Add DocumenterVitepress support and update documentation configuration

camilogarciabotero · Oct 30, 2024 · 734aa7a · 734aa7a
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diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,5 +1,6 @@
 [deps]
 BioMarkovChains = "f861b655-cb5f-42ce-b66a-341b542d4f2c"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterVitepress = "4710194d-e776-4893-9690-8d956a29c365"
 GeneFinder = "2bc6ee46-2158-4f5a-a720-91cb2d7cee64"
 LiveServer = "16fef848-5104-11e9-1b77-fb7a48bbb589"
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,30 +1,64 @@
 using GeneFinder
 using Documenter
+using DocumenterVitepress
 
 DocMeta.setdocmeta!(GeneFinder, :DocTestSetup, :(using GeneFinder); recursive = true)
 
+# makedocs(;
+#     modules = [GeneFinder],
+#     authors = "Camilo García-Botero",
+#     repo = "https://github.com/camilogarciabotero/GeneFinder.jl/",
+#     sitename = "GeneFinder.jl",
+#     format = Documenter.HTML(;
+#         mathengine=MathJax3(),
+#         # prettyurls = get(ENV, "CI", "false") == "true",
+#         canonical = "https://camilogarciabotero.github.io/GeneFinder.jl",
+#         repolink = "https://github.com/camilogarciabotero/GeneFinder.jl",
+#         edit_link = "main",
+#     ),
+#     pages = [
+#         "Home" => "index.md",
+#         "Finding ORFs" => "naivefinder.md",
+#         "Scoring ORFs" => "features.md",
+#         "A Simple Coding Rule" => "simplecodingrule.md",
+#         "Wrtiting ORFs In Files" => "iodocs.md",
+#         "API" => "api.md",
+#         # "Roadmap" => "roadmap.md",
+#     ],
+#     warnonly = true,
+# )
+
+deploydocs(; repo = "https://github.com/camilogarciabotero/GeneFinder.jl", devbranch = "main")
+
+
+fmt = DocumenterVitepress.MarkdownVitepress(
+    repo = "https://github.com/camilogarciabotero/GeneFinder.jl",
+    devbranch = "main",
+)
+
+pgs = [
+    "Home" => "index.md",
+    "Finding ORFs" => "naivefinder.md",
+    "Scoring ORFs" => "features.md",
+    "A Simple Coding Rule" => "simplecodingrule.md",
+    "Wrtiting ORFs In Files" => "iodocs.md",
+    "API" => "api.md",
+]
+
 makedocs(;
     modules = [GeneFinder],
     authors = "Camilo García-Botero",
-    repo = "https://github.com/camilogarciabotero/GeneFinder.jl/",
+    repo = Remotes.GitHub("camilogarciabotero", "GeneFinder.jl"),
     sitename = "GeneFinder.jl",
-    format = Documenter.HTML(;
-        mathengine=MathJax3(),
-        # prettyurls = get(ENV, "CI", "false") == "true",
-        canonical = "https://camilogarciabotero.github.io/GeneFinder.jl",
-        repolink = "https://github.com/camilogarciabotero/GeneFinder.jl",
-        edit_link = "main",
-    ),
-    pages = [
-        "Home" => "index.md",
-        "Finding ORFs" => "naivefinder.md",
-        "Scoring ORFs" => "features.md",
-        "A Simple Coding Rule" => "simplecodingrule.md",
-        "Wrtiting ORFs In Files" => "iodocs.md",
-        "API" => "api.md",
-        # "Roadmap" => "roadmap.md",
-    ],
+    format = fmt,
+    pages = pgs,
     warnonly = true,
 )
 
-deploydocs(; repo = "https://github.com/camilogarciabotero/GeneFinder.jl", devbranch = "main")
+deploydocs(; 
+    repo = "https://github.com/camilogarciabotero/GeneFinder.jl",
+    devbranch = "main",
+    target = "build", # this is where Vitepress stores its output
+    branch = "gh-pages",
+    push_preview = true
+)
diff --git a/docs/src/.vitepress/config.mts b/docs/src/.vitepress/config.mts
@@ -0,0 +1,49 @@
+import { defineConfig } from 'vitepress'
+import { tabsMarkdownPlugin } from 'vitepress-plugin-tabs'
+import mathjax3 from "markdown-it-mathjax3";
+import footnote from "markdown-it-footnote";
+
+// https://vitepress.dev/reference/site-config
+export default defineConfig({
+  base: 'REPLACE_ME_DOCUMENTER_VITEPRESS',// TODO: replace this in makedocs!
