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

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

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