Add tests for helper functions

pyproject.toml

@@ -31,7 +31,6 @@ disallow_untyped_defs = true
 exclude = [".venv/", "docs/"]
 
 [[tool.mypy.overrides]]
-module = "tests.*"
 disallow_untyped_defs = false
 
 [tool.pytest.ini_options]

tests/test_helpers.py

@@ -0,0 +1,69 @@
+"""Tests for helpers.py."""
+
+from pathlib import Path
+from unittest.mock import Mock, patch
+
+from muse2_data_analysis import helpers
+
+
+@patch("muse2_data_analysis.helpers.run_muse2")
+def test_get_example_input_dir_returns_existing_directory(
+    run_muse2_mock: Mock, tmp_path: Path
+) -> None:
+    """Check that get_example_input_dir returns an existing input directory."""
+    input_dir = tmp_path / "input"
+    input_dir.mkdir()
+
+    with patch.object(helpers, "_INPUT_DIR", input_dir):
+        assert helpers.get_example_input_dir() == input_dir
+
+    run_muse2_mock.assert_not_called()
+
+
+@patch("muse2_data_analysis.helpers.run_muse2")
+def test_get_example_input_dir_extracts_example_when_missing(
+    run_muse2_mock: Mock, tmp_path: Path
+) -> None:
+    """Check that get_example_input_dir extracts the example when missing."""
+    input_dir = tmp_path / "input"
+
+    with patch.object(helpers, "_INPUT_DIR", input_dir):
+        assert helpers.get_example_input_dir() == input_dir
+
+    run_muse2_mock.assert_called_once_with(
+        "example", "extract", helpers.EXAMPLE_NAME, str(input_dir)
+    )
+
+
+@patch("muse2_data_analysis.helpers.run_muse2")
+def test_get_example_output_dir_returns_existing_directory(
+    run_muse2_mock: Mock, tmp_path: Path
+) -> None:
+    """Check that get_example_output_dir returns an existing output directory."""
+    output_dir = tmp_path / "output"
+    output_dir.mkdir()
+
+    with patch.object(helpers, "_OUTPUT_DIR", output_dir):
+        assert helpers.get_example_output_dir() == output_dir
+
+    run_muse2_mock.assert_not_called()
+
+
+@patch("muse2_data_analysis.helpers.run_muse2")
+@patch("muse2_data_analysis.helpers.get_example_input_dir")
+def test_get_example_output_dir_runs_example_when_missing(
+    get_example_input_dir_mock: Mock, run_muse2_mock: Mock, tmp_path: Path
+) -> None:
+    """Check that get_example_output_dir ensures input exists and runs the model."""
+    input_dir = tmp_path / "input"
+    output_dir = tmp_path / "output"
+    get_example_input_dir_mock.return_value = input_dir
+
+    with patch.object(helpers, "_INPUT_DIR", input_dir):
+        with patch.object(helpers, "_OUTPUT_DIR", output_dir):
+            assert helpers.get_example_output_dir() == output_dir
+
+    get_example_input_dir_mock.assert_called_once_with()
+    run_muse2_mock.assert_called_once_with(
+        "run", str(input_dir), "--output-dir", str(output_dir)
+    )

tests/test_muse2.py

@@ -0,0 +1,101 @@
+"""Tests for muse2.py."""
+
+import subprocess as sp
+from collections.abc import Generator
+from pathlib import Path
+from unittest.mock import Mock, patch
+
+import pytest
+
+from muse2_data_analysis import muse2
+
+
+@pytest.fixture(autouse=True)
+def reset_muse2_path() -> Generator[None]:
+    """Reset the cached MUSE2 path before and after each test.
+
+    Note this won't work if tests are run in parallel.
+    """
+    previous = muse2._muse2_path
+    muse2._muse2_path = None
+    yield
+    muse2._muse2_path = previous
+
+
+@patch("muse2_data_analysis.muse2.shutil.which")
+@patch("muse2_data_analysis.muse2.os.getenv")
+def test_find_muse2_uses_environment_variable(
+    getenv_mock: Mock, which_mock: Mock
+) -> None:
+    """Check that find_muse2 prefers MUSE2_PATH over PATH lookup."""
+    getenv_mock.return_value = "/tmp/muse2-from-env"
+
+    assert muse2.find_muse2() == Path("/tmp/muse2-from-env")
+    which_mock.assert_not_called()
+
+
+@patch("muse2_data_analysis.muse2.shutil.which")
+@patch("muse2_data_analysis.muse2.os.getenv")
+def test_find_muse2_falls_back_to_path_lookup(
+    getenv_mock: Mock, which_mock: Mock
+) -> None:
+    """Check that find_muse2 uses PATH lookup when no env var is set."""
+    getenv_mock.return_value = None
+    which_mock.return_value = "/tmp/muse2-from-path"
+
+    assert muse2.find_muse2() == Path("/tmp/muse2-from-path")
+
+
+@patch("muse2_data_analysis.muse2.shutil.which")
+@patch("muse2_data_analysis.muse2.os.getenv")
+def test_find_muse2_raises_when_binary_is_not_available(
+    getenv_mock: Mock, which_mock: Mock
+) -> None:
+    """Check that find_muse2 raises if no muse2 binary can be found."""
+    getenv_mock.return_value = None
+    which_mock.return_value = None
+
+    with pytest.raises(RuntimeError, match="Could not find path to muse2"):
+        muse2.find_muse2()
+
+
+@patch("muse2_data_analysis.muse2.sp.run")
+@patch("muse2_data_analysis.muse2.find_muse2")
+def test_run_muse2_returns_stdout(find_muse2_mock: Mock, run_mock: Mock) -> None:
+    """Check that run_muse2 returns combined stdout/stderr output."""
+    find_muse2_mock.return_value = Path("/tmp/muse2")
+    run_mock.return_value = sp.CompletedProcess(
+        args=(Path("/tmp/muse2"), "--version"),
+        returncode=0,
+        stdout="muse2 version output",
+    )
+
+    assert muse2.run_muse2("--version") == "muse2 version output"
+    run_mock.assert_called_once_with(
+        (Path("/tmp/muse2"), "--version"),
+        text=True,
+        stdout=sp.PIPE,
+        stderr=sp.STDOUT,
+        env={
+            **muse2.os.environ,
+            "MUSE2_USE_DEFAULT_SETTINGS": "1",
+        },
+        check=True,
+    )
+
+
+@patch("muse2_data_analysis.muse2.sp.run")
+@patch("muse2_data_analysis.muse2.find_muse2")
+def test_run_muse2_raises_runtime_error_on_subprocess_failure(
+    find_muse2_mock: Mock, run_mock: Mock
+) -> None:
+    """Check that run_muse2 re-raises subprocess failures as RuntimeError."""
+    find_muse2_mock.return_value = Path("/tmp/muse2")
+    run_mock.side_effect = sp.CalledProcessError(
+        1,
+        (Path("/tmp/muse2"), "bad-arg"),
+        output="combined output",
+    )
+
+    with pytest.raises(RuntimeError, match="Error running muse2: combined output"):
+        muse2.run_muse2("bad-arg")