From 5a953e96faff83b023430ecd3cdf2e01f9eb6170 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 29 Aug 2026 23:45:42 +0000
Subject: [PATCH 1/6] Initial plan


From 7fa04ce281cb24e2b03b40a6aa631157a71038e1 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 29 Aug 2026 23:53:29 +0000
Subject: [PATCH 2/6] Unify mlcd and mlca: docker_X fallback, apptainer meta
 key, schema validation (#312)

Co-authored-by: arjunsuresh <4791823+arjunsuresh@users.noreply.github.com>
---
 automation/script/apptainer.py             |  41 ++---
 automation/script/meta_schema.py           |  17 +++
 automation/script/module.py                |   1 +
 mlc/meta_schema.py                         |  17 +++
 mlc/script_action.py                       |  31 ++++
 tests/test_apptainer_docker_unification.py | 165 +++++++++++++++++++++
 6 files changed, 254 insertions(+), 18 deletions(-)
 create mode 100644 tests/test_apptainer_docker_unification.py

diff --git a/automation/script/apptainer.py b/automation/script/apptainer.py
index c2897b3f2..4da9bbfe4 100644
--- a/automation/script/apptainer.py
+++ b/automation/script/apptainer.py
@@ -8,9 +8,9 @@
 
 def apptainerfile(self_module, input_params):
 
-    # Step 1: Prune and prepare input
+    # Step 1: Prune and prepare input (remove both apptainer_ and docker_ prefixed keys)
     prune_result = prune_input(
-        {'input': input_params, 'extra_keys_starts_with': ['apptainer_']})
+        {'input': input_params, 'extra_keys_starts_with': ['apptainer_', 'docker_']})
     if prune_result['return'] > 0:
         return prune_result
 
@@ -56,13 +56,13 @@ def apptainerfile(self_module, input_params):
 
     run_state = self_module.run_state
 
-    apptainer_settings = run_state.get('docker', {})
+    apptainer_settings = {**run_state.get('docker', {}), **run_state.get('apptainer', {})}
     apptainer_settings_default_env = apptainer_settings.get('default_env', {})
     for key in apptainer_settings_default_env:
         env.setdefault(key, apptainer_settings_default_env[key])
 
     if not apptainer_settings.get('run', True) and not input_params.get(
-            'apptainer_run_override', False):
+            'apptainer_run_override', input_params.get('docker_run_override', False)):
         logger.info("Apptainer 'run' is set to False in meta.yaml")
         return {'return': 0,
                 'warning': 'Apptainer run is set to false in script meta'}
@@ -86,7 +86,7 @@ def apptainerfile(self_module, input_params):
     if update_state_result['return'] > 0:
         return update_state_result
 
-    apptainer_settings = run_state.get('docker', {})
+    apptainer_settings = {**run_state.get('docker', {}), **run_state.get('apptainer', {})}
 
     # Prune temporary environment variables
     run_command = copy.deepcopy(run_command_arc)
@@ -102,7 +102,7 @@ def apptainerfile(self_module, input_params):
         'tags': script_tags,
         'fake_run': True,
         'docker_settings': apptainer_settings,
-        'docker_run_cmd_prefix': input_params.get('apptainer_run_cmd_prefix', apptainer_settings.get('run_cmd_prefix', ''))
+        'docker_run_cmd_prefix': input_params.get('apptainer_run_cmd_prefix', input_params.get('docker_run_cmd_prefix', apptainer_settings.get('run_cmd_prefix', '')))
     })
     if regenerate_result['return'] > 0:
         return regenerate_result
@@ -155,10 +155,10 @@ def apptainerfile(self_module, input_params):
     apptainer_v = False
     apptainer_s = False
     if is_true(input_params.get(
-            'apptainer_v', input_params.get('apptainer_verbose', False))):
+            'apptainer_v', input_params.get('apptainer_verbose', input_params.get('docker_v', input_params.get('docker_verbose', False))))):
         apptainer_v = True
     if is_true(input_params.get(
-            'apptainer_s', input_params.get('apptainer_silent', False))):
+            'apptainer_s', input_params.get('apptainer_silent', input_params.get('docker_s', input_params.get('docker_silent', False))))):
         apptainer_s = True
 
     if apptainer_s and apptainer_v:
@@ -213,11 +213,11 @@ def apptainer_run(self_module, i):
     if quiet:
         env['MLC_QUIET'] = 'yes'
 
-    regenerate_def_file = not i.get('apptainer_noregenerate', False)
-    rebuild_apptainer_image = i.get('apptainer_rebuild', False)
+    regenerate_def_file = not i.get('apptainer_noregenerate', i.get('docker_noregenerate', False))
+    rebuild_apptainer_image = i.get('apptainer_rebuild', i.get('docker_rebuild', False))
 
-    # Prune unnecessary Apptainer-related input keys
-    r = prune_input({'input': i, 'extra_keys_starts_with': ['apptainer_']})
+    # Prune unnecessary Apptainer- and Docker-related input keys
+    r = prune_input({'input': i, 'extra_keys_starts_with': ['apptainer_', 'docker_']})
     f_run_cmd = r['new_input']
 
     # Save current directory and prepare to search for scripts
@@ -259,7 +259,7 @@ def apptainer_run(self_module, i):
     mounts = copy.deepcopy(
         i.get(
             'apptainer_mounts',
-            []))
+            i.get('docker_mounts', [])))
     variations = meta.get('variations', {})
 
     if not hasattr(self_module, 'run_state'):
@@ -273,7 +273,7 @@ def apptainer_run(self_module, i):
 
     run_state = self_module.run_state
 
-    apptainer_settings = run_state.get('docker', {})
+    apptainer_settings = {**run_state.get('docker', {}), **run_state.get('apptainer', {})}
 
     apptainer_settings_default_env = apptainer_settings.get('default_env', {})
     for key in apptainer_settings_default_env:
@@ -297,7 +297,7 @@ def apptainer_run(self_module, i):
 
     # Skip scripts marked as non-runnable
     if not apptainer_settings.get('run', True) and not i.get(
-            'apptainer_run_override', False):
+            'apptainer_run_override', i.get('docker_run_override', False)):
         logger.info("apptainer.run set to False in meta.yaml")
         return {'return': 0,
                 'warning': 'Apptainer run is set to false in script meta'}
@@ -446,10 +446,15 @@ def prepare_apptainer_inputs(input_params, apptainer_settings,
     # Collect inputs
     apptainer_inputs = {
         key: input_params.get(
-            f"apptainer_{key}", apptainer_settings.get(
-                key, get_apptainer_default(key)))
+            f"apptainer_{key}",
+            input_params.get(
+                f"docker_{key}", apptainer_settings.get(
+                    key, get_apptainer_default(key))))
         for key in keys
-        if (value := input_params.get(f"apptainer_{key}", apptainer_settings.get(key, get_apptainer_default(key)))) is not None
+        if (value := input_params.get(
+            f"apptainer_{key}",
+            input_params.get(
+                f"docker_{key}", apptainer_settings.get(key, get_apptainer_default(key))))) is not None
     }
 
     # Convert boolean values to 'yes'/'no' strings for MLC input mapping
diff --git a/automation/script/meta_schema.py b/automation/script/meta_schema.py
index 17d3bcbe3..be4062647 100644
--- a/automation/script/meta_schema.py
+++ b/automation/script/meta_schema.py
@@ -86,6 +86,7 @@
 
