Docs astro site: first pass

Author: ewels

.github/workflows/docs.yml

@@ -0,0 +1,60 @@
+name: Deploy website
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - 'docs/**'
+      - '.github/workflows/docs.yml'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: docs
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install pnpm
+        uses: pnpm/action-setup@v4
+
+      - name: Setup Node
+        uses: actions/setup-node@v4
+        with:
+          node-version: 22
+          cache: pnpm
+          cache-dependency-path: docs/pnpm-lock.yaml
+
+      - name: Install dependencies
+        run: pnpm install --frozen-lockfile
+
+      - name: Build site
+        run: pnpm build
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/dist
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

README.md

@@ -1,4 +1,4 @@
-# ![rustar-aligner](docs/logo/rustar-logo.svg)
+# ![rustar-aligner](docs/src/assets/rustar-logo.svg)
 
 A Rust reimplementation of [STAR](https://github.com/alexdobin/STAR) (Spliced Transcripts Alignment to a Reference), the widely-used RNA-seq aligner originally written in C++ by Alexander Dobin.
 

docs-old/logo/rustar-icon.png

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+# Build output
+dist/
+
+# Dependencies
+node_modules/
+
+# Astro cache
+.astro/
+
+# Logs
+npm-debug.log*
+pnpm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+
+# Environment
+.env
+.env.production
+
+# OS
+.DS_Store

docs-old/logo/rustar-logo.png

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+// @ts-check
+import { defineConfig } from 'astro/config';
+import starlight from '@astrojs/starlight';
+
+export default defineConfig({
+  site: 'https://psy-fer.github.io',
+  base: '/rustar-aligner',
+  integrations: [
+    starlight({
+      title: 'rustar-aligner',
+      logo: {
+        src: './src/assets/rustar-icon.svg',
+      },
+      favicon: '/favicon.svg',
+      components: {
+        Header: './src/components/Header.astro',
+      },
+      customCss: ['./src/styles/custom.css'],
+      social: [
+        {
+          icon: 'github',
+          label: 'GitHub',
+          href: 'https://github.com/Psy-Fer/rustar-aligner',
+        },
+      ],
+      editLink: {
+        baseUrl: 'https://github.com/Psy-Fer/rustar-aligner/edit/main/docs/',
+      },
+      sidebar: [
+        {
+          label: 'Getting started',
+          items: [
+            { label: 'Introduction', slug: 'getting-started/introduction' },
+            { label: 'Installation', slug: 'getting-started/installation' },
+            { label: 'Quick start', slug: 'getting-started/quick-start' },
+          ],
+        },
+        {
+          label: 'Guides',
+          items: [
+            { label: 'Generating a genome index', slug: 'guides/genome-index' },
+            { label: 'Single-end alignment', slug: 'guides/single-end' },
+            { label: 'Paired-end alignment', slug: 'guides/paired-end' },
+            { label: 'Two-pass mode', slug: 'guides/two-pass' },
+            { label: 'Chimeric detection', slug: 'guides/chimeric' },
+            { label: 'Gene quantification', slug: 'guides/quantification' },
+            { label: 'Migrating from STAR', slug: 'guides/migrating-from-star' },
+          ],
+        },
+        {
+          label: 'Reference',
+          items: [
+            { label: 'CLI parameters', slug: 'reference/cli-parameters' },
+            { label: 'Output files', slug: 'reference/output-files' },
+            { label: 'STAR compatibility', slug: 'reference/star-compatibility' },
+            { label: 'Performance', slug: 'reference/performance' },
+          ],
+        },
+        {
+          label: 'About',
+          items: [
+            { label: 'Contributing', slug: 'about/contributing' },
+            { label: 'Changelog', slug: 'about/changelog' },
+            { label: 'License', slug: 'about/license' },
+          ],
+        },
+      ],
+    }),
+  ],
+});

docs/.gitignore

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+{
+  "name": "rustar-aligner",
+  "version": "0.0.1",
+  "private": true,
+  "type": "module",
+  "scripts": {
+    "dev": "astro dev",
+    "start": "astro dev",
+    "build": "astro build",
+    "preview": "astro preview",
+    "astro": "astro"
+  },
+  "dependencies": {
+    "@astrojs/starlight": "^0.38.4",
+    "astro": "^6.2.1",
+    "sharp": "^0.34.5"
+  },
+  "packageManager": "pnpm@10.33.2",
+  "pnpm": {
+    "onlyBuiltDependencies": ["esbuild", "sharp"]
+  }
+}