Apply the brand across the repo: reports, README, guide

* 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.
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kemal committed 2026-09-30 08:01:30 +01:00
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# SimurgArray
<p align="center"><img src="branding/templates/readme_banner_1280x320.png" alt="SimurgArray: Thirty birds, one picture." width="100%"></p>
Personal research toolkit for Illumina Infinium genotyping BeadChip data
(IDAT → normalization → genotype calling → BAF/LRR → QC → VCF/PLINK; CN/LOH/mosaicism, PGx, cluster training,
methylation control QC).
@@ -7,6 +9,7 @@ methylation control QC).
- **SIMURGARRAY_MASTER_PLAN.md** — architecture, algorithms, roadmap
- **SIMURGARRAY_FUNCTIONAL_SPEC.md** — 416 itemised requirements (CLI, inputs, outputs, QC, CN, PGx, methylation, edge cases)
- `docs/validation/` — per-phase validation reports · `docs/known_unknowns.md` — findings log · `docs/research/` — background
- `branding/` — logo, icons, templates and the brand guide · `blog/` — five posts about the project
## Status