From 99088af3bed40ce5c2e85c542b6fc0256380d61f Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 12 May 2026 16:59:20 +0000
Subject: [PATCH 1/9] Initial plan


From 82f46cc8c59070a3471a6cfe2c86eff9a43e10f1 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 12 May 2026 17:02:30 +0000
Subject: [PATCH 2/9] feat(submit): add --make-commit auto-commit option

Agent-Logs-Url: https://github.com/mila-iqia/cluv/sessions/664c8c45-1991-4e4a-b007-e1247faca220

Co-authored-by: lebrice <13387299+lebrice@users.noreply.github.com>
---
 cluv/__main__.py     |  5 ++++
 cluv/cli/submit.py   | 57 +++++++++++++++++++++++++++++++-----
 tests/test_submit.py | 69 ++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 124 insertions(+), 7 deletions(-)

diff --git a/cluv/__main__.py b/cluv/__main__.py
index 1c71424..af6aa1b 100644
--- a/cluv/__main__.py
+++ b/cluv/__main__.py
@@ -112,6 +112,11 @@ def add_submit_args(
         formatter_class=rich_argparse.RichHelpFormatter,
         usage="cluv submit <cluster> <job.sh> [sbatch-args...] [-- program-args...]",
     )
+    submit_parser.add_argument(
+        "--make-commit",
+        action="store_true",
+        help="Create a local commit with tracked changes before submitting the job.",
+    )
     submit_parser.add_argument(
         "cluster",
         metavar="<cluster>",
diff --git a/cluv/cli/submit.py b/cluv/cli/submit.py
index 53d5da1..11c04ca 100644
--- a/cluv/cli/submit.py
+++ b/cluv/cli/submit.py
@@ -25,6 +25,7 @@ async def submit(
     job_script: Path,
     sbatch_args: list[str],
     program_args: list[str],
+    make_commit: bool = False,
 ) -> int | None:
     """Submit a SLURM job on a remote cluster.
 
@@ -56,8 +57,12 @@ async def submit(
     )
     ```
     """
+    submit_command = build_submit_command(cluster, job_script, sbatch_args, program_args, make_commit)
+
     # Check git is clean locally (untracked files are fine) and capture current commit hash.
-    git_commit = ensure_clean_git_state()
+    git_commit = ensure_clean_git_state(
+        make_commit=make_commit, launched_job_command=submit_command
+    )
 
     if cluster == "first":
         return await submit_first(job_script, sbatch_args, program_args, git_commit)
@@ -186,17 +191,55 @@ async def submit_first(
     return start_job_id
 
 
-def ensure_clean_git_state() -> str:
+def build_submit_command(
+    cluster: str,
+    job_script: Path,
+    sbatch_args: list[str],
+    program_args: list[str],
+    make_commit: bool,
+) -> str:
+    """Build the local `cluv submit` command line used to launch the job."""
+    command_parts = ["cluv", "submit"]
+    if make_commit:
+        command_parts.append("--make-commit")
+    command_parts.extend([cluster, str(job_script), *sbatch_args])
+    if program_args:
+        command_parts.extend(["--", *program_args])
+    return shlex.join(command_parts)
+
+
+def create_submit_commit(launched_job_command: str) -> None:
+    """Create a commit with tracked changes and include the launched job command in the body."""
+    subprocess.run(["git", "add", "-u"], check=True)
+    subprocess.run(
+        [
+            "git",
+            "commit",
+            "-m",
+            "cluv submit: auto-commit tracked changes",
+            "-m",
+            f"Launched job command:\n\n{launched_job_command}",
+        ],
+        check=True,
+    )
+
+
+def ensure_clean_git_state(
+    make_commit: bool = False, launched_job_command: str | None = None
+) -> str:
     """
     Check git is clean locally and return the current commit hash.
     """
     git_status = subprocess.run(["git", "status", "--porcelain"], capture_output=True, text=True)
     dirty_lines = [line for line in git_status.stdout.splitlines() if not line.startswith("??")]
-    if dirty_lines and not (os.environ.get("SKIP_CLEAN_GIT_CHECK", "0") == "1"):
-        console.print(
-            "[red]Working directory is dirty. Please commit your changes before submitting.[/red]",
-        )
-        sys.exit(1)
+    if dirty_lines:
+        if make_commit:
+            create_submit_commit(launched_job_command=launched_job_command or "cluv submit")
+        elif not (os.environ.get("SKIP_CLEAN_GIT_CHECK", "0") == "1"):
+            console.print(
+                "[red]Working directory is dirty. Please commit your changes before submitting.[/red]",
+            )
+            sys.exit(1)
 
