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
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#!/usr/bin/env bash
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# Install (or remove) the nightly differential-testing run in the user's crontab (no root needed).
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# bash scripts/install_nightly.sh # add: every night at 02:30
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# bash scripts/install_nightly.sh --remove # remove the entry
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set -euo pipefail
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cd "$(dirname "$0")/.."
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REPO=$(pwd)
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TAG="# simurg-nightly"
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LINE="30 2 * * * cd $REPO && flock -n /tmp/simurg-nightly.lock .venv/bin/python scripts/nightly.py >> data/nightly/cron.log 2>&1 $TAG"
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current=$(crontab -l 2>/dev/null | grep -v -- "$TAG" || true)
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if [[ "${1:-}" == "--remove" ]]; then
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printf '%s\n' "$current" | sed '/^$/d' | crontab -
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echo "nightly entry removed"
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exit 0
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fi
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mkdir -p data/nightly
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printf '%s\n%s\n' "$current" "$LINE" | sed '/^$/d' | crontab -
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echo "installed: $LINE"
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crontab -l | grep -- "$TAG"
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@@ -0,0 +1,235 @@
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#!/usr/bin/env python3
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"""Nightly differential-testing run (plan §18 P7): P0 GSA demo + Omni2.5 subset, every result compared with its
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oracle by ``simurg compare``, one index page per night plus a history.
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Steps (each isolated; a failing step does not stop the others):
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unit pytest tests/unit (memory-capped)
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gsa_gtc simurg genotype on the 36 GSA IDATs → compare with the gtc2vcf oracle GTCs (expect PASS)
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gsa_vcf simurg gtc-to-vcf --unsquash-duplicates → semantic check vs gtc2vcf (scripts/validate_p6_vcf.py,
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expect 0 unexplained) and regression vs the golden VCFs of an earlier night (expect PASS)
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omni_gtc simurg genotype --preset autocall-1.6.2 on the local Omni2.5 subset → compare with the vendor GTCs
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Output: data/nightly/<YYYY-MM-DD>/{index.html, summary.json, <step>/...}, data/nightly/index.html (history).
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Usage: scripts/nightly.py [--root DIR] [--keep 14] [--steps unit,gsa_gtc,gsa_vcf,omni_gtc] [--update-golden]
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"""
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from __future__ import annotations
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import argparse
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import datetime as dt
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import html
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import json
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import shutil
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import subprocess
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import sys
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import time
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from pathlib import Path
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from typing import Any
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ROOT = Path(__file__).resolve().parents[1]
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PY = ROOT / ".venv" / "bin" / "python"
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SIMURG = ROOT / ".venv" / "bin" / "simurg"
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GSA = ROOT / "data/p0/gsa_v4_pgx"
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GSA_BPM = GSA / "GSA-PGx-48v4-0_20079540_E2_bpm/GSA-PGx-48v4-0_20079540_E2.bpm"
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GSA_CSV = GSA / "GSA-PGx-48v4-0_20079540_E2_csv/GSA-PGx-48v4-0_20079540_E2.csv"
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GSA_EGT = GSA / "GSA-PGx-48v4-0_20079540_E2_ClusterFile/GSA-PGx-48v4-0_20079540_E2_ClusterFile.egt"
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GSA_IDATS = GSA / "idats_Demo_36/idats_Demo_36"
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ORACLE_GTCS = ROOT / "data/p0/oracle/gsa_gt3_nofma"
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ORACLE_VCF = ROOT / "data/p6/oracle/gsa36_gtc2vcf.vcf.gz"
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FASTA = ROOT / "data/p6/GRCh38.primary.fa"
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BCFTOOLS = ROOT / "refs/tools/bcftools-1.22/bcftools"
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OMNI = ROOT / "data/p0/omni_head"
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MEM_CAP = "--as=5500000000" # 5.5 GB address-space cap per step (the Pi has 8 GB)
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def run(cmd: list[str], log: Path, timeout: int = 7200) -> tuple[int, float]:
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t = time.time()
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with log.open("a") as fh:
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fh.write(f"$ {' '.join(cmd)}\n")
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fh.flush()
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try:
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rc = subprocess.run(cmd, stdout=fh, stderr=subprocess.STDOUT, cwd=ROOT, timeout=timeout).returncode
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except subprocess.TimeoutExpired:
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fh.write("TIMEOUT\n")
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rc = 124
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return rc, round(time.time() - t, 1)
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def capped(cmd: list[str], cap: str = MEM_CAP) -> list[str]:
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return ["prlimit", cap, *cmd]
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# gtc-to-vcf memory-maps the whole genome cache (3.1 GB of file-backed address space that costs page cache, not RAM),
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# so its address-space cap must be larger
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VCF_CAP = "--as=12000000000"
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def compare_verdict(folder: Path) -> dict[str, Any]:
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p = folder / "summary.json"
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if not p.exists():
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return {"verdict": "ERROR"}
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s = json.loads(p.read_text())
