feat: warning if run in job (#78)

Already, two issues (#75 and #22) seem to result from running Snakemake
in a SLURM job context and using this executor plugin. This PR
introduces detecting if triggered within a SLURM job and issuing a
warning accordingly.

In principle, the plugin may work in job context. Submitting jobs from
jobs has always been a highlight of SLURM. However, settings may lead to
unintended behaviour (and would do so without Snakemake, presumably).
Hence, we can only warn from the executor.

Author: cmeesters

docs/further.md

@@ -291,6 +291,12 @@ set-resources:
 Be sure to use sensible settings for your cluster and make use of parallel execution (e.g. threads) and [global profiles](#using-profiles) to avoid I/O contention. 
 
 
+## Nesting Jobs (or Running this Plugin within a Job)
+
+Some environments provide a shell within a SLURM job, for instance, IDEs started in on-demand context. If Snakemake attempts to use this plugin to spawn jobs on the cluster, this may work just as intended. Or it might not: depending on cluster settings or individual settings, submitted jobs may be ill-parameterized or will not find the right environment.
+
+If the plugin detects to be running within a job, it will therefore issue a warning and stop for 5 seconds.
+
 ## Summary:
 
 When put together, a frequent command line looks like:

snakemake_executor_plugin_slurm/__init__.py

@@ -51,11 +51,24 @@
 # 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"