Compare commits
3
Commits
| Author | SHA1 | Date | |
|---|---|---|---|
 Eric Coissac
|
2417959fbd | ||
|
Eric Coissac
|
4e338bc1d4 | ||
|
Eric Coissac
|
053d2e28cb |
No files matched your search
@@ -3,6 +3,8 @@
|
||||
/jupyterhub_volumes/shared
|
||||
/jupyterhub_volumes/jupyterhub
|
||||
/jupyterhub_volumes/caddy
|
||||
/jupyterhub_volumes/course/data/Genbank
|
||||
/jupyterhub_volumes/web/
|
||||
/**/.DS_Store
|
||||
/web_src/**/*.RData
|
||||
/web_src/**/*.pdf
|
||||
@@ -11,3 +13,7 @@
|
||||
/.luarc.json
|
||||
/sandbox
|
||||
*.log
|
||||
ncbitaxo_*
|
||||
Readme_files
|
||||
Readme.html
|
||||
tmp.*
|
||||
+709
@@ -0,0 +1,709 @@
|
||||
<!DOCTYPE html>
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
|
||||
|
||||
<meta charset="utf-8">
|
||||
<meta name="generator" content="quarto-1.8.26">
|
||||
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
|
||||
|
||||
|
||||
<title>readme</title>
|
||||
<style>
|
||||
code{white-space: pre-wrap;}
|
||||
span.smallcaps{font-variant: small-caps;}
|
||||
div.columns{display: flex; gap: min(4vw, 1.5em);}
|
||||
div.column{flex: auto; overflow-x: auto;}
|
||||
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
|
||||
ul.task-list{list-style: none;}
|
||||
ul.task-list li input[type="checkbox"] {
|
||||
width: 0.8em;
|
||||
margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */
|
||||
vertical-align: middle;
|
||||
}
|
||||
/* CSS for syntax highlighting */
|
||||
html { -webkit-text-size-adjust: 100%; }
|
||||
pre > code.sourceCode { white-space: pre; position: relative; }
|
||||
pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
|
||||
pre > code.sourceCode > span:empty { height: 1.2em; }
|
||||
.sourceCode { overflow: visible; }
|
||||
code.sourceCode > span { color: inherit; text-decoration: inherit; }
|
||||
div.sourceCode { margin: 1em 0; }
|
||||
pre.sourceCode { margin: 0; }
|
||||
@media screen {
|
||||
div.sourceCode { overflow: auto; }
|
||||
}
|
||||
@media print {
|
||||
pre > code.sourceCode { white-space: pre-wrap; }
|
||||
pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
|
||||
}
|
||||
pre.numberSource code
|
||||
{ counter-reset: source-line 0; }
|
||||
pre.numberSource code > span
|
||||
{ position: relative; left: -4em; counter-increment: source-line; }
|
||||
pre.numberSource code > span > a:first-child::before
|
||||
{ content: counter(source-line);
|
||||
position: relative; left: -1em; text-align: right; vertical-align: baseline;
|
||||
border: none; display: inline-block;
|
||||
-webkit-touch-callout: none; -webkit-user-select: none;
|
||||
-khtml-user-select: none; -moz-user-select: none;
|
||||
-ms-user-select: none; user-select: none;
|
||||
padding: 0 4px; width: 4em;
|
||||
}
|
||||
pre.numberSource { margin-left: 3em; padding-left: 4px; }
|
||||
div.sourceCode
|
||||
{ }
|
||||
@media screen {
|
||||
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
|
||||
}
|
||||
</style>
|
||||
|
||||
|
||||
<script src="Readme_files/libs/clipboard/clipboard.min.js"></script>
|
||||
<script src="Readme_files/libs/quarto-html/quarto.js" type="module"></script>
|
||||
<script src="Readme_files/libs/quarto-html/tabsets/tabsets.js" type="module"></script>
|
||||
<script src="Readme_files/libs/quarto-html/axe/axe-check.js" type="module"></script>
|
||||
<script src="Readme_files/libs/quarto-html/popper.min.js"></script>
|
||||
<script src="Readme_files/libs/quarto-html/tippy.umd.min.js"></script>
|
||||
<script src="Readme_files/libs/quarto-html/anchor.min.js"></script>
|
||||
<link href="Readme_files/libs/quarto-html/tippy.css" rel="stylesheet">
|
||||
<link href="Readme_files/libs/quarto-html/quarto-syntax-highlighting-587c61ba64f3a5504c4d52d930310e48.css" rel="stylesheet" id="quarto-text-highlighting-styles">
|
||||
<script src="Readme_files/libs/bootstrap/bootstrap.min.js"></script>
|
||||
<link href="Readme_files/libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
|
||||
<link href="Readme_files/libs/bootstrap/bootstrap-d6a003b94517c951b2d65075d42fb01b.min.css" rel="stylesheet" append-hash="true" id="quarto-bootstrap" data-mode="light">
|
||||
|
||||
|
||||
</head>
|
||||
|
||||
<body class="fullcontent quarto-light">
|
||||
|
||||
<div id="quarto-content" class="page-columns page-rows-contents page-layout-article">
|
||||
|
||||
<main class="content" id="quarto-document-content">
|
||||
|
||||
|
||||
|
||||
|
||||
<section id="obijupyterhub---the-dna-metabarcoding-learning-server" class="level1">
|
||||
<h1>OBIJupyterHub - the DNA Metabarcoding Learning Server</h1>
|
||||
<section id="intended-use" class="level2">
|
||||
<h2 class="anchored" data-anchor-id="intended-use">Intended use</h2>
|
||||
<p>This project packages the MetabarcodingSchool training lab into one reproducible bundle. You get Python, R, and Bash kernels, a Quarto-built course website, and preconfigured admin/student accounts, so onboarding a class is a single command instead of a day of setup. Everything runs locally on a single machine, student work persists between sessions, and <code>./start-jupyterhub.sh</code> takes care of building images, rendering the site, preparing volumes, and bringing JupyterHub up at <code>http://localhost:8888</code>. Defaults (accounts, passwords, volumes) live in the repo so instructors can tweak them quickly.</p>
|
||||
</section>
|
||||
<section id="prerequisites-with-quick-checks" class="level2">
|
||||
<h2 class="anchored" data-anchor-id="prerequisites-with-quick-checks">Prerequisites (with quick checks)</h2>
|
||||
<p>You need Docker, Docker Compose, Quarto, and Python 3 available on the machine that will host the lab.</p>
|
||||
<ul>
|
||||
<li>macOS: install <a href="https://orbstack.dev/">OrbStack</a> (recommended) or Docker Desktop; both ship Docker Engine and Compose.</li>
|
||||
<li>Linux: install Docker Engine and the Compose plugin from your distribution (e.g., <code>sudo apt install docker.io docker-compose-plugin</code>) or from Docker’s official packages.</li>
|
||||
<li>Windows: install Docker Desktop with the WSL2 backend enabled.</li>
|
||||
<li>Quarto CLI: get installers from <a href="https://quarto.org/docs/get-started/" class="uri">https://quarto.org/docs/get-started/</a>.</li>
|
||||
<li>Python 3: any recent version is fine (only the standard library is used).</li>
|
||||
</ul>
|
||||
<p>Verify from a terminal; if a command is missing, install it before moving on:</p>
|
||||
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">docker</span> <span class="at">--version</span></span>
|
||||
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="ex">docker</span> compose version <span class="co"># or: docker-compose --version</span></span>
|
||||
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="ex">quarto</span> <span class="at">--version</span></span>
|
||||
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="ex">python3</span> <span class="at">--version</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
|
||||
</section>
|
||||
<section id="how-the-startup-script-works" class="level2">
|
||||
<h2 class="anchored" data-anchor-id="how-the-startup-script-works">How the startup script works</h2>
|
||||
<p><code>./start-jupyterhub.sh</code> is the single entry point. It builds the Docker images, renders the course website, prepares the volume folders, and starts the stack. Internally it:</p>
|
||||
<ul>
|
||||
<li>creates the <code>jupyterhub_volumes/</code> tree (caddy, course, shared, users, web…)</li>
|
||||
<li>builds <code>jupyterhub-student</code> and <code>jupyterhub-hub</code> images</li>
|
||||
<li>renders the Quarto site from <code>web_src/</code>, generates PDF galleries and <code>pages.json</code>, and copies everything into <code>jupyterhub_volumes/web/</code></li>
|
||||
<li>runs <code>docker-compose up -d --remove-orphans</code></li>
|
||||
</ul>
|
||||
<p>You can tailor what it does with a few flags:</p>
|
||||
<ul>
|
||||
<li><code>--no-build</code> (or <code>--offline</code>): skip Docker image builds and reuse existing images (useful when offline).</li>
|
||||
<li><code>--force-rebuild</code>: rebuild images without cache.</li>
|
||||
<li><code>--stop-server</code>: stop the stack and remove student containers, then exit.</li>
|
||||
<li><code>--update-lectures</code>: rebuild the course website only (no Docker stop/start).</li>
|
||||
</ul>
|
||||
</section>
|
||||
<section id="installation-and-first-run" class="level2">
|
||||
<h2 class="anchored" data-anchor-id="installation-and-first-run">Installation and first run</h2>
|
||||
<ol type="1">
|
||||
<li>Clone the project:</li>
|
||||
</ol>
|
||||
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb2"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> clone https://forge.metabarcoding.org/MetabarcodingSchool/OBIJupyterHub.git</span>
|
||||
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> OBIJupyterHub</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
|
||||
<ol start="2" type="1">
|
||||
<li>(Optional) glance at the structure you’ll populate:</li>
|
||||
</ol>
|
||||
<pre><code>OBIJupyterHub
|
||||
├── start-jupyterhub.sh - single entry point (build + render + start)
|
||||
├── obijupyterhub - Docker images and stack definitions
|
||||
│ ├── docker-compose.yml
|
||||
│ ├── Dockerfile
|
||||
│ ├── Dockerfile.hub
|
||||
│ └── jupyterhub_config.py
|
||||
├── jupyterhub_volumes - data persisted on the host
|
||||
│ ├── course - read-only for students (notebooks, data, bin, R packages)
|
||||
│ ├── shared - shared read/write space for everyone
|
||||
│ ├── users - per-user persistent data
|
||||
│ └── web - rendered course website
|
||||
└── web_src - Quarto sources for the course website</code></pre>
|
||||
<ol start="3" type="1">
|
||||
<li>Prepare course materials (optional before first run):</li>
|
||||
</ol>
|
||||
<ul>
|
||||
<li>Put notebooks, datasets, scripts, binaries, or PDFs for students under <code>jupyterhub_volumes/course/</code>. They will appear read-only at <code>/home/jovyan/work/course/</code>.</li>
|
||||
<li>For collaborative work, drop files in <code>jupyterhub_volumes/shared/</code> (read/write for all at <code>/home/jovyan/work/shared/</code>).</li>
|
||||
<li>Edit or add Quarto sources in <code>web_src/</code> to update the course website; the script will render them.</li>
|
||||
</ul>
|
||||
<ol start="4" type="1">
|
||||
<li>Start everything (build + render + launch):</li>
|
||||
</ol>
|
||||
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb4"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="ex">./start-jupyterhub.sh</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
|
||||
<ol start="5" type="1">
|
||||
<li><p>Access JupyterHub in a browser at <code>http://localhost:8888</code>.</p></li>
|
||||
<li><p>Stop the stack when you’re done (run from <code>obijupyterhub/</code>):</p></li>
|
||||
</ol>
|
||||
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb5"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="ex">docker-compose</span> down</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
|
||||
