Merge pull request #2964 from oesteban/enh/improved-File-Directory-tr…

…aits-addendum MAINT: Various minor improvements to complement previous PR
nipy · Jul 17, 2019 · bfbd0ab · bfbd0ab
2 parents 42b1239 + 9257f75
commit bfbd0ab
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Showing 776 changed files with 6,877 additions and 2,436 deletions.
diff --git a/Makefile b/Makefile
@@ -56,7 +56,7 @@ inplace:
 	$(PYTHON) setup.py build_ext -i
 
 test-code: in
-	py.test --doctest-module nipype
+	py.test --doctest-modules nipype
 
 test-coverage: clean-tests in
 	py.test --doctest-modules --cov-config .coveragerc --cov=nipype nipype

diff --git a/nipype/algorithms/tests/test_auto_ACompCor.py b/nipype/algorithms/tests/test_auto_ACompCor.py
@@ -22,7 +22,10 @@ def test_ACompCor_inputs():
         ),
         num_components=dict(xor=['variance_threshold'], ),
         pre_filter=dict(usedefault=True, ),
-        realigned_file=dict(mandatory=True, ),
+        realigned_file=dict(
+            extensions=None,
+            mandatory=True,
+        ),
         regress_poly_degree=dict(usedefault=True, ),
         repetition_time=dict(),
         save_metadata=dict(usedefault=True, ),
@@ -40,9 +43,9 @@ def test_ACompCor_inputs():
             assert getattr(inputs.traits()[key], metakey) == value
 def test_ACompCor_outputs():
     output_map = dict(
-        components_file=dict(),
-        metadata_file=dict(),
-        pre_filter_file=dict(),
+        components_file=dict(extensions=None, ),
+        metadata_file=dict(extensions=None, ),
+        pre_filter_file=dict(extensions=None, ),
     )
     outputs = ACompCor.output_spec()
 

diff --git a/nipype/algorithms/tests/test_auto_ActivationCount.py b/nipype/algorithms/tests/test_auto_ActivationCount.py
@@ -15,9 +15,9 @@ def test_ActivationCount_inputs():
             assert getattr(inputs.traits()[key], metakey) == value
 def test_ActivationCount_outputs():
     output_map = dict(
-        acm_neg=dict(),
-        acm_pos=dict(),
-        out_file=dict(),
+        acm_neg=dict(extensions=None, ),
+        acm_pos=dict(extensions=None, ),
+        out_file=dict(extensions=None, ),
     )
     outputs = ActivationCount.output_spec()
 

diff --git a/nipype/algorithms/tests/test_auto_AddCSVColumn.py b/nipype/algorithms/tests/test_auto_AddCSVColumn.py
@@ -7,16 +7,22 @@ def test_AddCSVColumn_inputs():
     input_map = dict(
         extra_column_heading=dict(),
         extra_field=dict(),
-        in_file=dict(mandatory=True, ),
-        out_file=dict(usedefault=True, ),
+        in_file=dict(
+            extensions=None,
+            mandatory=True,
+        ),
+        out_file=dict(
+            extensions=None,
+            usedefault=True,
+        ),
     )
     inputs = AddCSVColumn.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_AddCSVColumn_outputs():
-    output_map = dict(csv_file=dict(), )
+    output_map = dict(csv_file=dict(extensions=None, ), )
     outputs = AddCSVColumn.output_spec()
 
     for key, metadata in list(output_map.items()):

diff --git a/nipype/algorithms/tests/test_auto_AddCSVRow.py b/nipype/algorithms/tests/test_auto_AddCSVRow.py
@@ -14,7 +14,7 @@ def test_AddCSVRow_inputs():
         for metakey, value in list(metadata.items()):
             assert getattr(inputs.traits()[key], metakey) == value
 def test_AddCSVRow_outputs():
-    output_map = dict(csv_file=dict(), )
+    output_map = dict(csv_file=dict(extensions=None, ), )
     outputs = AddCSVRow.output_spec()
 
