feat: added requeue option to client (snakemake#136)

added option for users to indicate the sbatch requeue flag if the
cluster configuration does no re-queuing on default

this is a boolean flag. We wait for the interface_plugin to be fixed.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Introduced a new option to allow requeuing of preempted or failed jobs
in the job execution settings.
- Added a `--requeue` flag to the job submission command for enhanced
control over job handling.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: meesters <meesters@uni-mainz.de>
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
Co-authored-by: Christian Meesters <cmeesters@users.noreply.github.com>

Author: 3 people

snakemake_executor_plugin_slurm/__init__.py

@@ -42,6 +42,18 @@ class ExecutorSettings(ExecutorSettingsBase):
             "required": False,
         },
     )
+    requeue: bool = field(
+        default=False,
+        metadata={
+            "help": """
+                    Allow requeuing preempted of failed jobs,
+                    if no cluster default. Results in `sbatch ... --requeue ...`
+                    This flag has no effect, if not set.
+                    """,
+            "env_var": False,
+            "required": False,
+        },
+    )
 
 
 # Required:
@@ -79,8 +91,6 @@ def __post_init__(self):
         self._fallback_account_arg = None
         self._fallback_partition = None
         self._preemption_warning = False  # no preemption warning has been issued
-        # providing a short-hand, even if subsequent calls seem redundant
-        self.settings: ExecutorSettings = self.workflow.executor_settings
 
     def warn_on_jobcontext(self, done=None):
         if not done:
@@ -145,6 +155,9 @@ def run_job(self, job: JobExecutorInterface):
         call += self.get_account_arg(job)
         call += self.get_partition_arg(job)
 
+        if self.workflow.executor_settings.requeue:
+            call += " --requeue"
+
         if job.resources.get("clusters"):
             call += f" --clusters {job.resources.clusters}"
 

tests/tests.py

@@ -2,12 +2,19 @@
 import snakemake.common.tests
 from snakemake_interface_executor_plugins.settings import ExecutorSettingsBase
 
+from snakemake_executor_plugin_slurm import ExecutorSettings
 
-class TestWorkflowsBase(snakemake.common.tests.TestWorkflowsLocalStorageBase):
+
+class TestWorkflows(snakemake.common.tests.TestWorkflowsLocalStorageBase):
     __test__ = True
 
     def get_executor(self) -> str:
         return "slurm"
 
     def get_executor_settings(self) -> Optional[ExecutorSettingsBase]:
-        return None
+        return ExecutorSettings()
+
+
+class TestWorkflowsRequeue(TestWorkflows):
+    def get_executor_settings(self) -> Optional[ExecutorSettingsBase]:
+        return ExecutorSettings(requeue=True)