fixed serialization of task definitions

Author: tclose

pydra/compose/base/helpers.py

@@ -114,7 +114,13 @@ def ensure_field_objects(
             out_kwds = copy(out)
             if "help" not in out_kwds:
                 out_kwds["help"] = output_helps.get(output_name, "")
-            outputs[output_name] = out_type(
+            if "path_template" in out_kwds:
+                from pydra.compose.shell import outarg
+
+                out_type_ = outarg
+            else:
+                out_type_ = out_type
+            outputs[output_name] = out_type_(
                 name=output_name,
                 **out_kwds,
             )

pydra/compose/base/task.py

@@ -37,6 +37,7 @@ class Outputs:
     """Base class for all output definitions"""
 
     RESERVED_FIELD_NAMES = ("inputs",)
+    BASE_ATTRS = ()
 
     _cache_dir: Path = attrs.field(default=None, init=False, repr=False)
     _node = attrs.field(default=None, init=False, repr=False)
@@ -178,6 +179,7 @@ def _task_type(cls) -> str:
     _hashes = attrs.field(default=None, init=False, eq=False, repr=False)
 
     RESERVED_FIELD_NAMES = ("split", "combine")
+    BASE_ATTRS = ()
 
     def __call__(
         self,

pydra/compose/shell/builder.py

@@ -183,8 +183,8 @@ def make(
                 class_name = f"_{class_name}"
 
             # Add in fields from base classes
-            parsed_inputs.update({n: getattr(Task, n) for n in Task.BASE_NAMES})
-            parsed_outputs.update({n: getattr(Outputs, n) for n in Outputs.BASE_NAMES})
+            parsed_inputs.update({n: getattr(Task, n) for n in Task.BASE_ATTRS})
+            parsed_outputs.update({n: getattr(Outputs, n) for n in Outputs.BASE_ATTRS})
 
         if "executable" in parsed_inputs:
             raise ValueError(

pydra/compose/shell/field.py

@@ -134,7 +134,7 @@ def _callable_validator(self, _, value):
                 "stdout",
                 "stderr",
             ]
-        ):  # shell.Outputs.BASE_NAMES
+        ):  # shell.Outputs.BASE_ATTRS
             raise ValueError(
                 "A shell output field must have either a callable or a path_template"
             )

pydra/compose/shell/task.py

@@ -46,7 +46,7 @@
 class ShellOutputs(base.Outputs):
     """Output task of a generic shell process."""
 
-    BASE_NAMES = ["return_code", "stdout", "stderr"]
+    BASE_ATTRS = ["return_code", "stdout", "stderr"]
     RETURN_CODE_HELP = """The process' exit code."""
     STDOUT_HELP = """The standard output stream produced by the command."""
     STDERR_HELP = """The standard error stream produced by the command."""
@@ -234,7 +234,7 @@ class ShellTask(base.Task[ShellOutputsType]):
 
     _executor_name = "executable"
 
-    BASE_NAMES = ["append_args"]
+    BASE_ATTRS = ("append_args",)
 
     EXECUTABLE_HELP = (
         "the first part of the command, can be a string, "

pydra/utils/general.py

@@ -602,11 +602,22 @@ def task_def_as_dict(task_def: "type[Task]") -> ty.Dict[str, ty.Any]:
     dict[str, ty.Any]
         A dictionary representation of the Pydra task.
     """
+    from pydra.compose.base import Out
+
     input_fields = task_fields(task_def)
     executor = input_fields.pop(task_def._executor_name).default
-    input_dicts = [attrs.asdict(i, filter=_filter_defaults) for i in input_fields]
+    input_dicts = [
+        attrs.asdict(i, filter=_filter_defaults)
+        for i in input_fields
+        if (
+            not isinstance(i, Out)  # filter out outarg fields
+            and i.name not in task_def.BASE_ATTRS
+        )
+    ]
     output_dicts = [
-        attrs.asdict(o, filter=_filter_defaults) for o in task_fields(task_def.Outputs)
+        attrs.asdict(o, filter=_filter_defaults)
+        for o in task_fields(task_def.Outputs)
+        if o.name not in task_def.Outputs.BASE_ATTRS
     ]
     dct = {
         "type": task_def._task_type(),