fix: partition cluster selection

docs/further.md

@@ -70,6 +70,8 @@ The SLURM executor plugin supports automatic partition selection based on job re
 
 *Jobs that explicitly specify a `slurm_partition` resource will bypass automatic selection and use the specified partition directly.*
 
+> **Note:** Partition selection supports specifying the target cluster using any of the resource keys `cluster`, `clusters`, or `slurm_cluster` in your workflow profile or the partition configuration file. All three are treated equivalently by the plugin.
+
 ##### Partition Limits Specification
 
 To enable automatic partition selection, create a YAML configuration file that defines the available partitions and their resource limits. This file should be structured as follows:

snakemake_executor_plugin_slurm/__init__.py

@@ -868,10 +868,43 @@ def get_partition_arg(self, job: JobExecutorInterface):
         else raises an error - implicetly.
         """
         partition = None
+
+        # Check if a specific partition is requested
         if job.resources.get("slurm_partition"):
-            partition = job.resources.slurm_partition
-        elif self._partitions:
+            # But also check if there's a cluster requirement that might override it
+            job_cluster = (
+                job.resources.get("slurm_cluster")
+                or job.resources.get("cluster")
+                or job.resources.get("clusters")
+            )
+
+            if job_cluster and self._partitions:
+                # If a cluster is specified, verify the partition exists and matches
+                # Otherwise, use auto-selection to find a partition for that cluster
+                partition_obj = next(
+                    (
+                        p
+                        for p in self._partitions
+                        if p.name == job.resources.slurm_partition
+                    ),
+                    None,
+                )
+                if (
+                    partition_obj
+                    and partition_obj.partition_cluster
+                    and partition_obj.partition_cluster != job_cluster
+                ):
+                    # Partition exists but is for a different cluster - use auto-selection
+                    partition = get_best_partition(self._partitions, job, self.logger)
+                else:
+                    partition = job.resources.slurm_partition
+            else:
+                partition = job.resources.slurm_partition
+
+        # If no partition was selected yet, try auto-selection
+        if not partition and self._partitions:
             partition = get_best_partition(self._partitions, job, self.logger)
+
         # we didnt get a partition yet so try fallback.
         if not partition:
             if self._fallback_partition is None:

snakemake_executor_plugin_slurm/partitions.py

@@ -39,12 +39,16 @@ def read_partition_file(partition_file: Path) -> List["Partition"]:
             raise KeyError("Partition name cannot be empty")
 
         # Extract optional cluster name from partition config
-        cluster = partition_config.pop("cluster", None)
+        cluster = None
+        for key in ("slurm_cluster", "cluster", "clusters"):
+            if key in partition_config:
+                cluster = partition_config.pop(key)
+                break
 
         out.append(
             Partition(
                 name=partition_name,
-                cluster=cluster,
+                partition_cluster=cluster,
                 limits=PartitionLimits(**partition_config),
             )
         )
@@ -60,7 +64,7 @@ def get_best_partition(
     for p in candidate_partitions:
         score = p.score_job_fit(job)
         logger.debug(f"Partition '{p.name}' score for job {job.name}: {score}")
-        if score is not None:
+        if score is not None and score > 0:
             scored_partitions.append((p, score))
 
     if scored_partitions:
@@ -241,7 +245,7 @@ class Partition:
 
     name: str
     limits: PartitionLimits
-    cluster: Optional[str] = None
+    partition_cluster: Optional[str] = None
 
     def score_job_fit(self, job: JobExecutorInterface) -> Optional[float]:
         """
@@ -269,14 +273,19 @@ def score_job_fit(self, job: JobExecutorInterface) -> Optional[float]:
         # Accept multiple possible resource names for cluster specification
         job_cluster = (
             job.resources.get("slurm_cluster")
-            or job.resources.get("clusters")
             or job.resources.get("cluster")
+            or job.resources.get("clusters")
         )
 
+        # Enforce strict cluster eligibility:
+        # - If the job specifies a cluster, only partitions with a matching cluster are eligible
+        # - If the job does not specify a cluster, only partitions without a cluster are eligible
         if job_cluster is not None:
-            # Job specifies a cluster - partition must match
-            if self.cluster is not None and self.cluster != job_cluster:
-                return None  # Partition is for a different cluster
+            if self.partition_cluster != job_cluster:
+                return None  # Not eligible
+        else:
+            if self.partition_cluster is not None:
+                return None  # Not eligible
 
         for resource_key, limit in numerical_resources.items():
             job_requirement = job.resources.get(resource_key, 0)

snakemake_executor_plugin_slurm/submit_string.py

@@ -42,8 +42,15 @@ def get_submit_command(job, params):
     # "- p '{partition_name}'"
     call += f" {params.partition}"
 
