renamed make_task_spec to make_task_def

new-docs/source/tutorial/advanced-execution.ipynb

@@ -64,6 +64,10 @@
     "from fileformats.medimage import Nifti\n",
     "from pydra.engine.submitter import Submitter\n",
     "from pydra.tasks.mrtrix3.v3_0 import MrGrid\n",
+    "import nest_asyncio\n",
+    "\n",
+    "# Allow running async code in Jupyter notebooks\n",
+    "nest_asyncio.apply()\n",
     "\n",
     "# Make directory filled with nifti files\n",
     "test_dir = Path(tempfile.mkdtemp())\n",

new-docs/source/tutorial/canonical-form.ipynb

@@ -4,7 +4,7 @@
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "# Canonical (dataclass) task form\n",
+                "# Canonical task form\n",
                 "\n",
                 "Under the hood, all Python, shell and workflow task definitions generated by the\n",
                 "`pydra.design.*.define` decorators/functions are translated to\n",

new-docs/source/tutorial/getting-started.ipynb

@@ -38,6 +38,10 @@
     "from pathlib import Path\n",
     "from tempfile import mkdtemp\n",
     "import json\n",
+    "import nest_asyncio\n",
+    "\n",
+    "# Allow running async code in Jupyter notebooks\n",
+    "nest_asyncio.apply()\n",
     "\n",
     "JSON_CONTENTS = {'a': True, 'b': 'two', 'c': 3, 'd': [7, 0.55, 6]}\n",
     "\n",
@@ -57,9 +61,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "A newer version (0.25) of nipype/pydra is available. You are using 0.25.dev128+g1e817743.d20250104\n"
+     ]
+    }
+   ],
    "source": [
     "# Import the task definition\n",
     "from pydra.tasks.common import LoadJson\n",
@@ -83,13 +95,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
     "from pydra.engine.submitter import Submitter\n",
     "\n",
-    "with Submitter(plugin='cf', n_procs=1) as submitter:\n",
+    "with Submitter(plugin='serial', n_procs=1) as submitter:\n",
     "    result = submitter(load_json)"
    ]
   },
@@ -119,7 +131,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -142,14 +154,26 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "AttributeError",
+     "evalue": "'MrGrid' object has no attribute 'split'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[5], line 4\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mpydra\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mtasks\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmrtrix3\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mv3_0\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m MrGrid\n\u001b[1;32m      3\u001b[0m \u001b[38;5;66;03m# Instantiate the task definition, \"splitting\" over all NIfTI files in the test directory\u001b[39;00m\n\u001b[0;32m----> 4\u001b[0m mrgrid \u001b[38;5;241m=\u001b[39m \u001b[43mMrGrid\u001b[49m\u001b[43m(\u001b[49m\u001b[43mvoxel\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m0.5\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;241;43m0.5\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;241;43m0.5\u001b[39;49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msplit\u001b[49m(\u001b[38;5;28minput\u001b[39m\u001b[38;5;241m=\u001b[39mnifti_dir\u001b[38;5;241m.\u001b[39miterdir())\n\u001b[1;32m      6\u001b[0m \u001b[38;5;66;03m# Run the task to resample all NIfTI files\u001b[39;00m\n\u001b[1;32m      7\u001b[0m outputs \u001b[38;5;241m=\u001b[39m mrgrid()\n",
+      "\u001b[0;31mAttributeError\u001b[0m: 'MrGrid' object has no attribute 'split'"
+     ]
+    }
+   ],
    "source": [
     "from pydra.tasks.mrtrix3.v3_0 import MrGrid\n",
     "\n",
     "# Instantiate the task definition, \"splitting\" over all NIfTI files in the test directory\n",
-    "mrgrid = MrGrid(voxel=0.5).split(input=nifti_dir.iterdir())\n",
+    "mrgrid = MrGrid(voxel=(0.5,0.5,0.5)).split(input=nifti_dir.iterdir())\n",
     "\n",
     "# Run the task to resample all NIfTI files\n",
     "outputs = mrgrid()\n",

new-docs/source/tutorial/workflow.ipynb

@@ -414,7 +414,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "wf12",
    "language": "python",
    "name": "python3"
   },

pydra/design/base.py

@@ -34,7 +34,7 @@
     "Arg",
     "Out",
     "ensure_field_objects",
-    "make_task_spec",
+    "make_task_def",
 ]
 
 
@@ -349,7 +349,7 @@ def get_fields(klass, field_type, auto_attribs, helps) -> dict[str, Field]:
     return inputs, outputs
 
 
-def make_task_spec(
+def make_task_def(
     spec_type: type["TaskDef"],
     out_type: type["TaskOutputs"],
     task_type: type["Task"],
@@ -724,6 +724,8 @@ def allowed_values_validator(_, attribute, value):
     allowed = attribute.metadata[PYDRA_ATTR_METADATA].allowed_values
     if value is attrs.NOTHING or is_lazy(value):
         pass
+    elif value is None and is_optional(attribute.type):
+        pass
     elif value not in allowed:
         raise ValueError(
             f"value of {attribute.name} has to be from {allowed}, but {value} provided"

pydra/design/boutiques.py

@@ -7,7 +7,7 @@
 from fileformats.generic import File
 from pydra.engine.specs import ShellDef
 from pydra.engine.task import BoshTask
-from .base import make_task_spec
+from .base import make_task_def
 from . import shell
 
