feat: added validators for cli settigns

Author: cmeesters

snakemake_executor_plugin_slurm/__init__.py

@@ -46,7 +46,7 @@
 from .efficiency_report import create_efficiency_report
 from .submit_string import get_submit_command
 from .partitions import read_partition_file, get_best_partition
-from .validation import validate_slurm_extra
+from .validation import validate_slurm_extra, validate_executor_settings
 
 
 def _get_status_command_default():
@@ -266,8 +266,8 @@ class ExecutorSettings(ExecutorSettingsBase):
 
     def __post_init__(self):
         """Validate settings after initialization."""
-        # Add any validation logic here if needed in the future
-        pass
+        # Run all validation checks
+        validate_executor_settins(self)
 
 
 # Required:

snakemake_executor_plugin_slurm/validation.py

@@ -3,6 +3,7 @@
 """
 
 import re
+from pathlib import Path
 from snakemake_interface_common.exceptions import WorkflowError
 
 
@@ -73,3 +74,68 @@ def validate_slurm_extra(job):
                 f"specification instead. "
                 f"Consult the documentation for proper resource configuration."
             )
+
+
+def validate_executor_settings(settings):
+    """
+    Validate ExecutorSettings fields for correctness
+    (better user feedback in case of wrong inputs)
+
+    Args:
+        settings: ExecutorSettins instance to validate
+
+    Raises:
+        WorkflowError - if any validation check fails
+    """
+    # status_command: only allow known values
+    if settings.status_command is not None:
+        if settings.status_command not in {"sacct", "squeue"}:
+            raise WorkflowError(
+                "Invalid status command. Allowed values are 'sacct' or 'squeue'."
+            )
+
+    # status_attempts: require positive integer
+    if settings.status_attempts is not None:
+        if (
+            not isinstance(settings.status_attempts, int)
+            or settings.status_attempts < 1
+        ):
+            raise WorkflowError("status_attempts must be a positive integer")
+
+    # init_settings_befor_status_checks: require non-negative integer
+    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
+        ):
+            raise WorkflowError(
+                "init-seconds-before-status-checks must be a positive integer."
+            )
+
+    # efficiency_threshold, if set must be within (0, 1]
+    if settings.efficiency_threshold is not None:
+        try:
+            thr = float(settings.efficiency_threshold)
+        except (TypeError, ValueError):
+            raise WorkflowError(
+                "efficiency-threshold must be a number in range (0, 1]."
+            )
+        if not (0 < thr <= 1.0):
+            raise WorkflowError(
+                "efficiency-threshold must be a number in range (0, 1]."
+            )
+
+    # partition_config: if provided, it must exist
+    if settings.partition_config is not None:
+        p = Path(settings.partition_config)
+        if not p.exists():
+            raise WorkflowError(
+                f"Partition configuration file not found, given was {p}."
+            )
+
+    # delete_logfiles_older_than: if provided, should be reasonable
+    if settings.delete_logfiles_older_than is not None:
+        if not isinstance(settings.delete_logfiles_older_than, int):
+            raise WorkflowError(
+                "delete-logfiles-older-than must be an integer (days)."
+            )