-    if job.resources.get("clusters"):
-        call += f" --clusters {safe_quote(job.resources.clusters)}"
+    # Add cluster specification if provided
+    # Check for cluster first (singular), then fall back to clusters (plural) for backwards compatibility
+    cluster_val = (
+        job.resources.get("cluster")
+        or job.resources.get("clusters")
+        or job.resources.get("slurm_cluster")
+    )
+    if cluster_val:
+        call += f" --cluster {safe_quote(cluster_val)}"
 
     if job.resources.get("runtime"):
         call += f" -t {safe_quote(job.resources.runtime)}"

snakemake_executor_plugin_slurm/validation.py

@@ -132,7 +132,7 @@ def validate_executor_settings(settings, logger=None):
     if settings.init_seconds_before_status_checks is not None:
         if (
             not isinstance(settings.init_seconds_before_status_checks, int)
-            or settings.init_seconds_before_status_checks > 0
+            or settings.init_seconds_before_status_checks < 1
         ):
             raise WorkflowError(
                 "init-seconds-before-status-checks must be a positive integer."

tests/test_partition_selection.py

@@ -591,8 +591,8 @@ def test_cluster_specification_via_slurm_cluster(
             # Verify cluster field is read correctly
             # Find partitions by name instead of assuming order
             partition_map = {p.name: p for p in partitions}
-            assert partition_map["normal-small"].cluster == "normal"
-            assert partition_map["deviating-small"].cluster == "deviating"
+            assert partition_map["normal-small"].partition_cluster == "normal"
+            assert partition_map["deviating-small"].partition_cluster == "deviating"
 
             # Job targeting 'normal' cluster
             job = mock_job(threads=16, mem_mb=32000, slurm_cluster="normal")
@@ -664,10 +664,54 @@ def test_cluster_mismatch_excludes_partitions(
         finally:
             temp_path.unlink()
 
+    def test_job_with_cluster_does_not_select_partition_without_cluster(
+        self, multicluster_partition_config, temp_yaml_file, mock_job, mock_logger
+    ):
+        """
+        Test that jobs with a cluster requirement do not select partitions without a cluster.
+        """
+        config = dict(multicluster_partition_config)
+        config["partitions"]["no-cluster"] = {
+            "max_runtime": 360,
+            "max_threads": 32,
+            "max_mem_mb": 64000,
+        }
+        temp_path = temp_yaml_file(config)
+        try:
+            partitions = read_partition_file(temp_path)
+            job = mock_job(threads=16, mem_mb=32000, slurm_cluster="normal")
+            selected_partition = get_best_partition(partitions, job, mock_logger)
+            # Should select a partition with cluster 'normal', not 'no-cluster'
+            assert selected_partition in ["normal-small", "normal-large"]
+        finally:
+            temp_path.unlink()
+
+    def test_job_without_cluster_can_select_partition_without_cluster(
+        self, multicluster_partition_config, temp_yaml_file, mock_job, mock_logger
+    ):
+        """
+        Test that jobs without cluster requirement can select partitions without a cluster.
+        """
+        config = dict(multicluster_partition_config)
+        config["partitions"]["no-cluster"] = {
+            "max_runtime": 360,
+            "max_threads": 32,
+            "max_mem_mb": 64000,
+        }
+        temp_path = temp_yaml_file(config)
+        try:
+            partitions = read_partition_file(temp_path)
+            job = mock_job(threads=16, mem_mb=32000)
+            selected_partition = get_best_partition(partitions, job, mock_logger)
+            # Should be able to select 'no-cluster' partition
+            assert selected_partition in ["normal-small", "normal-large", "no-cluster"]
+        finally:
+            temp_path.unlink()
+
     def test_job_without_cluster_uses_any_partition(
         self, multicluster_partition_config, temp_yaml_file, mock_job, mock_logger
     ):
-        """Test that jobs without cluster specification can use any partition."""
+        """Test that jobs without cluster specification can use any partition without a cluster assignment."""
         temp_path = temp_yaml_file(multicluster_partition_config)
 
         try:
@@ -677,9 +721,8 @@ def test_job_without_cluster_uses_any_partition(
             job = mock_job(threads=16, mem_mb=32000)
             selected_partition = get_best_partition(partitions, job, mock_logger)
 
-            # Should select a partition (any cluster is acceptable)
-            assert selected_partition is not None
-            assert mock_logger.info.call_count >= 1
+            # Should return None since all partitions have a cluster assignment
+            assert selected_partition is None
         finally:
             temp_path.unlink()