disabled return dict unwrapping (used in _list_outputs) by default. Added copyfile to python functions

Author: tclose

nipype2pydra/interface/base.py

@@ -1280,12 +1280,12 @@ def process_method_body(
         input_names: ty.List[str],
         output_names: ty.List[str],
         super_base: ty.Optional[type] = None,
+        unwrap_return_dict: bool = False,
     ) -> str:
         if not method_body:
             return ""
         if super_base is None:
             super_base = self.nipype_interface
-        return_value = get_return_line(method_body)
         method_body = method_body.replace("if self.output_spec:", "if True:")
         # Replace self.inputs.<name> with <name> in the function body
         input_re = re.compile(r"self\.inputs\.(\w+)\b(?!\()")
@@ -1302,7 +1302,10 @@ def process_method_body(
         method_body = input_re.sub(r"\1", method_body)
         method_body = self.replace_supers(method_body, super_base)
 
-        if return_value:
+        if unwrap_return_dict:
+            return_value = get_return_line(method_body)
+            if return_value is None:
+                return_value = "outputs"
             output_re = re.compile(return_value + r"\[(?:'|\")(\w+)(?:'|\")\]")
             unrecognised_outputs = set(
                 m for m in output_re.findall(method_body) if m not in output_names

nipype2pydra/interface/function.py

@@ -65,7 +65,7 @@ def types_to_names(spec_fields):
         used = UsedSymbols.find(
             self.nipype_module,
             self.referenced_local_functions,
-            omit_classes=self.package.omit_classes + [BaseInterface, TraitedSpec],
+            omit_classes=self.package.omit_classes,  # + [BaseInterface, TraitedSpec],
             omit_modules=self.package.omit_modules,
             omit_functions=self.package.omit_functions,
             omit_constants=self.package.omit_constants,
@@ -81,7 +81,7 @@ def types_to_names(spec_fields):
             method_used = UsedSymbols.find(
                 method_module,
                 [ref_method],
-                omit_classes=self.package.omit_classes + [BaseInterface, TraitedSpec],
+                omit_classes=self.package.omit_classes,  #  + [BaseInterface, TraitedSpec],
                 omit_modules=self.package.omit_modules,
                 omit_functions=self.package.omit_functions,
                 omit_constants=self.package.omit_constants,
@@ -92,6 +92,9 @@ def types_to_names(spec_fields):
             used.update(method_used, from_other_module=False)
 
         method_body = ""
+        for field in input_fields:
+            if field[-1].get("copyfile"):
+                method_body += f"    {field[0]} = {field[0]}.copy(Path.cwd())\n"
         for field in output_fields:
             method_body += f"    {field[0]} = attrs.NOTHING\n"
 
@@ -150,7 +153,7 @@ def types_to_names(spec_fields):
             run_interface_used = UsedSymbols.find(
                 run_interface_class.__module__,
                 [run_interface_code],
-                omit_classes=self.package.omit_classes + [BaseInterface, TraitedSpec],
+                omit_classes=self.package.omit_classes,  #  + [BaseInterface, TraitedSpec],
                 omit_modules=self.package.omit_modules,
                 omit_functions=self.package.omit_functions,
                 omit_constants=self.package.omit_constants,
@@ -178,12 +181,13 @@ def types_to_names(spec_fields):
                 input_names,
                 output_names,
                 super_base=list_outputs_class,
+                unwrap_return_dict=True,
             )
 
             list_outputs_used = UsedSymbols.find(
                 list_outputs_class.__module__,
                 [list_outputs_code],
-                omit_classes=self.package.omit_classes + [BaseInterface, TraitedSpec],
+                omit_classes=self.package.omit_classes,  #  + [BaseInterface, TraitedSpec],
                 omit_modules=self.package.omit_modules,
                 omit_functions=self.package.omit_functions,
                 omit_constants=self.package.omit_constants,