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return {"verdict": s["verdict"], "discrepancies": s["discrepancies"], "unknown": s["unknown"],
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"report": str((folder / "dashboard.html").relative_to(folder.parents[1]))} # fmt: skip
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def step_unit(out: Path, log: Path) -> dict[str, Any]:
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rc, sec = run(capped([str(PY), "-m", "pytest", "-q", "-m", "not slow", "tests/unit"]), log, 3600)
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return {"verdict": "PASS" if rc == 0 else "FAIL", "seconds": sec}
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def step_gsa_gtc(out: Path, log: Path) -> dict[str, Any]:
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gt = out / "gt"
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rc, sec = run(capped([str(SIMURG), "genotype", "--bpm", str(GSA_BPM), "--egt", str(GSA_EGT), "--idats",
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str(GSA_IDATS), "--out", str(gt), "--threads", "2", "--quiet", "--force"]), log) # fmt: skip
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if rc not in (0,):
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return {"verdict": "ERROR", "seconds": sec, "exit": rc}
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_, sec2 = run(capped([str(SIMURG), "compare", str(gt / "samples"), str(ORACLE_GTCS), "--out", str(out / "compare"),
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"--bpm", str(GSA_BPM), "--threads", "2", "--title", "GSA GTCs vs gtc2vcf oracle",
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"--quiet", "--force"]), log) # fmt: skip
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return {**compare_verdict(out / "compare"), "seconds": sec + sec2}
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def step_gsa_vcf(out: Path, log: Path, golden: Path, update_golden: bool) -> dict[str, Any]:
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gt = out.parent / "gsa_gtc" / "gt" / "samples"
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if not gt.exists():
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return {"verdict": "SKIPPED", "reason": "gsa_gtc did not run"}
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vcf = out / "vcf"
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rc, sec = run(capped([str(SIMURG), "gtc-to-vcf", "--bpm", str(GSA_BPM), "--csv", str(GSA_CSV), "--fasta",
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str(FASTA), "--gtcs", str(gt), "--out", str(vcf), "--unsquash-duplicates", "--threads", "2",
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"--quiet", "--force"], VCF_CAP), log) # fmt: skip
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if rc != 0:
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return {"verdict": "ERROR", "seconds": sec, "exit": rc}
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res: dict[str, Any] = {"seconds": sec}
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if ORACLE_VCF.exists() and BCFTOOLS.exists():
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_, sec2 = run(capped([str(PY), "scripts/validate_p6_vcf.py", "--ours", str(vcf), "--oracle", str(ORACLE_VCF),
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"--fasta", str(FASTA), "--bcftools", str(BCFTOOLS), "--bpm", str(GSA_BPM),
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"--out", str(out / "vs_gtc2vcf.json")]), log) # fmt: skip
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d = json.loads((out / "vs_gtc2vcf.json").read_text()) if (out / "vs_gtc2vcf.json").exists() else {}
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res["vs_gtc2vcf_unexplained"] = d.get("unexplained", "ERROR")
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res["seconds"] += sec2
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if golden.exists() and not update_golden:
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run(capped([str(SIMURG), "compare", str(golden), str(vcf), "--out", str(out / "regression"), "--threads", "2",
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"--title", "GSA VCFs vs golden", "--quiet", "--force"]), log) # fmt: skip
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res["regression"] = compare_verdict(out / "regression")
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else:
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if golden.exists():
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shutil.rmtree(golden)
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golden.mkdir(parents=True)
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for f in vcf.glob("*.snv.vcf.gz"):
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shutil.copy2(f, golden / f.name)
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res["regression"] = {"verdict": "GOLDEN_CREATED"}
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ok = res.get("vs_gtc2vcf_unexplained", 0) == 0 and res["regression"]["verdict"] in ("PASS", "GOLDEN_CREATED")
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res["verdict"] = "PASS" if ok else "FAIL"
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return res
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def step_omni_gtc(out: Path, log: Path) -> dict[str, Any]:
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bpm, egt = OMNI / "HumanOmni2.5-4v1-Multi_B.bpm", OMNI / "HumanOmni2.5-4v1-Multi_B.egt"
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if not bpm.exists():
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return {"verdict": "SKIPPED", "reason": "no local Omni subset"}
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idats, vendor = out / "idats", out / "vendor"
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for d in (idats, vendor):
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d.mkdir(parents=True, exist_ok=True)
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for f in sorted(OMNI.rglob("*.idat")):
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(idats / f.name).unlink(missing_ok=True)
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(idats / f.name).symlink_to(f)
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for f in sorted(OMNI.rglob("*.gtc")):
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(vendor / f.name).unlink(missing_ok=True)
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(vendor / f.name).symlink_to(f)
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gt = out / "gt"
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rc, sec = run(capped([str(SIMURG), "genotype", "--bpm", str(bpm), "--egt", str(egt), "--idats", str(idats),
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"--out", str(gt), "--preset", "autocall-1.6.2", "--threads", "1", "--no-cohort-qc",
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"--quiet", "--force"]), log) # fmt: skip
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if rc != 0:
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return {"verdict": "ERROR", "seconds": sec, "exit": rc}
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run(capped([str(SIMURG), "compare", str(gt / "samples"), str(vendor), "--out", str(out / "compare"), "--bpm",
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str(bpm), "--threads", "1", "--title", "Omni2.5 subset vs vendor GTCs (AutoCall 1.6.2.2)",
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"--quiet", "--force"]), log) # fmt: skip
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return {**compare_verdict(out / "compare"), "seconds": sec}
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CSS = (
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"body{font:14px system-ui;margin:16px} td,th{border:1px solid #ccc;padding:3px 8px}"
