snakemake-executor-plugin-slurm 0.4.2__tar.gz → 0.4.4__tar.gz

{snakemake_executor_plugin_slurm-0.4.2 → snakemake_executor_plugin_slurm-0.4.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: snakemake-executor-plugin-slurm
-Version: 0.4.2
+Version: 0.4.4
 Summary: A Snakemake executor plugin for submitting jobs to a SLURM cluster.
 Home-page: https://github.com/snakemake/snakemake-executor-plugin-slurm
 License: MIT
@@ -12,9 +12,9 @@ Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Requires-Dist: snakemake-executor-plugin-slurm-jobstep (>=0.1.10,<0.2.0)
+Requires-Dist: snakemake-executor-plugin-slurm-jobstep (>=0.2.0,<0.3.0)
 Requires-Dist: snakemake-interface-common (>=1.13.0,<2.0.0)
-Requires-Dist: snakemake-interface-executor-plugins (>=9.0.0,<10.0.0)
+Requires-Dist: snakemake-interface-executor-plugins (>=9.1.1,<10.0.0)
 Requires-Dist: throttler (>=1.2.2,<2.0.0)
 Project-URL: Documentation, https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html
 Project-URL: Repository, https://github.com/snakemake/snakemake-executor-plugin-slurm

{snakemake_executor_plugin_slurm-0.4.2 → snakemake_executor_plugin_slurm-0.4.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "snakemake-executor-plugin-slurm"
-version = "0.4.2"
+version = "0.4.4"
 description = "A Snakemake executor plugin for submitting jobs to a SLURM cluster."
 authors = [
     "Christian Meesters <meesters@uni-mainz.de>",
@@ -16,8 +16,8 @@ keywords = ["snakemake", "plugin", "executor", "cluster", "slurm"]
 [tool.poetry.dependencies]
 python = "^3.11"
 snakemake-interface-common = "^1.13.0"
-snakemake-interface-executor-plugins = "^9.0.0"
-snakemake-executor-plugin-slurm-jobstep = "^0.1.10"
+snakemake-interface-executor-plugins = "^9.1.1"
+snakemake-executor-plugin-slurm-jobstep = "^0.2.0"
 throttler = "^1.2.2"
 
 [tool.poetry.group.dev.dependencies]

{snakemake_executor_plugin_slurm-0.4.2 → snakemake_executor_plugin_slurm-0.4.4}/snakemake_executor_plugin_slurm/__init__.py

@@ -18,6 +18,7 @@ from snakemake_interface_executor_plugins.jobs import (
     JobExecutorInterface,
 )
 from snakemake_interface_common.exceptions import WorkflowError
+from snakemake_executor_plugin_slurm_jobstep import get_cpus_per_task
 
 
 # Required:
@@ -65,7 +66,7 @@ class Executor(RemoteExecutor):
         # with job_info being of type
         # snakemake_interface_executor_plugins.executors.base.SubmittedJobInfo.
 
-        log_folder = f"group_{job.name}" if job.is_group() else f"rule_{job.name}"
+        group_or_rule = f"group_{job.name}" if job.is_group() else f"rule_{job.name}"
 
         try:
             wildcard_str = f"_{'_'.join(job.wildcards)}" if job.wildcards else ""
@@ -73,9 +74,17 @@ class Executor(RemoteExecutor):
             wildcard_str = ""
 
         slurm_logfile = os.path.abspath(
-            f".snakemake/slurm_logs/{log_folder}/%j{wildcard_str}.log"
+            f".snakemake/slurm_logs/{group_or_rule}/{wildcard_str}/%j.log"
         )
-        os.makedirs(os.path.dirname(slurm_logfile), exist_ok=True)
+        logdir = os.path.dirname(slurm_logfile)
+        # this behavior has been fixed in slurm 23.02, but there might be plenty of
+        # older versions around, hence we should rather be conservative here.
+        assert "%j" not in logdir, (
+            "bug: jobid placeholder in parent dir of logfile. This does not work as "
+            "we have to create that dir before submission in order to make sbatch "
+            "happy. Otherwise we get silent fails without logfiles being created."
+        )
+        os.makedirs(logdir, exist_ok=True)
 
         # generic part of a submission string:
         # we use a run_uuid as the job-name, to allow `--name`-based
@@ -118,18 +127,7 @@ class Executor(RemoteExecutor):
         # fixes #40 - set ntasks regarlless of mpi, because
         # SLURM v22.05 will require it for all jobs
         call += f" --ntasks={job.resources.get('tasks', 1)}"
-
-        cpus_per_task = job.threads
-        if job.resources.get("cpus_per_task"):
-            if not isinstance(cpus_per_task, int):
-                raise WorkflowError(
-                    f"cpus_per_task must be an integer, but is {cpus_per_task}"
-                )
-            cpus_per_task = job.resources.cpus_per_task
-        # ensure that at least 1 cpu is requested
-        # because 0 is not allowed by slurm
-        cpus_per_task = max(1, cpus_per_task)
-        call += f" --cpus-per-task={cpus_per_task}"
+        call += f" --cpus-per-task={get_cpus_per_task(job)}"
 
         if job.resources.get("slurm_extra"):
             call += f" {job.resources.slurm_extra}"