<section id="operating-the-stack-one-command-a-few-options" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="operating-the-stack-one-command-a-few-options">Operating the stack (one command, a few options)</h3>
|
||||
<ul>
|
||||
<li>Start or rebuild: <code>./start-jupyterhub.sh</code> (rebuilds images, regenerates the website, starts the stack).</li>
|
||||
<li>Start without rebuilding images (offline): <code>./start-jupyterhub.sh --no-build</code></li>
|
||||
<li>Force rebuild without cache: <code>./start-jupyterhub.sh --force-rebuild</code></li>
|
||||
<li>Stop only: <code>./start-jupyterhub.sh --stop-server</code></li>
|
||||
<li>Rebuild website only (no Docker stop/start): <code>./start-jupyterhub.sh --update-lectures</code></li>
|
||||
<li>Access at <code>http://localhost:8888</code> (students: any username / password <code>metabar2025</code>; admin: <code>admin</code> / <code>admin2025</code>).</li>
|
||||
<li>Check logs from <code>obijupyterhub/</code> with <code>docker-compose logs -f jupyterhub</code>.</li>
|
||||
<li>Stop with <code>docker-compose down</code> (from <code>obijupyterhub/</code>). Rerun <code>./start-jupyterhub.sh</code> to start again or after config changes.</li>
|
||||
</ul>
|
||||
</section>
|
||||
</section>
|
||||
<section id="managing-shared-data" class="level2">
|
||||
<h2 class="anchored" data-anchor-id="managing-shared-data">Managing shared data</h2>
|
||||
<p>Each student lands in <code>/home/jovyan/work/</code> with three key areas: their own files, a shared space, and a read-only course space. Everything under <code>work/</code> is persisted on the host in <code>jupyterhub_volumes</code>.</p>
|
||||
<pre><code>work/ # Personal workspace root (persistent)
|
||||
├── [student files] # Their own files and notebooks
|
||||
├── R_packages/ # Personal R packages (writable by student)
|
||||
├── shared/ # Shared workspace (read/write, shared with all)
|
||||
└── course/ # Course files (read-only, managed by admin)
|
||||
├── R_packages/ # Shared R packages (read-only, installed by prof)
|
||||
├── bin/ # Shared executables (in PATH)
|
||||
└── [course materials] # Your course files</code></pre>
|
||||
<p>R looks for packages in this order: personal <code>work/R_packages/</code>, then shared <code>work/course/R_packages/</code>, then system libraries. Because everything lives under <code>work/</code>, student files survive restarts.</p>
|
||||
<section id="user-accounts" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="user-accounts">User Accounts</h3>
|
||||
<p>Defaults are defined in <code>obijupyterhub/docker-compose.yml</code>: admin (<code>admin</code> / <code>admin2025</code>) with write access to <code>course/</code>, and students (any username, password <code>metabar2025</code>) with read-only access to <code>course/</code>. Adjust <code>JUPYTERHUB_ADMIN_PASSWORD</code> and <code>JUPYTERHUB_PASSWORD</code> there, then rerun <code>./start-jupyterhub.sh</code>.</p>
|
||||
</section>
|
||||
<section id="installing-r-packages-admin-only" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="installing-r-packages-admin-only">Installing R Packages (Admin Only)</h3>
|
||||
<p>From the host, install shared R packages into <code>course/R_packages/</code>:</p>
|
||||
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb7"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Install packages</span></span>
|
||||
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a><span class="ex">tools/install_packages.sh</span> reshape2 plotly knitr</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
|
||||
<p>Students can install their own packages into their personal <code>work/R_packages/</code>:</p>
|
||||
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb8"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Install in personal library (each student has their own)</span></span>
|
||||
<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">'mypackage'</span>) <span class="co"># Will install in work/R_packages/</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
|
||||
</section>
|
||||
<section id="using-r-packages-students" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="using-r-packages-students">Using R Packages (Students)</h3>
|
||||
<p>Students simply load packages normally:</p>
|
||||
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb9"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(reshape2) <span class="co"># R checks: 1) work/R_packages/ 2) work/course/R_packages/ 3) system</span></span>
|
||||
<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(plotly)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
|
||||
<p>R automatically searches in this order:</p>
|
||||
<ol type="1">
|
||||
<li>Personal packages: <code>/home/jovyan/work/R_packages/</code> (R_LIBS_USER)</li>
|
||||
<li>Prof packages: <code>/home/jovyan/work/course/R_packages/</code> (R_LIBS_SITE)</li>
|
||||
<li>System packages</li>
|
||||
</ol>
|
||||
</section>
|
||||
<section id="list-available-packages" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="list-available-packages">List Available Packages</h3>
|
||||
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb10"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="co"># List all available packages (personal + course + system)</span></span>
|
||||
<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a><span class="fu">installed.packages</span>()[,<span class="st">"Package"</span>]</span>
|
||||
<span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb10-4"><a href="#cb10-4" aria-hidden="true" tabindex="-1"></a><span class="co"># Check personal packages</span></span>
|
||||
<span id="cb10-5"><a href="#cb10-5" aria-hidden="true" tabindex="-1"></a><span class="fu">list.files</span>(<span class="st">"/home/jovyan/work/R_packages"</span>)</span>
|
||||
<span id="cb10-6"><a href="#cb10-6" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb10-7"><a href="#cb10-7" aria-hidden="true" tabindex="-1"></a><span class="co"># Check course packages (installed by prof)</span></span>
|
||||
<span id="cb10-8"><a href="#cb10-8" aria-hidden="true" tabindex="-1"></a><span class="fu">list.files</span>(<span class="st">"/home/jovyan/work/course/R_packages"</span>)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
|
||||
</section>
|
||||
<section id="deposit-or-retrieve-course-and-student-files" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="deposit-or-retrieve-course-and-student-files">Deposit or retrieve course and student files</h3>
|
||||
<p>On the host, place course files in <code>jupyterhub_volumes/course/</code> (they appear read-only to students), shared files in <code>jupyterhub_volumes/shared/</code>, and collect student work from <code>jupyterhub_volumes/users/</code>.</p>
|
||||
</section>
|
||||
</section>
|
||||
<section id="user-management" class="level2">
|
||||
<h2 class="anchored" data-anchor-id="user-management">User Management</h2>
|
||||
<section id="option-1-predefined-user-list" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="option-1-predefined-user-list">Option 1: Predefined User List</h3>
|
||||
<p>In <code>jupyterhub_config.py</code>, uncomment and modify:</p>
|
||||
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb11"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a>c.Authenticator.allowed_users <span class="op">=</span> {<span class="st">'student1'</span>, <span class="st">'student2'</span>, <span class="st">'student3'</span>}</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
|
||||
</section>
|
||||
<section id="option-2-allow-everyone-for-testing" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="option-2-allow-everyone-for-testing">Option 2: Allow Everyone (for testing)</h3>
|
||||
<p>By default, the configuration allows any user:</p>
|
||||
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb12"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a>c.Authenticator.allow_all <span class="op">=</span> <span class="va">True</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
|
||||
<p>⚠️ <strong>Warning</strong>: DummyAuthenticator is ONLY for local testing!</p>
|
||||
</section>
|
||||
</section>
|
||||
<section id="kernel-verification" class="level2">
|
||||
<h2 class="anchored" data-anchor-id="kernel-verification">Kernel Verification</h2>
|
||||
<p>Once logged in, create a new notebook and verify you have access to:</p>
|
||||
<ul>
|
||||
<li><strong>Python 3</strong> (default kernel)</li>
|
||||
<li><strong>R</strong> (R kernel)</li>
|
||||
<li><strong>Bash</strong> (bash kernel)</li>
|
||||
</ul>
|
||||
</section>
|
||||
<section id="customization-for-your-labs" class="level2">
|
||||
<h2 class="anchored" data-anchor-id="customization-for-your-labs">Customization for Your Labs</h2>
|
||||
<section id="add-additional-r-packages" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="add-additional-r-packages">Add Additional R Packages</h3>
|
||||
<p>Modify the <code>Dockerfile</code> (before <code>USER ${NB_UID}</code>):</p>
|
||||
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb13"><pre class="sourceCode dockerfile code-with-copy"><code class="sourceCode dockerfile"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="kw">RUN</span> <span class="ex">R</span> <span class="at">-e</span> <span class="st">"install.packages(c('your_package'), repos='http://cran.rstudio.com/')"</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
|
||||
<p>Then rerun <code>./start-jupyterhub.sh</code> to rebuild and restart.</p>
|
||||
</section>
|
||||
<section id="add-python-packages" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="add-python-packages">Add Python Packages</h3>
|
||||
<p>Add to the <code>Dockerfile</code> (before <code>USER ${NB_UID}</code>):</p>
|
||||
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb14"><pre class="sourceCode dockerfile code-with-copy"><code class="sourceCode dockerfile"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a><span class="kw">RUN</span> <span class="ex">pip</span> install numpy pandas matplotlib seaborn</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
|
||||
<p>Then rerun <code>./start-jupyterhub.sh</code> to rebuild and restart.</p>
|
||||
</section>
|
||||
<section id="change-port-if-8000-is-occupied" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="change-port-if-8000-is-occupied">Change Port (if 8000 is occupied)</h3>
|
||||
<p>Modify in <code>docker-compose.yml</code>:</p>
|
||||
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb15"><pre class="sourceCode yaml code-with-copy"><code class="sourceCode yaml"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ports</span><span class="kw">:</span></span>
|
||||
<span id="cb15-2"><a href="#cb15-2" aria-hidden="true" tabindex="-1"></a><span class="at"> </span><span class="kw">-</span><span class="at"> </span><span class="st">"8001:8000"</span><span class="co"> # Accessible on localhost:8001</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
|
||||
</section>
|
||||
</section>
|
||||
<section id="advantages-of-this-approach" class="level2">
|
||||
<h2 class="anchored" data-anchor-id="advantages-of-this-approach">Advantages of This Approach</h2>
