# Python
__pycache__/
*.py[cod]
*.egg-info/
.eggs/
build/
dist/
.venv/
venv/
.python-version

# Tooling caches
.pytest_cache/
.ruff_cache/
.mypy_cache/
.coverage
htmlcov/

# Secrets — never commit tokens, keys or server addresses
.env
.env.*
!.env.example
*.pem
*.key
.pypirc
secrets/

# BioHarbor runtime data (workspaces, job DB, caches, downloaded databases/weights)
.bioharbor/
bioharbor-data/
*.sqlite
*.sqlite3
*.db

# Large bio data files — keep them out of git (use tests/data for tiny fixtures)
*.h5ad
*.bam
*.cram
*.fastq
*.fastq.gz
*.fq.gz
*.pt
*.ckpt
*.safetensors

# Editors / OS
.idea/
.vscode/
*.swp
.DS_Store
Thumbs.db