 
@@ -113,7 +113,7 @@ def define(
     outputs = _prepare_output_spec(
         bosh_spec, input_keys, names_subset=output_spec_names
     )
-    return make_task_spec(
+    return make_task_def(
         spec_type=ShellDef,
         task_type=BoshTask,
         out_type=out,

pydra/design/python.py

@@ -6,7 +6,7 @@
     Arg,
     Out,
     ensure_field_objects,
-    make_task_spec,
+    make_task_def,
     parse_doc_string,
     extract_function_inputs_and_outputs,
     check_explicit_fields_are_none,
@@ -159,7 +159,7 @@ def make(wrapped: ty.Callable | type) -> PythonDef:
             name="function", type=ty.Callable, default=function
         )
 
-        interface = make_task_spec(
+        interface = make_task_def(
             PythonDef,
             PythonOutputs,
             PythonTask,

pydra/design/shell.py

@@ -19,7 +19,7 @@
     check_explicit_fields_are_none,
     extract_fields_from_class,
     ensure_field_objects,
-    make_task_spec,
+    make_task_def,
     EMPTY,
 )
 from pydra.utils.typing import is_fileset_or_union, MultiInputObj
@@ -373,7 +373,7 @@ def make(
             if inpt.position is None:
                 inpt.position = position_stack.pop(0)
 
-        interface = make_task_spec(
+        interface = make_task_def(
             ShellDef,
             ShellOutputs,
             ShellTask,

pydra/design/workflow.py

@@ -6,7 +6,7 @@
     Arg,
     Out,
     ensure_field_objects,
-    make_task_spec,
+    make_task_def,
     parse_doc_string,
     extract_function_inputs_and_outputs,
     check_explicit_fields_are_none,
@@ -171,7 +171,7 @@ def make(wrapped: ty.Callable | type) -> TaskDef:
         for inpt_name in lazy:
             parsed_inputs[inpt_name].lazy = True
 
-        interface = make_task_spec(
+        interface = make_task_def(
             WorkflowDef,
             WorkflowOutputs,
             WorkflowTask,

pydra/engine/submitter.py

@@ -50,8 +50,15 @@ def __init__(self, plugin: ty.Union[str, ty.Type[Worker]] = "cf", **kwargs):
 
     def __call__(self, runnable, cache_locations=None, rerun=False, environment=None):
         """Submitter run function."""
+        from pydra.engine.core import TaskDef
+
         if cache_locations is not None:
             runnable.cache_locations = cache_locations
+        if isinstance(runnable, TaskDef):
+            runnable = runnable.Task(
+                runnable,
+                cache_locations=cache_locations,
+            )
         self.loop.run_until_complete(
             self.submit_from_call(runnable, rerun, environment)
         )

pydra/engine/tests/test_dockertask.py

@@ -140,7 +140,6 @@ def test_docker_inputspec_1(tmp_path):
         shell.arg(
             name="file",
             type=File,
-            mandatory=True,
             position=1,
             argstr="",
             help="input file",
@@ -258,7 +257,6 @@ def test_docker_inputspec_2a_except(plugin, tmp_path):
         shell.arg(
             name="file2",
             type=File,
-            mandatory=True,
             position=2,
             argstr="",
             help="input file 2",
@@ -304,7 +302,6 @@ def test_docker_inputspec_2a(plugin, tmp_path):
         shell.arg(
             name="file2",
             type=File,
-            mandatory=True,
             position=2,
             argstr="",
             help="input file 2",
@@ -335,7 +332,6 @@ def test_docker_inputspec_3(plugin, tmp_path):
         shell.arg(
             name="file",
             type=File,
-            mandatory=True,
             position=1,
             argstr="",
             help="input file",
@@ -372,7 +368,6 @@ def test_docker_cmd_inputspec_copyfile_1(plugin, tmp_path):
         shell.arg(
             name="orig_file",
             type=File,
-            mandatory=True,
             position=1,
             argstr="",
             help="orig file",
@@ -423,7 +418,6 @@ def test_docker_inputspec_state_1(plugin, tmp_path):
         shell.arg(
             name="file",
             type=File,
-            mandatory=True,
             position=1,
             argstr="",
             help="input file",
@@ -460,7 +454,6 @@ def test_docker_inputspec_state_1b(plugin, tmp_path):
         shell.arg(
             name="file",
             type=File,
-            mandatory=True,
             position=1,
             argstr="",
             help="input file",
@@ -490,7 +483,6 @@ def test_docker_wf_inputspec_1(plugin, tmp_path):
         shell.arg(
             name="file",
             type=File,
-            mandatory=True,
             position=1,
             argstr="",
             help="input file",
@@ -533,7 +525,6 @@ def test_docker_wf_state_inputspec_1(plugin, tmp_path):
         shell.arg(
             name="file",
             type=File,
-            mandatory=True,
             position=1,
             argstr="",
             help="input file",
@@ -578,7 +569,6 @@ def test_docker_wf_ndst_inputspec_1(plugin, tmp_path):
         shell.arg(
             name="file",
             type=File,
-            mandatory=True,
             position=1,
             argstr="",
             help="input file",

pydra/engine/tests/test_environments.py

@@ -179,7 +179,6 @@ def create_shelly_inputfile(tempdir, filename, name, executable):
             type=File,
             position=1,
             help="files",
-            mandatory=True,
             argstr="",
         )
     ]

pydra/utils/typing.py

@@ -1042,6 +1042,8 @@ def is_fileset_or_union(type_: type) -> bool:
     """Check if the type is a FileSet or a Union containing a FileSet"""
     if is_union(type_):
         return any(is_fileset_or_union(t) for t in ty.get_args(type_))
+    elif not inspect.isclass(type_):
+        return False
     return issubclass(type_, core.FileSet)