     # Docker
     "docker": DICT,        # dict - see DOCKER_SCHEMA
+    "apptainer": DICT,     # dict - apptainer overrides; merges with docker settings
 
     # Output / debugging
     "print_env_at_the_end": DICT,        # dict[str, list[str]]
@@ -164,6 +165,7 @@
     "state": DICT,
     "const": DICT,
     "docker": DICT,
+    "apptainer": DICT,
     "alias": STR,
     "default_version": STR_OR_FLOAT,
     "required_disk_space": INT,
@@ -248,6 +250,7 @@
     "default_env": DICT,
     "default_variations": DICT,
     "docker": DICT,
+    "apptainer": DICT,
     "adr": DICT,
     "ad": DICT,
 }
@@ -403,6 +406,20 @@ def validate_meta(data, file_path=""):
                 errors.append(
                     f"{prefix}docker.{dk} has type '{actual}', expected {allowed}")
 
+    # Validate apptainer section (same schema as docker; apptainer overrides docker)
+    apptainer = data.get("apptainer")
+    if isinstance(apptainer, dict):
+        for ak, av in apptainer.items():
+            if ak not in DOCKER_SCHEMA:
+                warnings.append(
+                    f"{prefix}apptainer: unknown key '{ak}'")
+                continue
+            actual = type(av).__name__
+            allowed = DOCKER_SCHEMA[ak]
+            if actual not in allowed:
+                errors.append(
+                    f"{prefix}apptainer.{ak} has type '{actual}', expected {allowed}")
+
     # Validate tests section
     tests = data.get("tests")
     if isinstance(tests, dict):
diff --git a/automation/script/module.py b/automation/script/module.py
index 1686b7ed8..ff62167d1 100644
--- a/automation/script/module.py
+++ b/automation/script/module.py
@@ -778,6 +778,7 @@ def _run(self, i):
             variation_tags.append(f"version.{version}")
 
         run_state['docker'] = meta.get('docker', {})
+        run_state['apptainer'] = meta.get('apptainer', {})
 
         r = self._update_state_from_variations(
             i,
diff --git a/mlc/meta_schema.py b/mlc/meta_schema.py
index 500670f31..57a6b3eea 100644
--- a/mlc/meta_schema.py
+++ b/mlc/meta_schema.py
@@ -86,6 +86,7 @@
 
     # Docker
     "docker": DICT,        # dict - see DOCKER_SCHEMA
+    "apptainer": DICT,     # dict - apptainer overrides; merges with docker settings
 
     # Output / debugging
     "print_env_at_the_end": DICT,        # dict[str, list[str]]
@@ -164,6 +165,7 @@
     "state": DICT,
     "const": DICT,
     "docker": DICT,
+    "apptainer": DICT,
     "alias": STR,
     "default_version": STR_OR_FLOAT,
     "required_disk_space": INT,
@@ -248,6 +250,7 @@
     "default_env": DICT,
     "default_variations": DICT,
     "docker": DICT,
+    "apptainer": DICT,
     "adr": DICT,
     "ad": DICT,
 }
@@ -403,6 +406,20 @@ def validate_meta(data, file_path=""):
                 errors.append(
                     f"{prefix}docker.{dk} has type '{actual}', expected {allowed}")
 
+    # Validate apptainer section (same schema as docker; apptainer overrides docker)
+    apptainer = data.get("apptainer")
+    if isinstance(apptainer, dict):
+        for ak, av in apptainer.items():
+            if ak not in DOCKER_SCHEMA:
+                warnings.append(
+                    f"{prefix}apptainer: unknown key '{ak}'")
+                continue
+            actual = type(av).__name__
+            allowed = DOCKER_SCHEMA[ak]
+            if actual not in allowed:
+                errors.append(
+                    f"{prefix}apptainer.{ak} has type '{actual}', expected {allowed}")
+
     # Validate tests section
     tests = data.get("tests")
     if isinstance(tests, dict):
diff --git a/mlc/script_action.py b/mlc/script_action.py
index f0cf8e8dd..ab552996f 100644
--- a/mlc/script_action.py
+++ b/mlc/script_action.py
@@ -441,6 +441,37 @@ def apptainer_run(self, run_args):
     mlc apptainer script --tags=detect,os -j
     mlca detect,os -j
 
+    Flags Available (--apptainer_X takes priority over --docker_X for each option):
+
+    1. --apptainer_rebuild / --docker_rebuild:
+       Force rebuild of the Apptainer image even if it already exists.
+
+    2. --apptainer_noregenerate / --docker_noregenerate:
+       Skip regenerating the Apptainer definition file before running.
+
+    3. --apptainer_mounts / --docker_mounts:
+       List of bind mounts to pass to the container (host:container format).
+
+    4. --apptainer_run_cmd_prefix / --docker_run_cmd_prefix:
+       Command prefix to prepend before the mlcr command inside the container.
+
+    5. --apptainer_verbose / --apptainer_v / --docker_verbose / --docker_v:
+       Enable verbose output inside the container.
+
+    6. --apptainer_silent / --apptainer_s / --docker_silent / --docker_s:
+       Enable silent output inside the container.
+
+    7. --apptainer_run_override / --docker_run_override:
+       Force apptainer execution even if 'run' is set to False in script meta.
+
+    All --docker_X options are accepted and used as defaults when the
+    corresponding --apptainer_X option is not provided. This allows sharing
+    flags between mlcd and mlca invocations.
+
+    Script meta.yaml keys:
+    - ``docker``: base container settings (used by both mlcd and mlca).
+    - ``apptainer``: apptainer-specific overrides; merged over ``docker`` settings.
+
         """
         return self.call_script_module_function("apptainer", run_args)
 