|
||||
<p>✅ <strong>Everything in Docker</strong>: No need to install Python/JupyterHub on your computer<br>
|
||||
✅ <strong>Portable</strong>: Easy to deploy on another server<br>
|
||||
✅ <strong>Isolated</strong>: No pollution of your system environment<br>
|
||||
✅ <strong>Easy to Clean</strong>: A simple <code>docker-compose down</code> is enough<br>
|
||||
✅ <strong>Reproducible</strong>: Students will have exactly the same environment</p>
|
||||
</section>
|
||||
<section id="troubleshooting" class="level2">
|
||||
<h2 class="anchored" data-anchor-id="troubleshooting">Troubleshooting</h2>
|
||||
<ul>
|
||||
<li>Docker daemon unavailable: make sure OrbStack/Docker Desktop/daemon is running; verify <code>/var/run/docker.sock</code> exists.</li>
|
||||
<li>Student containers do not start: check <code>docker-compose logs jupyterhub</code> and confirm the images exist with <code>docker images | grep jupyterhub-student</code>.</li>
|
||||
<li>Port conflict: change the published port in <code>docker-compose.yml</code>.</li>
|
||||
</ul>
|
||||
<p><strong>I want to start from scratch</strong>:</p>
|
||||
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb16"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a><span class="bu">pushd</span> obijupyterhub</span>
|
||||
<span id="cb16-2"><a href="#cb16-2" aria-hidden="true" tabindex="-1"></a><span class="ex">docker-compose</span> down <span class="at">-v</span></span>
|
||||
<span id="cb16-3"><a href="#cb16-3" aria-hidden="true" tabindex="-1"></a><span class="ex">docker</span> rmi jupyterhub-hub jupyterhub-student</span>
|
||||
<span id="cb16-4"><a href="#cb16-4" aria-hidden="true" tabindex="-1"></a><span class="bu">popd</span></span>
|
||||
<span id="cb16-5"><a href="#cb16-5" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb16-6"><a href="#cb16-6" aria-hidden="true" tabindex="-1"></a><span class="co"># Then rebuild everything</span></span>
|
||||
<span id="cb16-7"><a href="#cb16-7" aria-hidden="true" tabindex="-1"></a><span class="ex">./start-jupyterhub.sh</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
|
||||
</section>
|
||||
</section>
|
||||
|
||||
</main>
|
||||
<!-- /main column -->
|
||||
<script id="quarto-html-after-body" type="application/javascript">
|
||||
window.document.addEventListener("DOMContentLoaded", function (event) {
|
||||
const icon = "";
|
||||
const anchorJS = new window.AnchorJS();
|
||||
anchorJS.options = {
|
||||
placement: 'right',
|
||||
icon: icon
|
||||
};
|
||||
anchorJS.add('.anchored');
|
||||
const isCodeAnnotation = (el) => {
|
||||
for (const clz of el.classList) {
|
||||
if (clz.startsWith('code-annotation-')) {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
return false;
|
||||
}
|
||||
const onCopySuccess = function(e) {
|
||||
// button target
|
||||
const button = e.trigger;
|
||||
// don't keep focus
|
||||
button.blur();
|
||||
// flash "checked"
|
||||
button.classList.add('code-copy-button-checked');
|
||||
var currentTitle = button.getAttribute("title");
|
||||
button.setAttribute("title", "Copied!");
|
||||
let tooltip;
|
||||
if (window.bootstrap) {
|
||||
button.setAttribute("data-bs-toggle", "tooltip");
|
||||
button.setAttribute("data-bs-placement", "left");
|
||||
button.setAttribute("data-bs-title", "Copied!");
|
||||
tooltip = new bootstrap.Tooltip(button,
|
||||
{ trigger: "manual",
|
||||
customClass: "code-copy-button-tooltip",
|
||||
offset: [0, -8]});
|
||||
tooltip.show();
|
||||
}
|
||||
setTimeout(function() {
|
||||
if (tooltip) {
|
||||
tooltip.hide();
|
||||
button.removeAttribute("data-bs-title");
|
||||
button.removeAttribute("data-bs-toggle");
|
||||
button.removeAttribute("data-bs-placement");
|
||||
}
|
||||
button.setAttribute("title", currentTitle);
|
||||
button.classList.remove('code-copy-button-checked');
|
||||
}, 1000);
|
||||
// clear code selection
|
||||
e.clearSelection();
|
||||
}
|
||||
const getTextToCopy = function(trigger) {
|
||||
const outerScaffold = trigger.parentElement.cloneNode(true);
|
||||
const codeEl = outerScaffold.querySelector('code');
|
||||
for (const childEl of codeEl.children) {
|
||||
if (isCodeAnnotation(childEl)) {
|
||||
childEl.remove();
|
||||
}
|
||||
}
|
||||
return codeEl.innerText;
|
||||
}
|
||||
const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
|
||||
text: getTextToCopy
|
||||
});
|
||||
clipboard.on('success', onCopySuccess);
|
||||
if (window.document.getElementById('quarto-embedded-source-code-modal')) {
|
||||
const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
|
||||
text: getTextToCopy,
|
||||
container: window.document.getElementById('quarto-embedded-source-code-modal')
|
||||
});
|
||||
clipboardModal.on('success', onCopySuccess);
|
||||
}
|
||||
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
|
||||
var mailtoRegex = new RegExp(/^mailto:/);
|
||||
var filterRegex = new RegExp('/' + window.location.host + '/');
|
||||
var isInternal = (href) => {
|
||||
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
|
||||
}
|
||||
// Inspect non-navigation links and adorn them if external
|
||||
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)');
|
||||
for (var i=0; i<links.length; i++) {
|
||||
const link = links[i];
|
||||
if (!isInternal(link.href)) {
|
||||
// undo the damage that might have been done by quarto-nav.js in the case of
|
||||
// links that we want to consider external
|
||||
if (link.dataset.originalHref !== undefined) {
|
||||
link.href = link.dataset.originalHref;
|
||||
}
|
||||
}
|
||||
}
|
||||
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
|
||||
const config = {
|
||||
allowHTML: true,
|
||||
maxWidth: 500,
|
||||
delay: 100,
|
||||
arrow: false,
|
||||
appendTo: function(el) {
|
||||
return el.parentElement;
|
||||
},
|
||||
interactive: true,
|
||||
interactiveBorder: 10,
|
||||
theme: 'quarto',
|
||||
placement: 'bottom-start',
|
||||
};
|
||||
if (contentFn) {
|
||||
config.content = contentFn;
|
||||
}
|
||||
if (onTriggerFn) {
|
||||
config.onTrigger = onTriggerFn;
|
||||
}
|
||||
if (onUntriggerFn) {
|
||||
config.onUntrigger = onUntriggerFn;
|
||||
}
|
||||
window.tippy(el, config);
|
||||
}
|
||||
const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
|
||||
for (var i=0; i<noterefs.length; i++) {
|
||||
const ref = noterefs[i];
|
||||
tippyHover(ref, function() {
|
||||
// use id or data attribute instead here
|
||||
let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href');
|
||||
try { href = new URL(href).hash; } catch {}
|
||||
const id = href.replace(/^#\/?/, "");
|
||||
const note = window.document.getElementById(id);
|
||||
if (note) {
|
||||
return note.innerHTML;
|
||||
} else {
|
||||
return "";
|
||||
}
|
||||
});
|
||||
}
|
||||
const xrefs = window.document.querySelectorAll('a.quarto-xref');
|
||||
const processXRef = (id, note) => {
|
||||
// Strip column container classes
|
||||
const stripColumnClz = (el) => {
|
||||
el.classList.remove("page-full", "page-columns");
|
||||
if (el.children) {
|
||||
for (const child of el.children) {
|
||||
stripColumnClz(child);
|
||||
}
|
||||
}
|
||||
}
|
||||
stripColumnClz(note)
|
||||
if (id === null || id.startsWith('sec-')) {
|
||||
// Special case sections, only their first couple elements
|
||||
const container = document.createElement("div");
|
||||
if (note.children && note.children.length > 2) {
|
||||
container.appendChild(note.children[0].cloneNode(true));
|
||||
for (let i = 1; i < note.children.length; i++) {
|
||||
const child = note.children[i];
|
||||
if (child.tagName === "P" && child.innerText === "") {
|
||||
continue;
|
||||
} else {
|
||||
container.appendChild(child.cloneNode(true));
|
||||
break;
|
||||
}
|
||||
}
|
||||
if (window.Quarto?.typesetMath) {
|
||||
window.Quarto.typesetMath(container);
|
||||
}
|
||||
return container.innerHTML
|
||||
} else {
|
||||
if (window.Quarto?.typesetMath) {
|
||||
window.Quarto.typesetMath(note);
|
||||
}
|
||||
return note.innerHTML;
|
||||
}
|
||||
} else {
|
||||
// Remove any anchor links if they are present
|
||||
const anchorLink = note.querySelector('a.anchorjs-link');
|
||||
if (anchorLink) {
|
||||
anchorLink.remove();
|
||||
}
|
||||
if (window.Quarto?.typesetMath) {
|
||||
window.Quarto.typesetMath(note);
|
||||
}
|
||||
if (note.classList.contains("callout")) {
|
||||
return note.outerHTML;
|
||||
} else {
|
||||
return note.innerHTML;
|
||||
}
|
||||
}
|
||||
}
|
||||
for (var i=0; i<xrefs.length; i++) {
|
||||
const xref = xrefs[i];
|
||||
tippyHover(xref, undefined, function(instance) {
|
||||
instance.disable();
|
||||
let url = xref.getAttribute('href');
|
||||
let hash = undefined;
|
||||
if (url.startsWith('#')) {
|
||||
hash = url;
|
||||
} else {
|
||||
try { hash = new URL(url).hash; } catch {}
|
||||
}
|
||||
if (hash) {
|
||||
const id = hash.replace(/^#\/?/, "");
|
||||
const note = window.document.getElementById(id);
|
||||
if (note !== null) {
|
||||
try {
|
||||
const html = processXRef(id, note.cloneNode(true));
|
||||
instance.setContent(html);
|
||||
} finally {
|
||||
instance.enable();
|
||||
instance.show();
|
||||
}
|
||||
} else {
|
||||
// See if we can fetch this
|
||||
fetch(url.split('#')[0])
|
||||
.then(res => res.text())
|
||||
.then(html => {
|
||||
const parser = new DOMParser();
|
||||
const htmlDoc = parser.parseFromString(html, "text/html");
|
||||
const note = htmlDoc.getElementById(id);
|
||||
if (note !== null) {
|
||||
const html = processXRef(id, note);
|
||||
instance.setContent(html);
|
||||
}
|
||||
}).finally(() => {
|
||||
instance.enable();
|
||||
instance.show();
|
||||
});
|
||||
}
|
||||
} else {
|
||||
// See if we can fetch a full url (with no hash to target)
|
||||
// This is a special case and we should probably do some content thinning / targeting
|
||||
fetch(url)
|
||||
.then(res => res.text())
|
||||
.then(html => {
|
||||
const parser = new DOMParser();
|
||||
const htmlDoc = parser.parseFromString(html, "text/html");
|
||||
const note = htmlDoc.querySelector('main.content');
|
||||
if (note !== null) {
|
||||
// This should only happen for chapter cross references
|
||||
// (since there is no id in the URL)
|
||||
// remove the first header
|
||||
if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
|
||||
note.children[0].remove();
|
||||
}
|
||||
const html = processXRef(null, note);
|
||||
instance.setContent(html);
|
||||
}
|
||||
}).finally(() => {
|
||||
instance.enable();
|
||||
instance.show();
|
||||
});
|
||||
}
|
||||
}, function(instance) {
|
||||
});
|
||||
}
|
||||
let selectedAnnoteEl;
|
||||
const selectorForAnnotation = ( cell, annotation) => {
|
||||
let cellAttr = 'data-code-cell="' + cell + '"';
|
||||
let lineAttr = 'data-code-annotation="' + annotation + '"';
|
||||
const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
|
||||
return selector;
|
||||
}
|
||||
const selectCodeLines = (annoteEl) => {
|
||||
const doc = window.document;
|
||||
const targetCell = annoteEl.getAttribute("data-target-cell");
|
||||
const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
|
||||
const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
|
||||
