# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg

# PyInstaller
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
coverage.json
.mypy_cache/
*.cover
*.py,cover
.hypothesis/
.pytest_cache/
.ruff_cache/

# Translations
*.mo
*.pot

# Environments
.env
.venv
env/
venv/
ENV/

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

# OS
.DS_Store
Thumbs.db

# API keys - NEVER commit these
*.key
itolapi.key
.itolapi.key

# Reference HTML
iTOL_Help.html

# Bundled reference implementations (for development reference only)
iTOL-API-4.1.6/
itol.toolkit-1.2.2/

# MkDocs
site/

# Session logs
.pyitol/

# IDE / AI assistant working directories
.workbuddy/

# Internal review documents (not for public repo)
PyiTOL_review_*.md

# Generated by setuptools_scm (do not track)
src/pyitol/_version.py

# Benchmark output
benchmarks/*.png
benchmarks/*.json
benchmarks/extreme_*tips.nwk
benchmarks/extreme_*tips_taxonomy.csv
# ... but keep the canonical result files referenced by the manuscript
!benchmarks/monophyly_comparison_results.json
!benchmarks/template_scalability_results.json
!benchmarks/extreme_scale_results.json
