.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

# head-to-head benchmark cache (examples + NetMHC scores)
bench/compare/_cache/

# private-sample concordance outputs (e.g. Alekseech patient data — never commit or share)
bench/results/private/

# Obsidian memory-sync marker (machine-local absolute paths + sync hashes)
.claude/obsidian-sync.json

# affinity training table (regenerable from the IEDB dump via bench/affinity/data.py)
bench/affinity/measured.tsv
# cached NetMHCpan/NetMHCIIpan predictions for the affinity head-to-head
bench/affinity/_cache/