const lines = annoteSpan.getAttribute("data-code-lines").split(",");
|
||||
const lineIds = lines.map((line) => {
|
||||
return targetCell + "-" + line;
|
||||
})
|
||||
let top = null;
|
||||
let height = null;
|
||||
let parent = null;
|
||||
if (lineIds.length > 0) {
|
||||
//compute the position of the single el (top and bottom and make a div)
|
||||
const el = window.document.getElementById(lineIds[0]);
|
||||
top = el.offsetTop;
|
||||
height = el.offsetHeight;
|
||||
parent = el.parentElement.parentElement;
|
||||
if (lineIds.length > 1) {
|
||||
const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
|
||||
const bottom = lastEl.offsetTop + lastEl.offsetHeight;
|
||||
height = bottom - top;
|
||||
}
|
||||
if (top !== null && height !== null && parent !== null) {
|
||||
// cook up a div (if necessary) and position it
|
||||
let div = window.document.getElementById("code-annotation-line-highlight");
|
||||
if (div === null) {
|
||||
div = window.document.createElement("div");
|
||||
div.setAttribute("id", "code-annotation-line-highlight");
|
||||
div.style.position = 'absolute';
|
||||
parent.appendChild(div);
|
||||
}
|
||||
div.style.top = top - 2 + "px";
|
||||
div.style.height = height + 4 + "px";
|
||||
div.style.left = 0;
|
||||
let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
|
||||
if (gutterDiv === null) {
|
||||
gutterDiv = window.document.createElement("div");
|
||||
gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
|
||||
gutterDiv.style.position = 'absolute';
|
||||
const codeCell = window.document.getElementById(targetCell);
|
||||
const gutter = codeCell.querySelector('.code-annotation-gutter');
|
||||
gutter.appendChild(gutterDiv);
|
||||
}
|
||||
gutterDiv.style.top = top - 2 + "px";
|
||||
gutterDiv.style.height = height + 4 + "px";
|
||||
}
|
||||
selectedAnnoteEl = annoteEl;
|
||||
}
|
||||
};
|
||||
const unselectCodeLines = () => {
|
||||
const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
|
||||
elementsIds.forEach((elId) => {
|
||||
const div = window.document.getElementById(elId);
|
||||
if (div) {
|
||||
div.remove();
|
||||
}
|
||||
});
|
||||
selectedAnnoteEl = undefined;
|
||||
};
|
||||
// Handle positioning of the toggle
|
||||
window.addEventListener(
|
||||
"resize",
|
||||
throttle(() => {
|
||||
elRect = undefined;
|
||||
if (selectedAnnoteEl) {
|
||||
selectCodeLines(selectedAnnoteEl);
|
||||
}
|
||||
}, 10)
|
||||
);
|
||||
function throttle(fn, ms) {
|
||||
let throttle = false;
|
||||
let timer;
|
||||
return (...args) => {
|
||||
if(!throttle) { // first call gets through
|
||||
fn.apply(this, args);
|
||||
throttle = true;
|
||||
} else { // all the others get throttled
|
||||
if(timer) clearTimeout(timer); // cancel #2
|
||||
timer = setTimeout(() => {
|
||||
fn.apply(this, args);
|
||||
timer = throttle = false;
|
||||
}, ms);
|
||||
}
|
||||
};
|
||||
}
|
||||
// Attach click handler to the DT
|
||||
const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
|
||||
for (const annoteDlNode of annoteDls) {
|
||||
annoteDlNode.addEventListener('click', (event) => {
|
||||
const clickedEl = event.target;
|
||||
if (clickedEl !== selectedAnnoteEl) {
|
||||
unselectCodeLines();
|
||||
const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
|
||||
if (activeEl) {
|
||||
activeEl.classList.remove('code-annotation-active');
|
||||
}
|
||||
selectCodeLines(clickedEl);
|
||||
clickedEl.classList.add('code-annotation-active');
|
||||
} else {
|
||||
// Unselect the line
|
||||
unselectCodeLines();
|
||||
clickedEl.classList.remove('code-annotation-active');
|
||||
}
|
||||
});
|
||||
}
|
||||
const findCites = (el) => {
|
||||
const parentEl = el.parentElement;
|
||||
if (parentEl) {
|
||||
const cites = parentEl.dataset.cites;
|
||||
if (cites) {
|
||||
return {
|
||||
el,
|
||||
cites: cites.split(' ')
|
||||
};
|
||||
} else {
|
||||
return findCites(el.parentElement)
|
||||
}
|
||||
} else {
|
||||
return undefined;
|
||||
}
|
||||
};
|
||||
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
|
||||
for (var i=0; i<bibliorefs.length; i++) {
|
||||
const ref = bibliorefs[i];
|
||||
const citeInfo = findCites(ref);
|
||||
if (citeInfo) {
|
||||
tippyHover(citeInfo.el, function() {
|
||||
var popup = window.document.createElement('div');
|
||||
citeInfo.cites.forEach(function(cite) {
|
||||
var citeDiv = window.document.createElement('div');
|
||||
citeDiv.classList.add('hanging-indent');
|
||||
citeDiv.classList.add('csl-entry');
|
||||
var biblioDiv = window.document.getElementById('ref-' + cite);
|
||||
if (biblioDiv) {
|
||||
citeDiv.innerHTML = biblioDiv.innerHTML;
|
||||
}
|
||||
popup.appendChild(citeDiv);
|
||||
});
|
||||
return popup.innerHTML;
|
||||
});
|
||||
}
|
||||
}
|
||||
});
|
||||
</script>
|
||||
</div> <!-- /content -->
|
||||
|
||||
|
||||
|
||||
|
||||
</body></html>
|
||||
@@ -1,146 +1,106 @@
|
||||
# JupyterHub Configuration with OrbStack on Mac (all in Docker)
|
||||
# OBIJupyterHub - the DNA Metabarcoding Learning Server
|
||||
|
||||
## Prerequisites
|
||||
## Intended use
|
||||
|
||||
You must have docker running on your computer
|
||||
This project packages the MetabarcodingSchool training lab into one reproducible bundle. You get Python, R, and Bash kernels, a Quarto-built course website, and preconfigured admin/student accounts, so onboarding a class is a single command instead of a day of setup. Everything runs locally on a single machine, student work persists between sessions, and `./start-jupyterhub.sh` takes care of building images, rendering the site, preparing volumes, and bringing JupyterHub up at `http://localhost:8888`. Defaults (accounts, passwords, volumes) live in the repo so instructors can tweak them quickly.
|
||||
|
||||
- On MacOS, [OrbStack](https://orbstack.dev/ "A Docker implementation optimised for MacOS") is recommanded
|
||||
## Prerequisites (with quick checks)
|
||||
|
||||
## Installation Steps
|
||||
You need Docker, Docker Compose, Quarto, and Python 3 available on the machine that will host the lab.
|
||||
|
||||
### 1. Create Directory Structure
|
||||
- macOS: install [OrbStack](https://orbstack.dev/) (recommended) or Docker Desktop; both ship Docker Engine and Compose.
|
||||
- Linux: install Docker Engine and the Compose plugin from your distribution (e.g., `sudo apt install docker.io docker-compose-plugin`) or from Docker’s official packages.
|
||||
- Windows: install Docker Desktop with the WSL2 backend enabled.
|
||||
- Quarto CLI: get installers from <https://quarto.org/docs/get-started/>.
|
||||
- Python 3: any recent version is fine (only the standard library is used).
|
||||
|
||||
Verify from a terminal; if a command is missing, install it before moving on:
|
||||
|
||||
```bash
|
||||
docker --version
|
||||
docker compose version # or: docker-compose --version
|
||||
quarto --version
|
||||
python3 --version
|
||||
```
|
||||
|
||||
## How the startup script works
|
||||
|
||||
`./start-jupyterhub.sh` is the single entry point. It builds the Docker images, renders the course website, prepares the volume folders, and starts the stack. Internally it:
|
||||
|
||||
- creates the `jupyterhub_volumes/` tree (caddy, course, shared, users, web…)
|
||||
- builds `jupyterhub-student` and `jupyterhub-hub` images
|
||||
- renders the Quarto site from `web_src/`, generates PDF galleries and `pages.json`, and copies everything into `jupyterhub_volumes/web/`
|
||||
- runs `docker-compose up -d --remove-orphans`
|
||||
|
||||
You can tailor what it does with a few flags:
|
||||
|
||||
- `--no-build` (or `--offline`): skip Docker image builds and reuse existing images (useful when offline).
|
||||
- `--force-rebuild`: rebuild images without cache.
|
||||
- `--stop-server`: stop the stack and remove student containers, then exit.
|
||||
- `--update-lectures`: rebuild the course website only (no Docker stop/start).
|
||||
- `--build-obidoc`: force rebuilding the obidoc documentation (auto-built if empty; skipped in offline mode).
|
||||
|
||||
## Installation and first run
|
||||
|
||||
1) Clone the project:
|
||||
|
||||
```bash
|
||||
git clone https://forge.metabarcoding.org/MetabarcodingSchool/OBIJupyterHub.git
|
||||
```
|
||||
|
||||
Enter into the `OBIJupyterHub` directory
|
||||
|
||||
```bash
|
||||
cd OBIJupyterHub
|
||||
```
|
||||
|
||||
#### File Structure
|
||||
|
||||
Your `OBIJupyterHub` directory should contain:
|
||||
2) (Optional) glance at the structure you’ll populate:
|
||||
|
||||
```
|
||||
OBIJupyterHub
|
||||
├── start-jupyterhub.sh - The script used to setup and start the server
|
||||
├── obijupyterhub - The files describing the docker images and the stack
|
||||
│ ├── Caddyfile
|
||||
├── start-jupyterhub.sh - single entry point (build + render + start)
|
||||
├── obijupyterhub - Docker images and stack definitions
|
||||
│ ├── docker-compose.yml
|
||||
│ ├── Dockerfile
|
||||
│ ├── Dockerfile.hub
|
||||
│ ├── jupyterhub_config.py
|
||||
│ ├── sftpgo_config.json
|
||||
│ └── start-notebook.sh
|
||||
├── jupyterhub_volumes - The directory containing the docker volumes
|
||||
│ ├── caddy
|
||||
│ ├── course - Read only volume mounted on every student container
|
||||
│ │ ├── bin
|
||||
│ │ └── R_packages
|
||||
│ ├── jupyterhub
|
||||
│ ├── shared - Read write volume shared in every student container
|
||||
│ ├── users
|
||||
│ └── web
|
||||
│ ├── img
|
||||
│ │ └── welcome_metabar.webp
|
||||
│ ├── index.html
|
||||
│ └── pages
|
||||
├── Readme.md - This documentation
|
||||
├── tools
|
||||
│ ├── generate_pages_json.py
|
||||
│ └── install_packages.sh
|
||||
└─── web_src - The quarto document sources used to build the web site
|
||||
├── _output
|
||||
├── _quarto.yml
|
||||
├── 00_home.qmd
|
||||
├── lectures
|
||||
│ └── computers
|
||||
│ └── regex
|
||||
│ ├── lecture_regex.qmd
|
||||
│ ├── slides_regex.qmd
|
||||
│ └── slides.css
|
||||
└── scripts
|
||||
└── copy-to-web.sh
|
||||
│ └── jupyterhub_config.py
|
||||
├── jupyterhub_volumes - data persisted on the host
|
||||
│ ├── course - read-only for students (notebooks, data, bin, R packages)
|
||||
│ ├── shared - shared read/write space for everyone
|
||||
│ ├── users - per-user persistent data
|
||||
│ └── web - rendered course website
|
||||
└── web_src - Quarto sources for the course website
|
||||
```
|
||||
|
||||
### 2. Start JupyterHub
|
||||
3) Prepare course materials (optional before first run):
|
||||
- Put notebooks, datasets, scripts, binaries, or PDFs for students under `jupyterhub_volumes/course/`. They will appear read-only at `/home/jovyan/work/course/`.
|
||||
- For collaborative work, drop files in `jupyterhub_volumes/shared/` (read/write for all at `/home/jovyan/work/shared/`).
|
||||
- Edit or add Quarto sources in `web_src/` to update the course website; the script will render them.
|
||||
|
||||
From the terminal, in the `OBIJupyterHub` directory, run the following command:
|
||||
4) Start everything (build + render + launch):
|
||||
|
||||
```bash
|
||||
./start-jupyterhub.sh
|
||||
```
|
||||
|
||||
### 3. Access JupyterHub
|
||||
5) Access JupyterHub in a browser at `http://localhost:8888`.
