fix: pipeline hangs when submitting from compute nodes (#450)

When running snakemake from within a SLURM job (e.g., an interactive
session on a compute node), the pipeline would submit jobs but never
detect their completion, hanging forever.

The RemoteExecutor base class starts a status-checking daemon thread in
`__init__` *before* `__post_init__` is called. The SLURM plugin's
`warn_on_jobcontext()` in `__post_init__` would sleep 5 seconds and then
delete SLURM environment variables, but by then the daemon thread had
already started and would silently die after its first polling cycle.

Fix: move the SLURM environment detection and cleanup into `__init__`,
before `super().__init__()` starts the daemon thread. Remove the now
unnecessary `warn_on_jobcontext()` method and its 5-second sleep.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

* **Bug Fixes**
* Cleaner SLURM environment detection and immediate cleanup during
executor startup, with an earlier warning when a SLURM job context is
present to improve job submission reliability.
* **Tests**
* Test suite updated to align with the revised executor initialization
and warning behavior; expectations remain unchanged.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-authored-by: Christian Meesters <cmeesters@users.noreply.github.com>

Author: 3 people

snakemake_executor_plugin_slurm/__init__.py

@@ -428,9 +428,22 @@ def _select_logdir(workflow):
 # Required:
 # Implementation of your executor
 class Executor(RemoteExecutor):
+    def __init__(self, workflow, logger):
+        # Must clean SLURM environment BEFORE super().__init__() starts
+        # the wait_thread, otherwise the thread races with __post_init__
+        # and silently dies, causing the pipeline to hang forever.
+        if "SLURM_JOB_ID" in os.environ:
+            logger.warning(
+                "You are running snakemake in a SLURM job context. "
+                "This is not recommended, as it may lead to unexpected "
+                "behavior. "
+                "If possible, please run Snakemake directly on the "
+                "login node."
+            )
+            delete_slurm_environment()
+        super().__init__(workflow, logger)
+
     def __post_init__(self, test_mode: bool = False):
-        # run check whether we are running in a SLURM job context
-        self.warn_on_jobcontext()
         self.test_mode = test_mode
 
         self.run_uuid = str(uuid.uuid4())
@@ -617,20 +630,6 @@ def clean_old_logs(self) -> None:
                 f"Could not delete empty directories in {self.slurm_logdir}: {e}"
             )
 
-    def warn_on_jobcontext(self, done=None):
-        if not done:
-            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. "
-                    "If possible, please run Snakemake directly on the "
-                    "login node."
-                )
-                time.sleep(5)
-                delete_slurm_environment()
-        done = True
-
     def additional_general_args(self):
         """
         This function defines additional arguments to be
@@ -1451,14 +1450,12 @@ async def check_active_jobs(
                             )
                 elif status == "PREEMPTED" and not self._preemption_warning:
                     self._preemption_warning = True
-                    self.logger.warning(
-                        """
+                    self.logger.warning("""
 ===== A Job preemption  occured! =====
 Leave Snakemake running, if possible. Otherwise Snakemake
 needs to restart this job upon a Snakemake restart.
 
-We leave it to SLURM to resume your job(s)"""
-                    )
+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

tests/test_cli.py

@@ -34,19 +34,17 @@ def _make_executor(jobname_prefix: str):
 def test_jobname_prefix_applied():
     executor = _make_executor("testprefix")
 
-    with patch.object(Executor, "warn_on_jobcontext", return_value=None):
-        with patch(
-            "snakemake_executor_plugin_slurm.uuid.uuid4",
-            return_value=uuid.UUID("00000000-0000-0000-0000-000000000000"),
-        ):
-            executor.__post_init__(test_mode=True)
+    with patch(
+        "snakemake_executor_plugin_slurm.uuid.uuid4",
+        return_value=uuid.UUID("00000000-0000-0000-0000-000000000000"),
+    ):
+        executor.__post_init__(test_mode=True)
 
     assert executor.run_uuid == "testprefix_00000000-0000-0000-0000-000000000000"
 
 
 def test_jobname_prefix_validation():
     executor = _make_executor("bad!prefix")
 
-    with patch.object(Executor, "warn_on_jobcontext", return_value=None):
-        with pytest.raises(WorkflowError, match="jobname_prefix"):
-            executor.__post_init__(test_mode=True)
+    with pytest.raises(WorkflowError, match="jobname_prefix"):
+        executor.__post_init__(test_mode=True)