Merge pull request #1813 from effigies/issue1348

BF: Run `make specs` with CWD in PYTHONPATH

Author: satra

Makefile

@@ -71,7 +71,7 @@ html:
 
 specs:
 	@echo "Checking specs and autogenerating spec tests"
-	python tools/checkspecs.py
+	env PYTHONPATH=".:$(PYTHONPATH)" python tools/checkspecs.py
 
 check: check-before-commit # just a shortcut
 check-before-commit: specs trailing-spaces html test

nipype/algorithms/tests/test_auto_ACompCor.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..confounds import ACompCor
 
 

nipype/algorithms/tests/test_auto_AddCSVColumn.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..misc import AddCSVColumn
 
 

nipype/algorithms/tests/test_auto_AddCSVRow.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..misc import AddCSVRow
 
 

nipype/algorithms/tests/test_auto_AddNoise.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..misc import AddNoise
 
 

nipype/algorithms/tests/test_auto_ArtifactDetect.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..rapidart import ArtifactDetect
 
 
@@ -16,7 +17,7 @@ def test_ArtifactDetect_inputs():
     mask_type=dict(mandatory=True,
     ),
     norm_threshold=dict(mandatory=True,
-    xor=[u'rotation_threshold', u'translation_threshold'],
+    xor=['rotation_threshold', 'translation_threshold'],
     ),
     parameter_source=dict(mandatory=True,
     ),
@@ -27,18 +28,18 @@ def test_ArtifactDetect_inputs():
     realignment_parameters=dict(mandatory=True,
     ),
     rotation_threshold=dict(mandatory=True,
-    xor=[u'norm_threshold'],
+    xor=['norm_threshold'],
     ),
     save_plot=dict(usedefault=True,
     ),
     translation_threshold=dict(mandatory=True,
-    xor=[u'norm_threshold'],
+    xor=['norm_threshold'],
     ),
     use_differences=dict(maxlen=2,
     minlen=2,
     usedefault=True,
     ),
-    use_norm=dict(requires=[u'norm_threshold'],
+    use_norm=dict(requires=['norm_threshold'],
     usedefault=True,
     ),
     zintensity_threshold=dict(mandatory=True,

nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..misc import CalculateNormalizedMoments
 
 

nipype/algorithms/tests/test_auto_CompCor.py

@@ -0,0 +1,37 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..confounds import CompCor
+
+
+def test_CompCor_inputs():
+    input_map = dict(components_file=dict(usedefault=True,
+    ),
+    header=dict(),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    mask_file=dict(),
+    num_components=dict(usedefault=True,
+    ),
+    realigned_file=dict(mandatory=True,
+    ),
+    regress_poly_degree=dict(usedefault=True,
+    ),
+    use_regress_poly=dict(usedefault=True,
+    ),
+    )
+    inputs = CompCor.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_CompCor_outputs():
+    output_map = dict(components_file=dict(),
+    )
+    outputs = CompCor.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/algorithms/tests/test_auto_ComputeDVARS.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..confounds import ComputeDVARS
 
 

nipype/algorithms/tests/test_auto_ComputeMeshWarp.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..mesh import ComputeMeshWarp
 
 

nipype/algorithms/tests/test_auto_CreateNifti.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..misc import CreateNifti
 
 

nipype/algorithms/tests/test_auto_Distance.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..misc import Distance
 
 

nipype/algorithms/tests/test_auto_ErrorMap.py

@@ -0,0 +1,35 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..metrics import ErrorMap
+
+
+def test_ErrorMap_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_ref=dict(mandatory=True,
+    ),
+    in_tst=dict(mandatory=True,
+    ),
+    mask=dict(),
+    metric=dict(mandatory=True,
+    usedefault=True,
+    ),
+    out_map=dict(),
+    )
+    inputs = ErrorMap.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_ErrorMap_outputs():
+    output_map = dict(distance=dict(),
+    out_map=dict(),
+    )
+    outputs = ErrorMap.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/algorithms/tests/test_auto_FramewiseDisplacement.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..confounds import FramewiseDisplacement
 
 

nipype/algorithms/tests/test_auto_FuzzyOverlap.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..misc import FuzzyOverlap
 
 

nipype/algorithms/tests/test_auto_Gunzip.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..misc import Gunzip
 
 

nipype/algorithms/tests/test_auto_ICC.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..icc import ICC
 
 

nipype/algorithms/tests/test_auto_Matlab2CSV.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..misc import Matlab2CSV
 
 

nipype/algorithms/tests/test_auto_MergeCSVFiles.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..misc import MergeCSVFiles
 
 

nipype/algorithms/tests/test_auto_MergeROIs.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..misc import MergeROIs
 