     # In GitHub Actions PR jobs we can be on a detached merge commit that doesn't exist on
     # the synced remote checkout. Prefer the branch tip commit in that case.
diff --git a/tests/test_submit.py b/tests/test_submit.py
index 8706ae4..3e98ca6 100644
--- a/tests/test_submit.py
+++ b/tests/test_submit.py
@@ -82,6 +82,75 @@ def test_only_override_slurm_vars_with_selected_cluster_vars(self, project_dir:
 
 
 class TestEnsureCleanGitState:
+    def test_dirty_repo_without_make_commit_exits(self, monkeypatch: pytest.MonkeyPatch) -> None:
+        def mock_subprocess_run(command: list[str], **kwargs) -> subprocess.CompletedProcess[str]:
+            assert kwargs.get("capture_output") is True
+            assert kwargs.get("text") is True
+            if command == ["git", "status", "--porcelain"]:
+                return subprocess.CompletedProcess(command, 0, stdout=" M cluv/cli/submit.py\n", stderr="")
+            raise AssertionError(f"Unexpected subprocess.run call: {command}")
+
+        monkeypatch.setattr(subprocess, "run", mock_subprocess_run)
+
+        with pytest.raises(SystemExit):
+            ensure_clean_git_state()
+
+    def test_make_commit_creates_commit_with_tracked_changes_and_command(
+        self, monkeypatch: pytest.MonkeyPatch
+    ) -> None:
+        command_calls: list[tuple[list[str], dict]] = []
+
+        def mock_subprocess_run(command: list[str], **kwargs) -> subprocess.CompletedProcess[str]:
+            command_calls.append((command, kwargs))
+            if command == ["git", "status", "--porcelain"]:
+                return subprocess.CompletedProcess(
+                    command, 0, stdout=" M cluv/cli/submit.py\n?? notes.txt\n", stderr=""
+                )
+            if command == ["git", "add", "-u"]:
+                assert kwargs.get("check") is True
+                return subprocess.CompletedProcess(command, 0, stdout="", stderr="")
+            if command[:2] == ["git", "commit"]:
+                assert kwargs.get("check") is True
+                assert command[2:4] == ["-m", "cluv submit: auto-commit tracked changes"]
+                assert command[4] == "-m"
+                assert (
+                    command[5]
+                    == "Launched job command:\n\ncluv submit --make-commit mila scripts/job.sh -- --flag"
+                )
+                return subprocess.CompletedProcess(command, 0, stdout="", stderr="")
+            raise AssertionError(f"Unexpected subprocess.run call: {command}")
+
+        def mock_subprocess_check_output(command: list[str], **kwargs) -> str:
+            assert kwargs.get("text") is True
+            if command == ["git", "rev-parse", "--abbrev-ref", "HEAD"]:
+                return "main\n"
+            if command == ["git", "rev-parse", "HEAD"]:
+                return "dddddddddddddddddddddddddddddddddddddddd\n"
+            raise AssertionError(f"Unexpected subprocess.check_output call: {command}")
+
+        monkeypatch.setattr(subprocess, "run", mock_subprocess_run)
+        monkeypatch.setattr(subprocess, "check_output", mock_subprocess_check_output)
+
+        assert (
+            ensure_clean_git_state(
+                make_commit=True,
+                launched_job_command="cluv submit --make-commit mila scripts/job.sh -- --flag",
+            )
+            == "dddddddddddddddddddddddddddddddddddddddd"
+        )
+        assert [call[0] for call in command_calls[:3]] == [
+            ["git", "status", "--porcelain"],
+            ["git", "add", "-u"],
+            [
+                "git",
+                "commit",
+                "-m",
+                "cluv submit: auto-commit tracked changes",
+                "-m",
+                "Launched job command:\n\ncluv submit --make-commit mila scripts/job.sh -- --flag",
+            ],
+        ]
+
     def test_prefers_branch_tip_in_github_actions_detached_head(
         self, monkeypatch: pytest.MonkeyPatch
     ) -> None:

