ripple_detection: Instructions file for Claude Code

CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

ripple_detection is a Python package for detecting sharp-wave ripple events (150-250 Hz) from local field potentials (LFPs) in neuroscience research. It implements detection algorithms from Karlsson et al. 2009 and Kay et al. 2016, along with other variants.

Development Commands

Setup

# Install from source (development mode with dev dependencies)
pip install -e .[dev,examples]

# Or create conda environment with all dependencies
conda env create -f environment.yml
conda activate ripple_detection
pip install -e .[dev,examples]

# Minimal install (runtime dependencies only)
pip install -e .

Testing

# Run all tests with coverage (93% coverage achieved!)
pytest --cov=ripple_detection tests/

# Run specific test module
pytest tests/test_core.py          # Core signal processing tests
pytest tests/test_detectors.py     # Detector integration tests
pytest tests/test_simulate.py      # Simulation module tests

# Run specific test class or function
pytest tests/test_core.py::TestGetEnvelope
pytest tests/test_detectors.py::TestKayRippleDetector::test_single_channel_with_ripples

# Generate HTML coverage report
pytest --cov=ripple_detection --cov-report=html tests/
open htmlcov/index.html

# Test notebooks (as done in CI)
jupyter nbconvert --to notebook --ExecutePreprocessor.kernel_name=python3 --execute examples/detection_examples.ipynb
jupyter nbconvert --to notebook --ExecutePreprocessor.kernel_name=python3 --execute examples/test_individual_algorithm_components.ipynb
jupyter nbconvert --to notebook --ExecutePreprocessor.kernel_name=python3 --execute examples/ripple_detection_tutorial.ipynb

Code Quality

# Format code with black
black ripple_detection/ tests/

# Check formatting without modifying files
black --check ripple_detection/ tests/

# Lint code with ruff (fast, modern linter - replaces flake8)
ruff check ripple_detection/ tests/

# Auto-fix ruff issues where possible
ruff check --fix ripple_detection/ tests/

# Type check with mypy
mypy ripple_detection/