target/
model.toml
build
*.rds
*.csv
*.tsv
t.py
calibrate/tests/__pycache__/
**/__pycache__/
/.worktrees/
report.md
diff.txt
.devcontainer/
**/proofs/lakefile.lean
**/proofs/lean-toolchain


# Lean
.lake/


# Jules automation
jules.patch
build.log

# Temporary tools
gh_*/
.lake/

# macOS Finder metadata
.DS_Store

# Ignore files whose names do not contain a dot
**/*
!**/
!**/*.*

# Local workspace/editor state (machine-specific, not project source)
/.claude/
/proofs/.claude/

# Lean/Lake build cache and vendored package checkouts (generated; huge/noisy)
/.lake/

# Scratch/debug files from ad-hoc investigations (ephemeral)
/proofs/.tmp_find.lean
/diff.txt

# Downloaded/generated research artifacts (large reproducible data, not source)
/data/snp_intersection_downloads/
/data/snp_intersection_downloads_v2/
/data/*.gnomon_cache/
/data/autosomal.txt
/data/genome_Joshua_Yoakem_v5_Full_20250129211749.txt
/data/arrays.snps_callrate_ge_0.9999.tsv
/local_power/
/examples/convert_score_output/
/sims/.cache/
/tmp/
/rust_digest.txt
/rustc-ice-*.txt

# Python bytecode cache (generated, interpreter-version specific)
/scripts/__pycache__/

# Local experiment outputs in repo root (analysis scratch, not canonical inputs)
/confounding.tsv
/divergence_g20.tsv

# Keep local build/dependency caches out of git status
/target/

# Final override: always ignore Python bytecode caches (after broad unignore rules above)
**/__pycache__/
**/__pycache__/**

# Final override: always ignore macOS Finder metadata (after broad unignore rules above)
.DS_Store
**/.DS_Store
proofs/.lake/

# Final override: data artifacts & OS junk. These MUST come after the `!**/*.*`
# whitelist above, which otherwise re-includes every dotted filename (so .parquet,
# .bed, ._* AppleDouble files, etc. would all be tracked). Later rules win.
# Large reproducible simulation outputs (regenerated by the sims pipeline):
/sims/results_hpc/
# PLINK / genotype binaries and columnar data dumps:
*.parquet
*.bed
*.bim
*.fam
# macOS AppleDouble resource forks (created when copying files off a Mac):
._*
**/._*
# Python bytecode (has a dot, so the whitelist re-includes it without this):
*.pyc

# maturin-built native extension (build artifact)
python/gnomon/_gnomon*.so

# Test fixtures: the PLINK 1.9 side of the pgen parity fixture is the ground
# truth those tests compare against, so it has to be tracked despite the
# blanket genotype-file ignores above.
!data/testdata/*.bed
!data/testdata/*.bim
!data/testdata/*.fam

# Toolchain clones that concurrent build sessions drop in the tree
/mathlib/

# Generated extraction tables. Produced from proofs/Calibrator/, which changes
# constantly; a committed snapshot drifts by six figures and reads as
# authoritative while being wrong. Regenerate per worktree -- each producer
# names its command in its own header.
proofs/validation/empirical/extract/lean_defs.py
proofs/validation/empirical/extract/defs.json
proofs/validation/empirical/extract/classes.json
proofs/validation/empirical/extract/ceiling.json
proofs/validation/empirical/extract/regime.json
proofs/validation/empirical/extract/reconcile.json
proofs/validation/empirical/extract/coverage.json

# Per-run validator output. These files are regenerated from the current Lean
# sources and must not masquerade as versioned evidence from an older revision.
proofs/validation/empirical/differential/results.json
proofs/validation/empirical/drift_diff/results_migration_mean.json
proofs/validation/empirical/invariants/defs.json
proofs/validation/empirical/invariants/results_ranges.json