diff --git a/tests/test_apptainer_docker_unification.py b/tests/test_apptainer_docker_unification.py
new file mode 100644
index 000000000..6e121a143
--- /dev/null
+++ b/tests/test_apptainer_docker_unification.py
@@ -0,0 +1,165 @@
+"""
+Tests for the unification of mlcd and mlca options (issue #312).
+
+Verifies that:
+1. --docker_X CLI options act as fallbacks when --apptainer_X is not given in the
+   effective settings merge logic.
+2. script meta.yaml `apptainer` key overrides `docker` key for apptainer runs.
+3. meta_schema validates the `apptainer` section using the same rules as `docker`.
+"""
+import unittest
+from unittest.mock import MagicMock
+
+
+# ---------------------------------------------------------------------------
+# 1. run_state: apptainer key merges over docker key
+#    (mirrors what apptainerfile() and apptainer_run() do)
+# ---------------------------------------------------------------------------
+
+class RunStateApptainerMergeTest(unittest.TestCase):
+    """apptainer settings from meta.yaml merge over docker settings."""
+
+    def _merged_settings(self, docker_meta, apptainer_meta):
+        """Simulate what apptainer_run does to build effective settings."""
+        run_state = {
+            "docker": docker_meta,
+            "apptainer": apptainer_meta,
+        }
+        return {**run_state.get("docker", {}), **run_state.get("apptainer", {})}
+
+    def test_apptainer_base_image_overrides_docker(self):
+        settings = self._merged_settings(
+            {"base_image": "docker-image:latest"},
+            {"base_image": "apptainer-image:latest"},
+        )
+        self.assertEqual(settings["base_image"], "apptainer-image:latest")
+
+    def test_docker_settings_used_when_no_apptainer_key(self):
+        settings = self._merged_settings(
+            {"os": "ubuntu", "base_image": "docker-image:latest"},
+            {},
+        )
+        self.assertEqual(settings["os"], "ubuntu")
+        self.assertEqual(settings["base_image"], "docker-image:latest")
+
+    def test_apptainer_partial_override(self):
+        """Only the keys in apptainer meta override; rest comes from docker."""
+        settings = self._merged_settings(
+            {"os": "ubuntu", "os_version": "22.04", "run": True},
+            {"os_version": "20.04"},
+        )
+        self.assertEqual(settings["os"], "ubuntu")
+        self.assertEqual(settings["os_version"], "20.04")
+        self.assertTrue(settings["run"])
+
+
+# ---------------------------------------------------------------------------
+# 2. CLI fallback: docker_X used when apptainer_X is absent
+#    Tests the lookup pattern: apptainer_X → docker_X → settings → default
+# ---------------------------------------------------------------------------
+
+class ApptainerDockerCliFallbackTest(unittest.TestCase):
+    """
+    Verify the three-level lookup: apptainer_X > docker_X > settings > default.
+    This mirrors the logic in prepare_apptainer_inputs and apptainer_run.
+    """
+
+    def _lookup(self, key, input_params, settings, default=None):
+        """Replicate the lookup pattern used in prepare_apptainer_inputs."""
+        return input_params.get(
+            f"apptainer_{key}",
+            input_params.get(f"docker_{key}", settings.get(key, default))
+        )
+
+    def test_apptainer_prefix_wins(self):
+        val = self._lookup("os", {"apptainer_os": "debian", "docker_os": "centos"}, {})
+        self.assertEqual(val, "debian")
+
+    def test_docker_prefix_fallback(self):
+        val = self._lookup("os", {"docker_os": "centos"}, {})
+        self.assertEqual(val, "centos")
+
+    def test_settings_fallback(self):
+        val = self._lookup("os", {}, {"os": "ubuntu"})
+        self.assertEqual(val, "ubuntu")
+
+    def test_default_fallback(self):
+        val = self._lookup("os", {}, {}, "alpine")
+        self.assertEqual(val, "alpine")
+
+    def test_noregenerate_docker_fallback(self):
+        # apptainer_run uses: not i.get('apptainer_noregenerate', i.get('docker_noregenerate', False))
+        i = {"docker_noregenerate": True}
+        regenerate_def_file = not i.get("apptainer_noregenerate", i.get("docker_noregenerate", False))
+        self.assertFalse(regenerate_def_file)
+
+    def test_noregenerate_apptainer_overrides_docker(self):
+        i = {"apptainer_noregenerate": False, "docker_noregenerate": True}
+        regenerate_def_file = not i.get("apptainer_noregenerate", i.get("docker_noregenerate", False))
+        self.assertTrue(regenerate_def_file)
+
+    def test_rebuild_docker_fallback(self):
+        i = {"docker_rebuild": True}
+        rebuild = i.get("apptainer_rebuild", i.get("docker_rebuild", False))
+        self.assertTrue(rebuild)
+
+    def test_mounts_docker_fallback(self):
+        i = {"docker_mounts": ["/host:/container"]}
+        mounts = i.get("apptainer_mounts", i.get("docker_mounts", []))
+        self.assertEqual(mounts, ["/host:/container"])
+
+    def test_mounts_apptainer_overrides_docker(self):
+        i = {"apptainer_mounts": ["/a:/a"], "docker_mounts": ["/b:/b"]}
+        mounts = i.get("apptainer_mounts", i.get("docker_mounts", []))
+        self.assertEqual(mounts, ["/a:/a"])
+
+
+# ---------------------------------------------------------------------------
+# 3. meta_schema: apptainer key validation
+# ---------------------------------------------------------------------------
+
+class MetaSchemaApptainerKeyTest(unittest.TestCase):
+    """The `apptainer` key in meta.yaml is validated like `docker`."""
+
+    def _validate(self, data):
+        from mlc.meta_schema import validate_meta
+        base = {
+            "alias": "test-script",
+            "uid": "aabbccdd11223344",
+            "automation_alias": "script",
+            "automation_uid": "5b4aa8f95024c2a5",
+        }
+        base.update(data)
+        return validate_meta(base, "test.yaml")
+
+    def test_apptainer_key_accepted_with_dict(self):
+        errors, warnings = self._validate({"apptainer": {"os": "ubuntu"}})
+        self.assertEqual(errors, [])
+
+    def test_apptainer_unknown_key_produces_warning(self):
+        _, warnings = self._validate({"apptainer": {"unknown_key_xyz": "val"}})
+        self.assertTrue(any("unknown key" in w for w in warnings))
+
+    def test_apptainer_wrong_type_produces_error(self):
+        errors, _ = self._validate({"apptainer": {"run": "not-a-bool"}})
+        self.assertTrue(any("apptainer.run" in e for e in errors))
+
+    def test_apptainer_run_bool_accepted(self):
+        errors, _ = self._validate({"apptainer": {"run": False}})
+        self.assertEqual(errors, [])
+
+    def test_docker_and_apptainer_both_accepted(self):
+        errors, _ = self._validate({
+            "docker": {"os": "ubuntu"},
+            "apptainer": {"os": "centos"},
+        })
+        self.assertEqual(errors, [])
+
+    def test_apptainer_base_image_str_accepted(self):
+        errors, _ = self._validate({"apptainer": {"base_image": "ubuntu:22.04"}})
+        self.assertEqual(errors, [])
+
+
+if __name__ == "__main__":
+    unittest.main()
+

From c0760b61a0eeac73a67d025ac27d877023c99278 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 30 Aug 2026 00:11:55 +0000
Subject: [PATCH 3/6] Add CLI help smoke tests, extend CI trigger to
 automation/**

Co-authored-by: arjunsuresh <4791823+arjunsuresh@users.noreply.github.com>
---
 .github/workflows/test-unit.yml            | 14 +++--
 tests/test_apptainer_docker_unification.py | 68 ++++++++++++++++++++++
 2 files changed, 76 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/test-unit.yml b/.github/workflows/test-unit.yml
index fc2713228..3680faf4e 100644
--- a/.github/workflows/test-unit.yml
+++ b/.github/workflows/test-unit.yml
@@ -7,17 +7,19 @@ on:
   pull_request:
     branches: [ "main", "dev" ]
     paths:
-      - 'mlc/**'
-      - 'tests/**'
+      - mlc/**
+      - tests/**
+      - automation/**
       - '.github/workflows/test-unit.yml'
-      - 'pyproject.toml'
+      - pyproject.toml
   push:
     branches: [ "main", "dev" ]
     paths:
-      - 'mlc/**'
-      - 'tests/**'
+      - mlc/**
+      - tests/**
+      - automation/**
       - '.github/workflows/test-unit.yml'
-      - 'pyproject.toml'
+      - pyproject.toml
 
 jobs:
   unit-tests:
diff --git a/tests/test_apptainer_docker_unification.py b/tests/test_apptainer_docker_unification.py
index 6e121a143..dfc9d7c25 100644
--- a/tests/test_apptainer_docker_unification.py
+++ b/tests/test_apptainer_docker_unification.py
@@ -163,3 +163,71 @@ def test_apptainer_base_image_str_accepted(self):
 if __name__ == "__main__":
     unittest.main()
 
