From aaa640365f2ea073922ea7e9f73007b6912c0b4c Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 4 Jul 2026 11:19:44 +0000
Subject: [PATCH 1/9] Initial plan


From 4df607a3c85f4f82b8dd56cc5abddc112c2fec28 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 4 Jul 2026 11:22:30 +0000
Subject: [PATCH 2/9] Add apptainer script action dispatch

---
 mlc/main.py                           |  2 +-
 mlc/script_action.py                  | 13 +++++++++++--
 tests/test_script_action_apptainer.py | 28 +++++++++++++++++++++++++++
 3 files changed, 40 insertions(+), 3 deletions(-)
 create mode 100644 tests/test_script_action_apptainer.py

diff --git a/mlc/main.py b/mlc/main.py
index 0250ad303..8c0f311fa 100644
--- a/mlc/main.py
+++ b/mlc/main.py
@@ -507,7 +507,7 @@ def main():
 
     | Target  | Actions                                                   |
     |---------|-----------------------------------------------------------|
-    | script  | run, find/search, rm, mv, cp, add, test, docker-run, show |
+    | script  | run, find/search, rm, mv, cp, add, test, docker-run, apptainer, show |
     | cache   | find/search, rm, show, list, prune, mark-tmp              |
     | repo    | pull, search, rm, list, find/search                       |
 
diff --git a/mlc/script_action.py b/mlc/script_action.py
index bee4d9f00..99f2c8d33 100644
--- a/mlc/script_action.py
+++ b/mlc/script_action.py
@@ -26,8 +26,9 @@ class ScriptAction(Action):
     6.  Copy(cp)
     7.  Run
     8.  Docker
-    9.  Test
-    10. Experiment
+    9.  Apptainer
+    10. Test
+    11. Experiment
 
     Scripts in MLCFlow can be identified using different methods:
 
@@ -414,6 +415,14 @@ def docker_run(self, run_args):
 
     docker.__doc__ = docker_run.__doc__
 
+    def apptainer(self, run_args):
+        return self.apptainer_run(run_args)
+
+    def apptainer_run(self, run_args):
+        return self.call_script_module_function("apptainer", run_args)
+
+    apptainer.__doc__ = docker_run.__doc__
+
     def remote_run(self, run_args):
         """
     ####################################################################################################################
diff --git a/tests/test_script_action_apptainer.py b/tests/test_script_action_apptainer.py
new file mode 100644
index 000000000..27b2bd27c
--- /dev/null
+++ b/tests/test_script_action_apptainer.py
@@ -0,0 +1,28 @@
+import unittest
+from unittest.mock import patch
+
+from mlc.script_action import ScriptAction
+
+
+class _Parent:
+    pass
+
+
+class ScriptActionApptainerTest(unittest.TestCase):
+    def test_apptainer_delegates_to_script_module(self):
+        action = ScriptAction(_Parent())
+        run_args = {"tags": "detect,os"}
+        expected = {"return": 0}
+
+        with patch.object(
+                ScriptAction,
+                "call_script_module_function",
+                return_value=expected) as call_script_module_function:
+            result = action.apptainer(run_args)
+
+        self.assertEqual(result, expected)
+        call_script_module_function.assert_called_once_with("apptainer", run_args)
+
+
+if __name__ == "__main__":
+    unittest.main()

From 100a42e7d42c709442e17e1b470dc09d2d6b2ec6 Mon Sep 17 00:00:00 2001
From: mlc-automations <3246381+mlc-automations@users.noreply.github.com>
Date: Sat, 4 Jul 2026 11:24:33 +0000
Subject: [PATCH 3/9] [Automated Commit] Format Codebase

---
 tests/test_script_action_apptainer.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/test_script_action_apptainer.py b/tests/test_script_action_apptainer.py
index 27b2bd27c..23403ebe1 100644
--- a/tests/test_script_action_apptainer.py
+++ b/tests/test_script_action_apptainer.py
@@ -21,7 +21,8 @@ def test_apptainer_delegates_to_script_module(self):
             result = action.apptainer(run_args)
 
         self.assertEqual(result, expected)
-        call_script_module_function.assert_called_once_with("apptainer", run_args)
+        call_script_module_function.assert_called_once_with(
+            "apptainer", run_args)
 
 
 if __name__ == "__main__":

From 55c2d56cbc668aae39a06cc53f5e7ddea0fa6c61 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 4 Jul 2026 11:24:43 +0000
Subject: [PATCH 4/9] Handle apptainer dispatch in ScriptAction

---
 mlc/script_action.py | 24 +++++++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

diff --git a/mlc/script_action.py b/mlc/script_action.py
index 99f2c8d33..9de4dcce4 100644
--- a/mlc/script_action.py
+++ b/mlc/script_action.py
@@ -286,6 +286,9 @@ def call_script_module_function(self, function_name, run_args):
                 elif function_name == "docker":
                     result = automation_instance.docker(
                         run_args)  # Pass args to the run method
+                elif function_name == "apptainer":
+                    result = automation_instance.apptainer(
+                        run_args)  # Pass args to the apptainer method
                 elif function_name == "test":
                     result = automation_instance.test(
                         run_args)  # Pass args to the run method
@@ -419,9 +422,28 @@ def apptainer(self, run_args):
         return self.apptainer_run(run_args)
 
     def apptainer_run(self, run_args):
+        """
+    ####################################################################################################################
+    Target: Script
+    Action: Apptainer
+    ####################################################################################################################
+
+    The `apptainer` action runs scripts inside an Apptainer containerized environment.
+
+    An MLCFlow script can be executed inside Apptainer using either of the following syntaxes:
+
+    1. Apptainer Run: mlc apptainer run --tags=<script tags> <run flags>
+    2. Apptainer Script: mlc apptainer script --tags=<script tags> <run flags>
+
+    Example Command:
+
+    mlc apptainer script --tags=detect,os -j
+    mlca detect,os -j
+
+        """
         return self.call_script_module_function("apptainer", run_args)
 
