Merge branch 'main' into feat/requeue-flag

CHANGELOG.md

@@ -1,5 +1,18 @@
 # Changelog
 
+## [0.10.0](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.9.0...v0.10.0) (2024-08-23)
+
+
+### Features
+
+* in job stability ([#137](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/137)) ([c27f5f8](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/c27f5f8b4dcf7c2d9bc34fd4870d13ff24c0dfae))
+
+
+### Bug Fixes
+
+* add --parsable to sbatch call for a more robust output parsing ([#125](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/125)) ([5e41d05](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/5e41d0577593909f8f0f255c8de29141bfd0bbe3))
+* issue [#109](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/109) - preemption is no longer considered a failed status ([#132](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/132)) ([6dad273](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/6dad273b2f09ed8f10e3c26b92e2963c382e9fb8))
+
 ## [0.9.0](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.8.0...v0.9.0) (2024-08-06)
 
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "snakemake-executor-plugin-slurm"
-version = "0.9.0"
+version = "0.10.0"
 description = "A Snakemake executor plugin for submitting jobs to a SLURM cluster."
 authors = [
     "Christian Meesters <[email protected]>",

snakemake_executor_plugin_slurm/__init__.py

@@ -26,6 +26,8 @@
 from snakemake_interface_common.exceptions import WorkflowError
 from snakemake_executor_plugin_slurm_jobstep import get_cpus_per_task
 
+from .utils import delete_slurm_environment
+
 
 @dataclass
 class ExecutorSettings(ExecutorSettingsBase):
@@ -97,10 +99,11 @@ def warn_on_jobcontext(self, done=None):
             if "SLURM_JOB_ID" in os.environ:
                 self.logger.warning(
                     "You are running snakemake in a SLURM job context. "
-                    "This is not recommended, as it may lead to unexpected behavior."
+                    "This is not recommended, as it may lead to unexpected behavior. "
                     "Please run Snakemake directly on the login node."
                 )
                 time.sleep(5)
+                delete_slurm_environment()
         done = True
 
     def additional_general_args(self):

snakemake_executor_plugin_slurm/utils.py

@@ -0,0 +1,16 @@
+# utility functions for the SLURM executor plugin
+
+import os
+
+
+def delete_slurm_environment():
+    """
+    Function to delete all environment variables
+    starting with 'SLURM_'. The parent shell will
+    still have this environment. This is needed to
+    submit within a SLURM job context to avoid
+    conflicting environments.
+    """
+    for var in os.environ:
+        if var.startswith("SLURM_"):
+            del os.environ[var]