Add documentation site (#786)

* add docs

* up

* update base

* update

* fix

* update

* fix

* u

* add build test

* up

* don't run e2e for docs

* adapt autogenerated astro readme

* Update README.md

.github/workflows/docs-build.yml

@@ -0,0 +1,27 @@
+name: Docs Build Check
+
+on:
+  push:
+    paths:
+      - 'docs/**'
+
+jobs:
+  check-docs-build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout Repository
+      uses: actions/checkout@v2
+
+    - name: Set up Node.js
+      uses: actions/setup-node@v2
+      with:
+        node-version: '20'
+
+    - name: Install Dependencies
+      run: npm install
+      working-directory: ./docs
+
+    - name: Check Build
+      run: npm run build
+      working-directory: ./docs

.github/workflows/docs-deploy.yml

@@ -0,0 +1,39 @@
+name: Builds and deploy documentation
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+
+jobs:
+  build-and-deploy:
+    permissions:
+      contents: write
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout Repository
+      uses: actions/checkout@v2
+
+    - name: Set up Node.js
+      uses: actions/setup-node@v2
+      with:
+        node-version: '20'
+
+    - name: Navigate to docs directory
+      run: cd docs
+
+    - name: Install Dependencies
+      run: npm install
+      working-directory: ./docs
+
+    - name: Build Project
+      run: npm run build
+      working-directory: ./docs
+
+    - name: Deploy to GitHub Pages
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./docs/dist  # Adjust if your build output directory is different

.github/workflows/e2e-k3d.yml

@@ -2,6 +2,11 @@ name: E2E test (on kubernetes)
 
 on:
   push:
+    paths:
+      - 'website/**'
+      - 'backend/**'
+      - 'kubernetes/**'
+      - 'preprocessing/**'
 
 concurrency:
   group: ci-${{ github.ref }}-e2e-k3d

docs/.gitignore

@@ -0,0 +1,21 @@
+# build output
+dist/
+# generated types
+.astro/
+
+# dependencies
+node_modules/
+
+# logs
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+pnpm-debug.log*
+
+
+# environment variables
+.env
+.env.production
+
+# macOS-specific files
+.DS_Store

docs/.vite/deps/_metadata.json

@@ -0,0 +1,8 @@
+{
+  "hash": "c1e8de51",
+  "configHash": "0c82321a",
+  "lockfileHash": "25f1fc72",
+  "browserHash": "cf2b5ff5",
+  "optimized": {},
+  "chunks": {}
+}

docs/.vite/deps/package.json

@@ -0,0 +1,3 @@
+{
+  "type": "module"
+}

docs/.vscode/extensions.json

@@ -0,0 +1,4 @@
+{
+  "recommendations": ["astro-build.astro-vscode"],
+  "unwantedRecommendations": []
+}

docs/.vscode/launch.json

@@ -0,0 +1,11 @@
+{
+  "version": "0.2.0",
+  "configurations": [
+    {
+      "command": "./node_modules/.bin/astro dev",
+      "name": "Development server",
+      "request": "launch",
+      "type": "node-terminal"
+    }
+  ]
+}

docs/README.md

@@ -0,0 +1,44 @@
+# Docs
+
+This directory is used to build the [Loculus documentation site](https://loculus-project.github.io/loculus/), which is based on [Starlight](https://starlight.astro.build/).
+
+## Project Structure
+
+The directory structure is as follows:
+
+```
+.
+├── public/
+├── src/
+│   ├── assets/
+│   ├── content/
+│   │   ├── docs/
+│   │   └── config.ts
+│   └── env.d.ts
+├── astro.config.mjs
+├── package.json
+└── tsconfig.json
+```
+
+Starlight looks for `.md` or `.mdx` files in the `src/content/docs/` directory. Each file is exposed as a route based on its file name.
+
+Images can be added to `src/assets/` and embedded in Markdown with a relative link.
+
+Static assets, like favicons, can be placed in the `public/` directory.
+
+## Commands
+
+All commands are run from the root of the project, from a terminal:
+
+| Command                   | Action                                           |
+| :------------------------ | :----------------------------------------------- |
+| `npm install`             | Installs dependencies                            |
+| `npm run dev`             | Starts local dev server at `localhost:4321`      |
+| `npm run build`           | Build your production site to `./dist/`          |
+| `npm run preview`         | Preview your build locally, before deploying     |
+| `npm run astro ...`       | Run CLI commands like `astro add`, `astro check` |
+| `npm run astro -- --help` | Get help using the Astro CLI                     |
+
+##  More information.
+
+Check out [Starlight’s docs](https://starlight.astro.build/), read [the Astro documentation](https://docs.astro.build).

docs/astro.config.mjs

@@ -0,0 +1,32 @@
+import { defineConfig } from "astro/config";
+import starlight from "@astrojs/starlight";
+
+// https://astro.build/config
+export default defineConfig({
+  base: "/loculus/",
+  integrations: [
+    starlight({
+      title: "Loculus",
+      editLink: {
+        baseUrl: "https://github.com/loculus-project/loculus/edit/main/docs/",
+      },
+
+      social: {
+        github: "https://github.com/loculus-project/loculus",
+      },
+      sidebar: [
+        {
+          label: "Guides",
+          items: [
+            // Each item here is one entry in the navigation menu.
+            { label: "Getting started", link: "/guides/getting-started/" },
+          ],
+        },
+        {
+          label: "Reference",
+          autogenerate: { directory: "reference" },
+        },
+      ],
+    }),
+  ],
+});