Merge pull request #3240 from effigies/fix/export_workflow

FIX: Serialize all interface arguments when exporting workflows

Author: effigies

nipype/pipeline/engine/tests/test_utils.py

@@ -11,7 +11,12 @@
 from ....interfaces import base as nib
 from ....interfaces import utility as niu
 from .... import config
-from ..utils import clean_working_directory, write_workflow_prov, load_resultfile
+from ..utils import (
+    clean_working_directory,
+    write_workflow_prov,
+    load_resultfile,
+    format_node,
+)
 
 
 class InputSpec(nib.TraitedSpec):
@@ -327,3 +332,11 @@ def test_save_load_resultfile(tmpdir, use_relative):
             )
 
     config.set("execution", "use_relative_paths", old_use_relative)
+
+
+def test_format_node():
+    node = pe.Node(niu.IdentityInterface(fields=["a", "b"]), name="node")
+    serialized = format_node(node)
+    workspace = {"Node": pe.Node}
+    exec("\n".join(serialized), workspace)
+    assert workspace["node"].interface._fields == node.interface._fields

nipype/pipeline/engine/utils.py

@@ -364,18 +364,12 @@ def format_node(node, format="python", include_config=False):
         importline = "from %s import %s" % (klass.__module__, klass.__class__.__name__)
         comment = "# Node: %s" % node.fullname
         spec = signature(node.interface.__init__)
-        args = [p.name for p in list(spec.parameters.values())]
-        args = args[1:]
-        if args:
-            filled_args = []
-            for arg in args:
-                if hasattr(node.interface, "_%s" % arg):
-                    filled_args.append(
-                        "%s=%s" % (arg, getattr(node.interface, "_%s" % arg))
-                    )
-            args = ", ".join(filled_args)
-        else:
-            args = ""
+        filled_args = []
+        for param in spec.parameters.values():
+            val = getattr(node.interface, f"_{param.name}", None)
+            if val is not None:
+                filled_args.append(f"{param.name}={val!r}")
+        args = ", ".join(filled_args)
         klass_name = klass.__class__.__name__
         if isinstance(node, MapNode):
             nodedef = '%s = MapNode(%s(%s), iterfield=%s, name="%s")' % (