[MAINT] Bump pydra to 0.23

clinica/pydra/engine_utils.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from os import PathLike
 from typing import Optional
 
@@ -50,7 +52,7 @@ def list_workflow_inputs(wf: Workflow) -> dict:
     return inputs
 
 
-def run(wf: Workflow, n_procs: Optional[int] = None) -> Result:
+def run(wf: Workflow, n_procs: int | None = None) -> Result:
     """Execute a Pydra workflow.
 
     If the execution of the workflow fails, the
@@ -62,19 +64,19 @@ def run(wf: Workflow, n_procs: Optional[int] = None) -> Result:
         The workflow to be executed.
 
     n_procs : int, optional
-        The number of CPU cores to be used to run the workflow.
-        If None, all available cores will be used.
+        The number of CPU cores used to run the workflow concurrently.
+        If None, the workflow is run sequentially.
 
     Returns
     -------
     Result :
         The result of running the Workflow
-
     """
     import re
 
     try:
-        with Submitter(plugin="cf", n_procs=n_procs) as submitter:
+        submitter_args = {"plugin": "cf", "n_procs": n_procs} if n_procs else {"plugin": "serial"}
+        with Submitter(**submitter_args) as submitter:
             submitter(wf)
     except Exception as e:
         path = re.search(r"/.*\.pklz", str(e))

clinica/pydra/pet_linear/pipeline.py

@@ -39,7 +39,7 @@ def build_core_workflow(name: str = "core", parameters: dict = {}) -> Workflow:
         name="Input",
         fields=[
             ("_graph_checksums", ty.Any),
-            ("T1w", str, {"mandatory": True}),
+            ("T1w", str, {"help_string": "T1w", "mandatory": True}),
             ("pet", dict, {"tracer": parameters["acq_label"]}, {"mandatory": True}),
             ("t1w_to_mni", dict, {}, {"mandatory": True}),
         ],

clinica/pydra/t1_linear/t1_linear.py

@@ -48,7 +48,7 @@ def build_core_workflow(name: str = "core", parameters={}) -> Workflow:
 
     input_spec = pydra.specs.SpecInfo(
         name="Input",
-        fields=[("T1w", str, {"mandatory": True})],
+        fields=[("T1w", str, {"help_string": "T1w", "mandatory": True})],
         bases=(pydra.specs.BaseSpec,),
     )
 

pyproject.toml

@@ -49,8 +49,8 @@ click-option-group = "^0.5"
 xlrd = "*"
 openpyxl = "*"
 fsspec = "*"
-pydra-nipype1 = "^0.2"
-pydra = "^0.22"
+pydra-nipype1 = "^0.3"
+pydra = "^0.23"
 pybids = "^0.16"
 joblib = "^1.2.0"
 attrs = ">=20.1.0"

test/unittests/pydra/test_engine.py

@@ -40,7 +40,7 @@ def pipeline():
 def core_workflow():
     input_spec = pydra.specs.SpecInfo(
         name="Input",
-        fields=[("T1w", str, {"mandatory": True})],
+        fields=[("T1w", str, {"help_string": "T1w", "mandatory": True})],
         bases=(pydra.specs.BaseSpec,),
     )
     wf = Workflow("smoothing_t1w", input_spec=input_spec)