From 3abb561b97b3dcede1aa57ae6bb89bdcc2eadda1 Mon Sep 17 00:00:00 2001
From: Johannes Koester <johannes.koester@uni-due.de>
Date: Fri, 29 Nov 2024 09:25:52 +0100
Subject: [PATCH 1/2] feat: job arrays

---
 snakemake_executor_plugin_slurm/__init__.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/snakemake_executor_plugin_slurm/__init__.py b/snakemake_executor_plugin_slurm/__init__.py
index e70b5a16..994874a7 100644
--- a/snakemake_executor_plugin_slurm/__init__.py
+++ b/snakemake_executor_plugin_slurm/__init__.py
@@ -5,6 +5,7 @@
 
 import csv
 from io import StringIO
+from itertools import groupby
 import os
 import re
 import shlex
@@ -107,6 +108,20 @@ def warn_on_jobcontext(self, done=None):
     def additional_general_args(self):
         return "--executor slurm-jobstep --jobs 1"
 
+    def run_jobs(self, jobs: List[JobExecutorInterface]):
+        for _, same_rule_jobs in groupby(jobs, key=lambda job: job.rule.name):
+            if len(same_rule_jobs) == 1:
+                self.run_job(same_rule_jobs[0])
+            else:
+                # TODO submit as array
+                # share code with run_job
+
+                # TODO in the future: give a hint to the scheduler to select preferably
+                # many jobs from the same rule if possible, in order to have
+                # more efficient array jobs. This should be somehow tunable, because
+                # it might contradict other efficiency goals.
+                ...
+
     def run_job(self, job: JobExecutorInterface):
         # Implement here how to run a job.
         # You can access the job's resources, etc.

From 5e8accaf954dfda1f437cfb1c8a60e5c2daf0d79 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20K=C3=B6ster?= <johannes.koester@uni-due.de>
Date: Fri, 20 Dec 2024 11:29:26 +0100
Subject: [PATCH 2/2] Update snakemake_executor_plugin_slurm/__init__.py

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
---
 snakemake_executor_plugin_slurm/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/snakemake_executor_plugin_slurm/__init__.py b/snakemake_executor_plugin_slurm/__init__.py
index 994874a7..561845af 100644
--- a/snakemake_executor_plugin_slurm/__init__.py
+++ b/snakemake_executor_plugin_slurm/__init__.py
@@ -109,7 +109,8 @@ def additional_general_args(self):
         return "--executor slurm-jobstep --jobs 1"
 
     def run_jobs(self, jobs: List[JobExecutorInterface]):
-        for _, same_rule_jobs in groupby(jobs, key=lambda job: job.rule.name):
+        for rule_name, group in groupby(jobs, key=lambda job: job.rule.name):
+            same_rule_jobs = list(group)  # Materialize the generator
             if len(same_rule_jobs) == 1:
                 self.run_job(same_rule_jobs[0])
             else:
@@ -121,7 +122,6 @@ def run_jobs(self, jobs: List[JobExecutorInterface]):
                 # more efficient array jobs. This should be somehow tunable, because
                 # it might contradict other efficiency goals.
                 ...
-
     def run_job(self, job: JobExecutorInterface):
         # Implement here how to run a job.
         # You can access the job's resources, etc.