# Build artifacts
build/
dist/
*.egg-info/
*.egg

# Python
__pycache__/
*.py[cod]
*$py.class
*.so
.Python

# Virtual environments
venv/
env/
ENV/
.venv

# IDE
.vscode/
.idea/
*.swp
*.swo
*~

# Testing
.coverage
.pytest_cache/
htmlcov/
.tox/

# Documentation
docs/_build/
docs/.doctrees/

# Temporary files
*.log
.DS_Store
.zenodo_doi
.zenodo_deposition_id
upload_to_zenodo.sh
.pypirc

# Generated files
*.bam
*.bai
*.fasta.gz
*.fai

# Project-specific files to exclude
CLAUDE.md
generate_bins.py