+  title: 'BioVossEncoder.jl',
+  description: "A VitePress Site",
+  lastUpdated: true,
+  cleanUrls: true,
+  outDir: 'REPLACE_ME_DOCUMENTER_VITEPRESS', // This is required for MarkdownVitepress to work correctly...
+  head: [['link', { rel: 'icon', href: 'REPLACE_ME_DOCUMENTER_VITEPRESS_FAVICON' }]],
+  ignoreDeadLinks: true,
+
+  markdown: {
+    math: true,
+    config(md) {
+      md.use(tabsMarkdownPlugin),
+      md.use(mathjax3),
+      md.use(footnote)
+    },
+    theme: {
+      light: "github-light",
+      dark: "github-dark"}
+  },
+  themeConfig: {
+    outline: 'deep',
+    logo: 'REPLACE_ME_DOCUMENTER_VITEPRESS',
+    // logo: { src: '/logo.png', width: 24, height: 24 },
+    search: {
+      provider: 'local',
+      options: {
+        detailedView: true
+      }
+    },
+    nav: 'REPLACE_ME_DOCUMENTER_VITEPRESS',
+    sidebar: 'REPLACE_ME_DOCUMENTER_VITEPRESS',
+    editLink: 'REPLACE_ME_DOCUMENTER_VITEPRESS',
+    socialLinks: [
+      { icon: 'github', link: 'REPLACE_ME_DOCUMENTER_VITEPRESS' }
+    ],
+    footer: {
+      message: 'Made with <a href="https://luxdl.github.io/DocumenterVitepress.jl/dev/" target="_blank"><strong>DocumenterVitepress.jl</strong></a><br>',
+      copyright: `© Copyright ${new Date().getUTCFullYear()}.`
+    }
+  }
+})
diff --git a/docs/src/.vitepress/theme/index.ts b/docs/src/.vitepress/theme/index.ts
@@ -0,0 +1,19 @@
+// .vitepress/theme/index.ts
+import { h } from 'vue'
+import type { Theme } from 'vitepress'
+import DefaultTheme from 'vitepress/theme'
+
+import { enhanceAppWithTabs } from 'vitepress-plugin-tabs/client'
+import './style.css'
+
+export default {
+  extends: DefaultTheme,
+  Layout() {
+    return h(DefaultTheme.Layout, null, {
+      // https://vitepress.dev/guide/extending-default-theme#layout-slots
+    })
+  },
+  enhanceApp({ app, router, siteData }) {
+    enhanceAppWithTabs(app)
+  }
+} satisfies Theme
diff --git a/docs/src/.vitepress/theme/style.css b/docs/src/.vitepress/theme/style.css
@@ -0,0 +1,171 @@
+@import url(https://fonts.googleapis.com/css?family=Space+Mono:regular,italic,700,700italic);
+@import url(https://fonts.googleapis.com/css?family=Space+Grotesk:regular,italic,700,700italic);
+
+/* Customize default theme styling by overriding CSS variables:
+https://github.com/vuejs/vitepress/blob/main/src/client/theme-default/styles/vars.css
+ */
+
+  /* Layouts */
+
+/* 
+ :root {
+  --vp-layout-max-width: 1440px;
+} */
+
+.VPHero .clip {
+  white-space: pre;
+  max-width: 500px;
+}
+
+/* Fonts */
+
+:root {
+  /* Typography */
+  --vp-font-family-base: "Barlow", "Inter var experimental", "Inter var",
+    -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu,
+    Cantarell, "Fira Sans", "Droid Sans", "Helvetica Neue", sans-serif;
+
+  /* Code Snippet font */
+  --vp-font-family-mono: "Fira Code", Menlo, Monaco, Consolas, "Courier New",
+    monospace;
+}
+
+/* Colors */
+/* more colors ansi colors = [209, 32, 81, 204, 249, 166, 37] */
+/* more colors colors = ["#ff875f", "#0087d7", "#5fd7ff", "#ff5f87", "#b2b2b2", "#d75f00", "#00afaf"] */
+:root {
+  --julia-blue: #5fd7ff ;
+  --julia-purple: #5fd7ff;
+  --julia-red: #CB3C33;
