snakemake-executor-plugin-slurm 0.5.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

snakemake_executor_plugin_slurm/__init__.py

@@ -6,6 +6,7 @@ __license__ = "MIT"
 import csv
 from io import StringIO
 import os
+import re
 import subprocess
 import time
 from datetime import datetime, timedelta
@@ -49,11 +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"
 
@@ -143,6 +157,7 @@ class Executor(RemoteExecutor):
         call += f" --cpus-per-task={get_cpus_per_task(job)}"
 
         if job.resources.get("slurm_extra"):
+            self.check_slurm_extra(job)
             call += f" {job.resources.slurm_extra}"
 
         exec_job = self.format_job_exec(job)
@@ -391,6 +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(
@@ -428,7 +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: "
@@ -488,3 +504,15 @@ class Executor(RemoteExecutor):
             "'slurm_partition=<your default partition>'."
         )
         return ""
+
+    def check_slurm_extra(self, job):
+        jobname = re.compile(r"--job-name[=?|\s+]|-J\s?")
+        if re.search(jobname, job.resources.slurm_extra):
+            raise WorkflowError(
+                "The '--job-name' option is not allowed in the 'slurm_extra' "
+                "parameter. The job name is set by snakemake and must not be "
+                "overwritten. It is internally used to check the stati of all "
+                "submitted jobs by this workflow."
+                "Please consult the documentation if you are unsure how to "
+                "query the status of your jobs."
+            )

{snakemake_executor_plugin_slurm-0.5.2.dist-info → snakemake_executor_plugin_slurm-0.7.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: snakemake-executor-plugin-slurm
-Version: 0.5.2
+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-0.7.0.dist-info/RECORD

@@ -0,0 +1,5 @@
+snakemake_executor_plugin_slurm/__init__.py,sha256=23xB0r9M9PqkM6g8sdOps_J6xKCwOUBOrNkZY9vJN_k,22157
+snakemake_executor_plugin_slurm-0.7.0.dist-info/LICENSE,sha256=YVc4xTLWMqGfFL36120k7rzXtsT6e4RkJsh68VVn12s,1076
+snakemake_executor_plugin_slurm-0.7.0.dist-info/METADATA,sha256=f77cauodNnBf_n9sGNgTkkiAhf_1A3-oAOQRtDioFZ0,1380
+snakemake_executor_plugin_slurm-0.7.0.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+snakemake_executor_plugin_slurm-0.7.0.dist-info/RECORD,,

snakemake_executor_plugin_slurm-0.5.2.dist-info/RECORD

@@ -1,5 +0,0 @@
-snakemake_executor_plugin_slurm/__init__.py,sha256=q25l-j-o7I4hjHIX8mIuyEqde4g_oz7_bjZuflcGTnU,20908
-snakemake_executor_plugin_slurm-0.5.2.dist-info/LICENSE,sha256=YVc4xTLWMqGfFL36120k7rzXtsT6e4RkJsh68VVn12s,1076
-snakemake_executor_plugin_slurm-0.5.2.dist-info/METADATA,sha256=7dUfUtoxbgD-ZluaigOJJAqKwMw1XJOXjJ0RJvCMVyo,1380
-snakemake_executor_plugin_slurm-0.5.2.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-snakemake_executor_plugin_slurm-0.5.2.dist-info/RECORD,,