# 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/
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/
cover/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# pipenv
Pipfile.lock

# poetry
poetry.lock

# pdm
.pdm.toml

# PEP 582
__pypackages__/

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

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

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

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

# Pyre type checker
.pyre/

# pytype static type analyzer
.pytype/

# Cython debug symbols
cython_debug/

# PyCharm
.idea/

# VS Code
.vscode/

# macOS
.DS_Store
.AppleDouble
.LSOverride

# Windows
Thumbs.db
Thumbs.db:encryptable
ehthumbs.db
ehthumbs_vista.db
*.stackdump
[Dd]esktop.ini
$RECYCLE.BIN/
*.cab
*.msi
*.msix
*.msm
*.msp
*.lnk

# Linux
*~

# Temporary files
*.tmp
*.temp
*.log
.temp_*/
.cache/

# DEBase specific
enzyme_pipeline*.log
temp_merged_input.csv
*.egg-info/

# Project data and examples
data/
examples/
!examples/test.csv  # Keep test.csv as example output

# Cache files
*.pkl
*_cache.pkl

# Large database files
*.db

# PDFs and Excel files
*.pdf
*.xlsx

# Backup files
*_backup.py
lineage_format_backup.py

# Temporary directories
.temp_*
enzyme_analysis_*