__pycache__/
build/
dist/
*egg-info
*.so
poetry.lock
.DS_Store
.pytest_cache

# Generated files (auto-generated by codegen/generate.py)
ciffy/src/hash/
ciffy/src/internal/bond_patterns.h
ciffy/biochemistry/_generated_*.py

# Version file (auto-generated by setuptools-scm)
ciffy/_version.py

# Test data (downloaded on demand from RCSB PDB)
tests/data/

# Generated documentation (mkdocs output)
site/

# Model training and inference outputs
checkpoints/
samples/
inference_output/
lightning_logs/
wandb/
outputs/
figures/

# Personal config files (use examples/configs as templates)
configs/
.rex.toml

# Scratch directory for local experiments
scratch/

# Science notes and experiment logs
science/

# Sanitizer test venv
.venv-asan/
