fixed handling of reserved attributes in python, shell and workflow tasks

Author: tclose

pydra/design/base.py

@@ -334,6 +334,7 @@ def extract_fields_from_class(
     arg_type: type[Arg],
     out_type: type[Out],
     auto_attribs: bool,
+    skip_fields: ty.Iterable[str] = (),
 ) -> tuple[dict[str, Arg], dict[str, Out]]:
     """Extract the input and output fields from an existing class
 
@@ -348,6 +349,8 @@ def extract_fields_from_class(
     auto_attribs : bool
         Whether to assume that all attribute annotations should be interpreted as
         fields or not
+    skip_fields : Iterable[str], optional
+        The names of attributes to skip when extracting the fields, by default ()
 
     Returns
     -------
@@ -364,10 +367,15 @@ def get_fields(klass, field_type, auto_attribs, helps) -> dict[str, Field]:
         fields_dict = {}
         # Get fields defined in base classes if present
         for field in list_fields(klass):
-            fields_dict[field.name] = field
+            if field.name not in skip_fields:
+                fields_dict[field.name] = field
         type_hints = ty.get_type_hints(klass)
         for atr_name in dir(klass):
-            if atr_name in ["Task", "Outputs"] or atr_name.startswith("__"):
+            if (
+                atr_name in ["Task", "Outputs"]
+                or atr_name in skip_fields
+                or atr_name.startswith("__")
+            ):
                 continue
             try:
                 atr = getattr(klass, atr_name)
@@ -394,7 +402,7 @@ def get_fields(klass, field_type, auto_attribs, helps) -> dict[str, Field]:
                     )
         if auto_attribs:
             for atr_name, type_ in type_hints.items():
-                if atr_name.startswith("_"):
+                if atr_name.startswith("_") or atr_name in skip_fields:
                     continue
                 if atr_name not in list(fields_dict) + ["Task", "Outputs"]:
                     fields_dict[atr_name] = field_type(

pydra/design/python.py

@@ -136,7 +136,13 @@ def make(wrapped: ty.Callable | type) -> PythonDef:
             name = klass.__name__
             check_explicit_fields_are_none(klass, inputs, outputs)
             parsed_inputs, parsed_outputs = extract_fields_from_class(
-                PythonDef, PythonOutputs, klass, arg, out, auto_attribs
+                PythonDef,
+                PythonOutputs,
+                klass,
+                arg,
+                out,
+                auto_attribs,
+                skip_fields=["function"],
             )
         else:
             if not isinstance(wrapped, ty.Callable):

pydra/design/shell.py

@@ -342,7 +342,13 @@ def make(
             class_name = klass.__name__
             check_explicit_fields_are_none(klass, inputs, outputs)
             parsed_inputs, parsed_outputs = extract_fields_from_class(
-                ShellDef, ShellOutputs, klass, arg, out, auto_attribs
+                ShellDef,
+                ShellOutputs,
+                klass,
+                arg,
+                out,
+                auto_attribs,
+                skip_fields=["executable"],
             )
         else:
             if not isinstance(wrapped, (str, list)):

pydra/design/workflow.py

@@ -145,7 +145,13 @@ def make(wrapped: ty.Callable | type) -> TaskDef:
             name = klass.__name__
             check_explicit_fields_are_none(klass, inputs, outputs)
             parsed_inputs, parsed_outputs = extract_fields_from_class(
-                WorkflowDef, WorkflowOutputs, klass, arg, out, auto_attribs
+                WorkflowDef,
+                WorkflowOutputs,
+                klass,
+                arg,
+                out,
+                auto_attribs,
+                skip_fields=["constructor"],
             )
         else:
             if not inspect.isfunction(wrapped):