     for key, metadata in list(output_map.items()):

diff --git a/nipype/algorithms/tests/test_auto_AddNoise.py b/nipype/algorithms/tests/test_auto_AddNoise.py
@@ -13,9 +13,12 @@ def test_AddNoise_inputs():
             mandatory=True,
             usedefault=True,
         ),
-        in_file=dict(mandatory=True, ),
-        in_mask=dict(),
-        out_file=dict(),
+        in_file=dict(
+            extensions=None,
+            mandatory=True,
+        ),
+        in_mask=dict(extensions=None, ),
+        out_file=dict(extensions=None, ),
         snr=dict(usedefault=True, ),
     )
     inputs = AddNoise.input_spec()
@@ -24,7 +27,7 @@ def test_AddNoise_inputs():
         for metakey, value in list(metadata.items()):
             assert getattr(inputs.traits()[key], metakey) == value
 def test_AddNoise_outputs():
-    output_map = dict(out_file=dict(), )
+    output_map = dict(out_file=dict(extensions=None, ), )
     outputs = AddNoise.output_spec()
 
     for key, metadata in list(output_map.items()):

diff --git a/nipype/algorithms/tests/test_auto_ArtifactDetect.py b/nipype/algorithms/tests/test_auto_ArtifactDetect.py
@@ -8,7 +8,7 @@ def test_ArtifactDetect_inputs():
         bound_by_brainmask=dict(usedefault=True, ),
         global_threshold=dict(usedefault=True, ),
         intersect_mask=dict(usedefault=True, ),
-        mask_file=dict(),
+        mask_file=dict(extensions=None, ),
         mask_threshold=dict(),
         mask_type=dict(mandatory=True, ),
         norm_threshold=dict(

diff --git a/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py b/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py
@@ -6,7 +6,10 @@
 def test_CalculateNormalizedMoments_inputs():
     input_map = dict(
         moment=dict(mandatory=True, ),
-        timeseries_file=dict(mandatory=True, ),
+        timeseries_file=dict(
+            extensions=None,
+            mandatory=True,
+        ),
     )
     inputs = CalculateNormalizedMoments.input_spec()
 

diff --git a/nipype/algorithms/tests/test_auto_ComputeDVARS.py b/nipype/algorithms/tests/test_auto_ComputeDVARS.py
@@ -8,8 +8,14 @@ def test_ComputeDVARS_inputs():
         figdpi=dict(usedefault=True, ),
         figformat=dict(usedefault=True, ),
         figsize=dict(usedefault=True, ),
-        in_file=dict(mandatory=True, ),
-        in_mask=dict(mandatory=True, ),
+        in_file=dict(
+            extensions=None,
+            mandatory=True,
+        ),
+        in_mask=dict(
+            extensions=None,
+            mandatory=True,
+        ),
         intensity_normalization=dict(usedefault=True, ),
         remove_zerovariance=dict(usedefault=True, ),
         save_all=dict(usedefault=True, ),
@@ -29,13 +35,13 @@ def test_ComputeDVARS_outputs():
         avg_nstd=dict(),
         avg_std=dict(),
         avg_vxstd=dict(),
-        fig_nstd=dict(),
-        fig_std=dict(),
-        fig_vxstd=dict(),
-        out_all=dict(),
-        out_nstd=dict(),
-        out_std=dict(),
-        out_vxstd=dict(),
+        fig_nstd=dict(extensions=None, ),
+        fig_std=dict(extensions=None, ),
+        fig_vxstd=dict(extensions=None, ),
+        out_all=dict(extensions=None, ),
+        out_nstd=dict(extensions=None, ),
+        out_std=dict(extensions=None, ),
+        out_vxstd=dict(extensions=None, ),
     )
     outputs = ComputeDVARS.output_spec()
 