 

nipype/algorithms/tests/test_auto_MeshWarpMaths.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..mesh import MeshWarpMaths
 
 

nipype/algorithms/tests/test_auto_ModifyAffine.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..misc import ModifyAffine
 
 

nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..misc import NormalizeProbabilityMapSet
 
 

nipype/algorithms/tests/test_auto_Overlap.py

@@ -0,0 +1,47 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..misc import Overlap
+
+
+def test_Overlap_inputs():
+    input_map = dict(bg_overlap=dict(mandatory=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    mask_volume=dict(),
+    out_file=dict(usedefault=True,
+    ),
+    vol_units=dict(mandatory=True,
+    usedefault=True,
+    ),
+    volume1=dict(mandatory=True,
+    ),
+    volume2=dict(mandatory=True,
+    ),
+    weighting=dict(usedefault=True,
+    ),
+    )
+    inputs = Overlap.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_Overlap_outputs():
+    output_map = dict(dice=dict(),
+    diff_file=dict(),
+    jaccard=dict(),
+    labels=dict(),
+    roi_di=dict(),
+    roi_ji=dict(),
+    roi_voldiff=dict(),
+    volume_difference=dict(),
+    )
+    outputs = Overlap.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/algorithms/tests/test_auto_P2PDistance.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..mesh import P2PDistance
 
 

nipype/algorithms/tests/test_auto_PickAtlas.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..misc import PickAtlas
 
 

nipype/algorithms/tests/test_auto_Similarity.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..metrics import Similarity
 
 

nipype/algorithms/tests/test_auto_SimpleThreshold.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..misc import SimpleThreshold
 
 

nipype/algorithms/tests/test_auto_SpecifyModel.py

@@ -1,10 +1,11 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..modelgen import SpecifyModel
 
 
 def test_SpecifyModel_inputs():
     input_map = dict(event_files=dict(mandatory=True,
-    xor=[u'subject_info', u'event_files'],
+    xor=['subject_info', 'event_files'],
     ),
     functional_runs=dict(copyfile=False,
     mandatory=True,
@@ -21,7 +22,7 @@ def test_SpecifyModel_inputs():
     realignment_parameters=dict(copyfile=False,
     ),
     subject_info=dict(mandatory=True,
-    xor=[u'subject_info', u'event_files'],
+    xor=['subject_info', 'event_files'],
     ),
     time_repetition=dict(mandatory=True,
     ),

nipype/algorithms/tests/test_auto_SpecifySPMModel.py

@@ -1,12 +1,13 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..modelgen import SpecifySPMModel
 
 
 def test_SpecifySPMModel_inputs():
     input_map = dict(concatenate_runs=dict(usedefault=True,
     ),
     event_files=dict(mandatory=True,
-    xor=[u'subject_info', u'event_files'],
+    xor=['subject_info', 'event_files'],
     ),
     functional_runs=dict(copyfile=False,
     mandatory=True,
@@ -25,7 +26,7 @@ def test_SpecifySPMModel_inputs():
     realignment_parameters=dict(copyfile=False,
     ),
     subject_info=dict(mandatory=True,
-    xor=[u'subject_info', u'event_files'],
+    xor=['subject_info', 'event_files'],
     ),
     time_repetition=dict(mandatory=True,
     ),

nipype/algorithms/tests/test_auto_SpecifySparseModel.py

@@ -1,10 +1,11 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..modelgen import SpecifySparseModel
 
 
 def test_SpecifySparseModel_inputs():
     input_map = dict(event_files=dict(mandatory=True,
-    xor=[u'subject_info', u'event_files'],
+    xor=['subject_info', 'event_files'],
     ),
     functional_runs=dict(copyfile=False,
     mandatory=True,
@@ -29,13 +30,13 @@ def test_SpecifySparseModel_inputs():
     stimuli_as_impulses=dict(usedefault=True,
     ),
     subject_info=dict(mandatory=True,
-    xor=[u'subject_info', u'event_files'],
+    xor=['subject_info', 'event_files'],
     ),
     time_acquisition=dict(mandatory=True,
     ),
     time_repetition=dict(mandatory=True,
     ),
-    use_temporal_deriv=dict(requires=[u'model_hrf'],
+    use_temporal_deriv=dict(requires=['model_hrf'],
     ),
     volumes_in_cluster=dict(usedefault=True,
     ),

nipype/algorithms/tests/test_auto_SplitROIs.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..misc import SplitROIs
 
 

nipype/algorithms/tests/test_auto_StimulusCorrelation.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..rapidart import StimulusCorrelation
 
 

nipype/algorithms/tests/test_auto_TCompCor.py

@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..confounds import TCompCor