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‎previews/PR57/.documenter/.vitepress/config.mts

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import { defineConfig } from 'vitepress'
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import { tabsMarkdownPlugin } from 'vitepress-plugin-tabs'
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import mathjax3 from "markdown-it-mathjax3";
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import footnote from "markdown-it-footnote";
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import path from 'path'
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function getBaseRepository(base: string): string {
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if (!base || base === '/') return '/';
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const parts = base.split('/').filter(Boolean);
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return parts.length > 0 ? `/${parts[0]}/` : '/';
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}
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const baseTemp = {
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base: '/MolecularEvolution.jl/previews/PR57/',// TODO: replace this in makedocs!
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}
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const navTemp = {
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nav: [
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{ text: 'Core Concepts', collapsed: false, items: [
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{ text: 'Intro', link: '/intro' },
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{ text: 'The MolecularEvolution.jl Framework', link: '/framework' },
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{ text: 'Models', link: '/models' }]
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},
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{ text: 'Methods & Algorithms', collapsed: false, items: [
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{ text: 'Simulation', link: '/simulation' },
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{ text: 'Optimization', link: '/optimization' },
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{ text: 'Ancestral Reconstruction', link: '/ancestors' }]
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},
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{ text: 'Extensions & Utilities', collapsed: false, items: [
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{ text: 'Input/Output', link: '/IO' },
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{ text: 'Visualization', link: '/generated/viz' },
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{ text: 'Updating a phylogenetic tree', link: '/generated/update' }]
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},
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{ text: 'Examples', link: '/examples' },
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{ text: 'Full API', link: '/api' }
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]
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,
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}
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const nav = [
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...navTemp.nav,
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{
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component: 'VersionPicker'
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}
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]
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// https://vitepress.dev/reference/site-config
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export default defineConfig({
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base: '/MolecularEvolution.jl/previews/PR57/',// TODO: replace this in makedocs!
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title: 'MolecularEvolution.jl',
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description: 'Documentation for MolecularEvolution.jl',
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lastUpdated: true,
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cleanUrls: true,
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outDir: '../1', // This is required for MarkdownVitepress to work correctly...
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head: [
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['link', { rel: 'icon', href: '/favicon.ico' }],
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['script', {src: `${getBaseRepository(baseTemp.base)}versions.js`}],
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// ['script', {src: '/versions.js'], for custom domains, I guess if deploy_url is available.
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['script', {src: `${baseTemp.base}siteinfo.js`}]
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],
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vite: {
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define: {
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__DEPLOY_ABSPATH__: JSON.stringify('/MolecularEvolution.jl'),
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},
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resolve: {
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alias: {
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'@': path.resolve(__dirname, '../components')
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}
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},
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optimizeDeps: {
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exclude: [
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'@nolebase/vitepress-plugin-enhanced-readabilities/client',
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'vitepress',
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'@nolebase/ui',
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],
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},
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ssr: {
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noExternal: [
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// If there are other packages that need to be processed by Vite, you can add them here.
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'@nolebase/vitepress-plugin-enhanced-readabilities',
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'@nolebase/ui',
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],
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},
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},
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markdown: {
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math: true,
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config(md) {
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md.use(tabsMarkdownPlugin),
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md.use(mathjax3),
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md.use(footnote)
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},
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theme: {
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light: "github-light",
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dark: "github-dark"}
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},
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themeConfig: {
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outline: 'deep',
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logo: { src: '/logo.png', width: 24, height: 24},
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search: {
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provider: 'local',
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options: {
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detailedView: true
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}
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},
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nav,
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sidebar: [
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{ text: 'Core Concepts', collapsed: false, items: [
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{ text: 'Intro', link: '/intro' },
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{ text: 'The MolecularEvolution.jl Framework', link: '/framework' },
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{ text: 'Models', link: '/models' }]
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},
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{ text: 'Methods & Algorithms', collapsed: false, items: [
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{ text: 'Simulation', link: '/simulation' },
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{ text: 'Optimization', link: '/optimization' },
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{ text: 'Ancestral Reconstruction', link: '/ancestors' }]
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},
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{ text: 'Extensions & Utilities', collapsed: false, items: [
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{ text: 'Input/Output', link: '/IO' },
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{ text: 'Visualization', link: '/generated/viz' },
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{ text: 'Updating a phylogenetic tree', link: '/generated/update' }]
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},
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{ text: 'Examples', link: '/examples' },
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{ text: 'Full API', link: '/api' }
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]
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,
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editLink: { pattern: "https://https://github.com/MurrellGroup/MolecularEvolution.jl/edit/main/docs/src/:path" },
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socialLinks: [
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{ icon: 'github', link: 'https://github.com/MurrellGroup/MolecularEvolution.jl' }
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],
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footer: {
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message: 'Made with <a href="https://luxdl.github.io/DocumenterVitepress.jl/dev/" target="_blank"><strong>DocumenterVitepress.jl</strong></a><br>',
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copyright: `© Copyright ${new Date().getUTCFullYear()}.`
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}
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}
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})