diff --git a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py
@@ -6,10 +6,22 @@
 def test_ComputeMeshWarp_inputs():
     input_map = dict(
         metric=dict(usedefault=True, ),
-        out_file=dict(usedefault=True, ),
-        out_warp=dict(usedefault=True, ),
-        surface1=dict(mandatory=True, ),
-        surface2=dict(mandatory=True, ),
+        out_file=dict(
+            extensions=None,
+            usedefault=True,
+        ),
+        out_warp=dict(
+            extensions=None,
+            usedefault=True,
+        ),
+        surface1=dict(
+            extensions=None,
+            mandatory=True,
+        ),
+        surface2=dict(
+            extensions=None,
+            mandatory=True,
+        ),
         weighting=dict(usedefault=True, ),
     )
     inputs = ComputeMeshWarp.input_spec()
@@ -20,8 +32,8 @@ def test_ComputeMeshWarp_inputs():
 def test_ComputeMeshWarp_outputs():
     output_map = dict(
         distance=dict(),
-        out_file=dict(),
-        out_warp=dict(),
+        out_file=dict(extensions=None, ),
+        out_warp=dict(extensions=None, ),
     )
     outputs = ComputeMeshWarp.output_spec()
 

diff --git a/nipype/algorithms/tests/test_auto_CreateNifti.py b/nipype/algorithms/tests/test_auto_CreateNifti.py
@@ -6,16 +6,22 @@
 def test_CreateNifti_inputs():
     input_map = dict(
         affine=dict(),
-        data_file=dict(mandatory=True, ),
-        header_file=dict(mandatory=True, ),
+        data_file=dict(
+            extensions=None,
+            mandatory=True,
+        ),
+        header_file=dict(
+            extensions=None,
+            mandatory=True,
+        ),
     )
     inputs = CreateNifti.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_CreateNifti_outputs():
-    output_map = dict(nifti_file=dict(), )
+    output_map = dict(nifti_file=dict(extensions=None, ), )
     outputs = CreateNifti.output_spec()
 
     for key, metadata in list(output_map.items()):

diff --git a/nipype/algorithms/tests/test_auto_Distance.py b/nipype/algorithms/tests/test_auto_Distance.py
@@ -5,10 +5,16 @@
 
 def test_Distance_inputs():
     input_map = dict(
-        mask_volume=dict(),
+        mask_volume=dict(extensions=None, ),
         method=dict(usedefault=True, ),
-        volume1=dict(mandatory=True, ),
-        volume2=dict(mandatory=True, ),
+        volume1=dict(
+            extensions=None,
+            mandatory=True,
+        ),
+        volume2=dict(
+            extensions=None,
+            mandatory=True,
+        ),
     )
     inputs = Distance.input_spec()
 
@@ -18,7 +24,7 @@ def test_Distance_inputs():
 def test_Distance_outputs():
     output_map = dict(
         distance=dict(),
-        histogram=dict(),
+        histogram=dict(extensions=None, ),
         point1=dict(),
         point2=dict(),
     )

diff --git a/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py b/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py
@@ -7,10 +7,19 @@ def test_FramewiseDisplacement_inputs():
     input_map = dict(
         figdpi=dict(usedefault=True, ),
         figsize=dict(usedefault=True, ),
-        in_file=dict(mandatory=True, ),
+        in_file=dict(
+            extensions=None,
+            mandatory=True,
+        ),
         normalize=dict(usedefault=True, ),
-        out_figure=dict(usedefault=True, ),
-        out_file=dict(usedefault=True, ),
+        out_figure=dict(
+            extensions=None,
+            usedefault=True,
+        ),
+        out_file=dict(
+            extensions=None,
+            usedefault=True,
+        ),
         parameter_source=dict(mandatory=True, ),
         radius=dict(usedefault=True, ),
         save_plot=dict(usedefault=True, ),
@@ -24,8 +33,8 @@ def test_FramewiseDisplacement_inputs():
 def test_FramewiseDisplacement_outputs():
     output_map = dict(
         fd_average=dict(),
-        out_figure=dict(),
-        out_file=dict(),
+        out_figure=dict(extensions=None, ),
+        out_file=dict(extensions=None, ),
     )
     outputs = FramewiseDisplacement.output_spec()
 