|
||||
|
||||
Open your browser and go to: **http://localhost:8888**
|
||||
|
||||
You can log in as a student with any username and password: `metabar2025`
|
||||
|
||||
## Useful Commands
|
||||
|
||||
### View JupyterHub logs
|
||||
6) Stop the stack when you’re done (run from `obijupyterhub/`):
|
||||
|
||||
```bash
|
||||
cd obijupyterhub
|
||||
docker-compose logs -f jupyterhub
|
||||
```
|
||||
|
||||
### View all containers (hub + students)
|
||||
|
||||
``` bash
|
||||
docker ps | grep jupyterhub
|
||||
```
|
||||
|
||||
### Stop JupyterHub
|
||||
|
||||
``` bash
|
||||
cd obijupyterhub
|
||||
docker-compose down
|
||||
```
|
||||
|
||||
### Restart JupyterHub (after config modification)
|
||||
### Operating the stack (one command, a few options)
|
||||
|
||||
``` bash
|
||||
cd obijupyterhub
|
||||
docker-compose restart jupyterhub
|
||||
```
|
||||
- Start or rebuild: `./start-jupyterhub.sh` (rebuilds images, regenerates the website, starts the stack).
|
||||
- Start without rebuilding images (offline): `./start-jupyterhub.sh --no-build`
|
||||
- Force rebuild without cache: `./start-jupyterhub.sh --force-rebuild`
|
||||
- Stop only: `./start-jupyterhub.sh --stop-server`
|
||||
- Rebuild website only (no Docker stop/start): `./start-jupyterhub.sh --update-lectures`
|
||||
- Rebuild obidoc docs: `./start-jupyterhub.sh --build-obidoc` (also builds automatically if `jupyterhub_volumes/web/obidoc` is empty; skipped in offline mode)
|
||||
- Access at `http://localhost:8888` (students: any username / password `metabar2025`; admin: `admin` / `admin2025`).
|
||||
- Check logs from `obijupyterhub/` with `docker-compose logs -f jupyterhub`.
|
||||
- Stop with `docker-compose down` (from `obijupyterhub/`). Rerun `./start-jupyterhub.sh` to start again or after config changes.
|
||||
|
||||
### View logs for a specific student
|
||||
## Managing shared data
|
||||
|
||||
``` bash
|
||||
docker logs jupyter-<username>
|
||||
```
|
||||
|
||||
Replace `<username>` by the actual username of the student.
|
||||
|
||||
### Clean up after lab
|
||||
|
||||
``` bash
|
||||
# Stop and remove all containers
|
||||
cd obijupyterhub
|
||||
docker-compose down
|
||||
|
||||
# Remove student containers
|
||||
docker ps -a | grep jupyter- | awk '{print $1}' | xargs docker rm -f
|
||||
|
||||
# Remove volumes (WARNING: deletes student data)
|
||||
docker volume ls | grep jupyterhub-user | awk '{print $2}' | xargs docker volume rm
|
||||
|
||||
# Clean everything (containers + volumes + network)
|
||||
docker-compose down -v
|
||||
docker ps -a | grep jupyter- | awk '{print $1}' | xargs docker rm -f
|
||||
docker volume prune -f
|
||||
```
|
||||
|
||||
## Managing Shared Data
|
||||
|
||||
### Directory Structure for Each Student
|
||||
|
||||
Each student will see this directory structure in their JupyterLab (everything under `work/` is persistent):
|
||||
Each student lands in `/home/jovyan/work/` with three key areas: their own files, a shared space, and a read-only course space. Everything under `work/` is persisted on the host in `jupyterhub_volumes`.
|
||||
|
||||
```
|
||||
work/ # Personal workspace root (persistent)
|
||||
@@ -153,42 +113,22 @@ work/ # Personal workspace root (persistent)
|
||||
└── [course materials] # Your course files
|
||||
```
|
||||
|
||||
**R Package Priority:**
|
||||
|
||||
1. R checks `work/R_packages/` first (personal, writable)
|
||||
1. Then `work/course/R_packages/` (shared, read-only, installed by prof)
|
||||
1. Then system libraries
|
||||
|
||||
**Important:** Everything is under `work/`, so all student files are automatically saved in their persistent volume.
|
||||
R looks for packages in this order: personal `work/R_packages/`, then shared `work/course/R_packages/`, then system libraries. Because everything lives under `work/`, student files survive restarts.
|
||||
|
||||
### User Accounts
|
||||
|
||||
**Admin Account:**
|
||||
|
||||
- Username: `admin`
|
||||
- Password: `admin2025` (change in docker-compose.yml: `JUPYTERHUB_ADMIN_PASSWORD`)
|
||||
- Can write to `course/` directory
|
||||
|
||||
**Student Accounts:**
|
||||
|
||||
- Username: any name
|
||||
- Password: `metabar2025` (change in docker-compose.yml: `JUPYTERHUB_PASSWORD`)
|
||||
- Read-only access to `course/` directory
|
||||
Defaults are defined in `obijupyterhub/docker-compose.yml`: admin (`admin` / `admin2025`) with write access to `course/`, and students (any username, password `metabar2025`) with read-only access to `course/`. Adjust `JUPYTERHUB_ADMIN_PASSWORD` and `JUPYTERHUB_PASSWORD` there, then rerun `./start-jupyterhub.sh`.
|
||||
|
||||
### Installing R Packages (Admin Only)
|
||||
|
||||
**From your Mac (recommended):**
|
||||
From the host, install shared R packages into `course/R_packages/`:
|
||||
|
||||
``` bash
|
||||
# Install packages
|
||||
tools/install_packages.sh reshape2 plotly knitr
|
||||
```
|
||||
|
||||
This script: - Installs packages in the `course/R_packages/` directory - All students can use them (read-only) - No need to rebuild the image
|
||||
|
||||
**Students can also install their own packages:**
|
||||
|
||||
Students can install packages in their personal `work/R_packages/`:
|
||||
Students can install their own packages into their personal `work/R_packages/`:
|
||||
|
||||
```r
|
||||
# Install in personal library (each student has their own)
|
||||
@@ -223,43 +163,9 @@ list.files("/home/jovyan/work/R_packages")
|
||||
list.files("/home/jovyan/work/course/R_packages")
|
||||
```
|
||||
|
||||
### Deposit Files for Course
|
||||
### Deposit or retrieve course and student files
|
||||
|
||||
To put files in the `course/` directory (accessible read-only):
|
||||
|
||||
``` bash
|
||||
# Create a temporary directory
|
||||
mkdir -p ~/jupyterhub-tp/course-files
|
||||
|
||||
# Copy your files into it
|
||||
cp my_notebooks.ipynb ~/jupyterhub-tp/course-files/
|
||||
cp my_data.csv ~/jupyterhub-tp/course-files/
|
||||
|
||||
# Copy into Docker volume
|
||||
docker run --rm \
|
||||
-v jupyterhub-course:/target \
|
||||
-v ~/jupyterhub-tp/course-files:/source \
|
||||
alpine sh -c "cp -r /source/* /target/"
|
||||
```
|
||||
|
||||
### Retrieve Student Work
|
||||
|
||||
``` bash
|
||||
# List user volumes
|
||||
docker volume ls | grep 'obijupyterhub_user-'
|
||||
|
||||
# Copy files from a specific student
|
||||
docker run --rm \
|
||||
-v obijupyterhub_user-alice:/source \
|
||||
-v ~/submissions:/target \
|
||||
alpine sh -c "cp -r /source/* /target/alice/"
|
||||
|
||||
# Copy all shared work
|
||||
docker run --rm \
|
||||
-v obijupyterhub_shared:/source \
|
||||
-v ~/submissions/shared:/target \
|
||||
alpine sh -c "cp -r /source/* /target/"
|
||||
```
|
||||
On the host, place course files in `jupyterhub_volumes/course/` (they appear read-only to students), shared files in `jupyterhub_volumes/shared/`, and collect student work from `jupyterhub_volumes/users/`.
|
||||
|
||||
## User Management
|
||||
|
||||
@@ -299,11 +205,7 @@ Modify the `Dockerfile` (before `USER ${NB_UID}`):
|
||||
RUN R -e "install.packages(c('your_package'), repos='http://cran.rstudio.com/')"
|
||||
```
|
||||
|
||||
Then restart the server (it rebuilds the images if needed):
|
||||
|
||||
```bash
|
||||
./start-jupyterhub.sh
|
||||
```
|
||||
Then rerun `./start-jupyterhub.sh` to rebuild and restart.
|
||||
|
||||
### Add Python Packages
|
||||
|
||||
@@ -313,14 +215,7 @@ Add to the `Dockerfile` (before `USER ${NB_UID}`):
|
||||
RUN pip install numpy pandas matplotlib seaborn
|
||||
```
|
||||
|
||||
### Distribute Files to Students
|
||||
|
||||
Create a `files_lab/` directory and add to the `Dockerfile`:
|
||||
|
||||
``` dockerfile
|
||||
COPY files_lab/ /home/${NB_USER}/lab/
|
||||
RUN chown -R ${NB_UID}:${NB_GID} /home/${NB_USER}/lab
|
||||
```
|
||||
Then rerun `./start-jupyterhub.sh` to rebuild and restart.
|
||||
|
||||
### Change Port (if 8000 is occupied)
|
||||
|
||||
@@ -341,25 +236,15 @@ ports:
|
||||
|
||||
## Troubleshooting
|
||||
|
||||
**Error "Cannot connect to Docker daemon"**:
|
||||
|
||||
- Check that OrbStack is running
|
||||
- Verify the socket exists: `ls -la /var/run/docker.sock`
|
||||
|
||||
**Student containers don't start**:
|
||||
|
||||
- Check logs: `docker-compose logs jupyterhub`
|
||||
- Verify student image exists: `docker images | grep jupyterhub-student`
|
||||
|
||||
**Port 8000 already in use**:
|
||||
|
||||
- Change port in `docker-compose.yml`
|
||||
- Docker daemon unavailable: make sure OrbStack/Docker Desktop/daemon is running; verify `/var/run/docker.sock` exists.
|
||||
- Student containers do not start: check `docker-compose logs jupyterhub` and confirm the images exist with `docker images | grep jupyterhub-student`.
|
||||
- Port conflict: change the published port in `docker-compose.yml`.
|
||||
|
||||
|
||||
**I want to start from scratch**:
|
||||
|
||||
``` bash
|
||||
push obijupyterhub
|
||||
pushd obijupyterhub
|
||||
docker-compose down -v
|
||||
docker rmi jupyterhub-hub jupyterhub-student
|
||||
popd
|
||||
|
||||
+12
@@ -0,0 +1,12 @@
|
||||
/*!