-    apptainer.__doc__ = docker_run.__doc__
+    apptainer.__doc__ = apptainer_run.__doc__
 
     def remote_run(self, run_args):
         """

From beb2735a9116d79f6525ce9d6e4afd651d2986bd Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 4 Jul 2026 11:34:03 +0000
Subject: [PATCH 5/9] Add GitHub Action test for apptainer CLI path

---
 .github/workflows/test-mlc-apptainer-core.yml | 46 +++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 .github/workflows/test-mlc-apptainer-core.yml

diff --git a/.github/workflows/test-mlc-apptainer-core.yml b/.github/workflows/test-mlc-apptainer-core.yml
new file mode 100644
index 000000000..b8e16f5aa
--- /dev/null
+++ b/.github/workflows/test-mlc-apptainer-core.yml
@@ -0,0 +1,46 @@
+name: MLC Apptainer core action tests
+
+on:
+  pull_request:
+    branches: [ "main", "dev" ]
+    paths:
+      - '.github/workflows/test-mlc-apptainer-core.yml'
+      - 'mlc/**'
+      - 'tests/**'
+      - 'pyproject.toml'
+      - '!**.md'
+
+permissions:
+  contents: read
+
+jobs:
+  test_mlc_apptainer_core:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.14", "3.9"]
+
+    steps:
+    - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4.3.1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install mlcflow from the pull request's source repository and branch
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install --ignore-installed --verbose pip setuptools
+        python -m pip install .
+
+    - name: Test apptainer delegation unit test
+      run: |
+        python -m unittest tests.test_script_action_apptainer -v
+
+    - name: Test apptainer CLI help paths
+      run: |
+        mlca --help | grep -q "apptainer"
+        mlc apptainer script --help | grep -q "apptainer"
+        mlc apptainer-run script --help | grep -q "apptainer"

From ad681ebe265f59574318bd2b808b6dff4e0b845b Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 4 Jul 2026 14:14:03 +0000
Subject: [PATCH 6/9] fix: add apptainer-run as a valid CLI command alias

---
 mlc/main.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/mlc/main.py b/mlc/main.py
index 8c0f311fa..f886a7598 100644
--- a/mlc/main.py
+++ b/mlc/main.py
@@ -390,7 +390,7 @@ def build_parser(pre_args):
     reindex_parser.add_argument('extra', nargs=argparse.REMAINDER)
 
     # Script-only
-    for action in ['docker', 'docker-run', 'apptainer',
+    for action in ['docker', 'docker-run', 'apptainer', 'apptainer-run',
                    'experiment', 'remote-run', 'remote-experiment',
                    'remote-docker', 'doc', 'lint']:
         p = subparsers.add_parser(action, add_help=False)
@@ -432,8 +432,8 @@ def build_run_args(args):
     if args.command in ['pull', 'rm', 'add', 'find'] and args.target == "repo":
         run_args['repo'] = args.details
 
-    if args.command in ['docker', 'docker-run', 'apptainer', 'experiment',
-                        'remote-run', 'remote-experiment',
+    if args.command in ['docker', 'docker-run', 'apptainer', 'apptainer-run',
+                        'experiment', 'remote-run', 'remote-experiment',
                         'remote-docker', 'doc', 'lint'] and args.target == "run":
         # run_args['target'] = 'script' #dont modify this as script might have
         # target as in input
@@ -560,7 +560,7 @@ def main():
         help_text = ""
         if pre_args.target == "run":
             if pre_args.action.startswith(
-                    "docker") or pre_args.action == "apptainer":
+                    "docker") or pre_args.action in ("apptainer", "apptainer-run"):
                 pre_args.target = "script"
             else:
                 logger.error(

From cb78ec701eb73530dfcc8fd357a359d4786e190a Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 4 Jul 2026 14:14:31 +0000
Subject: [PATCH 7/9] fix: update docstring to include apptainer-run alias

---
 mlc/main.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mlc/main.py b/mlc/main.py
index f886a7598..28fd4b3d6 100644
--- a/mlc/main.py
+++ b/mlc/main.py
@@ -507,7 +507,7 @@ def main():
 
     | Target  | Actions                                                   |
     |---------|-----------------------------------------------------------|
-    | script  | run, find/search, rm, mv, cp, add, test, docker-run, apptainer, show |
+    | script  | run, find/search, rm, mv, cp, add, test, docker-run, apptainer/apptainer-run, show |
     | cache   | find/search, rm, show, list, prune, mark-tmp              |
     | repo    | pull, search, rm, list, find/search                       |
 

From b25ff716ea908c187991308809832be1de006305 Mon Sep 17 00:00:00 2001
From: Arjun Suresh <arjun@gateoverflow.com>
Date: Sat, 4 Jul 2026 15:40:06 +0100
Subject: [PATCH 8/9] Update VERSION

---
 VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/VERSION b/VERSION
index e8ea05db8..c813fe116 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.2.4
+1.2.5

From e1669c93c1a72d37975cd8cb5899fc060e0a747d Mon Sep 17 00:00:00 2001
From: Arjun Suresh <arjun@gateoverflow.com>
Date: Sat, 4 Jul 2026 15:40:19 +0100
Subject: [PATCH 9/9] Update pyproject.toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 535fc8237..9d7953f66 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "mlcflow"
-version = "1.2.4"
+version = "1.2.5"
 
 description = "An automation interface tailored for CPU/GPU benchmarking"
 authors = [