* simurg/core/brand.py: single source of the mark geometry, colours, favicon
and the report header band (scripts/brand now load it from there).
* HTML reports (QC report, compare dashboard, methylation QC): offline SVG
favicon, indigo header band with the mark, version and a sha256 of the data
shown; Noto Sans font stack; methylation plots in Okabe-Ito colours.
* README banner, guide logo, brand/blog links; branding brief updated to the
final identity; Noto (OFL) and Okabe-Ito entries in THIRD_PARTY_NOTICES;
CHANGELOG (Unreleased).
Unit tests + P5 QC oracle: 285 passed; ruff and mypy clean.
- 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
kemal