Merge remote-tracking branch 'upstream/master' into fix/VirtualDisplay

Author: oesteban

nipype/interfaces/afni/preprocess.py

@@ -356,9 +356,17 @@ class AllineateInputSpec(AFNICommandInputSpec):
     weight_file = File(
         argstr='-weight %s',
         exists=True,
+        deprecated='1.0.0', new_name='weight',
         desc='Set the weighting for each voxel in the base dataset; '
              'larger weights mean that voxel count more in the cost function. '
              'Must be defined on the same grid as the base dataset')
+    weight = traits.Either(
+        File(exists=True), traits.Float(),
+        argstr='-weight %s',
+        desc='Set the weighting for each voxel in the base dataset; '
+             'larger weights mean that voxel count more in the cost function. '
+             'If an image file is given, the volume must be defined on the '
+             'same grid as the base dataset')
     out_weight_file = traits.File(
         argstr='-wtprefix %s',
         desc='Write the weight volume to disk as a dataset',

nipype/interfaces/afni/tests/test_auto_Allineate.py

@@ -117,7 +117,11 @@ def test_Allineate_inputs():
     ),
     warpfreeze=dict(argstr='-warpfreeze',
     ),
+    weight=dict(argstr='-weight %s',
+    ),
     weight_file=dict(argstr='-weight %s',
+    deprecated='1.0.0',
+    new_name='weight',
     ),
     zclip=dict(argstr='-zclip',
     ),