nipy · effigies · Jul 2, 2018 · May 25, 2018 · May 26, 2018 · Jun 16, 2018
diff --git a/.travis.yml b/.travis.yml
@@ -50,6 +50,7 @@ before_install:
 - conda config --add channels conda-forge
 - travis_retry conda install -y python=${TRAVIS_PYTHON_VERSION} icu
 - travis_retry pip install -r requirements.txt
+- travis_retry pip install grabbit==0.1.2
 - travis_retry git clone https://github.com/INCF/pybids.git ${HOME}/pybids &&
   pip install -e ${HOME}/pybids
 - travis_retry pip install codecov

diff --git a/docker/generate_dockerfiles.sh b/docker/generate_dockerfiles.sh
@@ -106,8 +106,10 @@ function generate_main_dockerfile() {
                              pandas psutil scikit-learn scipy traits=4.6.0' \
               pip_opts="-e" \
               pip_install="/src/nipype[all]" \
+  --miniconda env_name=neuro \
+              pip_install="grabbit==0.1.2" \
   --run-bash "mkdir -p /src/pybids
-         && curl -sSL --retry 5 https://github.com/INCF/pybids/tarball/master
+         && curl -sSL --retry 5 https://github.com/INCF/pybids/tarball/0.5.1
          | tar -xz -C /src/pybids --strip-components 1
          && source activate neuro
          && pip install --no-cache-dir -e /src/pybids" \

diff --git a/nipype/algorithms/tests/test_auto_ACompCor.py b/nipype/algorithms/tests/test_auto_ACompCor.py
@@ -8,11 +8,6 @@ def test_ACompCor_inputs():
         components_file=dict(usedefault=True, ),
         header_prefix=dict(),
         high_pass_cutoff=dict(usedefault=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         ignore_initial_volumes=dict(usedefault=True, ),
         mask_files=dict(),
         mask_index=dict(

diff --git a/nipype/algorithms/tests/test_auto_ActivationCount.py b/nipype/algorithms/tests/test_auto_ActivationCount.py
@@ -5,11 +5,6 @@
 
 def test_ActivationCount_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         in_files=dict(mandatory=True, ),
         threshold=dict(mandatory=True, ),
     )

diff --git a/nipype/algorithms/tests/test_auto_AddCSVRow.py b/nipype/algorithms/tests/test_auto_AddCSVRow.py
@@ -6,11 +6,6 @@
 def test_AddCSVRow_inputs():
     input_map = dict(
         _outputs=dict(usedefault=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         in_file=dict(mandatory=True, ),
     )
     inputs = AddCSVRow.input_spec()

diff --git a/nipype/algorithms/tests/test_auto_ArtifactDetect.py b/nipype/algorithms/tests/test_auto_ArtifactDetect.py
@@ -7,11 +7,6 @@ def test_ArtifactDetect_inputs():
     input_map = dict(
         bound_by_brainmask=dict(usedefault=True, ),
         global_threshold=dict(usedefault=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         intersect_mask=dict(usedefault=True, ),
         mask_file=dict(),
         mask_threshold=dict(),

diff --git a/nipype/algorithms/tests/test_auto_CalculateMedian.py b/nipype/algorithms/tests/test_auto_CalculateMedian.py
@@ -5,11 +5,6 @@
 
 def test_CalculateMedian_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         in_files=dict(),
         median_file=dict(),
         median_per_file=dict(usedefault=True, ),

diff --git a/nipype/algorithms/tests/test_auto_ComputeDVARS.py b/nipype/algorithms/tests/test_auto_ComputeDVARS.py
@@ -8,11 +8,6 @@ def test_ComputeDVARS_inputs():
         figdpi=dict(usedefault=True, ),
         figformat=dict(usedefault=True, ),
         figsize=dict(usedefault=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         in_file=dict(mandatory=True, ),
         in_mask=dict(mandatory=True, ),
         intensity_normalization=dict(usedefault=True, ),

diff --git a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py
@@ -5,11 +5,6 @@
 
 def test_ComputeMeshWarp_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         metric=dict(usedefault=True, ),
         out_file=dict(usedefault=True, ),
         out_warp=dict(usedefault=True, ),

