P7: differential-testing harness (simurg compare) and nightly run on the Pi

- compare/core: EXACT/NEAR/DISCREPANCY/UNKNOWN with the plan §16.3 tolerances (abs, float32 ULP), NaN = NaN, locus classes (assay, variant type, chromosome group, intensity-only); fields absent on both sides are not applicable - compare/records: GTC vs GTC (per-locus arrays, transforms per bin, controls, sample statistics; metadata listed, not counted) and VCF vs VCF (records keyed incl. ID; SNV/MNV/indel, merged, multi-allelic classes) - simurg compare A B (files or folders paired by name): summary.json, discrepancies.tsv.gz (never truncated), self-contained dashboard.html; --tolerance, --fail-on-discrepancy (exit 3) - scripts/nightly.py + install_nightly.sh (crontab 02:30): unit tests, GSA vs gtc2vcf (GTC + VCF), VCF regression vs golden, Omni2.5 subset vs vendor GTCs; first run PASS on every step - tests/unit/test_compare.py; docs/validation/P7.md, README Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
2026-09-28 17:00:37 +01:00
1 parent 2e8478cc6a
commit cd86681742
@@ -0,0 +1,19 @@
+#!/usr/bin/env bash
+# Install (or remove) the nightly differential-testing run in the user's crontab (no root needed).
+#   bash scripts/install_nightly.sh            # add: every night at 02:30
+#   bash scripts/install_nightly.sh --remove   # remove the entry
+set -euo pipefail
+cd "$(dirname "$0")/.."
+REPO=$(pwd)
+TAG="# simurg-nightly"
+LINE="30 2 * * * cd $REPO && flock -n /tmp/simurg-nightly.lock .venv/bin/python scripts/nightly.py >> data/nightly/cron.log 2>&1 $TAG"
+current=$(crontab -l 2>/dev/null | grep -v -- "$TAG" || true)
+if [[ "${1:-}" == "--remove" ]]; then
+  printf '%s\n' "$current" | sed '/^$/d' | crontab -
+  echo "nightly entry removed"
+  exit 0
+fi
+mkdir -p data/nightly
+printf '%s\n%s\n' "$current" "$LINE" | sed '/^$/d' | crontab -
+echo "installed: $LINE"
+crontab -l | grep -- "$TAG"