fix: fixed node configuration errors

Author: satra

nipype/pipeline/engine.py

@@ -143,7 +143,7 @@ def __init__(self, name=None, base_dir=None, **kwargs):
             special characters (e.g., '.', '@').
         """
         self.base_dir = base_dir
-        self.config = deepcopy(config._sections)
+        self.config = None #deepcopy(config._sections)
         if name is None:
             raise Exception("init requires a name for this %s" %
                             self.__class__.__name__)
@@ -215,6 +215,7 @@ class Workflow(WorkflowBase):
     def __init__(self, *args, **kwargs):
         super(Workflow, self).__init__(* args, **kwargs)
         self._graph = nx.DiGraph()
+        self.config = deepcopy(config._sections)
 
     # PUBLIC API
     def clone(self, name):
@@ -1205,7 +1206,10 @@ def run(self, updatehash=False):
             Update the hash stored in the output directory
         """
         # check to see if output directory and hash exist
-        self.config = merge_dict(deepcopy(config._sections), self.config)
+        if self.config is None:
+            self.config = deepcopy(config._sections)
+        else:
+            self.config = merge_dict(deepcopy(config._sections), self.config)
         if not self._got_inputs:
             self._get_inputs()
             self._got_inputs = True

nipype/pipeline/utils.py

@@ -729,6 +729,8 @@ def merge_dict(d1, d2, merge=lambda x, y: y):
     if not isinstance(d1, dict):
         return merge(d1, d2)
     result = dict(d1)
+    if d2 is None:
+        return result
     for k, v in d2.iteritems():
         if k in result:
             result[k] = merge_dict(result[k], v, merge=merge)