TESTING.md

Testing Guide for KLRfome

Quick Start

To run tests, use the provided test runner script:

./run_tests.sh

Or manually:

# Activate virtual environment
source venv/bin/activate

# Install package in editable mode (if not already installed)
pip install -e .

# Install test dependencies (if not already installed)
pip install -e ".[dev]"

# Run tests
pytest tests/ -v

# Run tests with coverage
pytest tests/ -v --cov=klrfome --cov-report=html --cov-report=term

Common Issues

"ERROR: file or directory not found: python"

This error typically occurs when:

1. pytest is run from outside the virtual environment
2. The package is not installed in the virtual environment
3. pytest-cov is having issues finding the Python executable

Solution:

• Always activate the virtual environment first: source venv/bin/activate
• Install the package: pip install -e .
• Use python -m pytest instead of just pytest

"ModuleNotFoundError: No module named 'jax'"

The virtual environment doesn't have dependencies installed.

Solution:

source venv/bin/activate
pip install -e .

"ModuleNotFoundError: No module named 'klrfome'"

The package is not installed in editable mode.

Solution:

source venv/bin/activate
pip install -e .

Running Specific Tests

# Run a specific test file
pytest tests/test_kernels.py -v

# Run a specific test function
pytest tests/test_kernels.py::test_rbf_kernel_properties -v

# Run tests matching a pattern
pytest tests/ -k "kernel" -v

Coverage Reports

After running tests with coverage, view the HTML report:

# Generate coverage report
pytest tests/ --cov=klrfome --cov-report=html

# Open the report (macOS)
open htmlcov/index.html

Test Structure

• tests/conftest.py - Shared fixtures
• tests/test_kernels.py - Kernel implementation tests
• tests/test_klr.py - Kernel Logistic Regression tests
• tests/test_prediction.py - Focal prediction tests
• tests/test_data.py - Data structure tests
• tests/test_integration.py - End-to-end workflow tests