Merge pull request #2533 from djarecka/default_value_2532

changing arguments names to default values for traits (closes #2532)

Author: satra

nipype/algorithms/confounds.py

@@ -390,13 +390,12 @@ class CompCorInputSpec(BaseInterfaceInputSpec):
         desc='Detrend time series prior to component '
         'extraction')
     use_regress_poly = traits.Bool(
-        True,
         deprecated='0.15.0',
         new_name='pre_filter',
         desc=('use polynomial regression '
               'pre-component extraction'))
     regress_poly_degree = traits.Range(
-        low=1, default=1, usedefault=True, desc='the degree polynomial to use')
+        low=1, value=1, usedefault=True, desc='the degree polynomial to use')
     header_prefix = traits.Str(
         desc=('the desired header for the output tsv '
               'file (one column). If undefined, will '

nipype/algorithms/mesh.py

@@ -289,6 +289,7 @@ class MeshWarpMathsInputSpec(BaseInterfaceInputSpec):
         float_trait,
         File(exists=True),
         default=1.0,
+        usedefault=True,
         mandatory=True,
         desc='image, float or tuple of floats to act as operator')
 

nipype/algorithms/rapidart.py

@@ -234,8 +234,9 @@ class ArtifactDetectInputSpec(BaseInterfaceInputSpec):
         desc=("Mask threshold to be used if mask_type"
               " is 'thresh'."))
     intersect_mask = traits.Bool(
-        True, desc=("Intersect the masks when computed from "
-                    "spm_global."))
+        True, usedefault=True,
+        desc=("Intersect the masks when computed from "
+              "spm_global."))
     save_plot = traits.Bool(
         True, desc="save plots containing outliers", usedefault=True)
     plot_type = traits.Enum(

nipype/algorithms/tests/test_auto_ArtifactDetect.py

@@ -12,7 +12,7 @@ def test_ArtifactDetect_inputs():
             nohash=True,
             usedefault=True,
         ),
-        intersect_mask=dict(),
+        intersect_mask=dict(usedefault=True, ),
         mask_file=dict(),
         mask_threshold=dict(),
         mask_type=dict(mandatory=True, ),

nipype/algorithms/tests/test_auto_MeshWarpMaths.py

@@ -13,7 +13,10 @@ def test_MeshWarpMaths_inputs():
         ),
         in_surf=dict(mandatory=True, ),
         operation=dict(usedefault=True, ),
-        operator=dict(mandatory=True, ),
+        operator=dict(
+            mandatory=True,
+            usedefault=True,
+        ),
         out_file=dict(usedefault=True, ),
         out_warp=dict(usedefault=True, ),
     )

nipype/interfaces/afni/preprocess.py

@@ -1606,6 +1606,7 @@ class OutlierCountInputSpec(CommandLineInputSpec):
         value=1e-3,
         low=0.0,
         high=1.0,
+        usedefault=True,
         argstr='-qthr %.5f',
         desc='indicate a value for q to compute alpha')
     autoclip = traits.Bool(
@@ -1675,7 +1676,7 @@ class OutlierCount(CommandLine):
     >>> toutcount = afni.OutlierCount()
     >>> toutcount.inputs.in_file = 'functional.nii'
     >>> toutcount.cmdline  # doctest: +ELLIPSIS
-    '3dToutcount functional.nii'
+    '3dToutcount -qthr 0.00100 functional.nii'
     >>> res = toutcount.run()  # doctest: +SKIP
 
     """

nipype/interfaces/afni/tests/test_auto_Cat.py

@@ -38,6 +38,7 @@ def test_Cat_inputs():
             argstr='> %s',
             mandatory=True,
             position=-1,
+            usedefault=True,
         ),
         out_fint=dict(
             argstr='-f',

nipype/interfaces/afni/tests/test_auto_NwarpApply.py

@@ -20,7 +20,10 @@ def test_NwarpApply_inputs():
             argstr='-source %s',
             mandatory=True,
         ),
-        interp=dict(argstr='-interp %s', ),
+        interp=dict(
+            argstr='-interp %s',
+            usedefault=True,
+        ),
         inv_warp=dict(argstr='-iwarp', ),
         master=dict(argstr='-master %s', ),
         out_file=dict(

nipype/interfaces/afni/tests/test_auto_NwarpCat.py

@@ -21,7 +21,10 @@ def test_NwarpCat_inputs():
             mandatory=True,
             position=-1,
         ),
-        interp=dict(argstr='-interp %s', ),
+        interp=dict(
+            argstr='-interp %s',
+            usedefault=True,
+        ),
         inv_warp=dict(argstr='-iwarp', ),
         num_threads=dict(
             nohash=True,

nipype/interfaces/afni/tests/test_auto_OneDToolPy.py

@@ -34,7 +34,6 @@ def test_OneDToolPy_inputs():
         show_cormat_warnings=dict(
             argstr='-show_cormat_warnings |& tee %s',
             position=-1,
-            usedefault=False,
             xor=['out_file'],
         ),
         show_indices_interest=dict(argstr='-show_indices_interest', ),