v28 scorched-earth audit: clean bill, no findings#49
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Follow-up to v27 (5 P0/P1 fixes across 4 commits). Repeated the full teardown → install → notebooks → MCP → applications walk on macOS arm64 to verify the v27 chain holds end-to-end on a fresh user install. Result: 0 findings. Verified: - README TLDR Steps 1-4 work first try, ~60 min unattended - All 3 shipped notebooks (quickstart / advanced / comprehensive) execute with 0 errors / 0 warnings - ChromBPNet HepG2 now pre-downloaded by `chorus setup` (per #9100964 prefetch fix); comprehensive notebook no longer blocks on HepG2 tarball mid-run - MCP E2E (stdio + fastmcp.Client + analyze_variant_multilayer) passes in 280s - Multi-oracle, fine-mapping/discover, CDF download all clean - Fast pytest 340/0 (regression on v27 fixes) - chorus --version, dead anchor, --help tool list all current First audit in the v22→v28 series with zero new bugs. Closes the audit chain that started with v25. Details: audits/2026-04-25_v28_scorched_earth_clean.md Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Apr 26, 2026
After audit/2026-04-26-bpnet-cdfs-complete merged into main, replayed
the full README quickstart from a fresh-install state (deleted 7 envs +
~53 GB of caches/downloads/genomes). Verified:
- Default `chorus setup --oracle chrombpnet` is back to the v27 fast
path (K562 + HepG2 DNase only, ~16 min, 3.5 GB) — no longer the
silent 30 GB / 3-hour download.
- `--all-chrombpnet` opt-in flag is properly advertised in
`chorus setup --help`.
- 786-track NPZ auto-downloads from HF (commit c1e5fc1) on chorus
setup --oracle chrombpnet.
- All 6 oracles ✓ Healthy in 67 min total.
- README Step 3 snippet: WT mean 0.468, 3 alts.
- All 3 shipped notebooks execute clean (single_oracle_quickstart,
advanced_multi_oracle_analysis, comprehensive_oracle_showcase).
- 4/4 integration tests pass (MCP E2E, SEI+LegNet CDF download,
ChromBPNet fresh single-model download).
- Fast pytest 340 / 1.
HTML walkthrough render audit (playwright on 18 shipped HTMLs):
- 18/18 loaded with 0 JS errors / 0 page errors
- 0/18 missing the glossary block
- 17/18 with valid IGV browser block (the one without is
batch_sort1_locus_scoring — by design, batch reports show a
multi-variant table, not per-variant tracks)
- All formula badges (log2FC / lnFC / Δ) and percentile columns
present where applicable.
Default disk footprint after install: ~25 GB (matches new README
claim). The 60 GB figure only applies to --all-chrombpnet opt-in.
This is the second consecutive scorched-earth audit (v28 was the
first) to return clean. Six bug-fix PRs (#48, #49, #50, #51, #52,
#53) plus the audit-fix branch all hold up end-to-end.
No findings. Code is shipping-ready.
Audit + screenshots: audits/2026-04-26_v29_scorched_earth/
Co-authored-by: lp698 <lp698@dimm2fv07n65x.partners.org>
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Follow-up to v27 (5 P0/P1 fixes across 4 commits: pip shadowing, FANTOM track validator, sei solver explosion, ChromBPNet HepG2 prefetch, --version flag). Repeated the full teardown → install → notebooks → MCP → applications walk on macOS arm64 to verify the v27 chain holds.
Result: 0 findings. First audit in the v22→v28 series to return clean.
What was verified
mamba env create+python -m pip install -e .) — 1.5 minchorus setup --oracle all) — 60 min, 6/6 ✓ Healthysingle_oracle_quickstart.ipynbadvanced_multi_oracle_analysis.ipynbcomprehensive_oracle_showcase.ipynbdiscover_variant_effects(SORT1 rs12740374) — 4 layer rankingschorus --version, dead anchor, MCP --help tool list — all currentWhat this PR adds
Single file:
audits/2026-04-25_v28_scorched_earth_clean.md. No code changes.🤖 Generated with Claude Code