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Merge pull request #2618 from effigies/deprecations
MAINT: Remove ignore_exception and terminal_output traits from input specs
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‎.travis.yml

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@@ -54,6 +54,7 @@ before_install:
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fi;
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- travis_retry pip install -r requirements.txt
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- travis_retry pip install grabbit==0.1.2
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- travis_retry git clone https://github.com/INCF/pybids.git ${HOME}/pybids &&
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pip install -e ${HOME}/pybids
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‎docker/generate_dockerfiles.sh

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@@ -106,8 +106,10 @@ function generate_main_dockerfile() {
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pandas psutil scikit-learn scipy traits=4.6.0' \
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pip_opts="-e" \
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pip_install="/src/nipype[all]" \
109+
--miniconda env_name=neuro \
110+
pip_install="grabbit==0.1.2" \
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--run-bash "mkdir -p /src/pybids
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&& curl -sSL --retry 5 https://github.com/INCF/pybids/tarball/master
112+
&& curl -sSL --retry 5 https://github.com/INCF/pybids/tarball/0.5.1
111113
| tar -xz -C /src/pybids --strip-components 1
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&& source activate neuro
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&& pip install --no-cache-dir -e /src/pybids" \

‎nipype/algorithms/tests/test_auto_ACompCor.py

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@@ -8,11 +8,6 @@ def test_ACompCor_inputs():
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components_file=dict(usedefault=True, ),
99
header_prefix=dict(),
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high_pass_cutoff=dict(usedefault=True, ),
11-
ignore_exception=dict(
12-
deprecated='1.0.0',
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nohash=True,
14-
usedefault=True,
15-
),
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ignore_initial_volumes=dict(usedefault=True, ),
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mask_files=dict(),
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mask_index=dict(

‎nipype/algorithms/tests/test_auto_ActivationCount.py

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@@ -5,11 +5,6 @@
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def test_ActivationCount_inputs():
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input_map = dict(
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ignore_exception=dict(
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deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
),
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in_files=dict(mandatory=True, ),
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threshold=dict(mandatory=True, ),
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)

‎nipype/algorithms/tests/test_auto_AddCSVRow.py

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@@ -6,11 +6,6 @@
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def test_AddCSVRow_inputs():
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input_map = dict(
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_outputs=dict(usedefault=True, ),
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ignore_exception=dict(
10-
deprecated='1.0.0',
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nohash=True,
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usedefault=True,
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),
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in_file=dict(mandatory=True, ),
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)
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inputs = AddCSVRow.input_spec()

‎nipype/algorithms/tests/test_auto_ArtifactDetect.py

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@@ -7,11 +7,6 @@ def test_ArtifactDetect_inputs():
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input_map = dict(
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bound_by_brainmask=dict(usedefault=True, ),
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global_threshold=dict(usedefault=True, ),
10-
ignore_exception=dict(
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deprecated='1.0.0',
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nohash=True,
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usedefault=True,
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),
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intersect_mask=dict(usedefault=True, ),
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mask_file=dict(),
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mask_threshold=dict(),

‎nipype/algorithms/tests/test_auto_CalculateMedian.py

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@@ -5,11 +5,6 @@
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def test_CalculateMedian_inputs():
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input_map = dict(
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ignore_exception=dict(
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deprecated='1.0.0',
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nohash=True,
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usedefault=True,
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),
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in_files=dict(),
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median_file=dict(),
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median_per_file=dict(usedefault=True, ),

‎nipype/algorithms/tests/test_auto_ComputeDVARS.py

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@@ -8,11 +8,6 @@ def test_ComputeDVARS_inputs():
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figdpi=dict(usedefault=True, ),
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figformat=dict(usedefault=True, ),
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figsize=dict(usedefault=True, ),
11-
ignore_exception=dict(
12-
deprecated='1.0.0',
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nohash=True,
14-
usedefault=True,
15-
),
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in_file=dict(mandatory=True, ),
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in_mask=dict(mandatory=True, ),
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intensity_normalization=dict(usedefault=True, ),

‎nipype/algorithms/tests/test_auto_ComputeMeshWarp.py

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@@ -5,11 +5,6 @@
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def test_ComputeMeshWarp_inputs():
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input_map = dict(
8-
ignore_exception=dict(
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deprecated='1.0.0',
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nohash=True,
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usedefault=True,
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),
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metric=dict(usedefault=True, ),
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out_file=dict(usedefault=True, ),
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out_warp=dict(usedefault=True, ),

‎nipype/algorithms/tests/test_auto_CreateNifti.py

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@@ -8,11 +8,6 @@ def test_CreateNifti_inputs():
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affine=dict(),
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data_file=dict(mandatory=True, ),
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header_file=dict(mandatory=True, ),
11-
ignore_exception=dict(
12-
deprecated='1.0.0',
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nohash=True,
14-
usedefault=True,
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),
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)
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inputs = CreateNifti.input_spec()
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‎nipype/algorithms/tests/test_auto_Distance.py

