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Add DocumenterVitepress support and update documentation configuration
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‎docs/Project.toml‎

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[deps]
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BioMarkovChains = "f861b655-cb5f-42ce-b66a-341b542d4f2c"
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Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
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DocumenterVitepress = "4710194d-e776-4893-9690-8d956a29c365"
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GeneFinder = "2bc6ee46-2158-4f5a-a720-91cb2d7cee64"
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LiveServer = "16fef848-5104-11e9-1b77-fb7a48bbb589"

‎docs/make.jl‎

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using GeneFinder
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using Documenter
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using DocumenterVitepress
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DocMeta.setdocmeta!(GeneFinder, :DocTestSetup, :(using GeneFinder); recursive = true)
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# makedocs(;
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# modules = [GeneFinder],
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# authors = "Camilo García-Botero",
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# repo = "https://github.com/camilogarciabotero/GeneFinder.jl/",
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# sitename = "GeneFinder.jl",
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# format = Documenter.HTML(;
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# mathengine=MathJax3(),
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# # prettyurls = get(ENV, "CI", "false") == "true",
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# canonical = "https://camilogarciabotero.github.io/GeneFinder.jl",
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# repolink = "https://github.com/camilogarciabotero/GeneFinder.jl",
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# edit_link = "main",
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# ),
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# pages = [
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# "Home" => "index.md",
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# "Finding ORFs" => "naivefinder.md",
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# "Scoring ORFs" => "features.md",
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# "A Simple Coding Rule" => "simplecodingrule.md",
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# "Wrtiting ORFs In Files" => "iodocs.md",
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# "API" => "api.md",
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# # "Roadmap" => "roadmap.md",
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# ],
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# warnonly = true,
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# )
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deploydocs(; repo = "https://github.com/camilogarciabotero/GeneFinder.jl", devbranch = "main")
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fmt = DocumenterVitepress.MarkdownVitepress(
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repo = "https://github.com/camilogarciabotero/GeneFinder.jl",
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devbranch = "main",
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)
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pgs = [
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"Home" => "index.md",
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"Finding ORFs" => "naivefinder.md",
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"Scoring ORFs" => "features.md",
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"A Simple Coding Rule" => "simplecodingrule.md",
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"Wrtiting ORFs In Files" => "iodocs.md",
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"API" => "api.md",
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]
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makedocs(;
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modules = [GeneFinder],
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authors = "Camilo García-Botero",
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repo = "https://github.com/camilogarciabotero/GeneFinder.jl/",
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repo = Remotes.GitHub("camilogarciabotero", "GeneFinder.jl"),
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sitename = "GeneFinder.jl",
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format = Documenter.HTML(;
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mathengine=MathJax3(),
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# prettyurls = get(ENV, "CI", "false") == "true",
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canonical = "https://camilogarciabotero.github.io/GeneFinder.jl",
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repolink = "https://github.com/camilogarciabotero/GeneFinder.jl",
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edit_link = "main",
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),
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pages = [
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"Home" => "index.md",
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"Finding ORFs" => "naivefinder.md",
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"Scoring ORFs" => "features.md",
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"A Simple Coding Rule" => "simplecodingrule.md",
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"Wrtiting ORFs In Files" => "iodocs.md",
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"API" => "api.md",
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# "Roadmap" => "roadmap.md",
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],
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format = fmt,
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pages = pgs,
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warnonly = true,
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)
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deploydocs(; repo = "https://github.com/camilogarciabotero/GeneFinder.jl", devbranch = "main")
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deploydocs(;
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repo = "https://github.com/camilogarciabotero/GeneFinder.jl",
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devbranch = "main",
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target = "build", # this is where Vitepress stores its output
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branch = "gh-pages",
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push_preview = true
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)

‎docs/src/.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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// https://vitepress.dev/reference/site-config
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export default defineConfig({
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base: 'REPLACE_ME_DOCUMENTER_VITEPRESS',// TODO: replace this in makedocs!
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title: 'BioVossEncoder.jl',
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description: "A VitePress Site",
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lastUpdated: true,
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cleanUrls: true,
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outDir: 'REPLACE_ME_DOCUMENTER_VITEPRESS', // This is required for MarkdownVitepress to work correctly...
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head: [['link', { rel: 'icon', href: 'REPLACE_ME_DOCUMENTER_VITEPRESS_FAVICON' }]],
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ignoreDeadLinks: true,
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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: 'REPLACE_ME_DOCUMENTER_VITEPRESS',
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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: 'REPLACE_ME_DOCUMENTER_VITEPRESS',
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sidebar: 'REPLACE_ME_DOCUMENTER_VITEPRESS',
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editLink: 'REPLACE_ME_DOCUMENTER_VITEPRESS',
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socialLinks: [
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{ icon: 'github', link: 'REPLACE_ME_DOCUMENTER_VITEPRESS' }
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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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})

