test: add shared fixtures and improve test infrastructure (#105)

- Add project-wide tests/conftest.py with common path fixtures,
  seed reset, mocks, and skip marks (skip_if_missing_testdata,
  skip_if_no_gpu)
- Implement --use-gpu pytest option via pytest_addoption and
  use_gpu fixture so the gpu_compatible marker is functional
- Guard all CUDA calls in reset_seed behind torch.cuda.is_available()
  to prevent failures in CPU-only environments
- Add CLI-specific tests/mussel/cli/conftest.py with test_data_path_cli
  alias fixture
- Register gpu_compatible marker in pyproject.toml

Addresses review comments:
- No unused heavy imports at collection time
- --use-gpu flag properly registered via pytest_addoption
- CUDA API calls guarded for CPU-only torch installs

Co-authored-by: Copilot <[email protected]>

Author: raylim

pyproject.toml

@@ -142,6 +142,7 @@ addopts = "-v --tb=short"
 markers = [
     "slow: marks tests as slow and require significant time to run (deselect with '-m \"not slow\"')",
     "integration: marks integration tests that perform actual model inference",
+    "gpu_compatible: marks tests that support --use-gpu flag for faster execution (use the use_gpu fixture to check)",
 ]
 
 [project.scripts]

tests/conftest.py

@@ -0,0 +1,133 @@
+"""
+Shared pytest configuration and fixtures for Mussel tests.
+
+This conftest.py provides common test fixtures and configuration
+used across multiple test files.
+"""
+
+import os
+from pathlib import Path
+from typing import Generator
+
+import pytest
+import torch
+
+
+@pytest.fixture
+def test_data_path() -> str:
+    """Return path to test data directory."""
+    return os.path.join(os.path.dirname(__file__), "testdata")
+
+
+@pytest.fixture
+def svs_slide_path(test_data_path: str) -> str:
+    """Return path to test slide file."""
+    return os.path.join(test_data_path, "948176.svs")
+
+
+@pytest.fixture
+def patch_h5_path(test_data_path: str) -> str:
+    """Return path to test patch HDF5 file."""
+    return os.path.join(test_data_path, "948176.patch.h5")
+
+
+@pytest.fixture
+def classifier_pkl_path(test_data_path: str) -> str:
+    """Return path to test classifier pickle file."""
+    return os.path.join(test_data_path, "simple_classifier.pkl")
+
+
+@pytest.fixture
+def annotation_csv_path(test_data_path: str) -> str:
+    """Return path to test annotation CSV file."""
+    return os.path.join(test_data_path, "948176.annotation.csv")
+
+
+@pytest.fixture
+def features_pt_path(test_data_path: str) -> str:
+    """Return path to test features pickle file."""
+    return os.path.join(test_data_path, "948176.features.pt")
+
+
+@pytest.fixture
+def class_embedding_pt_path(test_data_path: str) -> str:
+    """Return path to test class embedding file."""
+    return os.path.join(test_data_path, "class_embedding.pt")
+
+
+def pytest_addoption(parser: pytest.Parser) -> None:
+    parser.addoption(
+        "--use-gpu",
+        action="store_true",
+        default=False,
+        help="Run gpu_compatible tests on GPU instead of CPU.",
+    )
+
+
+@pytest.fixture
+def use_gpu(request: pytest.FixtureRequest) -> bool:
+    """Return True if --use-gpu was passed and a GPU is available."""
+    return request.config.getoption("--use-gpu") and torch.cuda.is_available()
+
+
+@pytest.fixture(autouse=True)
+def reset_seed() -> Generator[None, None, None]:
+    """Reset random seed to ensure reproducible test results."""
+    seed = 42
+    torch.manual_seed(seed)
+    if torch.cuda.is_available():
+        torch.cuda.manual_seed_all(seed)
+        torch.backends.cudnn.deterministic = True
+        torch.backends.cudnn.benchmark = False
+    yield
+    if torch.cuda.is_available():
+        torch.cuda.empty_cache()
+
+
+@pytest.fixture
+def cpu_device() -> torch.device:
+    """Return CPU device for testing."""
+    return torch.device("cpu")
+
+
+@pytest.fixture
+def mock_model_factory():
+    """Provide a mock model factory for testing without loading models."""
+    from unittest.mock import MagicMock
+
+    mock_model = MagicMock()
+    mock_model_fun = MagicMock(return_value=torch.randn(1, 2048))
+    mock_model.get_model_fun.return_value = mock_model_fun
+    mock_model.get_preprocessing_fun.return_value = None
+
+    mock_factory = MagicMock()
+    mock_factory.return_value = MagicMock(get_model=MagicMock(return_value=mock_model))
+
+    return mock_factory
+
+
+@pytest.fixture
+def mock_segment_tissue():
+    """Provide mock tissue segmentation results."""
+    from unittest.mock import MagicMock
+
+    mock_coords = [[0, 0], [256, 0], [0, 256]]
+    mock_polygon = MagicMock()
+    mock_grid = MagicMock()
+
+    mock_segment = MagicMock(return_value=(mock_polygon, mock_grid, mock_coords, None))
+
+    return mock_segment
+
+
+# Skip test if required test data is unavailable
+skip_if_missing_testdata = pytest.mark.skipif(
+    not Path(os.path.dirname(__file__), "testdata").exists(),
+    reason="Test data not available - requires testdata directory",
+)
+
+# Skip test if GPU is unavailable
+skip_if_no_gpu = pytest.mark.skipif(
+    not torch.cuda.is_available(),
+    reason="GPU is required for this test",
+)

tests/mussel/cli/conftest.py

@@ -0,0 +1,14 @@
+"""
+Shared pytest configuration and fixtures for CLI tests.
+
+Fixtures from tests/conftest.py are automatically available here via pytest's
+conftest discovery — no explicit imports needed.
+"""
+
+import pytest
+
+
+@pytest.fixture
+def test_data_path_cli(test_data_path: str) -> str:
+    """Return path to test data directory (alias for CLI tests)."""
+    return test_data_path