Merge pull request #2618 from effigies/deprecations

MAINT: Remove ignore_exception and terminal_output traits from input specs

Author: effigies

.travis.yml

@@ -54,6 +54,7 @@ before_install:
   fi;
 
 - 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
 

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" \

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(

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, ),
     )

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()

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(),

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, ),

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, ),

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, ),

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()