.venv/
__pycache__/
*.pyc
*.egg-info/
dist/
build/
docs/_build/
.pytest_cache/
.ruff_cache/
.DS_Store

# Large reference proteomes for source lookup are fetched, not committed
data/proteomes/
*.fasta
*.fasta.gz

# figure intermediates (keep the generated .pdf; regenerate via bench/*.py)
appendix/*.dat
appendix/*.gp
appendix/*.dot

# LaTeX build artifacts (keep .tex, .bib, .pdf)
appendix/*.aux
appendix/*.log
appendix/*.out
appendix/*.bbl
appendix/*.blg
appendix/*.fls
appendix/*.fdb_latexmk
