# Python
__pycache__/
*.py[cod]
*$py.class
*.so
.Python
.pytest_cache/
.coverage
.tox/
.nox/
htmlcov/
*.egg-info/
dist/
build/

# Models (v0.4-era local-PyTorch path; v0.5 is API-based and needs none of these).
# Kept so the [local] extra's legacy flow still works if users stage weights manually.
models/atlas_v8_4/
models/atlas_v9/
models/kestrel_v8_4/
models/bpe_vocab.json
models/*.pt

# Local test outputs
results/
results_test/
tests/data/mini_benchmark.fa

# Editor + OS
.DS_Store
.vscode/
.idea/
*.swp
*.swo

# Env + secrets
.env
*.key
*.pem

# Node (if any future web UI)
node_modules/

# Nextflow work dirs
work/
.nextflow*