From 4f7e771bd2253d4b2083d09543440c72e6bfd99e Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 12 May 2026 17:03:23 +0000
Subject: [PATCH 3/9] refactor(submit): tighten make-commit command handling

Agent-Logs-Url: https://github.com/mila-iqia/cluv/sessions/664c8c45-1991-4e4a-b007-e1247faca220

Co-authored-by: lebrice <13387299+lebrice@users.noreply.github.com>
---
 cluv/cli/submit.py   | 10 ++++++++--
 tests/test_submit.py | 15 +++++++++++++++
 2 files changed, 23 insertions(+), 2 deletions(-)

diff --git a/cluv/cli/submit.py b/cluv/cli/submit.py
index 11c04ca..40ff6f8 100644
--- a/cluv/cli/submit.py
+++ b/cluv/cli/submit.py
@@ -57,7 +57,11 @@ async def submit(
     )
     ```
     """
-    submit_command = build_submit_command(cluster, job_script, sbatch_args, program_args, make_commit)
+    submit_command: str | None = None
+    if make_commit:
+        submit_command = build_submit_command(
+            cluster, job_script, sbatch_args, program_args, make_commit
+        )
 
     # Check git is clean locally (untracked files are fine) and capture current commit hash.
     git_commit = ensure_clean_git_state(
@@ -234,7 +238,9 @@ def ensure_clean_git_state(
     dirty_lines = [line for line in git_status.stdout.splitlines() if not line.startswith("??")]
     if dirty_lines:
         if make_commit:
-            create_submit_commit(launched_job_command=launched_job_command or "cluv submit")
+            if launched_job_command is None:
+                raise ValueError("launched_job_command is required when make_commit=True")
+            create_submit_commit(launched_job_command=launched_job_command)
         elif not (os.environ.get("SKIP_CLEAN_GIT_CHECK", "0") == "1"):
             console.print(
                 "[red]Working directory is dirty. Please commit your changes before submitting.[/red]",
diff --git a/tests/test_submit.py b/tests/test_submit.py
index 3e98ca6..f0f3305 100644
--- a/tests/test_submit.py
+++ b/tests/test_submit.py
@@ -151,6 +151,21 @@ def mock_subprocess_check_output(command: list[str], **kwargs) -> str:
             ],
         ]
 
+    def test_make_commit_without_command_raises_value_error(
+        self, monkeypatch: pytest.MonkeyPatch
+    ) -> None:
+        def mock_subprocess_run(command: list[str], **kwargs) -> subprocess.CompletedProcess[str]:
+            assert kwargs.get("capture_output") is True
+            assert kwargs.get("text") is True
+            if command == ["git", "status", "--porcelain"]:
+                return subprocess.CompletedProcess(command, 0, stdout=" M cluv/cli/submit.py\n", stderr="")
+            raise AssertionError(f"Unexpected subprocess.run call: {command}")
+
+        monkeypatch.setattr(subprocess, "run", mock_subprocess_run)
+
+        with pytest.raises(ValueError, match="launched_job_command is required"):
+            ensure_clean_git_state(make_commit=True)
+
     def test_prefers_branch_tip_in_github_actions_detached_head(
         self, monkeypatch: pytest.MonkeyPatch
     ) -> None:

