Ignore shell in parallel command construction

CHANGELOG.md

@@ -22,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Applying filters for `merlin detailed-status` will now log debug statements instead of warnings
 - Modified the unit tests for the `merlin status` command to use pytest rather than unittest
 - Added fixtures for `merlin status` tests that copy the workspace to a temporary directory so you can see exactly what's run in a test
+- Ignore the shell keyword in parallel command construction
 
 ### Fixed
 - Bugfix for output of `merlin example openfoam_wf_singularity`

merlin/study/script_adapter.py

@@ -123,6 +123,11 @@ def __init__(self, **kwargs):
             "walltime",
         }
 
+        # These are known valid step keywords not used in batch
+        self._ignored:  Set[str] = {
+            "shell",
+        }
+
     def get_priority(self, priority):
         """This is implemented to override the abstract method and fix a pylint error"""
 
@@ -173,7 +178,9 @@ def get_parallelize_command(self, procs, nodes=None, **kwargs):
         for key in supported:
             value = kwargs.get(key)
             if key not in self._cmd_flags:
-                LOG.warning("'%s' is not supported -- ommitted.", key)
+                if key not in self._ignored:
+                    LOG.warning("'%s' is not supported in parallel command -- ommitted.", key)
+                LOG.debug("'%s' is not supported in parallel command -- ommitted.", key)
                 continue
             if value:
                 args += [self._cmd_flags[key], f"{str(value)}"]
@@ -236,6 +243,11 @@ def __init__(self, **kwargs):
         ]
         self._unsupported: Set[str] = set(list(self._unsupported) + new_unsupported)
 
+        # These are known valid step keywords not used in batch
+        self._ignored:  Set[str] = {
+            "shell",
+        }
+
     def get_priority(self, priority):
         """This is implemented to override the abstract method and fix a pylint error"""
 
@@ -282,7 +294,9 @@ def get_parallelize_command(self, procs, nodes=None, **kwargs):
                 continue
 
             if key not in self._cmd_flags:
-                LOG.warning("'%s' is not supported -- ommitted.", key)
+                if key not in self._ignored:
+                    LOG.warning("'%s' is not supported in parallel command -- ommitted.", key)
+                LOG.debug("'%s' is not supported in parallel command -- ommitted.", key)
                 continue
 
             if key == "walltime":