|
||||
* Bootstrap v5.3.1 (https://getbootstrap.com/)
|
||||
* Copyright 2011-2023 The Bootstrap Authors
|
||||
* Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
|
||||
*/:root,[data-bs-theme=light]{--bs-blue: #0d6efd;--bs-indigo: #6610f2;--bs-purple: #6f42c1;--bs-pink: #d63384;--bs-red: #dc3545;--bs-orange: #fd7e14;--bs-yellow: #ffc107;--bs-green: #198754;--bs-teal: #20c997;--bs-cyan: #0dcaf0;--bs-black: #000;--bs-white: #ffffff;--bs-gray: #6c757d;--bs-gray-dark: #343a40;--bs-gray-100: #f8f9fa;--bs-gray-200: #e9ecef;--bs-gray-300: #dee2e6;--bs-gray-400: #ced4da;--bs-gray-500: #adb5bd;--bs-gray-600: #6c757d;--bs-gray-700: #495057;--bs-gray-800: #343a40;--bs-gray-900: #212529;--bs-default: #dee2e6;--bs-primary: #0d6efd;--bs-secondary: #6c757d;--bs-success: #198754;--bs-info: #0dcaf0;--bs-warning: #ffc107;--bs-danger: #dc3545;--bs-light: #f8f9fa;--bs-dark: #212529;--bs-default-rgb: 222, 226, 230;--bs-primary-rgb: 13, 110, 253;--bs-secondary-rgb: 108, 117, 125;--bs-success-rgb: 25, 135, 84;--bs-info-rgb: 13, 202, 240;--bs-warning-rgb: 255, 193, 7;--bs-danger-rgb: 220, 53, 69;--bs-light-rgb: 248, 249, 250;--bs-dark-rgb: 33, 37, 41;--bs-primary-text-emphasis: rgb(5.2, 44, 101.2);--bs-secondary-text-emphasis: rgb(43.2, 46.8, 50);--bs-success-text-emphasis: rgb(10, 54, 33.6);--bs-info-text-emphasis: rgb(5.2, 80.8, 96);--bs-warning-text-emphasis: rgb(102, 77.2, 2.8);--bs-danger-text-emphasis: rgb(88, 21.2, 27.6);--bs-light-text-emphasis: #495057;--bs-dark-text-emphasis: #495057;--bs-primary-bg-subtle: rgb(206.6, 226, 254.6);--bs-secondary-bg-subtle: rgb(225.6, 227.4, 229);--bs-success-bg-subtle: rgb(209, 231, 220.8);--bs-info-bg-subtle: rgb(206.6, 244.4, 252);--bs-warning-bg-subtle: rgb(255, 242.6, 205.4);--bs-danger-bg-subtle: rgb(248, 214.6, 217.8);--bs-light-bg-subtle: rgb(251.5, 252, 252.5);--bs-dark-bg-subtle: #ced4da;--bs-primary-border-subtle: rgb(158.2, 197, 254.2);--bs-secondary-border-subtle: rgb(196.2, 199.8, 203);--bs-success-border-subtle: rgb(163, 207, 186.6);--bs-info-border-subtle: rgb(158.2, 233.8, 249);--bs-warning-border-subtle: rgb(255, 230.2, 155.8);--bs-danger-border-subtle: rgb(241, 174.2, 180.6);--bs-light-border-subtle: #e9ecef;--bs-dark-border-subtle: #adb5bd;--bs-white-rgb: 255, 255, 255;--bs-black-rgb: 0, 0, 0;--bs-font-sans-serif: system-ui, -apple-system, "Segoe UI", Roboto, "Helvetica Neue", "Noto Sans", "Liberation Sans", Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol", "Noto Color Emoji";--bs-font-monospace: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace;--bs-gradient: linear-gradient(180deg, rgba(255, 255, 255, 0.15), rgba(255, 255, 255, 0));--bs-root-font-size: 17px;--bs-body-font-family: system-ui, -apple-system, "Segoe UI", Roboto, "Helvetica Neue", "Noto Sans", "Liberation Sans", Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol", "Noto Color Emoji";--bs-body-font-size:1rem;--bs-body-font-weight: 400;--bs-body-line-height: 1.5;--bs-body-color: #212529;--bs-body-color-rgb: 33, 37, 41;--bs-body-bg: #ffffff;--bs-body-bg-rgb: 255, 255, 255;--bs-emphasis-color: #000;--bs-emphasis-color-rgb: 0, 0, 0;--bs-secondary-color: rgba(33, 37, 41, 0.75);--bs-secondary-color-rgb: 33, 37, 41;--bs-secondary-bg: #e9ecef;--bs-secondary-bg-rgb: 233, 236, 239;--bs-tertiary-color: rgba(33, 37, 41, 0.5);--bs-tertiary-color-rgb: 33, 37, 41;--bs-tertiary-bg: #f8f9fa;--bs-tertiary-bg-rgb: 248, 249, 250;--bs-heading-color: inherit;--bs-link-color: #0d6efd;--bs-link-color-rgb: 13, 110, 253;--bs-link-decoration: underline;--bs-link-hover-color: rgb(10.4, 88, 202.4);--bs-link-hover-color-rgb: 10, 88, 202;--bs-code-color: #7d12ba;--bs-highlight-bg: rgb(255, 242.6, 205.4);--bs-border-width: 1px;--bs-border-style: solid;--bs-border-color: rgb(221.7, 222.3, 222.9);--bs-border-color-translucent: rgba(0, 0, 0, 0.175);--bs-border-radius: 0.375rem;--bs-border-radius-sm: 0.25rem;--bs-border-radius-lg: 0.5rem;--bs-border-radius-xl: 1rem;--bs-border-radius-xxl: 2rem;--bs-border-radius-2xl: var(--bs-border-radius-xxl);--bs-border-radius-pill: 50rem;--bs-box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.15);--bs-box-shadow-sm: 0 0.125rem 0.25rem rgba(0, 0, 0, 0.075);--bs-box-shadow-lg: 0 1rem 3rem rgba(0, 0, 0, 0.175);--bs-box-shadow-inset: inset 0 1px 2px rgba(0, 0, 0, 0.075);--bs-focus-ring-width: 0.25rem;--bs-focus-ring-opacity: 0.25;--bs-focus-ring-color: rgba(13, 110, 253, 0.25);--bs-form-valid-color: #198754;--bs-form-valid-border-color: #198754;--bs-form-invalid-color: #dc3545;--bs-form-invalid-border-color: #dc3545}[data-bs-theme=dark]{color-scheme:dark;--bs-body-color: #dee2e6;--bs-body-color-rgb: 222, 226, 230;--bs-body-bg: #212529;--bs-body-bg-rgb: 33, 37, 41;--bs-emphasis-color: #ffffff;--bs-emphasis-color-rgb: 255, 255, 255;--bs-secondary-color: rgba(222, 226, 230, 0.75);--bs-secondary-color-rgb: 222, 226, 230;--bs-secondary-bg: #343a40;--bs-secondary-bg-rgb: 52, 58, 64;--bs-tertiary-color: rgba(222, 226, 230, 0.5);--bs-tertiary-color-rgb: 222, 226, 230;--bs-tertiary-bg: rgb(42.5, 47.5, 52.5);--bs-tertiary-bg-rgb: 43, 48, 53;--bs-primary-text-emphasis: rgb(109.8, 168, 253.8);--bs-secondary-tLine truncated
|
||||
*
|
||||
* ansi colors from IPython notebook's
|
||||
*
|
||||
* we also add `bright-[color]-` synonyms for the `-[color]-intense` classes since
|
||||
* that seems to be what ansi_up emits
|
||||
*
|
||||
*/.ansi-black-fg{color:#3e424d}.ansi-black-bg{background-color:#3e424d}.ansi-black-intense-black,.ansi-bright-black-fg{color:#282c36}.ansi-black-intense-black,.ansi-bright-black-bg{background-color:#282c36}.ansi-red-fg{color:#e75c58}.ansi-red-bg{background-color:#e75c58}.ansi-red-intense-red,.ansi-bright-red-fg{color:#b22b31}.ansi-red-intense-red,.ansi-bright-red-bg{background-color:#b22b31}.ansi-green-fg{color:#00a250}.ansi-green-bg{background-color:#00a250}.ansi-green-intense-green,.ansi-bright-green-fg{color:#007427}.ansi-green-intense-green,.ansi-bright-green-bg{background-color:#007427}.ansi-yellow-fg{color:#ddb62b}.ansi-yellow-bg{background-color:#ddb62b}.ansi-yellow-intense-yellow,.ansi-bright-yellow-fg{color:#b27d12}.ansi-yellow-intense-yellow,.ansi-bright-yellow-bg{background-color:#b27d12}.ansi-blue-fg{color:#208ffb}.ansi-blue-bg{background-color:#208ffb}.ansi-blue-intense-blue,.ansi-bright-blue-fg{color:#0065ca}.ansi-blue-intense-blue,.ansi-bright-blue-bg{background-color:#0065ca}.ansi-magenta-fg{color:#d160c4}.ansi-magenta-bg{background-color:#d160c4}.ansi-magenta-intense-magenta,.ansi-bright-magenta-fg{color:#a03196}.ansi-magenta-intense-magenta,.ansi-bright-magenta-bg{background-color:#a03196}.ansi-cyan-fg{color:#60c6c8}.ansi-cyan-bg{background-color:#60c6c8}.ansi-cyan-intense-cyan,.ansi-bright-cyan-fg{color:#258f8f}.ansi-cyan-intense-cyan,.ansi-bright-cyan-bg{background-color:#258f8f}.ansi-white-fg{color:#c5c1b4}.ansi-white-bg{background-color:#c5c1b4}.ansi-white-intense-white,.ansi-bright-white-fg{color:#a1a6b2}.ansi-white-intense-white,.ansi-bright-white-bg{background-color:#a1a6b2}.ansi-default-inverse-fg{color:#fff}.ansi-default-inverse-bg{background-color:#000}.ansi-bold{font-weight:bold}.ansi-underline{text-decoration:underline}:root{--quarto-body-bg: #ffffff;--quarto-body-color: #212529;--quarto-text-muted: rgba(33, 37, 41, 0.75);--quarto-border-color: rgb(221.7, 222.3, 222.9);--quarto-border-width: 1px;--quarto-border-radius: 0.375rem}table.gt_table{color:var(--quarto-body-color);font-size:1em;width:100%;background-color:rgba(0,0,0,0);border-top-width:inherit;border-bottom-width:inherit;border-color:var(--quarto-border-color)}table.gt_table th.gt_column_spanner_outer{color:var(--quarto-body-color);background-color:rgba(0,0,0,0);border-top-width:inherit;border-bottom-width:inherit;border-color:var(--quarto-border-color)}table.gt_table th.gt_col_heading{color:var(--quarto-body-color);font-weight:bold;background-color:rgba(0,0,0,0)}table.gt_table thead.gt_col_headings{border-bottom:1px solid currentColor;border-top-width:inherit;border-top-color:var(--quarto-border-color)}table.gt_table thead.gt_col_headings:not(:first-child){border-top-width:1px;border-top-color:var(--quarto-border-color)}table.gt_table td.gt_row{border-bottom-width:1px;border-bottom-color:var(--quarto-border-color);border-top-width:0px}table.gt_table tbody.gt_table_body{border-top-width:1px;border-bottom-width:1px;border-bottom-color:var(--quarto-border-color);border-top-color:currentColor}div.columns{display:initial;gap:initial}div.column{display:inline-block;overflow-x:initial;vertical-align:top;width:50%}.code-annotation-tip-content{word-wrap:break-word}.code-annotation-container-hidden{display:none !important}dl.code-annotation-container-grid{display:grid;grid-template-columns:min-content auto}dl.code-annotation-container-grid dt{grid-column:1}dl.code-annotation-container-grid dd{grid-column:2}pre.sourceCode.code-annotation-code{padding-right:0}code.sourceCode .code-annotation-anchor{z-index:100;position:relative;float:right;background-color:rgba(0,0,0,0)}input[type=checkbox]{margin-right:.5ch}:root{--mermaid-bg-color: #ffffff;--mermaid-edge-color: #6c757d;--mermaid-node-fg-color: #212529;--mermaid-fg-color: #212529;--mermaid-fg-color--lighter: rgb(55.7432432432, 62.5, 69.2567567568);--mermaid-fg-color--lightest: rgb(78.4864864865, 88, 97.5135135135);--mermaid-font-family: system-ui, -apple-system, Segoe UI, Roboto, Helvetica Neue, Noto Sans, Liberation Sans, Arial, sans-serif, Apple Color Emoji, Segoe UI Emoji, Segoe UI Symbol, Noto Color Emoji;--mermaid-label-bg-color: #ffffff;--mermaid-label-fg-color: #0d6efd;--mermaid-node-bg-color: rgba(13, 110, 253, 0.1);--mermaid-node-fg-color: #212529}@media print{:root{font-size:11pt}#quarto-sidebar,#TOC,.nav-page{display:none}.page-columns .content{grid-column-start:page-start}.fixed-top{position:relative}.panel-caption,.figure-caption,figcaption{color:#666}}.code-copy-button{position:absolute;top:0;right:0;border:0;margin-top:5px;margin-right:5px;background-color:rgba(0,0,0,0);z-index:3}.code-copy-button-tooltip{font-size:.75em}div.code-copy-outer-scaffold:hover>.code-copy-button>.bi::before{display:inline-block;height:1rem;width:1rem;content:"";vertical-align:-0.125em;background-image:url('data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="rgb(94, 94, 94)" viewBox="0 0 16 16"><path d="M4 1.5H3a2 2 0 0 0-2 2V14a2 2 0 0 0 2 2h10a2 2 0Line truncated
|
||||
+2106
File diff suppressed because it is too large.