+  --julia-green: #0087d7;
+
+  --vp-c-brand: #0087d7;
+  --vp-c-brand-light: #0087d7;
+  --vp-c-brand-lighter: #5fd7ff ;
+  --vp-c-brand-lightest: #5fd7ff ;
+  --vp-c-brand-dark: #5fd7ff;
+  --vp-c-brand-darker: #5fd7ff ;
+  --vp-c-brand-dimm: #212425;
+}
+
+ /* Component: Button */
+
+:root {
+  --vp-button-brand-border: var(--vp-c-brand-light);
+  --vp-button-brand-text: var(--vp-c-white);
+  --vp-button-brand-bg: var(--vp-c-brand);
+  --vp-button-brand-hover-border: var(--vp-c-brand-light);
+  --vp-button-brand-hover-text: var(--vp-c-white);
+  --vp-button-brand-hover-bg: var(--vp-c-brand-light);
+  --vp-button-brand-active-border: var(--vp-c-brand-light);
+  --vp-button-brand-active-text: var(--vp-c-white);
+  --vp-button-brand-active-bg: var(--vp-button-brand-bg);
+}
+
+/* Component: Home */
+
+:root {
+  --vp-home-hero-name-color: transparent;
+  --vp-home-hero-name-background: -webkit-linear-gradient(
+    120deg,
+    #ff875f 30%,
+    #ff875f 30%
+  );
+
+  --vp-home-hero-image-background-image: linear-gradient(
+    -45deg,
+    #0094ea11 15%,
+    #0094ea11 15%,
+    #0094ea11
+  );
+  --vp-home-hero-image-filter: blur(10px);
+}
+
+@media (min-width: 640px) {
+  :root {
+    --vp-home-hero-image-filter: blur(60px);
+  }
+}
+
+@media (min-width: 960px) {
+  :root {
+    --vp-home-hero-image-filter: blur(72px);
+  }
+}
+
+/* Component: Custom Block */
+
+:root.dark {
+  --vp-custom-block-tip-border: var(--vp-c-brand);
+  --vp-custom-block-tip-text: var(--vp-c-brand-lightest);
+  --vp-custom-block-tip-bg: var(--vp-c-brand-dimm);
+
+    /* // Tweak the color palette for blacks and dark grays */
+    --vp-c-black: hsl(220 20% 9%);
+    --vp-c-black-pure: hsl(220, 24%, 4%);
+    --vp-c-black-soft: hsl(220 16% 13%);
+    --vp-c-black-mute: hsl(220 14% 17%);
+    --vp-c-gray: hsl(220 8% 56%);
+    --vp-c-gray-dark-1: hsl(220 10% 39%);
+    --vp-c-gray-dark-2: hsl(220 12% 28%);
+    --vp-c-gray-dark-3: hsl(220 12% 23%);
+    --vp-c-gray-dark-4: hsl(220 14% 17%);
+    --vp-c-gray-dark-5: hsl(220 16% 13%);
+
+    /* // Backgrounds */
+    --vp-c-bg: hsl(240, 2%, 11%);
+    --vp-custom-block-info-bg: hsl(220 14% 17%);
+    --vp-c-gutter: hsl(220 20% 9%);
+
+    --vp-c-bg-alt: hsl(220 20% 9%);
+    --vp-c-bg-soft: hsl(220 14% 17%);
+    --vp-c-bg-mute: hsl(220 12% 23%);
+
+}
+
+ /* Component: Algolia */
+
+.DocSearch {
+  --docsearch-primary-color: var(--vp-c-brand) !important;
+}
+
+/* Component: MathJax */
+
+/* mjx-container > svg {
+  display: block;
+  margin: auto;
+}
+
+mjx-container {
+  padding: 0.5rem 0;
+}
+
+mjx-container {
+  display: inline-block;
+  margin: auto 2px -2px;
+}
+
+mjx-container > svg {
+  margin: auto;
+  display: inline-block;
+} */
+
+/**
+ * Colors links
+ * -------------------------------------------------------------------------- */
+
+ :root {
+  --vp-c-brand-1: #ff875f;
+  --vp-c-brand-2: #ff875f;
+  --vp-c-brand-3: #ff875f;
+  --vp-c-sponsor: #ca2971;
+  --vitest-c-sponsor-hover: #c13071;
+}
+
+.dark {
+  --vp-c-brand-1: #0087d7;
+  --vp-c-brand-2: #0087d7;
+  --vp-c-brand-3: #0087d7;
+  --vp-c-sponsor: #ee4e95;
+  --vitest-c-sponsor-hover: #e51370;
+}