allow graceful failure of workflows when not debugging

Author: tclose

new-docs/source/examples/glm.ipynb

@@ -56,6 +56,7 @@
     "from pathlib import Path\n",
     "\n",
     "from pydra.design import python, workflow\n",
+    "from pydra.engine.submitter import Submitter\n",
     "from fileformats.generic import File, Directory\n",
     "from fileformats.text import Csv\n",
     "import pandas as pd\n",
@@ -588,8 +589,10 @@
    "source": [
     "wf = FullWorkflow(output_dir=workflow_out_dir, n_subjects=1, contrast='StopSuccess - Go')\n",
     "\n",
-    "if False:\n",
-    "    results = wf(plugin='cf', n_procs=4)\n",
+    "if __name__ == \"__main__\":\n",
+    "    with Submitter(worker='cf', n_procs=4) as sub:\n",
+    "        results = sub(wf)\n",
+    "\n",
     "    print(results)"
    ]
   },
@@ -630,7 +633,7 @@
    },
    "outputs": [],
    "source": [
-    "!ls ../outputs/6_glm"
+    "! ls ../outputs/6_glm"
    ]
   },
   {
@@ -641,14 +644,6 @@
     "### Plot figures"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "dad22ca7",
-   "metadata": {},
-   "source": [
-    "#### First level contrast"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -662,73 +657,19 @@
    "source": [
     "from IPython.display import Image\n",
     "\n",
-    "Image(filename='../outputs/6_glm/firstlevel_contrast.jpg')"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "0cdfcc29",
-   "metadata": {},
-   "source": [
-    "#### Nilearn Z map"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "f08aa59f",
-   "metadata": {
-    "tags": [
-     "hide-input"
-    ]
-   },
-   "outputs": [],
-   "source": [
-    "Image(filename='../outputs/6_glm/nilearn_z_map.jpg')"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "ca1b896f",
-   "metadata": {},
-   "source": [
-    "#### FSL Z map"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "7d18b6ed",
-   "metadata": {
-    "tags": [
-     "hide-input"
-    ]
-   },
-   "outputs": [],
-   "source": [
-    "Image(filename='../outputs/6_glm/fsl_z_map.jpg')"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "fc68e7dc",
-   "metadata": {},
-   "source": [
-    "#### Nilearn FSL comparison"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "a37679ff",
-   "metadata": {
-    "tags": [
-     "hide-input"
-    ]
-   },
-   "outputs": [],
-   "source": [
-    "Image(filename='../outputs/6_glm/nilearn_fsl_comp.jpg')"
+    "\n",
+    "if not results.errored:\n",
+    "    # First-level contrast\n",
+    "    Image(filename='../outputs/6_glm/firstlevel_contrast.jpg')\n",
+    "\n",
+    "    # Nilearn Z map\n",
+    "    Image(filename='../outputs/6_glm/nilearn_z_map.jpg')\n",
+    "\n",
+    "    # FSL Z map\n",
+    "    Image(filename='../outputs/6_glm/fsl_z_map.jpg')\n",
+    "\n",
+    "    # Nilearn and FSL comparison\n",
+    "    Image(filename='../outputs/6_glm/nilearn_fsl_comp.jpg')"
    ]
   },
   {

pydra/engine/submitter.py

@@ -29,11 +29,12 @@
 
 if ty.TYPE_CHECKING:
     from .node import Node
-    from .specs import TaskDef, WorkflowDef, TaskHooks
+    from .specs import TaskDef, TaskOutputs, WorkflowDef, TaskHooks, Result
     from .environments import Environment
     from .state import State
 
 DefType = ty.TypeVar("DefType", bound="TaskDef")
+OutputType = ty.TypeVar("OutputType", bound="TaskOutputs")
 
 # Used to flag development mode of Audit
 develop = False
@@ -167,14 +168,34 @@ def worker(self):
 
     def __call__(
         self,
-        task_def: "TaskDef",
-        name: str | None = "task",
+        task_def: "TaskDef[OutputType]",
         hooks: "TaskHooks | None" = None,
-    ):
-        """Submitter run function."""
+        raise_errors: bool | None = None,
+    ) -> "Result[OutputType]":
+        """Submitter run function.
 
-        if name is None:
-            name = "task"
+        Parameters
+        ----------
+        task_def : :obj:`~pydra.engine.specs.TaskDef`
+            The task definition to run
+        hooks : :obj:`~pydra.engine.specs.TaskHooks`, optional
+            Task hooks, callable functions called as the task is setup and torn down,
+            by default no functions are called at the hooks
+        raise_errors : bool, optional
+            Whether to raise errors, by default True if the 'debug' worker is used,
+            otherwise False
+
+        Returns
+        -------
+        result : Any
+            The result of the task
+        """
+        if raise_errors is None:
+            raise_errors = self.worker_name == "debug"
+        if not isinstance(raise_errors, bool):
+            raise TypeError(
+                f"'raise_errors' must be a boolean or None, not {type(raise_errors)}"
+            )
 
         task_def._check_rules()
         # If the outer task is split, create an implicit workflow to hold the split nodes
@@ -198,7 +219,7 @@ def Split(defn: TaskDef, output_types: dict):
         task = Task(
             task_def,
             submitter=self,
-            name=name,
+            name="task",
             environment=self.environment,
             hooks=hooks,
         )
@@ -211,11 +232,15 @@ def Split(defn: TaskDef, output_types: dict):
             else:
                 self.worker.run(task, rerun=self.rerun)
         except Exception as e:
-            e.add_note(
+            msg = (
                 f"Full crash report for {type(task_def).__name__!r} task is here: "
                 + str(task.output_dir / "_error.pklz")
             )
-            raise e
+            if raise_errors:
+                e.add_note(msg)
+                raise e
+            else:
+                logger.error("\nTask execution failed\n" + msg)
         finally:
             self.run_start_time = None
         PersistentCache().clean_up()

pyproject.toml

@@ -48,6 +48,7 @@ doc = [
     "ipython",
     "ipykernel",
     "ipywidgets",
+    "matplotlib",
     "nbsphinx",
     "nest_asyncio",
     "nibabel",