fix: update a few more dynamic interfaces and allow for keyword arguments to be encoded

Author: satra

nipype/interfaces/utility.py

@@ -107,14 +107,14 @@ class Merge(IOBase):
 
     def __init__(self, numinputs=0, **inputs):
         super(Merge, self).__init__(**inputs)
-        self.numinputs = numinputs
+        self._numinputs = numinputs
         add_traits(self.inputs, ['in%d' % (i + 1) for i in range(numinputs)])
 
     def _list_outputs(self):
         outputs = self._outputs().get()
         out = []
         if self.inputs.axis == 'vstack':
-            for idx in range(self.numinputs):
+            for idx in range(self._numinputs):
                 value = getattr(self.inputs, 'in%d' % (idx + 1))
                 if isdefined(value):
                     if isinstance(value, list) and not self.inputs.no_flatten:
@@ -124,7 +124,7 @@ def _list_outputs(self):
         else:
             for i in range(len(filename_to_list(self.inputs.in1))):
                 out.insert(i, [])
-                for j in range(self.numinputs):
+                for j in range(self._numinputs):
                     out[i].append(filename_to_list(getattr(self.inputs, 'in%d' % (j + 1)))[i])
         if out:
             outputs['out'] = out

nipype/pipeline/engine.py

@@ -89,15 +89,13 @@ def format_node(node, format='python'):
                                             klass.__class__.__name__)
         comment = '# Node: %s' % node.fullname
         spec = inspect.getargspec(node._interface.__init__)
-        if spec.defaults:
-            args = spec.args[1:-len(spec.defaults)]
-        else:
-            args = spec.args[1:]
+        args = spec.args[1:]
         if args:
             filled_args = []
             for arg in args:
-                filled_args.append('%s=%s' % (arg, getattr(node._interface,
-                                                           '_%s' % arg)))
+                if  hasattr(node._interface, '_%s' % arg):
+                    filled_args.append('%s=%s' % (arg, getattr(node._interface,
+                                                               '_%s' % arg)))
             args = ', '.join(filled_args)
         else:
             args = ''