‎previews/PR57/.documenter/.vitepress/theme/docstrings.css

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.jldocstring.custom-block {
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border: 1px solid var(--vp-c-gray-2);
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color: var(--vp-c-text-1);
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overflow: hidden;
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}
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.jldocstring.custom-block summary {
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font-weight: 700;
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cursor: pointer;
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user-select: none;
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margin: 0 0 8px;
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}
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.jldocstring.custom-block summary a {
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pointer-events: none;
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text-decoration: none;
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}
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.jldocstring.custom-block .source-link {
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border: 1px solid var(--vp-c-gray-2);
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border-radius: 4px;
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text-decoration: none;
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background-color: #414040;
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float: right;
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opacity: 0;
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visibility: hidden;
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transform: translateY(-5px);
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transition: all 0.5s cubic-bezier(0.25, 0.1, 0.25, 1);
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}
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.jldocstring.custom-block .source-link a {
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text-decoration: none;
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color: #e5e5e5;
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}
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.jldocstring.custom-block .source-link a:hover {
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text-decoration: underline;
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}
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.jldocstring.custom-block:hover .source-link {
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opacity: 1;
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visibility: visible;
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transform: translateY(0);
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}
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@media (max-width: 768px) {
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.jldocstring.custom-block .source-link {
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opacity: 1;
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visibility: visible;
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transform: translateY(0);
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}
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}

‎previews/PR57/.documenter/.vitepress/theme/index.ts

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// .vitepress/theme/index.ts
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import { h } from 'vue'
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import DefaultTheme from 'vitepress/theme'
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import type { Theme as ThemeConfig } from 'vitepress'
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import {
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NolebaseEnhancedReadabilitiesMenu,
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NolebaseEnhancedReadabilitiesScreenMenu,
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} from '@nolebase/vitepress-plugin-enhanced-readabilities/client'
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import VersionPicker from "@/VersionPicker.vue"
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import AuthorBadge from '@/AuthorBadge.vue'
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import Authors from '@/Authors.vue'
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import { enhanceAppWithTabs } from 'vitepress-plugin-tabs/client'
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import '@nolebase/vitepress-plugin-enhanced-readabilities/client/style.css'
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import './style.css' // You could setup your own, or else a default will be copied.
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import './docstrings.css' // You could setup your own, or else a default will be copied.
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export const Theme: ThemeConfig = {
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extends: DefaultTheme,
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Layout() {
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return h(DefaultTheme.Layout, null, {
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'nav-bar-content-after': () => [
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h(NolebaseEnhancedReadabilitiesMenu), // Enhanced Readabilities menu
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],
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// A enhanced readabilities menu for narrower screens (usually smaller than iPad Mini)
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'nav-screen-content-after': () => h(NolebaseEnhancedReadabilitiesScreenMenu),
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})
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},
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enhanceApp({ app, router, siteData }) {
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enhanceAppWithTabs(app);
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app.component('VersionPicker', VersionPicker);
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app.component('AuthorBadge', AuthorBadge)
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app.component('Authors', Authors)
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}
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}
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export default Theme

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