From c2b1bb7d3b2eab4c7904cf2703fd8cc573871b13 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 12 May 2026 17:04:14 +0000
Subject: [PATCH 4/9] chore(submit): address review feedback on make-commit
 flow

Agent-Logs-Url: https://github.com/mila-iqia/cluv/sessions/664c8c45-1991-4e4a-b007-e1247faca220

Co-authored-by: lebrice <13387299+lebrice@users.noreply.github.com>
---
 cluv/cli/submit.py   | 12 ++++--------
 tests/test_submit.py | 11 +++++------
 2 files changed, 9 insertions(+), 14 deletions(-)

diff --git a/cluv/cli/submit.py b/cluv/cli/submit.py
index 40ff6f8..8421f24 100644
--- a/cluv/cli/submit.py
+++ b/cluv/cli/submit.py
@@ -57,15 +57,13 @@ async def submit(
     )
     ```
     """
-    submit_command: str | None = None
+    launched_job_command: str | None = None
     if make_commit:
-        submit_command = build_submit_command(
-            cluster, job_script, sbatch_args, program_args, make_commit
-        )
+        launched_job_command = build_submit_command(cluster, job_script, sbatch_args, program_args)
 
     # Check git is clean locally (untracked files are fine) and capture current commit hash.
     git_commit = ensure_clean_git_state(
-        make_commit=make_commit, launched_job_command=submit_command
+        make_commit=make_commit, launched_job_command=launched_job_command
     )
 
     if cluster == "first":
@@ -200,12 +198,10 @@ def build_submit_command(
     job_script: Path,
     sbatch_args: list[str],
     program_args: list[str],
-    make_commit: bool,
 ) -> str:
     """Build the local `cluv submit` command line used to launch the job."""
     command_parts = ["cluv", "submit"]
-    if make_commit:
-        command_parts.append("--make-commit")
+    command_parts.append("--make-commit")
     command_parts.extend([cluster, str(job_script), *sbatch_args])
     if program_args:
         command_parts.extend(["--", *program_args])
diff --git a/tests/test_submit.py b/tests/test_submit.py
index f0f3305..e7d6cd1 100644
--- a/tests/test_submit.py
+++ b/tests/test_submit.py
@@ -98,6 +98,8 @@ def mock_subprocess_run(command: list[str], **kwargs) -> subprocess.CompletedPro
     def test_make_commit_creates_commit_with_tracked_changes_and_command(
         self, monkeypatch: pytest.MonkeyPatch
     ) -> None:
+        launched_job_command = "cluv submit --make-commit mila scripts/job.sh -- --flag"
+        expected_commit_body = f"Launched job command:\n\n{launched_job_command}"
         command_calls: list[tuple[list[str], dict]] = []
 
         def mock_subprocess_run(command: list[str], **kwargs) -> subprocess.CompletedProcess[str]:
@@ -113,10 +115,7 @@ def mock_subprocess_run(command: list[str], **kwargs) -> subprocess.CompletedPro
                 assert kwargs.get("check") is True
                 assert command[2:4] == ["-m", "cluv submit: auto-commit tracked changes"]
                 assert command[4] == "-m"
-                assert (
-                    command[5]
-                    == "Launched job command:\n\ncluv submit --make-commit mila scripts/job.sh -- --flag"
-                )
+                assert command[5] == expected_commit_body
                 return subprocess.CompletedProcess(command, 0, stdout="", stderr="")
             raise AssertionError(f"Unexpected subprocess.run call: {command}")
 