diff --git a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py
@@ -5,10 +5,13 @@
 
 def test_FuzzyOverlap_inputs():
     input_map = dict(
-        in_mask=dict(),
+        in_mask=dict(extensions=None, ),
         in_ref=dict(mandatory=True, ),
         in_tst=dict(mandatory=True, ),
-        out_file=dict(usedefault=True, ),
+        out_file=dict(
+            extensions=None,
+            usedefault=True,
+        ),
         weighting=dict(usedefault=True, ),
     )
     inputs = FuzzyOverlap.input_spec()

diff --git a/nipype/algorithms/tests/test_auto_Gunzip.py b/nipype/algorithms/tests/test_auto_Gunzip.py
@@ -4,14 +4,18 @@
 
 
 def test_Gunzip_inputs():
-    input_map = dict(in_file=dict(mandatory=True, ), )
+    input_map = dict(
+        in_file=dict(
+            extensions=None,
+            mandatory=True,
+        ), )
     inputs = Gunzip.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_Gunzip_outputs():
-    output_map = dict(out_file=dict(), )
+    output_map = dict(out_file=dict(extensions=None, ), )
     outputs = Gunzip.output_spec()
 
     for key, metadata in list(output_map.items()):

diff --git a/nipype/algorithms/tests/test_auto_ICC.py b/nipype/algorithms/tests/test_auto_ICC.py
@@ -5,7 +5,10 @@
 
 def test_ICC_inputs():
     input_map = dict(
-        mask=dict(mandatory=True, ),
+        mask=dict(
+            extensions=None,
+            mandatory=True,
+        ),
         subjects_sessions=dict(mandatory=True, ),
     )
     inputs = ICC.input_spec()
@@ -15,9 +18,9 @@ def test_ICC_inputs():
             assert getattr(inputs.traits()[key], metakey) == value
 def test_ICC_outputs():
     output_map = dict(
-        icc_map=dict(),
-        session_var_map=dict(),
-        subject_var_map=dict(),
+        icc_map=dict(extensions=None, ),
+        session_var_map=dict(extensions=None, ),
+        subject_var_map=dict(extensions=None, ),
     )
     outputs = ICC.output_spec()
 

diff --git a/nipype/algorithms/tests/test_auto_Matlab2CSV.py b/nipype/algorithms/tests/test_auto_Matlab2CSV.py
@@ -5,7 +5,10 @@
 
 def test_Matlab2CSV_inputs():
     input_map = dict(
-        in_file=dict(mandatory=True, ),
+        in_file=dict(
+            extensions=None,
+            mandatory=True,
+        ),
         reshape_matrix=dict(usedefault=True, ),
     )
     inputs = Matlab2CSV.input_spec()

diff --git a/nipype/algorithms/tests/test_auto_MergeCSVFiles.py b/nipype/algorithms/tests/test_auto_MergeCSVFiles.py
@@ -9,7 +9,10 @@ def test_MergeCSVFiles_inputs():
         extra_column_heading=dict(),
         extra_field=dict(),
         in_files=dict(mandatory=True, ),
-        out_file=dict(usedefault=True, ),
+        out_file=dict(
+            extensions=None,
+            usedefault=True,
+        ),
         row_heading_title=dict(usedefault=True, ),
         row_headings=dict(),
     )
@@ -19,7 +22,7 @@ def test_MergeCSVFiles_inputs():
         for metakey, value in list(metadata.items()):
             assert getattr(inputs.traits()[key], metakey) == value
 def test_MergeCSVFiles_outputs():
-    output_map = dict(csv_file=dict(), )
+    output_map = dict(csv_file=dict(extensions=None, ), )
     outputs = MergeCSVFiles.output_spec()
 
     for key, metadata in list(output_map.items()):