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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@@ -19,6 +19,8 @@ used only as external subprocess oracles and are not copied or linked.
| [PharmVar](https://www.pharmvar.org) haplotype definitions (Gaedigk et al. 2018 CPT 103:399) | PharmVar terms of use (attribution) | per-gene zips downloaded by `scripts/pgx/fetch_sources.sh` into `data/` (never committed); `simurg pgx db build` derives core-allele definitions for genes CPIC does not define |
| [GeT-RM](https://www.cdc.gov/lab-quality/php/get-rm/reference-materials.html) consolidated PGx/HLA table (CDC) | US government work | validation truth only (`scripts/pgx/getrm_truth.py`), not redistributed |
| [ClinPGx](https://www.clinpgx.org) (formerly PharmGKB) clinical-annotation variants | CC BY-SA 4.0 (attribution: ClinPGx, https://www.clinpgx.org/page/citingClinpgx) | `clinicalVariants.zip` downloaded by `scripts/pgx/fetch_sources.sh` into `data/` (never committed); rsIDs become genotype-only variant-based genes in the local PGx DB |
| [Noto Sans, Noto Sans Mono](https://fonts.google.com/noto) — Copyright 2022 The Noto Project Authors | SIL Open Font License 1.1 | Glyph outlines of the wordmark in `branding/logo/` (converted to SVG paths by `scripts/brand/make_brand.py`); named in report CSS but never bundled |
| Okabe and Ito colour-universal-design palette (Okabe & Ito 2008, *Color Universal Design*) | free to use (cited) | Chart colours in `simurg/core/brand.py` and the HTML reports |
## BSD-2-Clause (BeadArrayFiles, verbatim from its README)