snakemake-executor-plugin-slurm 0.11.0__py3-none-any.whl → 0.11.2__py3-none-any.whl

snakemake_executor_plugin_slurm/__init__.py

@@ -217,12 +217,26 @@ class Executor(RemoteExecutor):
 
         self.logger.debug(f"sbatch call: {call}")
         try:
-            out = subprocess.check_output(
-                call, shell=True, text=True, stderr=subprocess.STDOUT
-            ).strip()
+            process = subprocess.Popen(
+                call,
+                shell=True,
+                text=True,
+                stdout=subprocess.PIPE,
+                stderr=subprocess.PIPE,
+            )
+            out, err = process.communicate()
+            if process.returncode != 0:
+                raise subprocess.CalledProcessError(
+                    process.returncode, call, output=err
+                )
         except subprocess.CalledProcessError as e:
             raise WorkflowError(
-                f"SLURM job submission failed. The error message was {e.output}"
+                f"SLURM sbatch failed. The error message was {e.output}"
+            )
+        # any other error message indicating failure?
+        if "submission failed" in err:
+            raise WorkflowError(
+                f"SLURM job submission failed. The error message was {err}"
             )
 
         # multicluster submissions yield submission infos like
@@ -230,7 +244,9 @@ class Executor(RemoteExecutor):
         # --parsable option it simply yields "<id>;<name>".
         # To extract the job id we split by semicolon and take the first element
         # (this also works if no cluster name was provided)
-        slurm_jobid = out.split(";")[0]
+        slurm_jobid = out.strip().split(";")[0]
+        if not slurm_jobid:
+            raise WorkflowError("Failed to retrieve SLURM job ID from sbatch output.")
         slurm_logfile = slurm_logfile.replace("%j", slurm_jobid)
         self.logger.info(
             f"Job {job.jobid} has been submitted with SLURM jobid {slurm_jobid} "

{snakemake_executor_plugin_slurm-0.11.0.dist-info → snakemake_executor_plugin_slurm-0.11.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: snakemake-executor-plugin-slurm
-Version: 0.11.0
+Version: 0.11.2
 Summary: A Snakemake executor plugin for submitting jobs to a SLURM cluster.
 Home-page: https://github.com/snakemake/snakemake-executor-plugin-slurm
 License: MIT
@@ -12,6 +12,7 @@ Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 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 (>=9.1.1,<10.0.0)

snakemake_executor_plugin_slurm-0.11.2.dist-info/RECORD

@@ -0,0 +1,6 @@
+snakemake_executor_plugin_slurm/__init__.py,sha256=Ui5xbATI0VfB93GTyy8RPNu6dSyB0ArwfPV5PJA5b4U,25543
+snakemake_executor_plugin_slurm/utils.py,sha256=DuJdFJsAmvFsrnpyb8kMoqxTEEmTsEVxroDS1t9qOGw,434
+snakemake_executor_plugin_slurm-0.11.2.dist-info/LICENSE,sha256=YVc4xTLWMqGfFL36120k7rzXtsT6e4RkJsh68VVn12s,1076
+snakemake_executor_plugin_slurm-0.11.2.dist-info/METADATA,sha256=fpd5ziYEmFkZkEwLrqYq2pJmGyeXfBDG7Xp-3pqMafA,1432
+snakemake_executor_plugin_slurm-0.11.2.dist-info/WHEEL,sha256=Nq82e9rUAnEjt98J6MlVmMCZb-t9cYE2Ir1kpBmnWfs,88
+snakemake_executor_plugin_slurm-0.11.2.dist-info/RECORD,,

{snakemake_executor_plugin_slurm-0.11.0.dist-info → snakemake_executor_plugin_slurm-0.11.2.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.9.0
+Generator: poetry-core 1.9.1
 Root-Is-Purelib: true
 Tag: py3-none-any

snakemake_executor_plugin_slurm-0.11.0.dist-info/RECORD

@@ -1,6 +0,0 @@
-snakemake_executor_plugin_slurm/__init__.py,sha256=FleQvFmJ6A2h2uCCTBD92T8cSb5Bcol-sgJ-ggs6ggA,24923
-snakemake_executor_plugin_slurm/utils.py,sha256=DuJdFJsAmvFsrnpyb8kMoqxTEEmTsEVxroDS1t9qOGw,434
-snakemake_executor_plugin_slurm-0.11.0.dist-info/LICENSE,sha256=YVc4xTLWMqGfFL36120k7rzXtsT6e4RkJsh68VVn12s,1076
-snakemake_executor_plugin_slurm-0.11.0.dist-info/METADATA,sha256=lUdtjmOC4hamB-4RiuWvExT5zyD1syFt_TYSK8gz-N0,1381
-snakemake_executor_plugin_slurm-0.11.0.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-snakemake_executor_plugin_slurm-0.11.0.dist-info/RECORD,,