snakemake-executor-plugin-slurm 0.10.0__tar.gz → 0.10.2__tar.gz

{snakemake_executor_plugin_slurm-0.10.0 → snakemake_executor_plugin_slurm-0.10.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: snakemake-executor-plugin-slurm
-Version: 0.10.0
+Version: 0.10.2
 Summary: A Snakemake executor plugin for submitting jobs to a SLURM cluster.
 Home-page: https://github.com/snakemake/snakemake-executor-plugin-slurm
 License: MIT

{snakemake_executor_plugin_slurm-0.10.0 → snakemake_executor_plugin_slurm-0.10.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "snakemake-executor-plugin-slurm"
-version = "0.10.0"
+version = "0.10.2"
 description = "A Snakemake executor plugin for submitting jobs to a SLURM cluster."
 authors = [
     "Christian Meesters <meesters@uni-mainz.de>",
@@ -25,7 +25,7 @@ black = "^23.7.0"
 flake8 = "^6.1.0"
 coverage = "^7.3.1"
 pytest = "^7.4.2"
-snakemake = {git = "https://github.com/snakemake/snakemake.git"}
+snakemake = "^8.20.0"
 
 [tool.coverage.run]
 omit = [".*", "*/site-packages/*", "Snakefile"]

{snakemake_executor_plugin_slurm-0.10.0 → snakemake_executor_plugin_slurm-0.10.2}/snakemake_executor_plugin_slurm/__init__.py

@@ -137,7 +137,7 @@ class Executor(RemoteExecutor):
             f"sbatch "
             f"--parsable "
             f"--job-name {self.run_uuid} "
-            f"--output {slurm_logfile} "
+            f"--output '{slurm_logfile}' "
             f"--export=ALL "
             f"--comment {comment_str}"
         )
@@ -361,6 +361,7 @@ needs to restart this job upon a Snakemake restart.
 
 We leave it to SLURM to resume your job(s)"""
                     )
+                    yield j
                 elif status == "UNKNOWN":
                     # the job probably does not exist anymore, but 'sacct' did not work
                     # so we assume it is finished
@@ -408,6 +409,14 @@ We leave it to SLURM to resume your job(s)"""
                 )
             except subprocess.TimeoutExpired:
                 self.logger.warning("Unable to cancel jobs within a minute.")
+            except subprocess.CalledProcessError as e:
+                msg = e.stderr.strip()
+                if msg:
+                    msg = f": {msg}"
+                raise WorkflowError(
+                    "Unable to cancel jobs with scancel "
+                    f"(exit code {e.returncode}){msg}"
+                ) from e
 
     async def job_stati(self, command):
         """Obtain SLURM job status of all submitted jobs with sacct