__pycache__/
*.pyc
*.pyo
.pytest_cache/
*.egg-info/
dist/
build/
.venv/
venv/
*_lacuna/
*.npz
*.npy
# The fitted sequence-ranker head is a shipped artifact, not a scratch file: the
# package is unusable with --rank-by learned-plm without it.
# Fitted models that ship with the package. Everything else matching
# *.npz is a cache or an analysis artifact and stays out.
!lacuna/pockets/plm_head.npz
!lacuna/pockets/surface_head.npz
!lacuna/pockets/fused_ranker.npz
*.log
benchmarks/pdb_cache/
benchmarks/pm_data/
# CryptoBench working data is downloaded on demand and stays out of the
# repository, except the fold assignments: every published split depends on
# them, and leaving them to a download made reproduction contingent on an
# external host staying up. Ignoring the directory itself would make the
# negation below unreachable, hence the glob.
benchmarks/cb_data/*
!benchmarks/cb_data/folds.json
benchmarks/coach420_data/
.joss_review_venv/
.joss_review_out/

# Figure generation scratch output; the canonical copies live one level up.
paper/figures/software/out/

# Analysis scratch: regenerable caches, not results
analysis/**/__pycache__/
analysis/moores_pocket_law/data/plm_emb/
analysis/moores_pocket_law/data/atom_feat/
analysis/moores_pocket_law/data/esmif_emb/
analysis/moores_pocket_law/data/atom_feat_v3/
analysis/moores_pocket_law/data/candidates_v3/
analysis/moores_pocket_law/data/candidates_ext/
analysis/moores_pocket_law/data/ca_coords/
analysis/moores_pocket_law/data/conf40/
analysis/moores_pocket_law/data/test_conf20/
analysis/moores_pocket_law/data/test_conf40/
benchmarks/holo_cache/