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@@ -5,11 +5,6 @@
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def test_Distance_inputs():
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input_map = dict(
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ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
),
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mask_volume=dict(),
149
method=dict(usedefault=True, ),
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volume1=dict(mandatory=True, ),

‎nipype/algorithms/tests/test_auto_FramewiseDisplacement.py

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Original file line numberDiff line numberDiff line change
@@ -7,11 +7,6 @@ def test_FramewiseDisplacement_inputs():
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input_map = dict(
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figdpi=dict(usedefault=True, ),
99
figsize=dict(usedefault=True, ),
10-
ignore_exception=dict(
11-
deprecated='1.0.0',
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nohash=True,
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usedefault=True,
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),
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in_file=dict(mandatory=True, ),
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normalize=dict(usedefault=True, ),
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out_figure=dict(usedefault=True, ),

‎nipype/algorithms/tests/test_auto_FuzzyOverlap.py

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@@ -5,11 +5,6 @@
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def test_FuzzyOverlap_inputs():
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input_map = dict(
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ignore_exception=dict(
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deprecated='1.0.0',
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nohash=True,
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usedefault=True,
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),
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in_mask=dict(),
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in_ref=dict(mandatory=True, ),
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in_tst=dict(mandatory=True, ),

‎nipype/algorithms/tests/test_auto_Gunzip.py

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@@ -4,14 +4,7 @@
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55

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def test_Gunzip_inputs():
7-
input_map = dict(
8-
ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
),
13-
in_file=dict(mandatory=True, ),
14-
)
7+
input_map = dict(in_file=dict(mandatory=True, ), )
158
inputs = Gunzip.input_spec()
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1710
for key, metadata in list(input_map.items()):

‎nipype/algorithms/tests/test_auto_ICC.py

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@@ -5,11 +5,6 @@
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def test_ICC_inputs():
77
input_map = dict(
8-
ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
),
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mask=dict(mandatory=True, ),
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subjects_sessions=dict(mandatory=True, ),
1510
)

‎nipype/algorithms/tests/test_auto_MeshWarpMaths.py

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@@ -6,11 +6,6 @@
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def test_MeshWarpMaths_inputs():
77
input_map = dict(
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float_trait=dict(),
9-
ignore_exception=dict(
10-
deprecated='1.0.0',
11-
nohash=True,
12-
usedefault=True,
13-
),
149
in_surf=dict(mandatory=True, ),
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operation=dict(usedefault=True, ),
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operator=dict(

‎nipype/algorithms/tests/test_auto_ModifyAffine.py

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@@ -5,11 +5,6 @@
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def test_ModifyAffine_inputs():
77
input_map = dict(
8-
ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
),
138
transformation_matrix=dict(usedefault=True, ),
149
volumes=dict(mandatory=True, ),
1510
)

‎nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py

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@@ -4,14 +4,7 @@
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def test_NonSteadyStateDetector_inputs():
7-
input_map = dict(
8-
ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
),
13-
in_file=dict(mandatory=True, ),
14-
)
7+
input_map = dict(in_file=dict(mandatory=True, ), )
158
inputs = NonSteadyStateDetector.input_spec()
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for key, metadata in list(input_map.items()):

‎nipype/algorithms/tests/test_auto_P2PDistance.py

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def test_P2PDistance_inputs():
77
input_map = dict(
8-
ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
),
138
metric=dict(usedefault=True, ),
149
out_file=dict(usedefault=True, ),
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out_warp=dict(usedefault=True, ),

‎nipype/algorithms/tests/test_auto_PickAtlas.py

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@@ -8,11 +8,6 @@ def test_PickAtlas_inputs():
88
atlas=dict(mandatory=True, ),
99
dilation_size=dict(usedefault=True, ),
1010
hemi=dict(usedefault=True, ),
11-
ignore_exception=dict(
12-
deprecated='1.0.0',
13-
nohash=True,
14-
usedefault=True,
15-
),
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labels=dict(mandatory=True, ),
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output_file=dict(),
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)

‎nipype/algorithms/tests/test_auto_Similarity.py

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def test_Similarity_inputs():
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input_map = dict(
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ignore_exception=dict(
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deprecated='1.0.0',
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nohash=True,
11-
usedefault=True,
12-
),
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mask1=dict(),
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mask2=dict(),
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metric=dict(usedefault=True, ),

‎nipype/algorithms/tests/test_auto_SimpleThreshold.py

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def test_SimpleThreshold_inputs():
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input_map = dict(
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ignore_exception=dict(
9-
deprecated='1.0.0',
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nohash=True,
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usedefault=True,
12-
),
138
threshold=dict(mandatory=True, ),
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volumes=dict(mandatory=True, ),
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)

