# 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/
pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# 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
*.cover
*.py,cover
.hypothesis/
.pytest_cache/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

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

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

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/

# Project specific - test outputs
complete_analysis_results/
output/
results/
data/
*.fasta
*.aln
*.nwk
*.tree
*.hmm
*.pdb
*.cif
*.log
*.png
*.html
*.json

# Old/backup files
*_old.md
README_old.md

# But keep example data
!examples/example_data/*.fasta
!examples/example_data/*.pdb

# Temp files
*.tmp
*.bak
*.swp
