Fix command prefix bug

src/submit_aml/aml.py

@@ -487,8 +487,14 @@ def submit_to_aml(
         return None
 
     # Build command that will be run
-    if project_dir != source_dir:
-        relative_project_dir = project_dir.relative_to(source_dir)
+    if command_prefix.startswith("uv run") and project_dir != source_dir:
+        try:
+            relative_project_dir = project_dir.relative_to(source_dir)
+        except ValueError as exc:
+            raise ValueError(
+                f"The project directory '{project_dir}' must be inside the source"
+                f" directory '{source_dir}' to append the uv --project flag."
+            ) from exc
         command_prefix += f" --project {relative_project_dir}"
 
     if services is None:

tests/test_aml.py

@@ -2,13 +2,15 @@
 
 from __future__ import annotations
 
+from pathlib import Path
 from unittest.mock import patch
 
 import pytest
 
 from submit_aml.aml import CredentialType
 from submit_aml.aml import _sanitize_experiment_name
 from submit_aml.aml import get_client
+from submit_aml.aml import submit_to_aml
 
 
 def test_sanitize_none_returns_none() -> None:
@@ -56,3 +58,90 @@ def test_get_client_msi_uses_managed_identity(
     """CredentialType.MANAGED_IDENTITY uses ManagedIdentityCredential."""
     get_client("sub", "rg", "ws", credential_type=CredentialType.MANAGED_IDENTITY)
     mock_msi_cred.assert_called_once()  # type: ignore[union-attr]
+
+
+@pytest.mark.parametrize(
+    ("command_prefix", "expected_in_command"),
+    [
+        ("uv run", "--project subproject"),
+        ("python", None),
+    ],
+    ids=["uv-run-appends-project", "non-uv-skips-project"],
+)
+@patch("submit_aml.aml._submit")
+@patch("submit_aml.aml.instantiate_command")
+@patch("submit_aml.aml.infer_environment")
+@patch("submit_aml.aml.setup")
+def test_project_flag_only_appended_for_uv_run(
+    mock_setup: object,
+    mock_infer_env: object,
+    mock_instantiate: object,
+    mock_submit: object,
+    command_prefix: str,
+    expected_in_command: str | None,
+) -> None:
+    """``--project`` is appended only for ``uv run`` prefixes."""
+    source_dir = Path("/repo")
+    project_dir = source_dir / "subproject"
+    mock_setup.return_value = (  # type: ignore[attr-defined]
+        source_dir,
+        project_dir,
+        "run.py",
+        object(),  # ml_client
+        "description",
+        1,  # instance_count
+        None,  # distribution
+        "experiment",
+    )
+
+    submit_to_aml(
+        command_prefix=command_prefix,
+        compute_target="cpu-cluster",
+        script_path="run.py",
+        subscription_id="sub",
+        resource_group="rg",
+        workspace_name="ws",
+        dry_run=True,
+    )
+
+    command = mock_instantiate.call_args.kwargs["command"]  # type: ignore[attr-defined]
+    if expected_in_command is None:
+        assert "--project" not in command
+    else:
+        assert expected_in_command in command
+
+
+@patch("submit_aml.aml._submit")
+@patch("submit_aml.aml.instantiate_command")
+@patch("submit_aml.aml.infer_environment")
+@patch("submit_aml.aml.setup")
+def test_uv_run_prefix_raises_when_project_not_under_source(
+    mock_setup: object,
+    mock_infer_env: object,
+    mock_instantiate: object,
+    mock_submit: object,
+) -> None:
+    """A clear ValueError is raised when project_dir is not inside source_dir."""
+    source_dir = Path("/repo")
+    project_dir = Path("/other/project")
+    mock_setup.return_value = (  # type: ignore[attr-defined]
+        source_dir,
+        project_dir,
+        "run.py",
+        object(),  # ml_client
+        "description",
+        1,  # instance_count
+        None,  # distribution
+        "experiment",
+    )
+
+    with pytest.raises(ValueError, match="must be inside the source directory"):
+        submit_to_aml(
+            command_prefix="uv run",
+            compute_target="cpu-cluster",
+            script_path="run.py",
+            subscription_id="sub",
+            resource_group="rg",
+            workspace_name="ws",
+            dry_run=True,
+        )