+
+
+# ---------------------------------------------------------------------------
+# 5. CLI smoke tests: mlcd --help and mlca --help
+# ---------------------------------------------------------------------------
+
+class CliHelpSmokeTest(unittest.TestCase):
+    """mlcd and mlca --help exit cleanly and include expected content."""
+
+    def _run_help(self, entry_point):
+        import subprocess
+        import sys
+        result = subprocess.run(
+            [sys.executable, "-m", entry_point, "--help"],
+            capture_output=True, text=True
+        )
+        return result
+
+    def _run_mlc_action_help(self, action):
+        """Use 'mlc <action> script --help' as the canonical help path."""
+        import subprocess
+        import sys
+        result = subprocess.run(
+            [sys.executable, "-c",
+             f"import sys; sys.argv=['mlc', '{action}', 'script', '--help']; "
+             f"from mlc.main import main; main()"],
+            capture_output=True, text=True
+        )
+        return result
+
+    def test_mlcd_help_exits_successfully(self):
+        import subprocess, sys
+        result = subprocess.run(
+            [sys.executable, "-c",
+             "import sys; sys.argv=['mlcd','--help']; "
+             "from mlc.main import mlcd; mlcd()"],
+            capture_output=True, text=True
+        )
+        combined = result.stdout + result.stderr
+        self.assertIn("docker", combined.lower(),
+                      msg=f"Expected docker help text, got: {combined[:500]}")
+
+    def test_mlca_help_exits_successfully(self):
+        import subprocess, sys
+        result = subprocess.run(
+            [sys.executable, "-c",
+             "import sys; sys.argv=['mlca','--help']; "
+             "from mlc.main import mlca; mlca()"],
+            capture_output=True, text=True
+        )
+        combined = result.stdout + result.stderr
+        self.assertIn("apptainer", combined.lower(),
+                      msg=f"Expected apptainer help text, got: {combined[:500]}")
+
+    def test_mlca_help_mentions_docker_fallback(self):
+        """mlca --help documents that --docker_X options are accepted."""
+        import subprocess, sys
+        result = subprocess.run(
+            [sys.executable, "-c",
+             "import sys; sys.argv=['mlca','--help']; "
+             "from mlc.main import mlca; mlca()"],
+            capture_output=True, text=True
+        )
+        combined = result.stdout + result.stderr
+        self.assertIn("docker_rebuild", combined,
+                      msg=f"Expected docker_rebuild in mlca help, got: {combined[:500]}")
+        self.assertIn("docker_noregenerate", combined,
+                      msg=f"Expected docker_noregenerate in mlca help, got: {combined[:500]}")

From b09e2441000395fbb6d1842f3aeab6834cb932cb Mon Sep 17 00:00:00 2001
From: mlc-automations <3246381+mlc-automations@users.noreply.github.com>
Date: Sun, 30 Aug 2026 00:13:15 +0000
Subject: [PATCH 4/6] [Automated Commit] Format Codebase

---
 tests/test_apptainer_docker_unification.py | 31 +++++++++++++++-------
 1 file changed, 21 insertions(+), 10 deletions(-)

diff --git a/tests/test_apptainer_docker_unification.py b/tests/test_apptainer_docker_unification.py
index dfc9d7c25..2d842fe57 100644
--- a/tests/test_apptainer_docker_unification.py
+++ b/tests/test_apptainer_docker_unification.py
@@ -25,7 +25,8 @@ def _merged_settings(self, docker_meta, apptainer_meta):
             "docker": docker_meta,
             "apptainer": apptainer_meta,
         }
-        return {**run_state.get("docker", {}), **run_state.get("apptainer", {})}
+        return {**run_state.get("docker", {}), **
+                run_state.get("apptainer", {})}
 
     def test_apptainer_base_image_overrides_docker(self):
         settings = self._merged_settings(
@@ -72,7 +73,9 @@ def _lookup(self, key, input_params, settings, default=None):
         )
 
     def test_apptainer_prefix_wins(self):
-        val = self._lookup("os", {"apptainer_os": "debian", "docker_os": "centos"}, {})
+        val = self._lookup(
+            "os", {
+                "apptainer_os": "debian", "docker_os": "centos"}, {})
         self.assertEqual(val, "debian")
 
     def test_docker_prefix_fallback(self):
@@ -88,14 +91,19 @@ def test_default_fallback(self):
         self.assertEqual(val, "alpine")
 
     def test_noregenerate_docker_fallback(self):
-        # apptainer_run uses: not i.get('apptainer_noregenerate', i.get('docker_noregenerate', False))
+        # apptainer_run uses: not i.get('apptainer_noregenerate',
+        # i.get('docker_noregenerate', False))
         i = {"docker_noregenerate": True}
-        regenerate_def_file = not i.get("apptainer_noregenerate", i.get("docker_noregenerate", False))
+        regenerate_def_file = not i.get(
+            "apptainer_noregenerate", i.get(
+                "docker_noregenerate", False))
         self.assertFalse(regenerate_def_file)
 
     def test_noregenerate_apptainer_overrides_docker(self):
         i = {"apptainer_noregenerate": False, "docker_noregenerate": True}
-        regenerate_def_file = not i.get("apptainer_noregenerate", i.get("docker_noregenerate", False))
+        regenerate_def_file = not i.get(
+            "apptainer_noregenerate", i.get(
+                "docker_noregenerate", False))
         self.assertTrue(regenerate_def_file)
 
     def test_rebuild_docker_fallback(self):
@@ -156,7 +164,8 @@ def test_docker_and_apptainer_both_accepted(self):
         self.assertEqual(errors, [])
 
     def test_apptainer_base_image_str_accepted(self):
-        errors, _ = self._validate({"apptainer": {"base_image": "ubuntu:22.04"}})
+        errors, _ = self._validate(
+            {"apptainer": {"base_image": "ubuntu:22.04"}})
         self.assertEqual(errors, [])
 
 
@@ -164,7 +173,6 @@ def test_apptainer_base_image_str_accepted(self):
     unittest.main()
 
 
-
 # ---------------------------------------------------------------------------
 # 5. CLI smoke tests: mlcd --help and mlca --help
 # ---------------------------------------------------------------------------
@@ -194,7 +202,8 @@ def _run_mlc_action_help(self, action):
         return result
 
     def test_mlcd_help_exits_successfully(self):
-        import subprocess, sys
+        import subprocess
+        import sys
         result = subprocess.run(
             [sys.executable, "-c",
              "import sys; sys.argv=['mlcd','--help']; "
@@ -206,7 +215,8 @@ def test_mlcd_help_exits_successfully(self):
                       msg=f"Expected docker help text, got: {combined[:500]}")
 
     def test_mlca_help_exits_successfully(self):
-        import subprocess, sys
+        import subprocess
+        import sys
         result = subprocess.run(
             [sys.executable, "-c",
              "import sys; sys.argv=['mlca','--help']; "
@@ -219,7 +229,8 @@ def test_mlca_help_exits_successfully(self):
 
     def test_mlca_help_mentions_docker_fallback(self):
         """mlca --help documents that --docker_X options are accepted."""
-        import subprocess, sys
+        import subprocess
+        import sys
         result = subprocess.run(
             [sys.executable, "-c",
              "import sys; sys.argv=['mlca','--help']; "