‎nipype/algorithms/tests/test_auto_SpecifyModel.py

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@@ -14,11 +14,6 @@ def test_SpecifyModel_inputs():
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mandatory=True,
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),
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high_pass_filter_cutoff=dict(mandatory=True, ),
17-
ignore_exception=dict(
18-
deprecated='1.0.0',
19-
nohash=True,
20-
usedefault=True,
21-
),
2217
input_units=dict(mandatory=True, ),
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outlier_files=dict(copyfile=False, ),
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parameter_source=dict(usedefault=True, ),

‎nipype/algorithms/tests/test_auto_SpecifySPMModel.py

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@@ -15,11 +15,6 @@ def test_SpecifySPMModel_inputs():
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mandatory=True,
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),
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high_pass_filter_cutoff=dict(mandatory=True, ),
18-
ignore_exception=dict(
19-
deprecated='1.0.0',
20-
nohash=True,
21-
usedefault=True,
22-
),
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input_units=dict(mandatory=True, ),
2419
outlier_files=dict(copyfile=False, ),
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output_units=dict(usedefault=True, ),

‎nipype/algorithms/tests/test_auto_SpecifySparseModel.py

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@@ -14,11 +14,6 @@ def test_SpecifySparseModel_inputs():
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mandatory=True,
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),
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high_pass_filter_cutoff=dict(mandatory=True, ),
17-
ignore_exception=dict(
18-
deprecated='1.0.0',
19-
nohash=True,
20-
usedefault=True,
21-
),
2217
input_units=dict(mandatory=True, ),
2318
model_hrf=dict(),
2419
outlier_files=dict(copyfile=False, ),

‎nipype/algorithms/tests/test_auto_StimulusCorrelation.py

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def test_StimulusCorrelation_inputs():
77
input_map = dict(
88
concatenated_design=dict(mandatory=True, ),
9-
ignore_exception=dict(
10-
deprecated='1.0.0',
11-
nohash=True,
12-
usedefault=True,
13-
),
149
intensity_values=dict(mandatory=True, ),
1510
realignment_parameters=dict(mandatory=True, ),
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spm_mat_file=dict(mandatory=True, ),

‎nipype/algorithms/tests/test_auto_TCompCor.py

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@@ -8,11 +8,6 @@ def test_TCompCor_inputs():
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components_file=dict(usedefault=True, ),
99
header_prefix=dict(),
1010
high_pass_cutoff=dict(usedefault=True, ),
11-
ignore_exception=dict(
12-
deprecated='1.0.0',
13-
nohash=True,
14-
usedefault=True,
15-
),
1611
ignore_initial_volumes=dict(usedefault=True, ),
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mask_files=dict(),
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mask_index=dict(

‎nipype/algorithms/tests/test_auto_TVTKBaseInterface.py

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@@ -4,12 +4,7 @@
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def test_TVTKBaseInterface_inputs():
7-
input_map = dict(
8-
ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
), )
7+
input_map = dict()
138
inputs = TVTKBaseInterface.input_spec()
149

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for key, metadata in list(input_map.items()):

‎nipype/algorithms/tests/test_auto_WarpPoints.py

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def test_WarpPoints_inputs():
77
input_map = dict(
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ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
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),
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interp=dict(
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mandatory=True,
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usedefault=True,

‎nipype/interfaces/afni/preprocess.py

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@@ -1811,12 +1811,6 @@ class ROIStatsInputSpec(CommandLineInputSpec):
18111811
argstr='-mask_f2short',
18121812
position=2)
18131813
quiet = traits.Bool(desc='execute quietly', argstr='-quiet', position=1)
1814-
terminal_output = traits.Enum(
1815-
'allatonce',
1816-
deprecated='1.0.0',
1817-
desc='Control terminal output:`allatonce` - waits till command is '
1818-
'finished to display output',
1819-
nohash=True)
18201814

18211815

18221816
class ROIStatsOutputSpec(TraitedSpec):

‎nipype/interfaces/afni/tests/test_auto_ABoverlap.py

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@@ -10,11 +10,6 @@ def test_ABoverlap_inputs():
1010
nohash=True,
1111
usedefault=True,
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),
13-
ignore_exception=dict(
14-
deprecated='1.0.0',
15-
nohash=True,
16-
usedefault=True,
17-
),
1813
in_file_a=dict(
1914
argstr='%s',
2015
copyfile=False,
@@ -38,10 +33,6 @@ def test_ABoverlap_inputs():
3833
),
3934
outputtype=dict(),
4035
quiet=dict(argstr='-quiet', ),
41-
terminal_output=dict(
42-
deprecated='1.0.0',
43-
nohash=True,
44-
),
4536
verb=dict(argstr='-verb', ),
4637
)
4738
inputs = ABoverlap.input_spec()

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