snakemake-executor-plugin-slurm 0.6.0__tar.gz → 0.7.0__tar.gz

{snakemake_executor_plugin_slurm-0.6.0 → snakemake_executor_plugin_slurm-0.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: snakemake-executor-plugin-slurm
-Version: 0.6.0
+Version: 0.7.0
 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-0.6.0 → snakemake_executor_plugin_slurm-0.7.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "snakemake-executor-plugin-slurm"
-version = "0.6.0"
+version = "0.7.0"
 description = "A Snakemake executor plugin for submitting jobs to a SLURM cluster."
 authors = [
     "Christian Meesters <meesters@uni-mainz.de>",

{snakemake_executor_plugin_slurm-0.6.0 → snakemake_executor_plugin_slurm-0.7.0}/snakemake_executor_plugin_slurm/__init__.py

@@ -50,11 +50,24 @@ common_settings = CommonSettings(
 # Implementation of your executor
 class Executor(RemoteExecutor):
     def __post_init__(self):
+        # run check whether we are running in a SLURM job context
+        self.warn_on_jobcontext()
         self.run_uuid = str(uuid.uuid4())
         self.logger.info(f"SLURM run ID: {self.run_uuid}")
         self._fallback_account_arg = None
         self._fallback_partition = None
 
+    def warn_on_jobcontext(self, done=None):
+        if not done:
+            if "SLURM_JOB_ID" in os.environ:
+                self.logger.warning(
+                    "Running Snakemake in a SLURM within a job may lead"
+                    " to unexpected behavior. Please run Snakemake directly"
+                    " on the head node."
+                )
+                time.sleep(5)
+        done = True
+
     def additional_general_args(self):
         return "--executor slurm-jobstep --jobs 1"
 
@@ -393,6 +406,7 @@ class Executor(RemoteExecutor):
                 account = self.get_account()
                 if account:
                     self.logger.warning(f"Guessed SLURM account: {account}")
+                    self.test_account(f"{account}")
                     self._fallback_account_arg = f" -A {account}"
                 else:
                     self.logger.warning(
@@ -430,7 +444,7 @@ class Executor(RemoteExecutor):
             sacct_out = subprocess.check_output(
                 cmd, shell=True, text=True, stderr=subprocess.PIPE
             )
-            return sacct_out.strip()
+            return sacct_out.replace("(null)", "").strip()
         except subprocess.CalledProcessError as e:
             self.logger.warning(
                 f"No account was given, not able to get a SLURM account via sacct: "