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‎dev/.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: '/BioTutorials/dev/',// 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: 'Rosalind.info', collapsed: false, items: [
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{ text: '🧑‍🔬 Getting Started with Rosalind.info Problems', link: '/rosalind/index' },
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{ text: '🧬 Problem 1: Counting DNA nucleotides', link: '/rosalind/01-dna' },
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{ text: '✍️ Problem 2: Transcription', link: '/rosalind/02-rna' },
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{ text: '😉 Problem 3 - Getting the complement', link: '/rosalind/03-revc' },
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{ text: '♻️ 🐇 Rabbits and Recurrence Relations', link: '/rosalind/04-fib' },
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{ text: '🧮 Computing GC content', link: '/rosalind/05-gc' }]
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}
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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: '/BioTutorials/dev/',// TODO: replace this in makedocs!
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title: 'BioTutorials',
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description: 'Documentation for BioTutorials',
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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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['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('/BioTutorials'),
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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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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: 'Rosalind.info', collapsed: false, items: [
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{ text: '🧑‍🔬 Getting Started with Rosalind.info Problems', link: '/rosalind/index' },
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{ text: '🧬 Problem 1: Counting DNA nucleotides', link: '/rosalind/01-dna' },
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{ text: '✍️ Problem 2: Transcription', link: '/rosalind/02-rna' },
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{ text: '😉 Problem 3 - Getting the complement', link: '/rosalind/03-revc' },
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{ text: '♻️ 🐇 Rabbits and Recurrence Relations', link: '/rosalind/04-fib' },
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{ text: '🧮 Computing GC content', link: '/rosalind/05-gc' }]
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}
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]
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,
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editLink: { pattern: "https://https://github.com/BioJulia/BioTutorials/edit/main/docs/src/:path" },
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socialLinks: [
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{ icon: 'github', link: 'https://github.com/BioJulia/BioTutorials' }
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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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})

‎dev/.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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}

‎dev/.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

‎dev/.documenter/.vitepress/theme/style.css‎

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/* Customize default theme styling by overriding CSS variables:
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https://github.com/vuejs/vitepress/blob/main/src/client/theme-default/styles/vars.css */
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/* Example */
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/* https://github.com/vuejs/vitepress/blob/main/template/.vitepress/theme/style.css */
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.VPHero .clip {
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white-space: pre;
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max-width: 600px;
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}
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/* Fonts */
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@font-face {
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font-family: JuliaMono-Regular;
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src: url("https://cdn.jsdelivr.net/gh/cormullion/juliamono/webfonts/JuliaMono-Regular.woff2");
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}
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:root {
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/* Typography */
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--vp-font-family-base: "Barlow", "Inter var experimental", "Inter var",
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-apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu,
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Cantarell, "Fira Sans", "Droid Sans", "Helvetica Neue", sans-serif;
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/* Code Snippet font */
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--vp-font-family-mono: JuliaMono-Regular, monospace;
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}
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/* Disable contextual alternates (kind of like ligatures but different) in monospace,
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which turns `/>` to an up arrow and `|>` (the Julia pipe symbol) to an up arrow as well. */
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.mono-no-substitutions {
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font-family: "JuliaMono-Regular", monospace;
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font-feature-settings: "calt" off;
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}
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.mono-no-substitutions-alt {
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font-family: "JuliaMono-Regular", monospace;
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font-variant-ligatures: none;
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}
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pre, code {
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font-family: "JuliaMono-Regular", monospace;
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font-feature-settings: "calt" off;
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}
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/* Colors */
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:root {
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--julia-blue: #4063D8;
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--julia-purple: #9558B2;
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--julia-red: #CB3C33;
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--julia-green: #389826;
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--vp-c-brand: #0087d7;
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--vp-c-brand-1: #0890df;
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--vp-c-brand-2: #0599ef;
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--vp-c-brand-3: #0c9ff4;
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--vp-c-brand-light: #0087d7;
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--vp-c-brand-dark: #5fd7ff;
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--vp-c-brand-dimm: #212425;
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/* Greens */
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--vp-dark-green: #155f3e; /* Main accent green */
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--vp-dark-green-dark: #2b855c;
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--vp-dark-green-light: #42d392;
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--vp-dark-green-lighter: #35eb9a;
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/* Complementary Colors */
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--vp-dark-gray: #1e1e1e;
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--vp-dark-gray-soft: #2a2a2a;
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--vp-dark-gray-mute: #242424;
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--vp-light-gray: #d1d5db;
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--vp-tip-bg: rgb(254, 254, 254);
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/* Text Colors */
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--vp-dark-text: #e5e5e5; /* Primary text color */
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--vp-dark-subtext: #c1c1c1; /* Subtle text */
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--vp-source-text: #e5e5e5;
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/* custom tip */
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--vp-custom-block-tip-border: var(--vp-c-brand-light);
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--vp-custom-block-tip-bg: var(--vp-tip-bg);
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}
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/* Component: Button */
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:root {
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--vp-button-brand-border: var(--vp-light-gray);
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--vp-button-brand-bg: var(--vp-c-brand-light);
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--vp-button-brand-hover-border: var(--vp-c-bg-alt);
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--vp-button-brand-hover-bg: var(--julia-blue);
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}
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/* Component: Home */
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:root {
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--vp-home-hero-name-color: transparent;
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--vp-home-hero-name-background: -webkit-linear-gradient(
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120deg,
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#9558B2 30%,
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#CB3C33
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);
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--vp-home-hero-image-background-image: linear-gradient(
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-145deg,
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#9558b282 30%,
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#3798269a 30%,
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#cb3d33e3
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);
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--vp-home-hero-image-filter: blur(40px);
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}
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/* Hero Section */
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:root.dark {
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--vp-home-hero-name-color: transparent;
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--vp-home-hero-name-background: -webkit-linear-gradient(
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120deg,
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var(--julia-purple) 15%,
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var(--vp-dark-green-light),
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var(--vp-dark-green)
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);
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--vp-home-hero-image-background-image: linear-gradient(
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-45deg,
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var(--vp-dark-green) 30%,
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var(--vp-dark-green-light),
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var(--vp-dark-gray) 30%
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);
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--vp-home-hero-image-filter: blur(56px);
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}
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:root.dark {
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/* custom tip */
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--vp-custom-block-tip-border: var(--vp-dark-green-dark);
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--vp-custom-block-tip-text: var(--vp-dark-subtext);
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--vp-custom-block-tip-bg: var(--vp-dark-gray-mute);
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}
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/**
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* Colors links
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* -------------------------------------------------------------------------- */
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.dark {
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--vp-c-brand: var(--vp-dark-green-light);
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--vp-button-brand-border: var(--vp-dark-green-lighter);
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--vp-button-brand-bg: var(--vp-dark-green);
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--vp-c-brand-1: var(--vp-dark-green-light);
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--vp-c-brand-2: var(--vp-dark-green-lighter);
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--vp-c-brand-3: var(--vp-dark-green);
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}
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@media (min-width: 640px) {
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:root {
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--vp-home-hero-image-filter: blur(56px);
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}
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}
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@media (min-width: 960px) {
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:root {
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--vp-home-hero-image-filter: blur(72px);
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}
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}
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/* Component: MathJax */
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mjx-container > svg {
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display: block;
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margin: auto;
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}
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mjx-container {
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padding: 0.5rem 0;
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}
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mjx-container {
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display: inline;
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margin: auto 2px -2px;
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}
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mjx-container > svg {
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margin: auto;
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display: inline-block;
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}

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