fix: reset only changed paths (workaround to preempt nipy#2968)

nipype/pipeline/engine/utils.py

@@ -248,12 +248,13 @@ def save_resultfile(result, cwd, name, rebase=True):
     try:
         with indirectory(cwd):
             # All the magic to fix #2944 resides here:
-            for key, val in list(outputs.items()):
-                val = rebase_path_traits(result.outputs.trait(key), val, cwd)
-                setattr(result.outputs, key, val)
+            for key, old in list(outputs.items()):
+                val = rebase_path_traits(result.outputs.trait(key), old, cwd)
+                if old != val:  # Workaround #2968: Reset only changed values
+                    setattr(result.outputs, key, val)
         savepkl(resultsfile, result)
     finally:
-        # Reset resolved paths from the outputs dict no matter what
+        # Restore resolved paths from the outputs dict no matter what
         for key, val in list(outputs.items()):
             setattr(result.outputs, key, val)
 
@@ -297,17 +298,18 @@ def load_resultfile(results_file, resolve=True):
         else:
             aggregate = False
 
-    if resolve and result.outputs:
-        try:
-            outputs = result.outputs.get()
-        except TypeError:  # This is a Bunch
-            return result, aggregate, attribute_error
-
-        logger.debug('Resolving paths in outputs loaded from results file.')
-        for trait_name, old_value in list(outputs.items()):
-            value = resolve_path_traits(result.outputs.trait(trait_name), old_value,
-                                        results_file.parent)
-            setattr(result.outputs, trait_name, value)
+        if resolve and result.outputs:
+            try:
+                outputs = result.outputs.get()
+            except TypeError:  # This is a Bunch
+                return result, aggregate, attribute_error
+
+            logger.debug('Resolving paths in outputs loaded from results file.')
+            for trait_name, old in list(outputs.items()):
+                value = resolve_path_traits(result.outputs.trait(trait_name), old,
+                                            results_file.parent)
+                if value != old:  # Workaround #2968: Reset only changed values
+                    setattr(result.outputs, trait_name, value)
 
     return result, aggregate, attribute_error