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" table{border-collapse:collapse} .PASS td:nth-child(2){background:#d6e6f5}"
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" .FAIL td:nth-child(2),.ERROR td:nth-child(2),.DISCREPANCIES td:nth-child(2){background:#f9d3ac}"
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)
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def render(night: dict[str, Any]) -> str:
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esc = html.escape
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rows = []
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for k, r in night["steps"].items():
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details = json.dumps({x: y for x, y in r.items() if x not in ("verdict", "seconds", "report")})
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link = f'<a href="{esc(r["report"])}">dashboard</a>' if r.get("report") else ""
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verdict = esc(str(r.get("verdict")))
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rows.append(
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f"<tr class='{verdict}'><td>{esc(k)}</td><td>{verdict}</td><td>{r.get('seconds', '')}</td>"
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f"<td>{esc(details)}</td><td>{link}</td></tr>"
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)
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return (
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"<!doctype html><meta charset=utf-8><meta name=viewport content='width=device-width,initial-scale=1'>"
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f"<title>Nightly {night['date']}</title><style>{CSS}</style>"
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f"<h1>Nightly {night['date']} — {esc(night['overall'])}</h1>"
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f"<p>{esc(night['version'])} · {night['seconds']} s</p>"
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"<table><tr><th>step</th><th>verdict</th><th>seconds</th><th>details</th><th></th></tr>"
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+ "".join(rows)
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+ "</table>"
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)
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def main() -> int:
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ap = argparse.ArgumentParser()
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ap.add_argument("--root", type=Path, default=ROOT / "data" / "nightly")
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ap.add_argument("--keep", type=int, default=14, help="nights to keep")
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ap.add_argument("--steps", default="unit,gsa_gtc,gsa_vcf,omni_gtc")
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ap.add_argument("--update-golden", action="store_true")
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a = ap.parse_args()
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day = dt.date.today().isoformat()
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base = a.root / day
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base.mkdir(parents=True, exist_ok=True)
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log = base / "run.log"
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t0 = time.time()
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version = subprocess.run([str(SIMURG), "version"], capture_output=True, text=True, cwd=ROOT).stdout.strip()
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steps: dict[str, Any] = {}
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for name in a.steps.split(","):
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out = base / name
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out.mkdir(exist_ok=True)
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try:
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if name == "unit":
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steps[name] = step_unit(out, log)
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elif name == "gsa_gtc":
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steps[name] = step_gsa_gtc(out, log)
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elif name == "gsa_vcf":
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steps[name] = step_gsa_vcf(out, log, a.root / "golden" / "gsa_vcf", a.update_golden)
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elif name == "omni_gtc":
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steps[name] = step_omni_gtc(out, log)
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except Exception as e: # a crashing step must not stop the others
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steps[name] = {"verdict": "ERROR", "error": f"{type(e).__name__}: {e}"}
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overall = "PASS" if all(s.get("verdict") in ("PASS", "SKIPPED") for s in steps.values()) else "FAIL"
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night = {"date": day, "version": version, "overall": overall, "seconds": round(time.time() - t0), "steps": steps}
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(base / "summary.json").write_text(json.dumps(night, indent=2) + "\n")
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(base / "index.html").write_text(render(night))
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# large intermediates are not kept (reports and summaries are)
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for heavy in ("gsa_gtc/gt/samples", "gsa_vcf/vcf", "omni_gtc/gt/samples"):
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shutil.rmtree(base / heavy, ignore_errors=True)
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nights = sorted(p for p in a.root.iterdir() if p.is_dir() and len(p.name) == 10 and p.name[4] == "-")
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for old in nights[: max(0, len(nights) - a.keep)]:
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shutil.rmtree(old, ignore_errors=True)
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hist = []
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for p in sorted(a.root.glob("????-??-??/summary.json"), reverse=True)[:30]:
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s = json.loads(p.read_text())
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cells = "".join(f"<td>{html.escape(str(s['steps'].get(k, {}).get('verdict', '')))}</td>" for k in steps)
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hist.append(f"<tr><td><a href='{s['date']}/index.html'>{s['date']}</a></td><td>{s['overall']}</td>{cells}</tr>")
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head = "".join(f"<th>{html.escape(k)}</th>" for k in steps)
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(a.root / "index.html").write_text(
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f"<!doctype html><meta charset=utf-8><title>SimurgArray nightly</title><style>{CSS}</style>"
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"<h1>SimurgArray nightly history</h1>"
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f"<table><tr><th>night</th><th>overall</th>{head}</tr>{''.join(hist)}</table>"
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)
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print(json.dumps({"overall": overall, **{k: v.get("verdict") for k, v in steps.items()}}))
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return 0 if overall == "PASS" else 1
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if __name__ == "__main__":
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sys.exit(main())
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