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Contributing to snakesee

Thank you for your interest in contributing to snakesee!

Development Setup

Prerequisites

  • Python 3.11 or later
  • pixi (recommended) or uv

Setup with pixi

# Clone the repository
git clone https://github.com/nh13/snakesee.git
cd snakesee

# Install development environment
pixi run install-dev

# Run all checks (lint, type check, tests)
pixi run check

# Run tests only
pixi run test

# Auto-fix linting issues
pixi run fix

# Build documentation
pixi run docs

Setup with uv

# Clone the repository
git clone https://github.com/nh13/snakesee.git
cd snakesee

# Create virtual environment and install
uv sync --group dev --group docs
uv pip install -e '.[logo]'

# Run checks
uv run poe check-all

Code Style

This project uses:

  • ruff for linting and formatting
  • mypy for type checking
  • pytest for testing

All code should:

  • Pass ruff format (formatting)
  • Pass ruff check (linting)
  • Pass mypy (type checking)
  • Have tests with >65% coverage

Running Checks

# Run all checks
pixi run check
# or
uv run poe check-all

# Auto-fix linting issues
pixi run fix
# or
uv run poe fix-all

# Run just tests
pixi run test
# or
uv run pytest

Pull Request Process

  1. Fork the repository and create a feature branch
  2. Make your changes
  3. Ensure all checks pass: pixi run check
  4. Update documentation if needed
  5. Submit a pull request

Release Process

Releases are automated via GitHub Actions when a SemVer tag is pushed:

# Ensure everything is committed and pushed
git push origin main

# Create and push a tag
git tag 0.2.0
git push origin 0.2.0

The CI will automatically:

  1. Run all tests
  2. Build the source distribution
  3. Publish to PyPI
  4. Generate changelog with git-cliff
  5. Create a GitHub release

Commit Messages

We use Conventional Commits for generating changelogs:

  • feat: New features
  • fix: Bug fixes
  • docs: Documentation changes
  • test: Test changes
  • refactor: Code refactoring
  • style: Code style changes
  • chore: Maintenance tasks

Examples:

feat: add support for filtering by rule name
fix: handle missing log files gracefully
docs: update keyboard shortcuts table

Logger Plugin Development

The repository includes an optional Snakemake logger plugin in snakemake-logger-plugin-snakesee/.

Plugin Setup

# Install the plugin in development mode
cd snakemake-logger-plugin-snakesee
pip install -e .

# Run plugin tests
pytest tests/

Plugin Structure

  • src/snakemake_logger_plugin_snakesee/handler.py - Main LogHandler implementation
  • src/snakemake_logger_plugin_snakesee/events.py - Event types and serialization
  • src/snakemake_logger_plugin_snakesee/writer.py - JSONL event file writer

The plugin writes events to .snakesee_events.jsonl which snakesee reads via snakesee/events.py.

Questions?

Open an issue at https://github.com/nh13/snakesee/issues