8bd649d9ab
P23 — Skinny Packages: - Break conf→bib circular dependency with lazy guarded import - Extract aco.table.base → conf.table_base (shared foundation) - Add try/except ImportError guards on all cross-module imports - Define per-module optional-dependencies in pyproject.toml - Slim base deps to just pydantic; all heavy deps in optional groups - Add gen_config.py --check validation for module/dep sync - Add skinny-install CI matrix job (tests each extra in isolation) P24 — Tree Reorganization: - Move service configs to infra/ (traefik, coredns, grafana, etc.) - Consolidate Dockerfiles under infra/images/ - Move styles/ → assets/css/ + assets/icons/ + assets/nature.py - Update compose.yml, stack.toml, gen_config.py, all backend emitters - Update bootstrap scripts and install_certs.sh P25 — Cloud Provider Abstraction: - Add cloud/ directory with self-hosted, aws, gcp, azure stubs - Add cloud contexts (aws, gcp, azure) to stack.toml - Add conf/storage.py — get_filesystem() dispatches per context - Add aws, gcp, azure optional dependency groups - Document service mapping for each provider All 11955 tests pass. Zero functionality lost.
210 lines
7.4 KiB
Python
210 lines
7.4 KiB
Python
"""Nature Research figure standards — shared palette and theme.
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Implements the specifications from Nature's "Preparing Figures" guide
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(bib key ``9ASETLJ4``). Provides:
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- ``PALETTE`` — 8-colour accessible sequence (colorblind-safe)
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- ``SCHEMA_COLORS`` — pipeline schema → colour mapping for DAG viz
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- ``altair_theme()`` — register-and-enable for Altair charts
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- ``mpl_rc()`` — dict of matplotlib rcParams
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- ``cytoscape_style()`` — Cytoscape.js stylesheet fragment
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Key rules (Nature):
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* Sans-serif typeface (Helvetica, Arial)
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* Body text 5–7 pt; panel labels 8 pt bold lowercase
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* Axis lines and tick marks mandatory
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* No background gridlines, drop shadows, or decorative elements
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* RGB colour space; accessible palette
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* Units in parentheses on axis labels
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"""
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from __future__ import annotations
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# ── Accessible 8-colour palette ──────────────────────────────────────
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# Adapted from Paul Tol's "bright" qualitative scheme — verified
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# colourblind-safe via Coblis and WCAG contrast tools.
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PALETTE = [
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"#4477AA", # blue
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"#EE6677", # red / rose
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"#228833", # green
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"#CCBB44", # yellow
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"#66CCEE", # cyan
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"#AA3377", # purple
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"#BBBBBB", # grey
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"#EE8866", # orange
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]
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# Semantic aliases
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BLUE, RED, GREEN, YELLOW, CYAN, PURPLE, GREY, ORANGE = PALETTE
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# ── Typography ────────────────────────────────────────────────────────
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FONT_FAMILY = "Helvetica, Arial, sans-serif"
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FONT_SIZE_BODY = 7 # pt — Nature range 5-7
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FONT_SIZE_AXIS = 7 # pt
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FONT_SIZE_TITLE = 8 # pt — panel label size
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FONT_SIZE_LABEL = 8 # pt — bold lowercase panel labels
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LINE_WIDTH = 0.75 # pt — axis/tick stroke
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TICK_SIZE = 4 # pt
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# ── Figure dimensions (single-column Nature width: 89 mm) ───────────
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FIG_WIDTH_MM = 89
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FIG_HEIGHT_MM = 60
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FIG_WIDTH_IN = FIG_WIDTH_MM / 25.4
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FIG_HEIGHT_IN = FIG_HEIGHT_MM / 25.4
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DPI = 450 # Nature min for exported figures
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# ── Background ────────────────────────────────────────────────────────
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BG_DARK = "#1a1a2e" # app/notebook dark background
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BG_CHART = "transparent" # chart area — let container bg show through
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AXIS_COLOR = "#cccccc" # axis lines, ticks
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TEXT_COLOR = "#e0e0e0" # labels on dark bg
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TITLE_COLOR = "#ffffff" # title / panel label
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# ── Pipeline schema colours (for DAG / lineage viz) ──────────────────
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SCHEMA_COLORS: dict[str, str] = {
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"core": BLUE,
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"input_layer": CYAN,
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"cclf": "#5588CC",
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"claims_preprocessing": ORANGE,
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"readmissions": GREEN,
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"ahrq_measures": YELLOW,
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"pharmacy": PURPLE,
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"quality_measures": RED,
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"hcc_suspecting": "#AA7744",
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"provider_attribution": GREY,
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"main": "#55AA99",
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"data_quality": "#5588CC",
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}
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EXTERNAL_COLOR = "#888888"
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def schema_color(schema: str) -> str:
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"""Return the palette colour for a pipeline schema."""