Load diff
Binary file not shown.
@@ -0,0 +1,7 @@
|
||||
/*!
|
||||
* Bootstrap v5.3.1 (https://getbootstrap.com/)
|
||||
* Copyright 2011-2023 The Bootstrap Authors (https://github.com/twbs/bootstrap/graphs/contributors)
|
||||
* Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
|
||||
*/
|
||||
!function(t,e){"object"==typeof exports&&"undefined"!=typeof module?module.exports=e():"function"==typeof define&&define.amd?define(e):(t="undefined"!=typeof globalThis?globalThis:t||self).bootstrap=e()}(this,(function(){"use strict";const t=new Map,e={set(e,i,n){t.has(e)||t.set(e,new Map);const s=t.get(e);s.has(i)||0===s.size?s.set(i,n):console.error(`Bootstrap doesn't allow more than one instance per element. Bound instance: ${Array.from(s.keys())[0]}.`)},get:(e,i)=>t.has(e)&&t.get(e).get(i)||null,remove(e,i){if(!t.has(e))return;const n=t.get(e);n.delete(i),0===n.size&&t.delete(e)}},i="transitionend",n=t=>(t&&window.CSS&&window.CSS.escape&&(t=t.replace(/#([^\s"#']+)/g,((t,e)=>`#${CSS.escape(e)}`))),t),s=t=>{t.dispatchEvent(new Event(i))},o=t=>!(!t||"object"!=typeof t)&&(void 0!==t.jquery&&(t=t[0]),void 0!==t.nodeType),r=t=>o(t)?t.jquery?t[0]:t:"string"==typeof t&&t.length>0?document.querySelector(n(t)):null,a=t=>{if(!o(t)||0===t.getClientRects().length)return!1;const e="visible"===getComputedStyle(t).getPropertyValue("visibility"),i=t.closest("details:not([open])");if(!i)return e;if(i!==t){const e=t.closest("summary");if(e&&e.parentNode!==i)return!1;if(null===e)return!1}return e},l=t=>!t||t.nodeType!==Node.ELEMENT_NODE||!!t.classList.contains("disabled")||(void 0!==t.disabled?t.disabled:t.hasAttribute("disabled")&&"false"!==t.getAttribute("disabled")),c=t=>{if(!document.documentElement.attachShadow)return null;if("function"==typeof t.getRootNode){const e=t.getRootNode();return e instanceof ShadowRoot?e:null}return t instanceof ShadowRoot?t:t.parentNode?c(t.parentNode):null},h=()=>{},d=t=>{t.offsetHeight},u=()=>window.jQuery&&!document.body.hasAttribute("data-bs-no-jquery")?window.jQuery:null,f=[],p=()=>"rtl"===document.documentElement.dir,m=t=>{var e;e=()=>{const e=u();if(e){const i=t.NAME,n=e.fn[i];e.fn[i]=t.jQueryInterface,e.fn[i].Constructor=t,e.fn[i].noConflict=()=>(e.fn[i]=n,t.jQueryInterface)}},"loading"===document.readyState?(f.length||document.addEventListener("DOMContentLoaded",(()=>{for(const t of f)t()})),f.push(e)):e()},g=(t,e=[],i=t)=>"function"==typeof t?t(...e):i,_=(t,e,n=!0)=>{if(!n)return void g(t);const o=(t=>{if(!t)return 0;let{transitionDuration:e,transitionDelay:i}=window.getComputedStyle(t);const n=Number.parseFloat(e),s=Number.parseFloat(i);return n||s?(e=e.split(",")[0],i=i.split(",")[0],1e3*(Number.parseFloat(e)+Number.parseFloat(i))):0})(e)+5;let r=!1;const a=({target:n})=>{n===e&&(r=!0,e.removeEventListener(i,a),g(t))};e.addEventListener(i,a),setTimeout((()=>{r||s(e)}),o)},b=(t,e,i,n)=>{const s=t.length;let o=t.indexOf(e);return-1===o?!i&&n?t[s-1]:t[0]:(o+=i?1:-1,n&&(o=(o+s)%s),t[Math.max(0,Math.min(o,s-1))])},v=/[^.]*(?=\..*)\.|.*/,y=/\..*/,w=/::\d+$/,A={};let E=1;const T={mouseenter:"mouseover",mouseleave:"mouseout"},C=new Set(["click","dblclick","mouseup","mousedown","contextmenu","mousewheel","DOMMouseScroll","mouseover","mouseout","mousemove","selectstart","selectend","keydown","keypress","keyup","orientationchange","touchstart","touchmove","touchend","touchcancel","pointerdown","pointermove","pointerup","pointerleave","pointercancel","gesturestart","gesturechange","gestureend","focus","blur","change","reset","select","submit","focusin","focusout","load","unload","beforeunload","resize","move","DOMContentLoaded","readystatechange","error","abort","scroll"]);function O(t,e){return e&&`${e}::${E++}`||t.uidEvent||E++}function x(t){const e=O(t);return t.uidEvent=e,A[e]=A[e]||{},A[e]}function k(t,e,i=null){return Object.values(t).find((t=>t.callable===e&&t.delegationSelector===i))}function L(t,e,i){const n="string"==typeof e,s=n?i:e||i;let o=I(t);return C.has(o)||(o=t),[n,s,o]}function S(t,e,i,n,s){if("string"!=typeof e||!t)return;let[o,r,a]=L(e,i,n);if(e in T){const t=t=>function(e){if(!e.relatedTarget||e.relatedTarget!==e.delegateTarget&&!e.delegateTarget.contains(e.relatedTarget))return t.call(this,e)};r=t(r)}const l=x(t),c=l[a]||(l[a]={}),h=k(c,r,o?i:null);if(h)return void(h.oneOff=h.oneOff&&s);const d=O(r,e.replace(v,"")),u=o?function(t,e,i){return function n(s){const o=t.querySelectorAll(e);for(let{target:r}=s;r&&r!==this;r=r.parentNode)for(const a of o)if(a===r)return P(s,{delegateTarget:r}),n.oneOff&&N.off(t,s.type,e,i),i.apply(r,[s])}}(t,i,r):function(t,e){return function i(n){return P(n,{delegateTarget:t}),i.oneOff&&N.off(t,n.type,e),e.apply(t,[n])}}(t,r);u.delegationSelector=o?i:null,u.callable=r,u.oneOff=s,u.uidEvent=d,c[d]=u,t.addEventListener(a,u,o)}function D(t,e,i,n,s){const o=k(e[i],n,s);o&&(t.removeEventListener(i,o,Boolean(s)),delete e[i][o.uidEvent])}function $(t,e,i,n){const s=e[i]||{};for(const[o,r]of Object.entries(s))o.includes(n)&&D(t,e,i,r.callable,r.delegationSelector)}function I(t){return t=t.replace(y,""),T[t]||t}const N={on(t,e,i,n){S(t,e,i,n,!1)},one(t,e,i,n){S(t,e,i,n,!0)},off(t,e,i,n){if("string"!=typeof e||!t)return;const[s,o,r]=L(e,i,n),a=r!==e,l=x(t),c=l[r]||{},h=e.startsWith(".");if(void 0===o){if(h)for(const i of Object.keys(l))$(t,l,i,e.slLine truncated
|
||||
//# sourceMappingURL=bootstrap.bundle.min.js.map
|
||||
@@ -0,0 +1,7 @@
|
||||
/*!