@@ -134,7 +133,7 @@ def mock_subprocess_check_output(command: list[str], **kwargs) -> str:
         assert (
             ensure_clean_git_state(
                 make_commit=True,
-                launched_job_command="cluv submit --make-commit mila scripts/job.sh -- --flag",
+                launched_job_command=launched_job_command,
             )
             == "dddddddddddddddddddddddddddddddddddddddd"
         )
@@ -147,7 +146,7 @@ def mock_subprocess_check_output(command: list[str], **kwargs) -> str:
                 "-m",
                 "cluv submit: auto-commit tracked changes",
                 "-m",
-                "Launched job command:\n\ncluv submit --make-commit mila scripts/job.sh -- --flag",
+                expected_commit_body,
             ],
         ]
 

From f76658d9601660db71ff33f0ddd800d8171419da Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 12 May 2026 17:05:05 +0000
Subject: [PATCH 5/9] fix(submit): store launched command without make-commit
 flag

Agent-Logs-Url: https://github.com/mila-iqia/cluv/sessions/664c8c45-1991-4e4a-b007-e1247faca220

Co-authored-by: lebrice <13387299+lebrice@users.noreply.github.com>
---
 cluv/cli/submit.py   |  1 -
 tests/test_submit.py | 13 +++++++++++--
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/cluv/cli/submit.py b/cluv/cli/submit.py
index 8421f24..81c9dc1 100644
--- a/cluv/cli/submit.py
+++ b/cluv/cli/submit.py
@@ -201,7 +201,6 @@ def build_submit_command(
 ) -> str:
     """Build the local `cluv submit` command line used to launch the job."""
     command_parts = ["cluv", "submit"]
-    command_parts.append("--make-commit")
     command_parts.extend([cluster, str(job_script), *sbatch_args])
     if program_args:
         command_parts.extend(["--", *program_args])
diff --git a/tests/test_submit.py b/tests/test_submit.py
index e7d6cd1..bc83e8d 100644
--- a/tests/test_submit.py
+++ b/tests/test_submit.py
@@ -2,7 +2,7 @@
 import subprocess
 from pathlib import Path
 
-from cluv.cli.submit import ensure_clean_git_state, get_sbatch_command, get_config
+from cluv.cli.submit import build_submit_command, ensure_clean_git_state, get_sbatch_command, get_config
 
 import pytest
 
@@ -98,9 +98,18 @@ def mock_subprocess_run(command: list[str], **kwargs) -> subprocess.CompletedPro
     def test_make_commit_creates_commit_with_tracked_changes_and_command(
         self, monkeypatch: pytest.MonkeyPatch
     ) -> None:
-        launched_job_command = "cluv submit --make-commit mila scripts/job.sh -- --flag"
+        launched_job_command = "cluv submit mila scripts/job.sh -- --flag"
         expected_commit_body = f"Launched job command:\n\n{launched_job_command}"
         command_calls: list[tuple[list[str], dict]] = []
+        assert (
+            build_submit_command(
+                cluster="mila",
+                job_script=Path("scripts/job.sh"),
+                sbatch_args=[],
+                program_args=["--flag"],
+            )
+            == launched_job_command
+        )
 
         def mock_subprocess_run(command: list[str], **kwargs) -> subprocess.CompletedProcess[str]:
             command_calls.append((command, kwargs))

From efab1eb1890b3f5c3fe66360bb3d1df27d1a7b51 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 12 May 2026 17:05:57 +0000
Subject: [PATCH 6/9] test(submit): clarify command reconstruction coverage

Agent-Logs-Url: https://github.com/mila-iqia/cluv/sessions/664c8c45-1991-4e4a-b007-e1247faca220

