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Merged
merged 31 commits into from
Dec 5, 2017
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7b2b350
move _exists_in_path to filemanip, and update
oesteban Nov 22, 2017
f6f97b6
use nipype's which in nifty package
oesteban Nov 22, 2017
a984f9f
ensure which call in ants/segmentation is correct)
oesteban Nov 22, 2017
8b56e12
ensure which calls in interfaces/base are correct
oesteban Nov 22, 2017
6676d22
cleaning up imports
oesteban Nov 22, 2017
d6a4b90
move from base with deprecation the load_template method
oesteban Nov 23, 2017
833d716
mv Multi- traits to traits_extension
oesteban Nov 23, 2017
82411ae
deep refactor of nipype.interfaces.base
oesteban Nov 23, 2017
d9c7f3d
fix final errors and wrong imports
oesteban Nov 23, 2017
d663e2f
test passing locally
oesteban Nov 23, 2017
8629376
remove some unicode prefixes
oesteban Nov 23, 2017
6949323
simplify fname_presuffix adding test
oesteban Nov 23, 2017
4e37641
run test in temp directory
oesteban Nov 23, 2017
672d1a0
add some docstrings
oesteban Nov 23, 2017
92a8ce5
fixup DictStrStr
oesteban Nov 26, 2017
3b83940
member could be function, and use filemanip.hash_infile
oesteban Nov 26, 2017
59ae74c
amend to previous commit
oesteban Nov 26, 2017
290eb77
minor fixes
oesteban Nov 26, 2017
67491af
Merge remote-tracking branch 'upstream/master' into ref/interface-base
oesteban Nov 29, 2017
e5bb856
Merge branch 'ref/interface-base' of github.com:oesteban/nipype into …
oesteban Nov 29, 2017
281c0e7
Merge remote-tracking branch 'upstream/master' into ref/interface-base
oesteban Dec 2, 2017
5758373
change dict_ when they are list_
oesteban Dec 2, 2017
b454961
set base_dir
oesteban Dec 3, 2017
98f5c31
move fsl.model templates
oesteban Dec 3, 2017
79c22ee
final fixes
oesteban Dec 3, 2017
9147408
move tests, update specs
oesteban Dec 4, 2017
86792b9
split huge test_base into pieces
oesteban Dec 4, 2017
15cd86f
fix imports in new tests
oesteban Dec 4, 2017
609c505
Merge branch 'ref/interface-base' of github.com:oesteban/nipype into …
oesteban Dec 4, 2017
50580aa
fix tests
oesteban Dec 4, 2017
5512779
update specs [skip ci]
oesteban Dec 5, 2017
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3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_ACompCor.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
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3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_AddCSVRow.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
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3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_ArtifactDetect.py
Original file line number Diff line number Diff line change
Expand Up @@ -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(),
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3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_CalculateMedian.py
Original file line number Diff line number Diff line change
Expand Up @@ -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(),
Expand Down
3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_ComputeDVARS.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
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3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_ComputeMeshWarp.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
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3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_CreateNifti.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
),
)
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3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_Distance.py
Original file line number Diff line number Diff line change
Expand Up @@ -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(),
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3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_FramewiseDisplacement.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
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3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_FuzzyOverlap.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
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3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_Gunzip.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_ICC.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_MeshWarpMaths.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_ModifyAffine.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_P2PDistance.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_PickAtlas.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_Similarity.py
Original file line number Diff line number Diff line change
Expand Up @@ -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(),
Expand Down
3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_SimpleThreshold.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_SpecifyModel.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_SpecifySPMModel.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_SpecifySparseModel.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_StimulusCorrelation.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_TCompCor.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_TVTKBaseInterface.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
),
)
Expand Down
3 changes: 2 additions & 1 deletion nipype/algorithms/tests/test_auto_WarpPoints.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
3 changes: 2 additions & 1 deletion nipype/interfaces/afni/tests/test_auto_ABoverlap.py
Original file line number Diff line number Diff line change
Expand Up @@ -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',
Expand Down
3 changes: 2 additions & 1 deletion nipype/interfaces/afni/tests/test_auto_AFNICommand.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
3 changes: 2 additions & 1 deletion nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py
Original file line number Diff line number Diff line change
Expand Up @@ -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',
Expand Down
3 changes: 2 additions & 1 deletion nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
3 changes: 2 additions & 1 deletion nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py
Original file line number Diff line number Diff line change
Expand Up @@ -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',
Expand Down
3 changes: 2 additions & 1 deletion nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py
Original file line number Diff line number Diff line change
Expand Up @@ -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',
Expand Down
3 changes: 2 additions & 1 deletion nipype/interfaces/afni/tests/test_auto_Allineate.py
Original file line number Diff line number Diff line change
Expand Up @@ -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',
Expand Down
3 changes: 2 additions & 1 deletion nipype/interfaces/afni/tests/test_auto_AutoTLRC.py
Original file line number Diff line number Diff line change
Expand Up @@ -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',
Expand Down
3 changes: 2 additions & 1 deletion nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py
Original file line number Diff line number Diff line change
Expand Up @@ -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',
Expand Down
3 changes: 2 additions & 1 deletion nipype/interfaces/afni/tests/test_auto_Autobox.py
Original file line number Diff line number Diff line change
Expand Up @@ -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',
Expand Down
3 changes: 2 additions & 1 deletion nipype/interfaces/afni/tests/test_auto_Automask.py
Original file line number Diff line number Diff line change
Expand Up @@ -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',
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3 changes: 2 additions & 1 deletion nipype/interfaces/afni/tests/test_auto_Axialize.py
Original file line number Diff line number Diff line change
Expand Up @@ -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',
Expand Down
3 changes: 2 additions & 1 deletion nipype/interfaces/afni/tests/test_auto_Bandpass.py
Original file line number Diff line number Diff line change
Expand Up @@ -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',
Expand Down
3 changes: 2 additions & 1 deletion nipype/interfaces/afni/tests/test_auto_BlurInMask.py
Original file line number Diff line number Diff line change
Expand Up @@ -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',
Expand Down
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