From ba09b8a407067de8f2d8200d7777876943933cec Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 30 Aug 2026 17:07:05 +0000
Subject: [PATCH 5/6] Fix apptainer meta key propagation, deep merge, test
 quality, and CI coverage

Co-authored-by: arjunsuresh <4791823+arjunsuresh@users.noreply.github.com>
---
 .github/workflows/test-mlc-apptainer-core.yml |   1 +
 .github/workflows/test-unit.yml               |  16 +-
 automation/script/apptainer.py                |  30 +--
 automation/script/module.py                   |  18 +-
 mlc/script_action.py                          |   7 +-
 tests/test_apptainer_docker_unification.py    | 206 ++++++++++--------
 6 files changed, 161 insertions(+), 117 deletions(-)

diff --git a/.github/workflows/test-mlc-apptainer-core.yml b/.github/workflows/test-mlc-apptainer-core.yml
index b8e16f5aa..61eb187c5 100644
--- a/.github/workflows/test-mlc-apptainer-core.yml
+++ b/.github/workflows/test-mlc-apptainer-core.yml
@@ -6,6 +6,7 @@ on:
     paths:
       - '.github/workflows/test-mlc-apptainer-core.yml'
       - 'mlc/**'
+      - 'automation/**'
       - 'tests/**'
       - 'pyproject.toml'
       - '!**.md'
diff --git a/.github/workflows/test-unit.yml b/.github/workflows/test-unit.yml
index 3680faf4e..57b4f1480 100644
--- a/.github/workflows/test-unit.yml
+++ b/.github/workflows/test-unit.yml
@@ -7,19 +7,19 @@ on:
   pull_request:
     branches: [ "main", "dev" ]
     paths:
-      - mlc/**
-      - tests/**
-      - automation/**
+      - 'mlc/**'
+      - 'tests/**'
+      - 'automation/**'
       - '.github/workflows/test-unit.yml'
-      - pyproject.toml
+      - 'pyproject.toml'
   push:
     branches: [ "main", "dev" ]
     paths:
-      - mlc/**
-      - tests/**
-      - automation/**
+      - 'mlc/**'
+      - 'tests/**'
+      - 'automation/**'
       - '.github/workflows/test-unit.yml'
-      - pyproject.toml
+      - 'pyproject.toml'
 
 jobs:
   unit-tests:
diff --git a/automation/script/apptainer.py b/automation/script/apptainer.py
index 4da9bbfe4..9440dc052 100644
--- a/automation/script/apptainer.py
+++ b/automation/script/apptainer.py
@@ -56,7 +56,9 @@ def apptainerfile(self_module, input_params):
 
     run_state = self_module.run_state
 
-    apptainer_settings = {**run_state.get('docker', {}), **run_state.get('apptainer', {})}
+    apptainer_settings = copy.deepcopy(run_state.get('docker', {}))
+    utils.merge_dicts({'dict1': apptainer_settings, 'dict2': run_state.get('apptainer', {}),
+                       'append_lists': True, 'append_unique': True})
     apptainer_settings_default_env = apptainer_settings.get('default_env', {})
     for key in apptainer_settings_default_env:
         env.setdefault(key, apptainer_settings_default_env[key])
@@ -86,7 +88,9 @@ def apptainerfile(self_module, input_params):
     if update_state_result['return'] > 0:
         return update_state_result
 
-    apptainer_settings = {**run_state.get('docker', {}), **run_state.get('apptainer', {})}
+    apptainer_settings = copy.deepcopy(run_state.get('docker', {}))
+    utils.merge_dicts({'dict1': apptainer_settings, 'dict2': run_state.get('apptainer', {}),
+                       'append_lists': True, 'append_unique': True})
 
     # Prune temporary environment variables
     run_command = copy.deepcopy(run_command_arc)
@@ -273,7 +277,9 @@ def apptainer_run(self_module, i):
 
     run_state = self_module.run_state
 
-    apptainer_settings = {**run_state.get('docker', {}), **run_state.get('apptainer', {})}
+    apptainer_settings = copy.deepcopy(run_state.get('docker', {}))
+    utils.merge_dicts({'dict1': apptainer_settings, 'dict2': run_state.get('apptainer', {}),
+                       'append_lists': True, 'append_unique': True})
 
     apptainer_settings_default_env = apptainer_settings.get('default_env', {})
     for key in apptainer_settings_default_env:
@@ -443,19 +449,15 @@ def prepare_apptainer_inputs(input_params, apptainer_settings,
             "network", "security_opt"
         ]
 
-    # Collect inputs
-    apptainer_inputs = {
-        key: input_params.get(
+    # Collect inputs: apptainer_X > docker_X > meta settings > default
+    apptainer_inputs = {}
+    for key in keys:
+        value = input_params.get(
             f"apptainer_{key}",
             input_params.get(
-                f"docker_{key}", apptainer_settings.get(
-                    key, get_apptainer_default(key))))
-        for key in keys
-        if (value := input_params.get(
-            f"apptainer_{key}",
-            input_params.get(
-                f"docker_{key}", apptainer_settings.get(key, get_apptainer_default(key))))) is not None
-    }
+                f"docker_{key}", apptainer_settings.get(key, get_apptainer_default(key))))
+        if value is not None:
+            apptainer_inputs[key] = value
 
     # Convert boolean values to 'yes'/'no' strings for MLC input mapping
     for key in list(apptainer_inputs.keys()):
diff --git a/automation/script/module.py b/automation/script/module.py
index ff62167d1..d5f414c2b 100644
--- a/automation/script/module.py
+++ b/automation/script/module.py
@@ -151,7 +151,7 @@ def init_run_state(self, run_state):
         for f in ['fake_deps', 'cache']:
             run_state.setdefault(f, False)
 
-        for d in ['input_mapping', 'docker', 'remote_run']:
+        for d in ['input_mapping', 'docker', 'remote_run', 'apptainer']:
             run_state.setdefault(d, {})
 
         for l in ['deps', 'post_deps', 'prehook_deps', 'posthook_deps',
@@ -778,7 +778,6 @@ def _run(self, i):
             variation_tags.append(f"version.{version}")
 
         run_state['docker'] = meta.get('docker', {})
-        run_state['apptainer'] = meta.get('apptainer', {})
 
         r = self._update_state_from_variations(
             i,
@@ -5769,6 +5768,14 @@ def _apply_conditional_meta_updates(update_meta_if_env, default_env, env, const,
                                'append_lists': True,
                                'append_unique': True})
 
+        if c_meta.get('apptainer', {}):
+            if not run_state.get('apptainer', {}):
+                run_state['apptainer'] = {}
+            utils.merge_dicts({'dict1': run_state['apptainer'],
+                               'dict2': c_meta['apptainer'],
+                               'append_lists': True,
+                               'append_unique': True})
+
         c_add_deps_info = c_meta.get('ad', {})
         if not c_add_deps_info:
             c_add_deps_info = c_meta.get('add_deps', {})
@@ -5976,6 +5983,13 @@ def update_state_from_meta(meta, env, state, const, const_state, run_state, i):
         if remote_run_settings.get('deps', []):
             update_deps(remote_run_settings['deps'], add_deps_info, False, env)
 
+    new_apptainer_settings = meta.get('apptainer')
+    if new_apptainer_settings:
+        utils.merge_dicts({'dict1': run_state['apptainer'],
+                           'dict2': new_apptainer_settings,
+                           'append_lists': True,
+                           'append_unique': True})
+
     new_env_keys_from_meta = meta.get('new_env_keys', [])
     if new_env_keys_from_meta:
         run_state['new_env_keys'] += new_env_keys_from_meta
diff --git a/mlc/script_action.py b/mlc/script_action.py
index ab552996f..125b99cd1 100644
--- a/mlc/script_action.py
+++ b/mlc/script_action.py
@@ -464,9 +464,10 @@ def apptainer_run(self, run_args):
     7. --apptainer_run_override / --docker_run_override:
        Force apptainer execution even if 'run' is set to False in script meta.
 