Co-authored-by: lebrice <13387299+lebrice@users.noreply.github.com>
---
 cluv/cli/submit.py   |  6 +++---
 tests/test_submit.py | 22 +++++++++++++---------
 2 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/cluv/cli/submit.py b/cluv/cli/submit.py
index 81c9dc1..3b3ce66 100644
--- a/cluv/cli/submit.py
+++ b/cluv/cli/submit.py
@@ -57,9 +57,9 @@ async def submit(
     )
     ```
     """
-    launched_job_command: str | None = None
-    if make_commit:
-        launched_job_command = build_submit_command(cluster, job_script, sbatch_args, program_args)
+    launched_job_command = (
+        build_submit_command(cluster, job_script, sbatch_args, program_args) if make_commit else None
+    )
 
     # Check git is clean locally (untracked files are fine) and capture current commit hash.
     git_commit = ensure_clean_git_state(
diff --git a/tests/test_submit.py b/tests/test_submit.py
index bc83e8d..58c00a3 100644
--- a/tests/test_submit.py
+++ b/tests/test_submit.py
@@ -81,6 +81,19 @@ def test_only_override_slurm_vars_with_selected_cluster_vars(self, project_dir:
         )
 
 
+class TestBuildSubmitCommand:
+    def test_build_submit_command_with_program_args(self) -> None:
+        assert (
+            build_submit_command(
+                cluster="mila",
+                job_script=Path("scripts/job.sh"),
+                sbatch_args=[],
+                program_args=["--flag"],
+            )
+            == "cluv submit mila scripts/job.sh -- --flag"
+        )
+
+
 class TestEnsureCleanGitState:
     def test_dirty_repo_without_make_commit_exits(self, monkeypatch: pytest.MonkeyPatch) -> None:
         def mock_subprocess_run(command: list[str], **kwargs) -> subprocess.CompletedProcess[str]:
@@ -101,15 +114,6 @@ def test_make_commit_creates_commit_with_tracked_changes_and_command(
         launched_job_command = "cluv submit mila scripts/job.sh -- --flag"
         expected_commit_body = f"Launched job command:\n\n{launched_job_command}"
         command_calls: list[tuple[list[str], dict]] = []
-        assert (
-            build_submit_command(
-                cluster="mila",
-                job_script=Path("scripts/job.sh"),
-                sbatch_args=[],
-                program_args=["--flag"],
-            )
-            == launched_job_command
-        )
 
         def mock_subprocess_run(command: list[str], **kwargs) -> subprocess.CompletedProcess[str]:
             command_calls.append((command, kwargs))

From c19e0d5cb5d27129203cd2918f38224750d2ab6c Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 12 May 2026 17:06:59 +0000
Subject: [PATCH 7/9] perf(submit): defer command reconstruction until dirty
 check

Agent-Logs-Url: https://github.com/mila-iqia/cluv/sessions/664c8c45-1991-4e4a-b007-e1247faca220

Co-authored-by: lebrice <13387299+lebrice@users.noreply.github.com>
---
 cluv/cli/submit.py   | 19 +++++++++++--------
 tests/test_submit.py |  4 ++--
 2 files changed, 13 insertions(+), 10 deletions(-)

diff --git a/cluv/cli/submit.py b/cluv/cli/submit.py
index 3b3ce66..472bdad 100644
--- a/cluv/cli/submit.py
+++ b/cluv/cli/submit.py
@@ -6,6 +6,7 @@
 import subprocess
 import sys
 from pathlib import Path
+from typing import Callable
 
 from cluv.cli.sync import sync
 from cluv.config import ClusterConfig, find_pyproject, get_config
@@ -57,13 +58,14 @@ async def submit(
     )
     ```
     """
-    launched_job_command = (
-        build_submit_command(cluster, job_script, sbatch_args, program_args) if make_commit else None
-    )
-
     # Check git is clean locally (untracked files are fine) and capture current commit hash.
     git_commit = ensure_clean_git_state(
-        make_commit=make_commit, launched_job_command=launched_job_command
+        make_commit=make_commit,
+        launched_job_command_builder=(
+            (lambda: build_submit_command(cluster, job_script, sbatch_args, program_args))
+            if make_commit
+            else None
+        ),
     )
 
