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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"""Geometry of the SimurgArray mark on its dot grid (no dependencies beyond the standard library).
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"""The mark geometry for the image scripts; the single source is ``src/simurg/core/brand.py``.
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A frontal simurg with raised wings (three feathers each), a three-dot crown and three tail plumes: red channel,
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gold, green channel, each ending in a peacock eye. Shapes are capsules, circles and an ellipse in grid units; a cell
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belongs to the first shape that contains its centre. ``SIMPLE`` and ``MICRO`` are hand-drawn small versions.
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Loaded straight from the file, so these scripts run with any Python that has Pillow, without installing SimurgArray.
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"""
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from __future__ import annotations
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import math
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from typing import Any
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import importlib.util
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from pathlib import Path
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_path = Path(__file__).resolve().parents[2] / "src" / "simurg" / "core" / "brand.py"
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_spec = importlib.util.spec_from_file_location("simurg_brand", _path)
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assert _spec is not None and _spec.loader is not None
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_brand = importlib.util.module_from_spec(_spec)
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_spec.loader.exec_module(_brand)
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def _seg(px: float, py: float, a: tuple[float, float], b: tuple[float, float]) -> float:
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dx, dy = b[0] - a[0], b[1] - a[1]
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t = max(0.0, min(1.0, ((px - a[0]) * dx + (py - a[1]) * dy) / ((dx * dx + dy * dy) or 1.0)))
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return math.hypot(px - a[0] - t * dx, py - a[1] - t * dy)
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COLOURS = _brand.COLOURS
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MICRO = _brand.MICRO
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SIMPLE = _brand.SIMPLE
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Grid = _brand.Grid
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art = _brand.art
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detailed = _brand.detailed
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CX = 15.5
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_WING = [([(13.6, 9.6), (8, 5.2), (1.8, 1.4)], 1.25), ([(13.4, 11), (7.5, 8.4), (1.2, 6.6)], 1.25),
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([(13.4, 12.6), (8, 12), (2.6, 11.8)], 1.2)] # fmt: skip
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SHAPES: list[tuple[str, Any, str]] = []
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for pts, r in _WING:
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SHAPES.append(("cap", (pts, r), "gold"))
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SHAPES.append(("cap", ([(2 * CX - x, y) for x, y in pts], r), "gold"))
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SHAPES += [
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("circ", (CX, 4.4, 2.3), "gold"), ("cap", ([(CX, 6), (CX, 8)], 1.3), "gold"), # head, neck
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("circ", (CX, 1.2, 0.62), "gold"), ("circ", (13.6, 1.9, 0.62), "gold"), ("circ", (17.4, 1.9, 0.62), "gold"),
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("ell", (CX, 12.5, 2.9, 5.4), "gold"), # body
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("cap", ([(14.8, 17), (12.6, 20.5), (10.4, 23.2)], 0.7), "red"), ("circ", (10, 24.3, 1.6), "red"),
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("cap", ([(CX, 17.5), (CX, 23.2)], 0.7), "gold"), ("circ", (CX, 24.6, 1.6), "gold"),
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("cap", ([(16.2, 17), (18.4, 20.5), (20.6, 23.2)], 0.7), "green"), ("circ", (21, 24.3, 1.6), "green"),
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] # fmt: skip
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DETAILED_SIZE = (31, 27)
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SIMPLE = """
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X.........X
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XX.......XX
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.XX..X..XX.
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..XXXXXXX..
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XXXXXXXXXXX
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...XXXXX...
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....XXX....
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...R.X.G...
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..R..X..G..
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.RR.XXX.GG.
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"""
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MICRO = """
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X.....X
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XX.X.XX
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.XXXXX.
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..XXX..
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...X...
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.R.X.G.
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R..X..G
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"""
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Grid = dict[tuple[int, int], str]
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def _inside(x: float, y: float, kind: str, p: Any) -> bool:
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if kind == "circ":
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return math.hypot(x - p[0], y - p[1]) <= p[2]
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if kind == "cap":
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pts, r = p
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return min(_seg(x, y, pts[i], pts[i + 1]) for i in range(len(pts) - 1)) <= r
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cx, cy, rx, ry = p
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return ((x - cx) / rx) ** 2 + ((y - cy) / ry) ** 2 <= 1
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def detailed() -> tuple[Grid, int, int]:
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cols, rows = DETAILED_SIZE
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g: Grid = {}
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for r in range(rows):
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for c in range(cols):
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for kind, p, layer in SHAPES:
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if _inside(c + 0.5, r + 0.5, kind, p):
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g[(c, r)] = layer
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break
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return g, cols, rows
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def art(s: str) -> tuple[Grid, int, int]:
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lines = s.strip().splitlines()
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g = {(c, r): {"X": "gold", "R": "red", "G": "green"}[ch] for r, ln in enumerate(lines) for c, ch in enumerate(ln)
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if ch != "."} # fmt: skip
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return g, len(lines[0]), len(lines)
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__all__ = ["COLOURS", "MICRO", "SIMPLE", "Grid", "art", "detailed"]
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