# Git
.git/
.github/
.gitignore
.gitattributes

# Python cache and build artifacts
**/__pycache__/
**/*.pyc
**/*.pyo
**/*.pyd
*.so
*.egg-info/
*.egg
.eggs/
dist/
build/
*.whl

# Testing and coverage
.pytest_cache/
.coverage
coverage.xml
htmlcov/
.tox/
tests/

# Documentation
docs/
*.md
!README.md
!LICENSE

# Development tools
.vscode/
.idea/
.ideas/
*.swp
*.swo
*~

# Environment and package management
.conda/
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/
environment.yml

# Project specific
.pre-commit-config.yaml
CITATION.cff
node_modules/
pkg-mgt/

# Nextflow
.nextflow.log
.nextflow/
examples/
results/
work/