     if cluster == "first":
@@ -224,7 +226,7 @@ def create_submit_commit(launched_job_command: str) -> None:
 
 
 def ensure_clean_git_state(
-    make_commit: bool = False, launched_job_command: str | None = None
+    make_commit: bool = False, launched_job_command_builder: Callable[[], str] | None = None
 ) -> str:
     """
     Check git is clean locally and return the current commit hash.
@@ -233,8 +235,9 @@ def ensure_clean_git_state(
     dirty_lines = [line for line in git_status.stdout.splitlines() if not line.startswith("??")]
     if dirty_lines:
         if make_commit:
-            if launched_job_command is None:
-                raise ValueError("launched_job_command is required when make_commit=True")
+            if launched_job_command_builder is None:
+                raise ValueError("launched_job_command_builder is required when make_commit=True")
+            launched_job_command = launched_job_command_builder()
             create_submit_commit(launched_job_command=launched_job_command)
         elif not (os.environ.get("SKIP_CLEAN_GIT_CHECK", "0") == "1"):
             console.print(
diff --git a/tests/test_submit.py b/tests/test_submit.py
index 58c00a3..33b71cb 100644
--- a/tests/test_submit.py
+++ b/tests/test_submit.py
@@ -146,7 +146,7 @@ def mock_subprocess_check_output(command: list[str], **kwargs) -> str:
         assert (
             ensure_clean_git_state(
                 make_commit=True,
-                launched_job_command=launched_job_command,
+                launched_job_command_builder=lambda: launched_job_command,
             )
             == "dddddddddddddddddddddddddddddddddddddddd"
         )
@@ -175,7 +175,7 @@ def mock_subprocess_run(command: list[str], **kwargs) -> subprocess.CompletedPro
 
         monkeypatch.setattr(subprocess, "run", mock_subprocess_run)
 
-        with pytest.raises(ValueError, match="launched_job_command is required"):
+        with pytest.raises(ValueError, match="launched_job_command_builder is required"):
             ensure_clean_git_state(make_commit=True)
 
     def test_prefers_branch_tip_in_github_actions_detached_head(

From dfbce420a4be20af2f4142f3939da64b70240105 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 12 May 2026 17:07:41 +0000
Subject: [PATCH 8/9] test(submit): improve ensure_clean_git_state test naming

Agent-Logs-Url: https://github.com/mila-iqia/cluv/sessions/664c8c45-1991-4e4a-b007-e1247faca220

Co-authored-by: lebrice <13387299+lebrice@users.noreply.github.com>
---
 tests/test_submit.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/tests/test_submit.py b/tests/test_submit.py
index 33b71cb..de1d2dd 100644
--- a/tests/test_submit.py
+++ b/tests/test_submit.py
@@ -95,7 +95,9 @@ def test_build_submit_command_with_program_args(self) -> None:
 
 
 class TestEnsureCleanGitState:
-    def test_dirty_repo_without_make_commit_exits(self, monkeypatch: pytest.MonkeyPatch) -> None:
+    def test_ensure_clean_git_state_exits_when_repo_dirty_without_make_commit(
+        self, monkeypatch: pytest.MonkeyPatch
+    ) -> None:
         def mock_subprocess_run(command: list[str], **kwargs) -> subprocess.CompletedProcess[str]:
             assert kwargs.get("capture_output") is True
             assert kwargs.get("text") is True
@@ -108,7 +110,7 @@ def mock_subprocess_run(command: list[str], **kwargs) -> subprocess.CompletedPro
         with pytest.raises(SystemExit):
             ensure_clean_git_state()
 
-    def test_make_commit_creates_commit_with_tracked_changes_and_command(
+    def test_ensure_clean_git_state_creates_commit_when_make_commit_enabled(
         self, monkeypatch: pytest.MonkeyPatch
     ) -> None:
         launched_job_command = "cluv submit mila scripts/job.sh -- --flag"
@@ -163,7 +165,7 @@ def mock_subprocess_check_output(command: list[str], **kwargs) -> str:
             ],
         ]
 