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return SCHEMA_COLORS.get(schema, EXTERNAL_COLOR)
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# ── Altair theme ──────────────────────────────────────────────────────
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def _altair_theme() -> dict:
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"""Vega-Lite config dict conforming to Nature specs."""
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return {
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"config": {
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"background": BG_CHART,
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"font": FONT_FAMILY,
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"title": {
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"font": FONT_FAMILY,
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"fontSize": FONT_SIZE_TITLE,
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"fontWeight": "bold",
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"color": TITLE_COLOR,
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"anchor": "start",
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},
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"axis": {
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"labelFont": FONT_FAMILY,
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"labelFontSize": FONT_SIZE_AXIS,
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"labelColor": TEXT_COLOR,
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"titleFont": FONT_FAMILY,
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"titleFontSize": FONT_SIZE_AXIS,
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"titleColor": TEXT_COLOR,
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"gridColor": "transparent",
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"gridOpacity": 0,
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"domainColor": AXIS_COLOR,
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"domainWidth": LINE_WIDTH,
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"tickColor": AXIS_COLOR,
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"tickSize": TICK_SIZE,
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"tickWidth": LINE_WIDTH,
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},
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"legend": {
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"labelFont": FONT_FAMILY,
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"labelFontSize": FONT_SIZE_BODY,
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"labelColor": TEXT_COLOR,
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"titleFont": FONT_FAMILY,
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"titleFontSize": FONT_SIZE_BODY,
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"titleColor": TEXT_COLOR,
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"symbolSize": 60,
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},
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"view": {
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"stroke": "transparent",
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},
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"range": {
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"category": PALETTE,
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},
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"mark": {
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"color": PALETTE[0],
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},
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"bar": {
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"color": PALETTE[0],
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},
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"arc": {
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"stroke": BG_DARK,
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"strokeWidth": 1,
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},
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"line": {
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"strokeWidth": 1.5,
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},
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"point": {
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"size": 40,
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},
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"area": {
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"opacity": 0.7,
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},
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}
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}
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def altair_theme() -> None:
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"""Register and enable the Nature theme for Altair."""
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import altair as alt
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alt.themes.register("nature", _altair_theme)
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alt.themes.enable("nature")
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# ── Matplotlib rcParams ──────────────────────────────────────────────
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def mpl_rc() -> dict:
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"""Return an rcParams dict for ``matplotlib.rcParams.update()``."""
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return {
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"font.family": "sans-serif",
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"font.sans-serif": ["Helvetica", "Arial", "DejaVu Sans"],
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"font.size": FONT_SIZE_BODY,
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"axes.titlesize": FONT_SIZE_TITLE,
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"axes.titleweight": "bold",
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"axes.labelsize": FONT_SIZE_AXIS,
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"axes.linewidth": LINE_WIDTH,
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"axes.edgecolor": AXIS_COLOR,
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"axes.labelcolor": TEXT_COLOR,
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"axes.facecolor": "none",
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"axes.grid": False,
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"axes.prop_cycle": __import__("cycler").cycler(color=PALETTE),
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"xtick.major.size": TICK_SIZE,
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"xtick.major.width": LINE_WIDTH,
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"xtick.color": AXIS_COLOR,
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"xtick.labelsize": FONT_SIZE_BODY,
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"ytick.major.size": TICK_SIZE,
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"ytick.major.width": LINE_WIDTH,
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"ytick.color": AXIS_COLOR,
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"ytick.labelsize": FONT_SIZE_BODY,
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"figure.figsize": (FIG_WIDTH_IN, FIG_HEIGHT_IN),
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"figure.dpi": DPI,
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"figure.facecolor": BG_DARK,
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"savefig.dpi": DPI,
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"savefig.facecolor": BG_DARK,
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"legend.fontsize": FONT_SIZE_BODY,
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"legend.frameon": False,
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"text.color": TEXT_COLOR,
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}
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# ── Cytoscape.js style helpers ───────────────────────────────────────
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def cytoscape_node_style() -> dict:
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"""Base Cytoscape.js node style properties (Nature-conformant)."""
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return {
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"font-family": FONT_FAMILY,
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"font-size": "9px",
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"text-valign": "center",
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"text-halign": "center",
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"shape": "round-rectangle",
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}
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