feat: added requeue option to client

slaube-jgu commented 3 months ago

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.

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.

coderabbitai[bot] commented 3 months ago

Walkthrough

The recent changes introduce a requeue boolean field to the ExecutorSettings class, allowing users to specify whether preempted or failed jobs should be requeued. This field is initialized with a default value of False and integrates with the SLURM job scheduler by adding the --requeue flag to the sbatch command when enabled. The logic in the run_job method has been updated to reflect this new functionality.

Changes

Files	Change Summary
`snakemake_executor_plugin_slurm/__init__.py`	Introduced a `requeue` boolean field to `ExecutorSettings`, defaulting to `False`, and modified `run_job` to append `--requeue` to the command if the flag is enabled.
`tests/tests.py`	Renamed `TestWorkflowsBase` to `TestWorkflows`, updated `get_executor_settings` to return `ExecutorSettings`, and added `TestWorkflowsRequeue` subclass to test the `requeue` functionality.

Possibly related PRs

137: This PR involves modifications to the warn_on_jobcontext method in the ExecutorSettings class, which may interact with job submission processes, although it does not directly relate to the new requeue functionality.
140: This PR alters the run_job method in the ExecutorSettings class, which is directly related to job submission and may be impacted by the new requeue feature introduced in the main PR.

Poem

🐰 In code we hop, with settings bright,
A requeue flag brings jobs to light.
When failures strike, don’t fear the fall,
With SLURM’s help, we’ll stand up tall!
So here’s to changes, swift and neat,
Let’s celebrate with a happy beat! 🎉

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cmeesters commented 3 months ago

@johanneskoester I requested your review, because locally testworkflows run just fine and our change yields valid Python types, where the CI thinks a None-Type is given. Ideas?

cmeesters commented 2 months ago

The tests still fail - while working locally, the CI claims

FAILED tests/tests.py::TestWorkflowsBase::test_simple_workflow - AttributeError: 'NoneType' object has no attribute 'requeue'

cmeesters commented 2 months ago

ah, wanted to look into this CI issue - turns out, I cannot find this branch. WTF???

cmeesters commented 1 month ago

I see. Cool! Thanks!

snakemake / snakemake-executor-plugin-slurm