-    def test_make_commit_without_command_raises_value_error(
+    def test_ensure_clean_git_state_raises_when_make_commit_without_builder(
         self, monkeypatch: pytest.MonkeyPatch
     ) -> None:
         def mock_subprocess_run(command: list[str], **kwargs) -> subprocess.CompletedProcess[str]:

From 5b049f9f9ae60d28e8676245e2211a178092ff63 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 12 May 2026 17:08:38 +0000
Subject: [PATCH 9/9] docs(submit): document make-commit arg and improve commit
 error output

Agent-Logs-Url: https://github.com/mila-iqia/cluv/sessions/664c8c45-1991-4e4a-b007-e1247faca220

Co-authored-by: lebrice <13387299+lebrice@users.noreply.github.com>
---
 cluv/cli/submit.py   | 35 +++++++++++++++++++++++------------
 tests/test_submit.py |  4 ++++
 2 files changed, 27 insertions(+), 12 deletions(-)

diff --git a/cluv/cli/submit.py b/cluv/cli/submit.py
index 472bdad..65c191f 100644
--- a/cluv/cli/submit.py
+++ b/cluv/cli/submit.py
@@ -43,6 +43,7 @@ async def submit(
         job_script: Path to the job script to submit, relative to the project root.
         sbatch_args: List of additional flags to pass to `sbatch`.
         program_args: List of arguments to pass to the job script, for example `["python", "main.py"]`.
+        make_commit: If True, automatically create a local commit with tracked changes before submitting.
 
     Returns:
         The job ID of the submitted job or None if the sbatch command fails.
@@ -211,18 +212,28 @@ def build_submit_command(
 
 def create_submit_commit(launched_job_command: str) -> None:
     """Create a commit with tracked changes and include the launched job command in the body."""
-    subprocess.run(["git", "add", "-u"], check=True)
-    subprocess.run(
-        [
-            "git",
-            "commit",
-            "-m",
-            "cluv submit: auto-commit tracked changes",
-            "-m",
-            f"Launched job command:\n\n{launched_job_command}",
-        ],
-        check=True,
-    )
+    try:
+        subprocess.run(["git", "add", "-u"], check=True, capture_output=True, text=True)
+        subprocess.run(
+            [
+                "git",
+                "commit",
+                "-m",
+                "cluv submit: auto-commit tracked changes",
+                "-m",
+                f"Launched job command:\n\n{launched_job_command}",
+            ],
+            check=True,
+            capture_output=True,
+            text=True,
+        )
+    except subprocess.CalledProcessError as err:
+        error_text = (err.stderr or err.stdout or str(err)).strip()
+        console.print(
+            "[red]Failed to create automatic submit commit before job submission:[/red] "
+            f"{error_text}"
+        )
+        raise
 
 
 def ensure_clean_git_state(
diff --git a/tests/test_submit.py b/tests/test_submit.py
index de1d2dd..926918d 100644
--- a/tests/test_submit.py
+++ b/tests/test_submit.py
@@ -125,9 +125,13 @@ def mock_subprocess_run(command: list[str], **kwargs) -> subprocess.CompletedPro
                 )
             if command == ["git", "add", "-u"]:
                 assert kwargs.get("check") is True
+                assert kwargs.get("capture_output") is True
+                assert kwargs.get("text") is True
                 return subprocess.CompletedProcess(command, 0, stdout="", stderr="")
             if command[:2] == ["git", "commit"]:
                 assert kwargs.get("check") is True
+                assert kwargs.get("capture_output") is True
+                assert kwargs.get("text") is True
                 assert command[2:4] == ["-m", "cluv submit: auto-commit tracked changes"]
                 assert command[4] == "-m"
                 assert command[5] == expected_commit_body