feat(core): make toil the default workflow backend (#3220)

Author: Panaetius

poetry.lock

@@ -136,7 +136,7 @@ sphinx-click = { version = "^4.3.0", optional = true }
 sphinx-rtd-theme = { version = "<1.1,>=0.5.0", optional = true }
 sphinx-tabs = { version = "==3.2.0", optional = true }
 tabulate = ">=0.7.7,<0.8.11"
-toil = { version = "==5.7.1", optional = true }
+toil = "5.7.1"
 tqdm = "<4.62.4,>=4.48.1"
 types-python-dateutil = { version="^2.8.10", optional = true }
 types-PyYAML = { version="<6.1.0,>=5.4", optional = true }
@@ -205,7 +205,6 @@ tests = [
     "types-requests",
     "types-tabulate"
 ]
-toil = ["toil"]
 docs = ["plantweb", "renku-sphinx-theme", "sphinx-click", "sphinx-rtd-theme", "sphinxcontrib-spelling", "sphinx-tabs"]
 all = [
     "apispec",

pyproject.toml

@@ -69,14 +69,14 @@ def available_workflow_providers() -> List[str]:
     return [p[1] for p in providers]
 
 
-def execute(dag: "nx.DiGraph", basedir: Path, config: Dict[str, Any], provider: str = "cwltool") -> List[str]:
+def execute(dag: "nx.DiGraph", basedir: Path, config: Dict[str, Any], provider: str = "toil") -> List[str]:
     """Executes a given workflow using the selected provider.
 
     Args:
         dag("nx.DiGraph"): The workflow graph to execute.
         basedir(Path): The root directory of the renku project.
         config(Dict[str, Any]): Configuration values for the workflow provider.
-        provider(str, optional): The workflow executor engine to be used (Default value = "cwltool").
+        provider(str, optional): The workflow executor engine to be used (Default value = "toil").
 
     Returns:
         List[str]: List of paths that has been modified.

renku/core/plugin/provider.py

@@ -52,7 +52,7 @@ def execute_workflow_graph(
     dag: "DiGraph",
     activity_gateway: IActivityGateway,
     plan_gateway: IPlanGateway,
-    provider="cwltool",
+    provider="toil",
     config=None,
     workflow_file_plan: Optional[WorkflowFileCompositePlan] = None,
 ):
@@ -62,7 +62,7 @@ def execute_workflow_graph(
         dag(DiGraph): The workflow graph to execute.
         activity_gateway(IActivityGateway): The injected activity gateway.
         plan_gateway(IPlanGateway): The injected plan gateway.
-        provider: Provider to run the workflow with (Default value = "cwltool").
+        provider: Provider to run the workflow with (Default value = "toil").
         config: Path to config for the workflow provider (Default value = None).
         workflow_file_plan (Optional[WorkflowFileCompositePlan): If passed, a workflow file is executed, so, store
             related metadata.

renku/core/workflow/execute.py

@@ -96,7 +96,7 @@
     "provider",
     "-p",
     "--provider",
-    default="cwltool",
+    default="toil",
     show_default=True,
     type=click.Choice(Proxy(available_workflow_providers), case_sensitive=False),
     help="The workflow engine to use.",

renku/ui/cli/rerun.py

@@ -173,7 +173,7 @@
     "provider",
     "-p",
     "--provider",
-    default="cwltool",
+    default="toil",
     show_default=True,
     type=click.Choice(Proxy(available_workflow_providers), case_sensitive=False),
     help="The workflow engine to use.",

renku/ui/cli/update.py

@@ -1135,7 +1135,7 @@ def outputs(ctx, paths):
     "provider",
     "-p",
     "--provider",
-    default="cwltool",
+    default="toil",
     show_default=True,
     type=click.Choice(Proxy(available_workflow_providers), case_sensitive=False),
     help="The workflow engine to use.",
@@ -1311,7 +1311,7 @@ def visualize(sources, columns, exclude_files, ascii, revision, format, interact
     "provider",
     "-p",
     "--provider",
-    default="cwltool",
+    default="toil",
     show_default=True,
     type=click.Choice(Proxy(available_workflow_providers), case_sensitive=False),
     help="The workflow engine to use.",