feat: Set up comprehensive Python testing infrastructure

.gitignore

@@ -131,3 +131,13 @@ dmypy.json
 # Ignore directories
 samples/
 .snakemake/
+
+# Claude Code settings
+.claude/*
+
+# Additional testing artifacts
+htmlcov/
+.coverage
+.coverage.*
+coverage.xml
+.pytest_cache/

pyproject.toml

@@ -0,0 +1,79 @@
+[tool.poetry]
+name = "princess"
+version = "0.1.0"
+description = "A bioinformatics tool for variant analysis and processing"
+authors = ["Princess Team"]
+readme = "README.md"
+packages = [{include = "scripts"}, {include = "cluster"}]
+
+[tool.poetry.dependencies]
+python = "^3.8"
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^7.4.0"
+pytest-cov = "^4.1.0"
+pytest-mock = "^3.11.0"
+
+# Poetry scripts are not needed for pytest - use 'poetry run pytest' directly
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py", "*_test.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = [
+    "--strict-markers",
+    "--strict-config",
+    "--cov=scripts",
+    "--cov=cluster",
+    "--cov-report=term-missing",
+    "--cov-report=html:htmlcov",
+    "--cov-report=xml:coverage.xml",
+    "--cov-fail-under=80",
+    "-v"
+]
+markers = [
+    "unit: Unit tests that test individual functions/classes",
+    "integration: Integration tests that test component interactions",
+    "slow: Tests that take a long time to run"
+]
+filterwarnings = [
+    "error",
+    "ignore::UserWarning",
+    "ignore::DeprecationWarning"
+]
+
+[tool.coverage.run]
+source = ["scripts", "cluster"]
+omit = [
+    "*/tests/*",
+    "*/test_*",
+    "*/__pycache__/*",
+    "*/venv/*",
+    "*/.venv/*",
+    "*/envs/*"
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "if self.debug:",
+    "if settings.DEBUG",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if 0:",
+    "if __name__ == .__main__.:"
+]
+show_missing = true
+skip_covered = false
+
+[tool.coverage.html]
+directory = "htmlcov"
+
+[tool.coverage.xml]
+output = "coverage.xml"

tests/conftest.py

@@ -0,0 +1,87 @@
+"""Shared pytest fixtures for the test suite."""
+
+import os
+import tempfile
+from pathlib import Path
+from typing import Generator
+
+import pytest
+
+
+@pytest.fixture
+def temp_dir() -> Generator[Path, None, None]:
+    """Create a temporary directory for testing."""
+    with tempfile.TemporaryDirectory() as tmp_dir:
+        yield Path(tmp_dir)
+
+
+@pytest.fixture
+def temp_file(temp_dir: Path) -> Path:
+    """Create a temporary file for testing."""
+    temp_file_path = temp_dir / "test_file.txt"
+    temp_file_path.write_text("test content")
+    return temp_file_path
+
+
+@pytest.fixture
+def sample_vcf_content() -> str:
+    """Sample VCF file content for testing."""
+    return """##fileformat=VCFv4.2
+##source=test
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE1
+chr1	100	.	A	G	250	.	DP=30	GT	0/1
+chr1	200	.	T	C	150	.	DP=25	GT	1/1
+chr1	300	.	G	<DEL>	300	.	DP=35	GT	0/1
+"""
+
+
+@pytest.fixture
+def sample_vcf_file(temp_dir: Path, sample_vcf_content: str) -> Path:
+    """Create a sample VCF file for testing."""
+    vcf_file = temp_dir / "sample.vcf"
+    vcf_file.write_text(sample_vcf_content)
+    return vcf_file
+
+
+@pytest.fixture
+def mock_args():
+    """Mock argument parser arguments."""
+    class MockArgs:
+        def __init__(self, input_file=None, output_file=None, filter_threshold=200):
+            self.input = input_file
+            self.output = output_file
+            self.filter = filter_threshold
+
+    return MockArgs
+
+
+@pytest.fixture
+def capture_stdout():
+    """Fixture to capture stdout for testing."""
+    import io
+    import sys
+
+    old_stdout = sys.stdout
+    sys.stdout = captured_output = io.StringIO()
+    yield captured_output
+    sys.stdout = old_stdout
+
+
+@pytest.fixture
+def env_backup():
+    """Backup and restore environment variables."""
+    original_env = os.environ.copy()
+    yield
+    os.environ.clear()
+    os.environ.update(original_env)
+
+
+@pytest.fixture
+def working_directory(temp_dir: Path):
+    """Change to a temporary working directory for testing."""
+    original_cwd = os.getcwd()
+    os.chdir(temp_dir)
+    yield temp_dir
+    os.chdir(original_cwd)

tests/test_infrastructure.py

@@ -0,0 +1,66 @@
+"""Test file to validate the testing infrastructure setup."""
+
+import pytest
+import sys
+from pathlib import Path
+
+
+class TestInfrastructure:
+    """Test the testing infrastructure is working correctly."""
+
+    def test_pytest_is_working(self):
+        """Test that pytest is functioning."""
+        assert True
+
+    def test_fixtures_are_available(self, temp_dir):
+        """Test that fixtures are available and working."""
+        assert temp_dir.exists()
+        assert temp_dir.is_dir()
+
+    def test_temp_file_fixture(self, temp_file):
+        """Test that temp file fixture works."""
+        assert temp_file.exists()
+        assert temp_file.read_text() == "test content"
+
+    def test_sample_vcf_content(self, sample_vcf_content):
+        """Test that sample VCF content fixture works."""
+        assert "##fileformat=VCFv4.2" in sample_vcf_content
+        assert "#CHROM" in sample_vcf_content
+
+    def test_sample_vcf_file(self, sample_vcf_file):
+        """Test that sample VCF file fixture works."""
+        assert sample_vcf_file.exists()
+        content = sample_vcf_file.read_text()
+        assert "##fileformat=VCFv4.2" in content
+
+    def test_mock_args_fixture(self, mock_args):
+        """Test that mock args fixture works."""
+        args = mock_args()
+        assert hasattr(args, 'filter')
+        assert args.filter == 200
+
+    @pytest.mark.unit
+    def test_unit_marker(self):
+        """Test that unit marker is available."""
+        assert True
+
+    @pytest.mark.integration
+    def test_integration_marker(self):
+        """Test that integration marker is available."""
+        assert True
+
+    def test_python_path_includes_project_root(self):
+        """Test that the project root is in Python path."""
+        project_root = Path(__file__).parent.parent
+        assert str(project_root) in sys.path or any(
+            str(project_root) in path for path in sys.path
+        )
+
+    def test_coverage_will_run(self):
+        """Test that coverage reporting will work."""
+        # This is just a placeholder to ensure coverage can track this file
+        def dummy_function():
+            return "covered"
+
+        result = dummy_function()
+        assert result == "covered"