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jsneljsnel
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Fix pre-commit issues
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‎.pre-commit-config.yaml‎

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args: ["--ignore-words-list=doas"]
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- repo: https://github.com/rhysd/actionlint
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rev: "v1.7.10"
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rev: "v1.7.11"
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hooks:
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- id: actionlint
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‎docs/notebooks/kinetic_scheme_visualization.ipynb‎

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"cells": [
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{
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"cell_type": "markdown",
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"id": "intro-title",
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"id": "0",
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"metadata": {},
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"source": [
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"# Kinetic Scheme Visualization\n",
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},
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{
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"cell_type": "markdown",
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"id": "basics-heading",
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"id": "1",
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"metadata": {},
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"source": [
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"## Basics\n",
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "import-basics",
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"id": "2",
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "markdown",
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"id": "basic-call-heading",
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"id": "3",
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"metadata": {},
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"source": [
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"### Minimal call\n",
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "basic-sequential",
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"id": "4",
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "markdown",
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"id": "parallel-heading",
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"id": "5",
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"metadata": {},
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"source": [
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"A parallel decay model has independent decay channels. All compartments appear side by side,\n",
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "basic-parallel",
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"id": "6",
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "markdown",
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"id": "dataset-heading",
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"id": "7",
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"metadata": {},
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"source": [
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"### Dataset-level entry point\n",
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "basic-dataset",
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"id": "8",
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "markdown",
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"id": "gs-heading",
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"id": "9",
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"metadata": {},
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"source": [
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"### Ground state bar\n",
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "gs-shared",
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"id": "10",
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "markdown",
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"id": "rate-labels-heading",
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"id": "11",
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"metadata": {},
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"source": [
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"### Rate labels\n",
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "rate-labels",
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"id": "12",
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "markdown",
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"id": "export-heading",
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"id": "13",
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"metadata": {},
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"source": [
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"### Exporting figures\n",
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "export-demo",
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"id": "14",
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "markdown",
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"id": "real-world-heading",
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"id": "15",
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"metadata": {},
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"source": [
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"## Real-world example: target analysis of carotenoid triads\n",
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "load-target",
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"id": "16",
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "markdown",
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"id": "17",
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"metadata": {},
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"source": [
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"### Single megacomplex: RCG triad\n",
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "single-mc",
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"id": "18",
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"source": [
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},
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{
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"cell_type": "markdown",
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"id": "dataset-real-heading",
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"id": "19",
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"metadata": {},
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"source": [
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"### Dataset-level: automatically skip non-decay megacomplexes\n",
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "dataset-real",
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"id": "20",
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "markdown",
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"id": "all-mc-heading",
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"id": "21",
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"metadata": {},
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"source": [
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"### Multiple megacomplexes: all three triads together\n",
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "all-mc",
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"id": "22",
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "markdown",
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"id": "config-heading",
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"id": "23",
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"metadata": {},
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"source": [
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"## Customization with `KineticSchemeConfig`\n",
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},
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{
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"cell_type": "markdown",
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"id": "color-mapping-heading",
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"id": "24",
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"metadata": {},
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"source": [
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"### Color mapping\n",
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{
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"execution_count": null,
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"id": "25",
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "markdown",
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"id": "node-styles-heading",
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"id": "26",
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"### Per-node styling and display labels\n",
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{
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"cell_type": "code",
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"id": "27",
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"metadata": {},
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"outputs": [],
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"source": [
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},
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"cell_type": "markdown",
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"id": "28",
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"metadata": {},
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"source": [
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"### Layout hints\n",
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "layout-hint",
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"id": "29",
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},
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"cell_type": "markdown",
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"metadata": {},
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"### Spring layout for complex graphs\n",
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{
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"cell_type": "code",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "markdown",
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"id": "32",
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"metadata": {},
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"source": [
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"### Ground state bar on a real model\n",
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{
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"cell_type": "code",
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},
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"cell_type": "markdown",
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"metadata": {},
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"### Omitting specific rate parameters\n",
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},
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"cell_type": "markdown",
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"### Side-by-side comparison with subplots\n",
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"cell_type": "markdown",
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"## Configuration reference\n",

‎pyglotaran_extras/inspect/kinetic_scheme/_kinetic_graph.py‎

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gray: set[str] = set()
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def _has_cycle(node: str) -> bool:
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"""Check if a cycle is reachable from ``node`` via DFS."""
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"""Check if a cycle is reachable from ``node`` via DFS.
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Parameters
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----------
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node : str
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The starting node for cycle detection.
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Returns
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-------
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bool
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True if a cycle is reachable from the node.
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"""
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white.discard(node)
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gray.add(node)
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for neighbor in self._adjacency.get(node, []):

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