-    All --docker_X options are accepted and used as defaults when the
-    corresponding --apptainer_X option is not provided. This allows sharing
-    flags between mlcd and mlca invocations.
+    All --docker_X options listed above are accepted as defaults when the
+    corresponding --apptainer_X option is not provided. Docker-only options
+    (e.g. --docker_dt, --docker_cache, --docker_shm_size) are not applicable
+    to Apptainer and are ignored.
 
     Script meta.yaml keys:
     - ``docker``: base container settings (used by both mlcd and mlca).
diff --git a/tests/test_apptainer_docker_unification.py b/tests/test_apptainer_docker_unification.py
index 2d842fe57..a35f7688d 100644
--- a/tests/test_apptainer_docker_unification.py
+++ b/tests/test_apptainer_docker_unification.py
@@ -2,80 +2,138 @@
 Tests for the unification of mlcd and mlca options (issue #312).
 
 Verifies that:
-1. --docker_X CLI options act as fallbacks when --apptainer_X is not given in the
-   effective settings merge logic.
-2. script meta.yaml `apptainer` key overrides `docker` key for apptainer runs.
+1. --docker_X CLI options act as fallbacks when --apptainer_X is not given.
+2. script meta.yaml `apptainer` key reaches run_state via update_state_from_meta
+   and overrides `docker` key for apptainer runs.
 3. meta_schema validates the `apptainer` section using the same rules as `docker`.
+4. mlcd --help and mlca --help work as expected.
 """
+import copy
 import unittest
-from unittest.mock import MagicMock
+import mlc.utils as mlc_utils
 
 
 # ---------------------------------------------------------------------------
-# 1. run_state: apptainer key merges over docker key
-#    (mirrors what apptainerfile() and apptainer_run() do)
+# 1. run_state population from meta.yaml — calls real mlc.utils.merge_dicts
+#    to exercise the same code path as update_state_from_meta in module.py
 # ---------------------------------------------------------------------------
 
-class RunStateApptainerMergeTest(unittest.TestCase):
-    """apptainer settings from meta.yaml merge over docker settings."""
+class RunStateApptainerKeyTest(unittest.TestCase):
+    """
+    Verifies that the apptainer key in meta.yaml reaches run_state via the
+    same merge_dicts pattern used in update_state_from_meta.
+    This mirrors module.py:update_state_from_meta exactly.
+    """
 
-    def _merged_settings(self, docker_meta, apptainer_meta):
-        """Simulate what apptainer_run does to build effective settings."""
-        run_state = {
-            "docker": docker_meta,
-            "apptainer": apptainer_meta,
-        }
-        return {**run_state.get("docker", {}), **
-                run_state.get("apptainer", {})}
+    def _apply_meta_to_run_state(self, meta, run_state=None):
+        """Replicate the apptainer and docker blocks in update_state_from_meta."""
+        if run_state is None:
+            run_state = {'docker': {}, 'apptainer': {}}
+
+        new_docker = meta.get('docker')
+        if new_docker:
+            mlc_utils.merge_dicts({'dict1': run_state.get('docker', {}),
+                                   'dict2': new_docker,
+                                   'append_lists': True, 'append_unique': True})
+
+        new_apptainer = meta.get('apptainer')
+        if new_apptainer:
+            mlc_utils.merge_dicts({'dict1': run_state.get('apptainer', {}),
+                                   'dict2': new_apptainer,
+                                   'append_lists': True, 'append_unique': True})
+        return run_state
+
+    def _effective_settings(self, run_state):
+        """Replicate the merge in apptainer.py: docker overridden by apptainer."""
+        effective = copy.deepcopy(run_state.get('docker', {}))
+        mlc_utils.merge_dicts({'dict1': effective,
+                               'dict2': run_state.get('apptainer', {}),
+                               'append_lists': True, 'append_unique': True})
+        return effective
 
     def test_apptainer_base_image_overrides_docker(self):
-        settings = self._merged_settings(
-            {"base_image": "docker-image:latest"},
-            {"base_image": "apptainer-image:latest"},
-        )
-        self.assertEqual(settings["base_image"], "apptainer-image:latest")
+        meta = {
+            'docker': {'os': 'ubuntu', 'base_image': 'ubuntu:22.04'},
+            'apptainer': {'base_image': 'docker://ubuntu:20.04'},
+        }
+        run_state = self._apply_meta_to_run_state(meta)
+        self.assertEqual(run_state['apptainer']['base_image'], 'docker://ubuntu:20.04')
+        effective = self._effective_settings(run_state)
+        self.assertEqual(effective['base_image'], 'docker://ubuntu:20.04')
+        self.assertEqual(effective['os'], 'ubuntu')
 
     def test_docker_settings_used_when_no_apptainer_key(self):
-        settings = self._merged_settings(
-            {"os": "ubuntu", "base_image": "docker-image:latest"},
-            {},
-        )
-        self.assertEqual(settings["os"], "ubuntu")
-        self.assertEqual(settings["base_image"], "docker-image:latest")
-
-    def test_apptainer_partial_override(self):
-        """Only the keys in apptainer meta override; rest comes from docker."""
-        settings = self._merged_settings(
-            {"os": "ubuntu", "os_version": "22.04", "run": True},
-            {"os_version": "20.04"},
-        )
-        self.assertEqual(settings["os"], "ubuntu")
-        self.assertEqual(settings["os_version"], "20.04")
-        self.assertTrue(settings["run"])
+        meta = {'docker': {'os': 'ubuntu', 'base_image': 'ubuntu:22.04'}}
+        run_state = self._apply_meta_to_run_state(meta)
+        effective = self._effective_settings(run_state)
+        self.assertEqual(effective['os'], 'ubuntu')
+        self.assertEqual(effective['base_image'], 'ubuntu:22.04')
+
+    def test_apptainer_key_missing_from_meta_leaves_run_state_empty(self):
+        meta = {'docker': {'os': 'ubuntu'}}
+        run_state = self._apply_meta_to_run_state(meta)
+        self.assertEqual(run_state['apptainer'], {})
+
+    def test_deep_merge_preserves_docker_subkeys_not_in_apptainer(self):
+        """apptainer.default_env.B overrides docker.default_env.B; A is preserved."""
+        meta = {
+            'docker': {'default_env': {'A': '1', 'B': '2'}},
+            'apptainer': {'default_env': {'B': 'override'}},
+        }
+        run_state = self._apply_meta_to_run_state(meta)
+        effective = self._effective_settings(run_state)
+        self.assertEqual(effective['default_env']['A'], '1')
+        self.assertEqual(effective['default_env']['B'], 'override')
+
+    def test_init_run_state_seeds_apptainer_key(self):
+        """init_run_state in module.py must initialise run_state['apptainer'] to {}."""
+        import sys, importlib.util, os
+
+        # Load automation/utils.py as 'utils' so module.py can do `from utils import *`
+        automation_path = os.path.join(
+            os.path.dirname(os.path.dirname(__file__)), 'automation')
+        utils_spec = importlib.util.spec_from_file_location(
+            'utils', os.path.join(automation_path, 'utils.py'))
+        utils_mod = importlib.util.module_from_spec(utils_spec)
+        sys.modules.setdefault('utils', utils_mod)
+        utils_spec.loader.exec_module(utils_mod)
+
+        # Also add automation/script to sys.path so `from script.X import *` works
+        script_path = os.path.join(automation_path, 'script')
+        for p in [automation_path, script_path]:
+            if p not in sys.path:
+                sys.path.insert(0, p)
+
+        # Dynamically load automation/script/module.py
+        module_spec = importlib.util.spec_from_file_location(
+            '_test_module',
+            os.path.join(automation_path, 'script', 'module.py'))
+        module_mod = importlib.util.module_from_spec(module_spec)
+        module_spec.loader.exec_module(module_mod)
+
+        sa = module_mod.ScriptAutomation.__new__(module_mod.ScriptAutomation)
+        result = sa.init_run_state(None)
+        self.assertIn('apptainer', result,
+                      "init_run_state must seed run_state['apptainer']")
+        self.assertEqual(result['apptainer'], {})
 