diff --git a/nipype/algorithms/tests/test_auto_CreateNifti.py b/nipype/algorithms/tests/test_auto_CreateNifti.py
@@ -8,11 +8,6 @@ def test_CreateNifti_inputs():
         affine=dict(),
         data_file=dict(mandatory=True, ),
         header_file=dict(mandatory=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
     )
     inputs = CreateNifti.input_spec()
 

diff --git a/nipype/algorithms/tests/test_auto_Distance.py b/nipype/algorithms/tests/test_auto_Distance.py
@@ -5,11 +5,6 @@
 
 def test_Distance_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         mask_volume=dict(),
         method=dict(usedefault=True, ),
         volume1=dict(mandatory=True, ),

diff --git a/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py b/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py
@@ -7,11 +7,6 @@ def test_FramewiseDisplacement_inputs():
     input_map = dict(
         figdpi=dict(usedefault=True, ),
         figsize=dict(usedefault=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         in_file=dict(mandatory=True, ),
         normalize=dict(usedefault=True, ),
         out_figure=dict(usedefault=True, ),

diff --git a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py
@@ -5,11 +5,6 @@
 
 def test_FuzzyOverlap_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         in_mask=dict(),
         in_ref=dict(mandatory=True, ),
         in_tst=dict(mandatory=True, ),

diff --git a/nipype/algorithms/tests/test_auto_Gunzip.py b/nipype/algorithms/tests/test_auto_Gunzip.py
@@ -4,14 +4,7 @@
 
 
 def test_Gunzip_inputs():
-    input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
-        in_file=dict(mandatory=True, ),
-    )
+    input_map = dict(in_file=dict(mandatory=True, ), )
     inputs = Gunzip.input_spec()
 
     for key, metadata in list(input_map.items()):

diff --git a/nipype/algorithms/tests/test_auto_ICC.py b/nipype/algorithms/tests/test_auto_ICC.py
@@ -5,11 +5,6 @@
 
 def test_ICC_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         mask=dict(mandatory=True, ),
         subjects_sessions=dict(mandatory=True, ),
     )

diff --git a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py
@@ -6,11 +6,6 @@
 def test_MeshWarpMaths_inputs():
     input_map = dict(
         float_trait=dict(),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         in_surf=dict(mandatory=True, ),
         operation=dict(usedefault=True, ),
         operator=dict(

diff --git a/nipype/algorithms/tests/test_auto_ModifyAffine.py b/nipype/algorithms/tests/test_auto_ModifyAffine.py
@@ -5,11 +5,6 @@
 
 def test_ModifyAffine_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         transformation_matrix=dict(usedefault=True, ),
         volumes=dict(mandatory=True, ),
     )

diff --git a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py
@@ -4,14 +4,7 @@
 
 
 def test_NonSteadyStateDetector_inputs():
-    input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
-        in_file=dict(mandatory=True, ),
-    )
+    input_map = dict(in_file=dict(mandatory=True, ), )
     inputs = NonSteadyStateDetector.input_spec()
 
     for key, metadata in list(input_map.items()):

diff --git a/nipype/algorithms/tests/test_auto_P2PDistance.py b/nipype/algorithms/tests/test_auto_P2PDistance.py
@@ -5,11 +5,6 @@
 
 def test_P2PDistance_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         metric=dict(usedefault=True, ),
         out_file=dict(usedefault=True, ),
         out_warp=dict(usedefault=True, ),

diff --git a/nipype/algorithms/tests/test_auto_PickAtlas.py b/nipype/algorithms/tests/test_auto_PickAtlas.py
@@ -8,11 +8,6 @@ def test_PickAtlas_inputs():
         atlas=dict(mandatory=True, ),
         dilation_size=dict(usedefault=True, ),
         hemi=dict(usedefault=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         labels=dict(mandatory=True, ),
         output_file=dict(),
     )

diff --git a/nipype/algorithms/tests/test_auto_Similarity.py b/nipype/algorithms/tests/test_auto_Similarity.py
@@ -5,11 +5,6 @@
 
 def test_Similarity_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         mask1=dict(),
         mask2=dict(),
         metric=dict(usedefault=True, ),

diff --git a/nipype/algorithms/tests/test_auto_SimpleThreshold.py b/nipype/algorithms/tests/test_auto_SimpleThreshold.py
@@ -5,11 +5,6 @@
 
