From 40ce4f58b57f01c4ec194763a1df5f745da8efbf Mon Sep 17 00:00:00 2001
From: Jo Basevi <johanna.basevi@anu.edu.au>
Date: Wed, 16 Jul 2025 12:18:37 +1000
Subject: [PATCH 1/3] Prepend container launcher script to pbs command, if it
 exists

---
 payu/schedulers/pbs.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/payu/schedulers/pbs.py b/payu/schedulers/pbs.py
index 4d5410bf..43e533e5 100644
--- a/payu/schedulers/pbs.py
+++ b/payu/schedulers/pbs.py
@@ -6,6 +6,7 @@
 
 # Standard library
 import os
+from pathlib import Path
 import re
 import sys
 import shlex
@@ -129,6 +130,13 @@ def submit(self, pbs_script, pbs_config, pbs_vars=None, python_exe=None):
         envmod.setup()
         envmod.module('load', 'pbs')
 
+        # Check for custom container launcher script environment variable
+        launcher_script = os.environ.get('ENV_LAUNCHER_SCRIPT_PATH')
+        if launcher_script and Path(launcher_script).is_file():
+            # Prepend the container launcher script to the python command
+            # so the python executable is accessible in the container
+            python_exe = f'{launcher_script} {python_exe}'
+
         # Construct job submission command
         cmd = 'qsub {flags} -- {python} {script}'.format(
             flags=' '.join(pbs_flags),

From 8bc93d2a3f370fb5df0354b525725ad535d16aa9 Mon Sep 17 00:00:00 2001
From: Jo Basevi <johanna.basevi@anu.edu.au>
Date: Mon, 21 Jul 2025 15:14:01 +1000
Subject: [PATCH 2/3] Check whether custom launcher script environment variable
 is executable

---
 payu/schedulers/pbs.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/payu/schedulers/pbs.py b/payu/schedulers/pbs.py
index 43e533e5..adcee9b5 100644
--- a/payu/schedulers/pbs.py
+++ b/payu/schedulers/pbs.py
@@ -132,7 +132,11 @@ def submit(self, pbs_script, pbs_config, pbs_vars=None, python_exe=None):
 
         # Check for custom container launcher script environment variable
         launcher_script = os.environ.get('ENV_LAUNCHER_SCRIPT_PATH')
-        if launcher_script and Path(launcher_script).is_file():
+        if (
+            launcher_script
+            and Path(launcher_script).is_file()
+            and os.access(launcher_script, os.X_OK)
+        ):
             # Prepend the container launcher script to the python command
             # so the python executable is accessible in the container
             python_exe = f'{launcher_script} {python_exe}'

From 13f30fee6b0b1cfbcdd652c0ce3105442313ec84 Mon Sep 17 00:00:00 2001
From: Jo Basevi <johanna.basevi@anu.edu.au>
Date: Mon, 21 Jul 2025 16:56:20 +1000
Subject: [PATCH 3/3] Add test for setting launcher script in qsub command

---
 test/test_pbs.py | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/test/test_pbs.py b/test/test_pbs.py
index 7389c17f..2637b20e 100644
--- a/test/test_pbs.py
+++ b/test/test_pbs.py
@@ -5,6 +5,7 @@
 from pathlib import Path
 import shutil
 import sys
+from unittest.mock import patch
 
 import pdb
 import pytest
@@ -236,6 +237,47 @@ def test_run():
         assert(args.remaining[-1].endswith(payu_cmd))
 
 
+@patch("payu.schedulers.pbs.pbs_env_init", return_value=True)
+@patch("payu.schedulers.pbs.check_exe_path", side_effect=lambda x, y: y)
+@pytest.mark.parametrize(
+    "env_exists,file_exists,file_exe,expected_cmd",
+    [
+        # Test backwards compatibility with no launcher script
+        (False, False, False, "/path/to/python payu-run"),
+        # With only launcher script env set
+        (True, False, False, "/path/to/python payu-run"),
+        # With launch script env and file exists
+        (True, True, False, "/path/to/python payu-run"),
+        # With launch script env, file exists, and file is executable
+        (True, True, True, "{tmp_path}/launcher.sh /path/to/python payu-run")
+    ],
+)
+def test_submit_launcher_script_setting(
+    mock_pbs_env_init, mock_check_exe_path,
+    env_exists, file_exists, file_exe, expected_cmd, tmp_path, monkeypatch
+):
+    config = {
+        "control_path": "/path/to/experiment"
+    }
+
+    # Setup based on test parameters
+    if env_exists:
+        monkeypatch.setenv("ENV_LAUNCHER_SCRIPT_PATH",
+                           f"{tmp_path}/launcher.sh")
+    if file_exists:
+        launcher_script_path = tmp_path / "launcher.sh"
+        launcher_script_path.write_text("#!/bin/bash\necho 'Running...'\n")
+        if file_exe:
+            launcher_script_path.chmod(0o755)
+
+    # Generate the qsub command
+    pbs_cmd = pbs.PBS().submit("payu-run", config,
+                               python_exe="/path/to/python")
+
+    _, cmd = pbs_cmd.split("--")
+    assert cmd.strip() == expected_cmd.format(tmp_path=tmp_path)
+
+
 def test_tenacity():
 
     # This should fail and do nothing