 
 # ---------------------------------------------------------------------------
 # 2. CLI fallback: docker_X used when apptainer_X is absent
-#    Tests the lookup pattern: apptainer_X → docker_X → settings → default
+#    Tests the three-level lookup: apptainer_X > docker_X > settings > default
 # ---------------------------------------------------------------------------
 
 class ApptainerDockerCliFallbackTest(unittest.TestCase):
-    """
-    Verify the three-level lookup: apptainer_X > docker_X > settings > default.
-    This mirrors the logic in prepare_apptainer_inputs and apptainer_run.
-    """
 
     def _lookup(self, key, input_params, settings, default=None):
-        """Replicate the lookup pattern used in prepare_apptainer_inputs."""
+        """Replicates the lookup used in prepare_apptainer_inputs."""
         return input_params.get(
             f"apptainer_{key}",
             input_params.get(f"docker_{key}", settings.get(key, default))
         )
 
     def test_apptainer_prefix_wins(self):
-        val = self._lookup(
-            "os", {
-                "apptainer_os": "debian", "docker_os": "centos"}, {})
+        val = self._lookup("os", {"apptainer_os": "debian", "docker_os": "centos"}, {})
         self.assertEqual(val, "debian")
 
     def test_docker_prefix_fallback(self):
@@ -91,19 +149,13 @@ def test_default_fallback(self):
         self.assertEqual(val, "alpine")
 
     def test_noregenerate_docker_fallback(self):
-        # apptainer_run uses: not i.get('apptainer_noregenerate',
-        # i.get('docker_noregenerate', False))
         i = {"docker_noregenerate": True}
-        regenerate_def_file = not i.get(
-            "apptainer_noregenerate", i.get(
-                "docker_noregenerate", False))
+        regenerate_def_file = not i.get("apptainer_noregenerate", i.get("docker_noregenerate", False))
         self.assertFalse(regenerate_def_file)
 
     def test_noregenerate_apptainer_overrides_docker(self):
         i = {"apptainer_noregenerate": False, "docker_noregenerate": True}
-        regenerate_def_file = not i.get(
-            "apptainer_noregenerate", i.get(
-                "docker_noregenerate", False))
+        regenerate_def_file = not i.get("apptainer_noregenerate", i.get("docker_noregenerate", False))
         self.assertTrue(regenerate_def_file)
 
     def test_rebuild_docker_fallback(self):
@@ -123,11 +175,10 @@ def test_mounts_apptainer_overrides_docker(self):
 
 
 # ---------------------------------------------------------------------------
-# 3. meta_schema: apptainer key validation
+# 3. meta_schema: apptainer key validation (calls real validate_meta)
 # ---------------------------------------------------------------------------
 
 class MetaSchemaApptainerKeyTest(unittest.TestCase):
-    """The `apptainer` key in meta.yaml is validated like `docker`."""
 
     def _validate(self, data):
         from mlc.meta_schema import validate_meta
@@ -164,46 +215,19 @@ def test_docker_and_apptainer_both_accepted(self):
         self.assertEqual(errors, [])
 
     def test_apptainer_base_image_str_accepted(self):
-        errors, _ = self._validate(
-            {"apptainer": {"base_image": "ubuntu:22.04"}})
+        errors, _ = self._validate({"apptainer": {"base_image": "ubuntu:22.04"}})
         self.assertEqual(errors, [])
 
 
-if __name__ == "__main__":
-    unittest.main()
-
-
 # ---------------------------------------------------------------------------
-# 5. CLI smoke tests: mlcd --help and mlca --help
+# 4. CLI smoke tests: mlcd --help and mlca --help
 # ---------------------------------------------------------------------------
 
 class CliHelpSmokeTest(unittest.TestCase):
     """mlcd and mlca --help exit cleanly and include expected content."""
 
-    def _run_help(self, entry_point):
-        import subprocess
-        import sys
-        result = subprocess.run(
-            [sys.executable, "-m", entry_point, "--help"],
-            capture_output=True, text=True
-        )
-        return result
-
-    def _run_mlc_action_help(self, action):
-        """Use 'mlc <action> script --help' as the canonical help path."""
-        import subprocess
-        import sys
-        result = subprocess.run(
-            [sys.executable, "-c",
-             f"import sys; sys.argv=['mlc', '{action}', 'script', '--help']; "
-             f"from mlc.main import main; main()"],
-            capture_output=True, text=True
-        )
-        return result
-
     def test_mlcd_help_exits_successfully(self):
-        import subprocess
-        import sys
+        import subprocess, sys
         result = subprocess.run(
             [sys.executable, "-c",
              "import sys; sys.argv=['mlcd','--help']; "
@@ -215,8 +239,7 @@ def test_mlcd_help_exits_successfully(self):
                       msg=f"Expected docker help text, got: {combined[:500]}")
 
     def test_mlca_help_exits_successfully(self):
-        import subprocess
-        import sys
+        import subprocess, sys
         result = subprocess.run(
             [sys.executable, "-c",
              "import sys; sys.argv=['mlca','--help']; "
@@ -229,8 +252,7 @@ def test_mlca_help_exits_successfully(self):
 
     def test_mlca_help_mentions_docker_fallback(self):
         """mlca --help documents that --docker_X options are accepted."""
-        import subprocess
-        import sys
+        import subprocess, sys
         result = subprocess.run(
             [sys.executable, "-c",
              "import sys; sys.argv=['mlca','--help']; "
@@ -242,3 +264,7 @@ def test_mlca_help_mentions_docker_fallback(self):
                       msg=f"Expected docker_rebuild in mlca help, got: {combined[:500]}")
         self.assertIn("docker_noregenerate", combined,
                       msg=f"Expected docker_noregenerate in mlca help, got: {combined[:500]}")
+
+
+if __name__ == "__main__":
+    unittest.main()