‎docs/src/.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 type { Theme } from 'vitepress'
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import DefaultTheme from 'vitepress/theme'
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import { enhanceAppWithTabs } from 'vitepress-plugin-tabs/client'
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import './style.css'
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export default {
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extends: DefaultTheme,
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Layout() {
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return h(DefaultTheme.Layout, null, {
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// https://vitepress.dev/guide/extending-default-theme#layout-slots
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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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}
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} satisfies Theme

‎docs/src/.vitepress/theme/style.css‎

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@import url(https://fonts.googleapis.com/css?family=Space+Mono:regular,italic,700,700italic);
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@import url(https://fonts.googleapis.com/css?family=Space+Grotesk:regular,italic,700,700italic);
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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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*/
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/* Layouts */
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/*
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:root {
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--vp-layout-max-width: 1440px;
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} */
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.VPHero .clip {
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white-space: pre;
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max-width: 500px;
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}
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/* Fonts */
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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: "Fira Code", Menlo, Monaco, Consolas, "Courier New",
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monospace;
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}
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/* Colors */
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/* more colors ansi colors = [209, 32, 81, 204, 249, 166, 37] */
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/* more colors colors = ["#ff875f", "#0087d7", "#5fd7ff", "#ff5f87", "#b2b2b2", "#d75f00", "#00afaf"] */
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:root {
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--julia-blue: #5fd7ff ;
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--julia-purple: #5fd7ff;
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--julia-red: #CB3C33;
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--julia-green: #0087d7;
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--vp-c-brand: #0087d7;
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--vp-c-brand-light: #0087d7;
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--vp-c-brand-lighter: #5fd7ff ;
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--vp-c-brand-lightest: #5fd7ff ;
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--vp-c-brand-dark: #5fd7ff;
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--vp-c-brand-darker: #5fd7ff ;
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--vp-c-brand-dimm: #212425;
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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-c-brand-light);
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--vp-button-brand-text: var(--vp-c-white);
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--vp-button-brand-bg: var(--vp-c-brand);
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--vp-button-brand-hover-border: var(--vp-c-brand-light);
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--vp-button-brand-hover-text: var(--vp-c-white);
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--vp-button-brand-hover-bg: var(--vp-c-brand-light);
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--vp-button-brand-active-border: var(--vp-c-brand-light);
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--vp-button-brand-active-text: var(--vp-c-white);
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--vp-button-brand-active-bg: var(--vp-button-brand-bg);
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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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#ff875f 30%,
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#ff875f 30%
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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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#0094ea11 15%,
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#0094ea11 15%,
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#0094ea11
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);
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--vp-home-hero-image-filter: blur(10px);
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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(60px);
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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: Custom Block */
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:root.dark {
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--vp-custom-block-tip-border: var(--vp-c-brand);
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--vp-custom-block-tip-text: var(--vp-c-brand-lightest);
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--vp-custom-block-tip-bg: var(--vp-c-brand-dimm);
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/* // Tweak the color palette for blacks and dark grays */
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--vp-c-black: hsl(220 20% 9%);
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--vp-c-black-pure: hsl(220, 24%, 4%);
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--vp-c-black-soft: hsl(220 16% 13%);
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--vp-c-black-mute: hsl(220 14% 17%);
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--vp-c-gray: hsl(220 8% 56%);
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--vp-c-gray-dark-1: hsl(220 10% 39%);
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--vp-c-gray-dark-2: hsl(220 12% 28%);
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--vp-c-gray-dark-3: hsl(220 12% 23%);
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--vp-c-gray-dark-4: hsl(220 14% 17%);
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--vp-c-gray-dark-5: hsl(220 16% 13%);
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/* // Backgrounds */
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--vp-c-bg: hsl(240, 2%, 11%);
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--vp-custom-block-info-bg: hsl(220 14% 17%);
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--vp-c-gutter: hsl(220 20% 9%);
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--vp-c-bg-alt: hsl(220 20% 9%);
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--vp-c-bg-soft: hsl(220 14% 17%);
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--vp-c-bg-mute: hsl(220 12% 23%);
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}
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/* Component: Algolia */
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.DocSearch {
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--docsearch-primary-color: var(--vp-c-brand) !important;
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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-block;
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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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/**
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* Colors links
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* -------------------------------------------------------------------------- */
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:root {
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--vp-c-brand-1: #ff875f;
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--vp-c-brand-2: #ff875f;
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--vp-c-brand-3: #ff875f;
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--vp-c-sponsor: #ca2971;
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--vitest-c-sponsor-hover: #c13071;
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}
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.dark {
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--vp-c-brand-1: #0087d7;
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--vp-c-brand-2: #0087d7;
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--vp-c-brand-3: #0087d7;
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--vp-c-sponsor: #ee4e95;
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--vitest-c-sponsor-hover: #e51370;
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}

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