* 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.
User guide: ArrayTrain section, v2 commands in the table, v2 accuracy rows,
updated limitations. README status for v2.0.0. Version 2.0.0 (Python package);
the Rust kernels are unchanged and stay simurg_core 1.1.0. uv.lock committed
(uv lock --check clean).
Full suite on the Pi, file by file under the memory guard: 29 files exit 0
(unit: 282 passed), ruff and mypy clean.
Wheels (pure + manylinux_2_28 kernels), sdist, Docker image and conda packages built and
installed on fresh Ubuntu 24.04 machines; 225 unit tests pass against the installed
package; the tutorial runs with pip (with and without kernels); GTC/VCF content digests are
identical across pip, Docker and conda on both architectures and equal to the Pi's run.
docs/validation/P10.md; guide: install from wheels, Docker, conda; exit code 141.
docs/user_guide.md (install, inputs, complete run, commands, presets, QC, outputs,
accuracy, limitations, troubleshooting), examples/gsa_demo.sh (end-to-end run on the
public GSA demo, verified on the Pi), examples/sample_sheet.csv, CHANGELOG.md; version 1.0.0.
kemal