 def test_SimpleThreshold_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         threshold=dict(mandatory=True, ),
         volumes=dict(mandatory=True, ),
     )

diff --git a/nipype/algorithms/tests/test_auto_SpecifyModel.py b/nipype/algorithms/tests/test_auto_SpecifyModel.py
@@ -14,11 +14,6 @@ def test_SpecifyModel_inputs():
             mandatory=True,
         ),
         high_pass_filter_cutoff=dict(mandatory=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         input_units=dict(mandatory=True, ),
         outlier_files=dict(copyfile=False, ),
         parameter_source=dict(usedefault=True, ),

diff --git a/nipype/algorithms/tests/test_auto_SpecifySPMModel.py b/nipype/algorithms/tests/test_auto_SpecifySPMModel.py
@@ -15,11 +15,6 @@ def test_SpecifySPMModel_inputs():
             mandatory=True,
         ),
         high_pass_filter_cutoff=dict(mandatory=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         input_units=dict(mandatory=True, ),
         outlier_files=dict(copyfile=False, ),
         output_units=dict(usedefault=True, ),

diff --git a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py
@@ -14,11 +14,6 @@ def test_SpecifySparseModel_inputs():
             mandatory=True,
         ),
         high_pass_filter_cutoff=dict(mandatory=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         input_units=dict(mandatory=True, ),
         model_hrf=dict(),
         outlier_files=dict(copyfile=False, ),

diff --git a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py
@@ -6,11 +6,6 @@
 def test_StimulusCorrelation_inputs():
     input_map = dict(
         concatenated_design=dict(mandatory=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         intensity_values=dict(mandatory=True, ),
         realignment_parameters=dict(mandatory=True, ),
         spm_mat_file=dict(mandatory=True, ),

diff --git a/nipype/algorithms/tests/test_auto_TCompCor.py b/nipype/algorithms/tests/test_auto_TCompCor.py
@@ -8,11 +8,6 @@ def test_TCompCor_inputs():
         components_file=dict(usedefault=True, ),
         header_prefix=dict(),
         high_pass_cutoff=dict(usedefault=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         ignore_initial_volumes=dict(usedefault=True, ),
         mask_files=dict(),
         mask_index=dict(

diff --git a/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py b/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py
@@ -4,12 +4,7 @@
 
 
 def test_TVTKBaseInterface_inputs():
-    input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ), )
+    input_map = dict()
     inputs = TVTKBaseInterface.input_spec()
 
     for key, metadata in list(input_map.items()):

diff --git a/nipype/algorithms/tests/test_auto_WarpPoints.py b/nipype/algorithms/tests/test_auto_WarpPoints.py
@@ -5,11 +5,6 @@
 
 def test_WarpPoints_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         interp=dict(
             mandatory=True,
             usedefault=True,

diff --git a/nipype/interfaces/afni/preprocess.py b/nipype/interfaces/afni/preprocess.py
@@ -1810,12 +1810,6 @@ class ROIStatsInputSpec(CommandLineInputSpec):
         argstr='-mask_f2short',
         position=2)
     quiet = traits.Bool(desc='execute quietly', argstr='-quiet', position=1)
-    terminal_output = traits.Enum(
-        'allatonce',
-        deprecated='1.0.0',
-        desc='Control terminal output:`allatonce` - waits till command is '
-        'finished to display output',
-        nohash=True)
 
 
 class ROIStatsOutputSpec(TraitedSpec):

diff --git a/nipype/interfaces/afni/tests/test_auto_ABoverlap.py b/nipype/interfaces/afni/tests/test_auto_ABoverlap.py
@@ -10,11 +10,6 @@ def test_ABoverlap_inputs():
             nohash=True,
             usedefault=True,
         ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         in_file_a=dict(
             argstr='%s',
             copyfile=False,
@@ -38,10 +33,6 @@ def test_ABoverlap_inputs():
         ),
         outputtype=dict(),
         quiet=dict(argstr='-quiet', ),
-        terminal_output=dict(
-            deprecated='1.0.0',
-            nohash=True,
-        ),
         verb=dict(argstr='-verb', ),
     )
     inputs = ABoverlap.input_spec()