From fa1df9e4eff7965dff13eee231dd567ca67f4433 Mon Sep 17 00:00:00 2001
From: mlc-automations <3246381+mlc-automations@users.noreply.github.com>
Date: Sun, 30 Aug 2026 17:14:45 +0000
Subject: [PATCH 6/6] [Automated Commit] Format Codebase

---
 automation/script/apptainer.py             | 14 +++++---
 tests/test_apptainer_docker_unification.py | 38 +++++++++++++++-------
 2 files changed, 37 insertions(+), 15 deletions(-)

diff --git a/automation/script/apptainer.py b/automation/script/apptainer.py
index 9440dc052..c63b8b7cf 100644
--- a/automation/script/apptainer.py
+++ b/automation/script/apptainer.py
@@ -8,7 +8,8 @@
 
 def apptainerfile(self_module, input_params):
 
-    # Step 1: Prune and prepare input (remove both apptainer_ and docker_ prefixed keys)
+    # Step 1: Prune and prepare input (remove both apptainer_ and docker_
+    # prefixed keys)
     prune_result = prune_input(
         {'input': input_params, 'extra_keys_starts_with': ['apptainer_', 'docker_']})
     if prune_result['return'] > 0:
@@ -217,11 +218,16 @@ def apptainer_run(self_module, i):
     if quiet:
         env['MLC_QUIET'] = 'yes'
 
-    regenerate_def_file = not i.get('apptainer_noregenerate', i.get('docker_noregenerate', False))
-    rebuild_apptainer_image = i.get('apptainer_rebuild', i.get('docker_rebuild', False))
+    regenerate_def_file = not i.get(
+        'apptainer_noregenerate', i.get(
+            'docker_noregenerate', False))
+    rebuild_apptainer_image = i.get(
+        'apptainer_rebuild', i.get(
+            'docker_rebuild', False))
 
     # Prune unnecessary Apptainer- and Docker-related input keys
-    r = prune_input({'input': i, 'extra_keys_starts_with': ['apptainer_', 'docker_']})
+    r = prune_input(
+        {'input': i, 'extra_keys_starts_with': ['apptainer_', 'docker_']})
     f_run_cmd = r['new_input']
 
     # Save current directory and prepare to search for scripts
diff --git a/tests/test_apptainer_docker_unification.py b/tests/test_apptainer_docker_unification.py
index a35f7688d..6e09a3802 100644
--- a/tests/test_apptainer_docker_unification.py
+++ b/tests/test_apptainer_docker_unification.py
@@ -57,7 +57,9 @@ def test_apptainer_base_image_overrides_docker(self):
             'apptainer': {'base_image': 'docker://ubuntu:20.04'},
         }
         run_state = self._apply_meta_to_run_state(meta)
-        self.assertEqual(run_state['apptainer']['base_image'], 'docker://ubuntu:20.04')
+        self.assertEqual(
+            run_state['apptainer']['base_image'],
+            'docker://ubuntu:20.04')
         effective = self._effective_settings(run_state)
         self.assertEqual(effective['base_image'], 'docker://ubuntu:20.04')
         self.assertEqual(effective['os'], 'ubuntu')
@@ -87,9 +89,12 @@ def test_deep_merge_preserves_docker_subkeys_not_in_apptainer(self):
 
     def test_init_run_state_seeds_apptainer_key(self):
         """init_run_state in module.py must initialise run_state['apptainer'] to {}."""
-        import sys, importlib.util, os
+        import sys
+        import importlib.util
+        import os
 
-        # Load automation/utils.py as 'utils' so module.py can do `from utils import *`
+        # Load automation/utils.py as 'utils' so module.py can do `from utils
+        # import *`
         automation_path = os.path.join(
             os.path.dirname(os.path.dirname(__file__)), 'automation')
         utils_spec = importlib.util.spec_from_file_location(
@@ -98,7 +103,8 @@ def test_init_run_state_seeds_apptainer_key(self):
         sys.modules.setdefault('utils', utils_mod)
         utils_spec.loader.exec_module(utils_mod)
 
-        # Also add automation/script to sys.path so `from script.X import *` works
+        # Also add automation/script to sys.path so `from script.X import *`
+        # works
         script_path = os.path.join(automation_path, 'script')
         for p in [automation_path, script_path]:
             if p not in sys.path:
@@ -133,7 +139,9 @@ def _lookup(self, key, input_params, settings, default=None):
         )
 
     def test_apptainer_prefix_wins(self):
-        val = self._lookup("os", {"apptainer_os": "debian", "docker_os": "centos"}, {})
+        val = self._lookup(
+            "os", {
+                "apptainer_os": "debian", "docker_os": "centos"}, {})
         self.assertEqual(val, "debian")
 
     def test_docker_prefix_fallback(self):
@@ -150,12 +158,16 @@ def test_default_fallback(self):
 
     def test_noregenerate_docker_fallback(self):
         i = {"docker_noregenerate": True}
-        regenerate_def_file = not i.get("apptainer_noregenerate", i.get("docker_noregenerate", False))
+        regenerate_def_file = not i.get(
+            "apptainer_noregenerate", i.get(
+                "docker_noregenerate", False))
         self.assertFalse(regenerate_def_file)
 
     def test_noregenerate_apptainer_overrides_docker(self):
         i = {"apptainer_noregenerate": False, "docker_noregenerate": True}
-        regenerate_def_file = not i.get("apptainer_noregenerate", i.get("docker_noregenerate", False))
+        regenerate_def_file = not i.get(
+            "apptainer_noregenerate", i.get(
+                "docker_noregenerate", False))
         self.assertTrue(regenerate_def_file)
 
     def test_rebuild_docker_fallback(self):
@@ -215,7 +227,8 @@ def test_docker_and_apptainer_both_accepted(self):
         self.assertEqual(errors, [])
 
     def test_apptainer_base_image_str_accepted(self):
-        errors, _ = self._validate({"apptainer": {"base_image": "ubuntu:22.04"}})
+        errors, _ = self._validate(
+            {"apptainer": {"base_image": "ubuntu:22.04"}})
         self.assertEqual(errors, [])
 
 
@@ -227,7 +240,8 @@ class CliHelpSmokeTest(unittest.TestCase):
     """mlcd and mlca --help exit cleanly and include expected content."""
 
     def test_mlcd_help_exits_successfully(self):
-        import subprocess, sys
+        import subprocess
+        import sys
         result = subprocess.run(
             [sys.executable, "-c",
              "import sys; sys.argv=['mlcd','--help']; "
@@ -239,7 +253,8 @@ def test_mlcd_help_exits_successfully(self):
                       msg=f"Expected docker help text, got: {combined[:500]}")
 
     def test_mlca_help_exits_successfully(self):
-        import subprocess, sys
+        import subprocess
+        import sys
         result = subprocess.run(
             [sys.executable, "-c",
              "import sys; sys.argv=['mlca','--help']; "
@@ -252,7 +267,8 @@ def test_mlca_help_exits_successfully(self):
 
     def test_mlca_help_mentions_docker_fallback(self):
         """mlca --help documents that --docker_X options are accepted."""
-        import subprocess, sys
+        import subprocess
+        import sys
         result = subprocess.run(
             [sys.executable, "-c",
              "import sys; sys.argv=['mlca','--help']; "