__pycache__/
*.pyc
*.pyo
.Python
*.egg-info/
build/
dist/
.pytest_cache/
.mypy_cache/
.ruff_cache/
.coverage
htmlcov/
.venv/
venv/

# OS / editor
.DS_Store
.vscode/
.idea/
*.swp

# Outputs / runs
outputs/
runs/
wandb/
multirun/
lightning_logs/
*.npz
*.pt
*.ckpt
checkpoints/

# Data caches (fetched at runtime)
data/raw/
data/processed/
data/cache/
*.h5ad

# Scratch figures (paper-ready figures under figures/E1/, figures/E2/, ... are committed)
figures/scratch/
figures/*.pdf
figures/*.png
!figures/E1/**
!figures/E2/**
!figures/E3/**
!figures/E4/**

# Local scratch
scratch/
notebooks/.ipynb_checkpoints/

# Claude / local assistant
.claude/
CLAUDE.md
