_callback.py index 46f3608746..7212ff7302 100644 --- a/nipype/pipeline/plugins/tests/test_callback.py +++ b/nipype/pipeline/plugins/tests/test_callback.py @@ -31,6 +31,8 @@ def callback(self, node, status, result=None): def test_callback_normal(tmpdir): + tmpdir.chdir() + so = Status() wf = pe.Workflow(name='test', base_dir=tmpdir.strpath) f_node = pe.Node(niu.Function(function=func, input_names=[], @@ -47,6 +49,8 @@ def test_callback_normal(tmpdir): def test_callback_exception(tmpdir): + tmpdir.chdir() + so = Status() wf = pe.Workflow(name='test', base_dir=tmpdir.strpath) f_node = pe.Node(niu.Function(function=bad_func, input_names=[], @@ -65,6 +69,8 @@ def test_callback_exception(tmpdir): assert so.statuses[1][1] == 'exception' def test_callback_multiproc_normal(tmpdir): + tmpdir.chdir() + so = Status() wf = pe.Workflow(name='test', base_dir=tmpdir.strpath) f_node = pe.Node(niu.Function(function=func, input_names=[], @@ -84,11 +90,13 @@ def test_callback_multiproc_exception(tmpdir): tmpdir.chdir() so = Status() - wf = pe.Workflow(name='test') + wf = pe.Workflow(name='test', base_dir=tmpdir.strpath) f_node = pe.Node(niu.Function(function=bad_func, input_names=[], output_names=[]), name='f_node') wf.add_nodes([f_node]) + wf.config['execution'] = {'crashdump_dir': wf.base_dir} + try: wf.run(plugin='MultiProc', plugin_args={'status_callback': so.callback}) diff --git a/nipype/interfaces/tests/realign_json.json b/nipype/testing/data/realign_json.json similarity index 100% rename from nipype/interfaces/tests/realign_json.json rename to nipype/testing/data/realign_json.json diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py index 16eabbb69c..d721b740a9 100644 --- a/nipype/utils/filemanip.py +++ b/nipype/utils/filemanip.py @@ -8,7 +8,7 @@ import sys import pickle -import subprocess +import subprocess as sp import gzip import hashlib import locale @@ -24,8 +24,6 @@ from .. import logging, config from .misc import is_container -from ..interfaces.traits_extension import isdefined - from future import standard_library standard_library.install_aliases() @@ -93,6 +91,7 @@ def split_filename(fname): return pth, fname, ext + def to_str(value): """ Manipulates ordered dicts before they are hashed (Py2/3 compat.) @@ -104,6 +103,7 @@ def to_str(value): retval = to_str_py27(value) return retval + def to_str_py27(value): """ Encode dictionary for python 2 @@ -121,7 +121,7 @@ def to_str_py27(value): venc = to_str_py27(val) if venc.startswith(("u'", 'u"')): venc = venc[1:] - retval+= entry(kenc, venc) + retval += entry(kenc, venc) retval += '}' return retval @@ -148,6 +148,7 @@ def to_str_py27(value): retval = retval[1:] return retval + def fname_presuffix(fname, prefix='', suffix='', newpath=None, use_ext=True): """Manipulates path and name of input filename @@ -174,11 +175,17 @@ def fname_presuffix(fname, prefix='', suffix='', newpath=None, use_ext=True): >>> fname_presuffix(fname,'pre','post','/tmp') '/tmp/prefoopost.nii.gz' + >>> from nipype.interfaces.base import Undefined + >>> fname_presuffix(fname, 'pre', 'post', Undefined) == fname_presuffix(fname, 'pre', 'post') + True + """ pth, fname, ext = split_filename(fname) if not use_ext: ext = '' - if newpath and isdefined(newpath): + + # No need for isdefined: bool(Undefined) evaluates to False + if newpath: pth = os.path.abspath(newpath) return os.path.join(pth, prefix + fname + suffix + ext) @@ -250,7 +257,7 @@ def _generate_cifs_table(): On systems without a ``mount`` command, or with no CIFS mounts, returns an empty list. """ - exit_code, output = subprocess.getstatusoutput("mount") + exit_code, output = sp.getstatusoutput("mount") # Not POSIX if exit_code != 0: return [] @@ -626,6 +633,7 @@ def savepkl(filename, record): pickle.dump(record, pkl_file) pkl_file.close() + rst_levels = ['=', '-', '~', '+'] @@ -663,3 +671,90 @@ def dist_is_editable(dist): if os.path.isfile(egg_link): return True return False + + +def which(cmd, env=None, pathext=None): + """ + Return the path to an executable which would be run if the given + cmd was called. If no cmd would be called, return ``None``. + + Code for Python < 3.3 is based on a code snippet from + http://orip.org/2009/08/python-checking-if-executable-exists-in.html + + """ + + if pathext is None: + pathext = os.getenv('PATHEXT', '').split(os.pathsep) + pathext.insert(0, '') + + path = os.getenv("PATH", os.defpath) + if env and 'PATH' in env: + path = env.get("PATH") + + if sys.version_info >= (3, 3): + for ext in pathext: + filename = shutil.which(cmd + ext, path=path) + if filename: + return filename + return None + + for ext in pathext: + extcmd = cmd + ext + for directory in path.split(os.pathsep): + filename = os.path.join(directory, extcmd) + if os.path.exists(filename): + return filename + return None + + +def get_dependencies(name, environ): + """Return library dependencies of a dynamically linked executable + + Uses otool on darwin, ldd on linux. Currently doesn't support windows. + + """ + if sys.platform == 'darwin': + proc = sp.Popen('otool -L `which %s`' % name, + stdout=sp.PIPE, + stderr=sp.PIPE, + shell=True, + env=environ) + elif 'linux' in sys.platform: + proc = sp.Popen('ldd `which %s`' % name, + stdout=sp.PIPE, + stderr=sp.PIPE, + shell=True, + env=environ) + else: + return 'Platform %s not supported' % sys.platform + o, e = proc.communicate() + return o.rstrip() + + +def canonicalize_env(env): + """Windows requires that environment be dicts with bytes as keys and values + This function converts any unicode entries for Windows only, returning the + dictionary untouched in other environments. + + Parameters + ---------- + env : dict + environment dictionary with unicode or bytes keys and values + + Returns + ------- + env : dict + Windows: environment dictionary with bytes keys and values + Other: untouched input ``env`` + """ + if os.name != 'nt': + return env + + out_env = {} + for key, val in env.items(): + if not isinstance(key, bytes): + key = key.encode('utf-8') + if not isinstance(val, bytes): + val = val.encode('utf-8') + out_env[key] = val + return out_env diff --git a/setup.py b/setup.py index 8bca901a4a..012efd2722 100755 --- a/setup.py +++ b/setup.py @@ -103,11 +103,11 @@ def main(): pjoin('testing', 'data', 'brukerdir', 'fid'), pjoin('testing', 'data', 'brukerdir', 'pdata', '1', '*'), pjoin('testing', 'data', 'ds005', '*'), + pjoin('testing', 'data', 'realign_json.json'), pjoin('workflows', 'data', '*'), pjoin('pipeline', 'engine', 'report_template.html'), pjoin('external', 'd3.js'), - pjoin('interfaces', 'script_templates', '*'), - pjoin('interfaces', 'tests', 'realign_json.json'), + pjoin('interfaces', 'fsl', 'model_templates', '*'), pjoin('interfaces', 'tests', 'use_resources'), 'pytest.ini', 'conftest.py',