Runner refac

bclenet · Jan 29, 2024 · c2610e1 · c2610e1
1 parent 5563921
commit c2610e1
Show file tree

Hide file tree

Showing 2 changed files with 28 additions and 25 deletions.
diff --git a/narps_open/runner.py b/narps_open/runner.py
@@ -106,38 +106,38 @@ def start(self, first_level_only: bool = False, group_level_only: bool = False)
         if first_level_only and group_level_only:
             raise AttributeError('first_level_only and group_level_only cannot both be True')
 
-        # Generate workflow list
-        workflow_list = []
+        # Generate workflow lists
+        first_level_workflows = []
+        group_level_workflows = []
+
         if not group_level_only:
-            workflow_list += [
+            for workflow in [
                 self._pipeline.get_preprocessing(),
                 self._pipeline.get_run_level_analysis(),
-                self._pipeline.get_subject_level_analysis(),
-            ]
-        if not first_level_only:
-            workflow_list += [
-                self._pipeline.get_group_level_analysis()
-            ]
+                self._pipeline.get_subject_level_analysis()]:
 
-        nb_procs = Configuration()['runner']['nb_procs']
+                if isinstance(workflow, list):
+                    for sub_workflow in workflow:
+                        first_level_workflows.append(sub_workflow)
+                else:
+                    first_level_workflows.append(workflow)
+
+        if not first_level_only:
+            for workflow in [self._pipeline.get_group_level_analysis()]:
+                if isinstance(workflow, list):
+                    for sub_workflow in workflow:
+                        group_level_workflows.append(sub_workflow)
+                else:
+                    group_level_workflows.append(workflow)
 
         # Launch workflows
-        for workflow in workflow_list:
+        for workflow in first_level_workflows + group_level_workflows:
             if workflow is None:
                 pass
-            elif isinstance(workflow, list):
-                for sub_workflow in workflow:
-                    if not isinstance(sub_workflow, Workflow):
-                        raise AttributeError('Workflow must be of type nipype.Workflow')
-
-                    if nb_procs > 1:
-                        sub_workflow.run('MultiProc', plugin_args = {'n_procs': nb_procs})
-                    else:
-                        sub_workflow.run()
+            elif not isinstance(workflow, Workflow):
+                raise AttributeError('Workflow must be of type nipype.Workflow')
             else:
-                if not isinstance(workflow, Workflow):
-                    raise AttributeError('Workflow must be of type nipype.Workflow')
-
+                nb_procs = Configuration()['runner']['nb_procs']
                 if nb_procs > 1:
                     workflow.run('MultiProc', plugin_args = {'n_procs': nb_procs})
                 else:

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -44,8 +44,11 @@ def test_pipeline_execution(
         - keep intermediate levels : boolean in PipelineRunner
     """
     # A list of number of subject to iterate over
-    nb_subjects_subgroup = Configuration()['testing']['pipelines']['nb_subjects_per_group']
-    nb_subjects_list = [s for s in range(nb_subjects_subgroup, nb_subjects, nb_subjects_subgroup)]
+    nb_subjects_list = list(range(
+        Configuration()['testing']['pipelines']['nb_subjects_per_group'],
+        nb_subjects,
+        Configuration()['testing']['pipelines']['nb_subjects_per_group'])
+        )
     nb_subjects_list.append(nb_subjects)
 
     # Initialize the pipeline