# Python bytecode
__pycache__/
*.py[cod]
*$py.class

# Distribution / packaging
dist/
/build/
*.egg-info/
.eggs/

# Testing
.pytest_cache/
.coverage
htmlcov/
.tox/

# Type checking
.mypy_cache/
.dmypy.json
dmypy.json

# Virtual environments (if created inside this subdirectory)
venv/
env/
ENV/

*.h5ad
*.gz
*.txt.gz
data/
datasets/
tutorials/data/
**/__pycache__/
.DS_Store
**/.DS_Store
.vscode/
.idea/
.ruff_cache/
**/.doctrees/
docs/build/

# Manuscript figure computation cache
_cache/
manuscript_figures/_cache/

# Run scripts (local convenience only)
run_nb*.sh

# Jupyter notebook artifacts
*.nbconvert.ipynb
.ipynb_checkpoints/

# Claude Code
CLAUDE.md
.claude/
.mcp.json
