.DS_Store
__pycache__/
*.pyc
*.pyo
.venv/
.venv-*/
*.egg-info/
dist/
build/
.eggs/
uv.lock
*.h5ad
*.pt
*.pkl
.env
.pytest_cache/
*.aux
*.bbl
*.blg
*.log
*.out
*.fls
*.fdb_latexmk
*.synctex*
*.pdf
*.zip

# Submission dirs (compiled PDFs, zips, cover letters — not tracked)
submission/genome-biology/
submission/zenodo/
submission/plos-comp-bio/