|
||||
* clipboard.js v2.0.11
|
||||
* https://clipboardjs.com/
|
||||
*
|
||||
* Licensed MIT © Zeno Rocha
|
||||
*/
|
||||
!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return b}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),r=n.n(e);function c(t){try{return document.execCommand(t)}catch(t){return}}var a=function(t){t=r()(t);return c("cut"),t};function o(t,e){var n,o,t=(n=t,o="rtl"===document.documentElement.getAttribute("dir"),(t=document.createElement("textarea")).style.fontSize="12pt",t.style.border="0",t.style.padding="0",t.style.margin="0",t.style.position="absolute",t.style[o?"right":"left"]="-9999px",o=window.pageYOffset||document.documentElement.scrollTop,t.style.top="".concat(o,"px"),t.setAttribute("readonly",""),t.value=n,t);return e.container.appendChild(t),e=r()(t),c("copy"),t.remove(),e}var f=function(t){var e=1<arguments.length&&void 0!==arguments[1]?arguments[1]:{container:document.body},n="";return"string"==typeof t?n=o(t,e):t instanceof HTMLInputElement&&!["text","search","url","tel","password"].includes(null==t?void 0:t.type)?n=o(t.value,e):(n=r()(t),c("copy")),n};function l(t){return(l="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(t){return typeof t}:function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":typeof t})(t)}var s=function(){var t=0<arguments.length&&void 0!==arguments[0]?arguments[0]:{},e=t.action,n=void 0===e?"copy":e,o=t.container,e=t.target,t=t.text;if("copy"!==n&&"cut"!==n)throw new Error('Invalid "action" value, use either "copy" or "cut"');if(void 0!==e){if(!e||"object"!==l(e)||1!==e.nodeType)throw new Error('Invalid "target" value, use a valid Element');if("copy"===n&&e.hasAttribute("disabled"))throw new Error('Invalid "target" attribute. Please use "readonly" instead of "disabled" attribute');if("cut"===n&&(e.hasAttribute("readonly")||e.hasAttribute("disabled")))throw new Error('Invalid "target" attribute. You can\'t cut text from elements with "readonly" or "disabled" attributes')}return t?f(t,{container:o}):e?"cut"===n?a(e):f(e,{container:o}):void 0};function p(t){return(p="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(t){return typeof t}:function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":typeof t})(t)}function d(t,e){for(var n=0;n<e.length;n++){var o=e[n];o.enumerable=o.enumerable||!1,o.configurable=!0,"value"in o&&(o.writable=!0),Object.defineProperty(t,o.key,o)}}function y(t,e){return(y=Object.setPrototypeOf||function(t,e){return t.__proto__=e,t})(t,e)}function h(n){var o=function(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return Date.prototype.toString.call(Reflect.construct(Date,[],function(){})),!0}catch(t){return!1}}();return function(){var t,e=v(n);return t=o?(t=v(this).constructor,Reflect.construct(e,arguments,t)):e.apply(this,arguments),e=this,!(t=t)||"object"!==p(t)&&"function"!=typeof t?function(t){if(void 0!==t)return t;throw new ReferenceError("this hasn't been initialised - super() hasn't been called")}(e):t}}function v(t){return(v=Object.setPrototypeOf?Object.getPrototypeOf:function(t){return t.__proto__||Object.getPrototypeOf(t)})(t)}function m(t,e){t="data-clipboard-".concat(t);if(e.hasAttribute(t))return e.getAttribute(t)}var b=function(){!function(t,e){if("function"!=typeof e&&null!==e)throw new TypeError("Super expression must either be null or a function");t.prototype=Object.create(e&&e.prototype,{constructor:{value:t,writable:!0,configurable:!0}}),e&&y(t,e)}(r,i());var t,e,n,o=h(r);function r(t,e){var n;return function(t){if(!(t instanceof r))throw new TypeError("Cannot call a class as a function")}(this),(n=o.call(this)).resolveOptions(e),n.listenClick(t),n}return t=r,n=[{key:"copy",value:function(t){var e=1<arguments.length&&void 0!==arguments[1]?arguments[1]:{container:document.body};return f(t,e)}},{key:"cut",value:function(t){return a(t)}},{key:"isSupported",value:function(){var t=0<arguments.length&&void 0!==arguments[0]?arguments[0]:["copy","cut"],t="string"==typeof t?[t]:t,e=!!document.queryCommandSupported;return t.forEach(function(t){e=e&&!!document.queryCommandSupported(t)}),e}}],(e=[{key:"resolveOptions",value:function(){var t=0<arguments.length&&void 0!==arguments[0]?arguments[0]:{};this.action="function"==typeof t.action?t.action:this.defaultAction,this.target="function"==typeof t.target?t.target:this.defaultTarget,this.text="function"==typeof t.text?t.text:this.defaultText,this.container="object"===p(t.container)?t.container:document.body}},{key:"listenClick",value:function(t){var e=this;this.listener=u()(t,"click",function(t){return e.onClick(t)})}},{key:"onClick",value:function(t){var e=t.delegateTarget||t.currentTarget,n=this.action(e)||"copy",t=s({action:n,container:thLine truncated
|
||||
+9
@@ -0,0 +1,9 @@
|
||||
// @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&dn=expat.txt Expat
|
||||
//
|
||||
// AnchorJS - v5.0.0 - 2023-01-18
|
||||
// https://www.bryanbraun.com/anchorjs/
|
||||
// Copyright (c) 2023 Bryan Braun; Licensed MIT
|
||||
//
|
||||
// @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&dn=expat.txt Expat
|
||||
!function(A,e){"use strict";"function"==typeof define&&define.amd?define([],e):"object"==typeof module&&module.exports?module.exports=e():(A.AnchorJS=e(),A.anchors=new A.AnchorJS)}(globalThis,function(){"use strict";return function(A){function u(A){A.icon=Object.prototype.hasOwnProperty.call(A,"icon")?A.icon:"",A.visible=Object.prototype.hasOwnProperty.call(A,"visible")?A.visible:"hover",A.placement=Object.prototype.hasOwnProperty.call(A,"placement")?A.placement:"right",A.ariaLabel=Object.prototype.hasOwnProperty.call(A,"ariaLabel")?A.ariaLabel:"Anchor",A.class=Object.prototype.hasOwnProperty.call(A,"class")?A.class:"",A.base=Object.prototype.hasOwnProperty.call(A,"base")?A.base:"",A.truncate=Object.prototype.hasOwnProperty.call(A,"truncate")?Math.floor(A.truncate):64,A.titleText=Object.prototype.hasOwnProperty.call(A,"titleText")?A.titleText:""}function d(A){var e;if("string"==typeof A||A instanceof String)e=[].slice.call(document.querySelectorAll(A));else{if(!(Array.isArray(A)||A instanceof NodeList))throw new TypeError("The selector provided to AnchorJS was invalid.");e=[].slice.call(A)}return e}this.options=A||{},this.elements=[],u(this.options),this.add=function(A){var e,t,o,i,n,s,a,r,l,c,h,p=[];if(u(this.options),0!==(e=d(A=A||"h2, h3, h4, h5, h6")).length){for(null===document.head.querySelector("style.anchorjs")&&((A=document.createElement("style")).className="anchorjs",A.appendChild(document.createTextNode("")),void 0===(h=document.head.querySelector('[rel="stylesheet"],style'))?document.head.appendChild(A):document.head.insertBefore(A,h),A.sheet.insertRule(".anchorjs-link{opacity:0;text-decoration:none;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale}",A.sheet.cssRules.length),A.sheet.insertRule(":hover>.anchorjs-link,.anchorjs-link:focus{opacity:1}",A.sheet.cssRules.length),A.sheet.insertRule("[data-anchorjs-icon]::after{content:attr(data-anchorjs-icon)}",A.sheet.cssRules.length),A.sheet.insertRule('@font-face{font-family:anchorjs-icons;src:url(data:n/a;base64,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) format("truetype")}',A.sheet.cssRules.length)),h=document.querySelectorAll("[id]"),t=[].map.call(h,function(A){return A.id}),i=0;i<e.length;i++)if(this.hasAnchorJSLink(e[i]))p.push(i);else{if(e[i].hasAttribute("id"))o=e[i].getAttribute("id");else if(e[i].hasAttribute("data-anchor-id"))o=e[i].getAttribute("data-anchor-id");else{for(r=a=this.urlify(e[i].textContent),s=0;n=t.indexOf(r=void 0!==n?a+"-"+s:r),s+=1,-1!==n;);n=void 0,t.push(r),e[i].setAttribute("id",r),o=r}(l=document.createElement("a")).className="anchorjs-link "+this.options.class,l.setAttribute("aria-label",this.options.ariaLabel),l.setAttribute("data-anchorjs-icon",this.options.icon),this.options.titleText&&(l.title=this.options.titleText),c=document.querySelector("base")?window.location.pathname+window.location.search:"",c=this.options.base||c,l.href=c+"#"+o,"always"===this.options.visible&&(l.style.opacity="1"),""===this.options.icon&&(l.style.font="1em/1 anchorjs-icons","left"===this.options.placement)&&(l.style.lineHeight="inherit"),"left"===this.options.placement?(l.style.position="absolute",l.style.marginLeft="-1.25em",l.style.paddingRight=".25em",l.style.paddingLeft=".25em",e[i].insertBefore(l,e[i].firstChild)):(l.style.marginLeft=".1875em",l.style.paddingRight=".1875em",l.style.paddingLeft=".1875em",e[i].appendChild(l))}for(i=0;i<p.length;i++)e.splice(p[i]-i,1);this.elements=this.elements.concat(e)}return this},this.remove=function(A){for(var e,t,o=d(A),i=0;i<o.length;i++)(t=o[i].querySelector(".anchorjs-link"))&&(-1!==(e=this.elements.indexOf(o[i]))&&this.elements.splice(e,1),o[i].removeChild(t));return this},this.removeAll=function(){thisLine truncated
|
||||
// @license-end
|
||||
@@ -0,0 +1,145 @@
|
||||
class QuartoAxeReporter {
|
||||
constructor(axeResult, options) {
|
||||
this.axeResult = axeResult;
|
||||
this.options = options;
|
||||
}
|
||||
|
||||
report() {
|
||||
throw new Error("report() is an abstract method");
|
||||
}
|
||||
}
|
||||
|
||||
class QuartoAxeJsonReporter extends QuartoAxeReporter {
|
||||
constructor(axeResult, options) {
|
||||
super(axeResult, options);
|
||||
}
|
||||
|
||||
report() {
|
||||
console.log(JSON.stringify(this.axeResult, null, 2));
|
||||
}
|
||||
}
|
||||
|
||||
class QuartoAxeConsoleReporter extends QuartoAxeReporter {
|
||||
constructor(axeResult, options) {
|
||||
super(axeResult, options);
|
||||
}
|
||||
|
||||
report() {
|
||||
for (const violation of this.axeResult.violations) {
|
||||
console.log(violation.description);
|
||||
for (const node of violation.nodes) {
|
||||
for (const target of node.target) {
|
||||
console.log(target);
|
||||
console.log(document.querySelector(target));
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
class QuartoAxeDocumentReporter extends QuartoAxeReporter {
|
||||
constructor(axeResult, options) {
|
||||
super(axeResult, options);
|
||||
}
|
||||
|
||||
createViolationElement(violation) {
|
||||
const violationElement = document.createElement("div");
|
||||
|
||||
const descriptionElement = document.createElement("div");
|
||||
descriptionElement.className = "quarto-axe-violation-description";
|
||||
descriptionElement.innerText = `${violation.impact.replace(/^[a-z]/, match => match.toLocaleUpperCase())}: ${violation.description}`;
|
||||
violationElement.appendChild(descriptionElement);
|
||||
|
||||
const helpElement = document.createElement("div");
|
||||
helpElement.className = "quarto-axe-violation-help";
|
||||
helpElement.innerText = violation.help;
|
||||
violationElement.appendChild(helpElement);
|
||||
|
||||
const nodesElement = document.createElement("div");
|
||||
nodesElement.className = "quarto-axe-violation-nodes";
|
||||
violationElement.appendChild(nodesElement);
|
||||
const nodeElement = document.createElement("div");
|
||||
nodeElement.className = "quarto-axe-violation-selector";
|
||||
for (const node of violation.nodes) {
|
||||
for (const target of node.target) {
|
||||
const targetElement = document.createElement("span");
|
||||
targetElement.className = "quarto-axe-violation-target";
|
||||
targetElement.innerText = target;
|
||||
nodeElement.appendChild(targetElement);
|
||||
nodeElement.addEventListener("mouseenter", () => {
|
||||
const element = document.querySelector(target);
|
||||
if (element) {
|
||||
element.scrollIntoView({ behavior: "smooth", block: "center" });
|
||||
element.classList.add("quarto-axe-hover-highlight");
|
||||
setTimeout(() => {
|
||||
element.style.border = "";
|
||||
}, 2000);
|
||||
}
|
||||
});
|
||||
nodeElement.addEventListener("mouseleave", () => {
|
||||
const element = document.querySelector(target);
|
||||
if (element) {
|
||||
element.classList.remove("quarto-axe-hover-highlight");
|
||||
}
|
||||
});
|
||||
nodeElement.addEventListener("click", () => {
|
||||
console.log(document.querySelector(target));
|
||||
});
|
||||
nodeElement.appendChild(targetElement);
|
||||
}
|
||||
nodesElement.appendChild(nodeElement);
|
||||
}
|
||||
return violationElement;
|
||||
}
|
||||
|
||||
report() {
|
||||
const violations = this.axeResult.violations;
|
||||
const reportElement = document.createElement("div");
|
||||
reportElement.className = "quarto-axe-report";
|
||||
if (violations.length === 0) {
|
||||
const noViolationsElement = document.createElement("div");
|
||||
noViolationsElement.className = "quarto-axe-no-violations";
|
||||
noViolationsElement.innerText = "No axe-core violations found.";
|
||||
reportElement.appendChild(noViolationsElement);
|
||||
}
|
||||
violations.forEach((violation) => {
|
||||
reportElement.appendChild(this.createViolationElement(violation));
|
||||
});
|
||||
document.querySelector("main").appendChild(reportElement);
|
||||
}
|
||||
}
|
||||
|
||||
const reporters = {
|
||||
json: QuartoAxeJsonReporter,
|
||||
console: QuartoAxeConsoleReporter,
|
||||
document: QuartoAxeDocumentReporter,
|
||||
};
|
||||
|
||||
class QuartoAxeChecker {
|
||||
constructor(opts) {
|
||||
this.options = opts;
|
||||
}
|
||||
async init() {
|
||||
const axe = (await import("https://cdn.skypack.dev/pin/axe-core@v4.10.3-aVOFXWsJaCpVrtv89pCa/mode=imports,min/optimized/axe-core.js")).default;
|
||||
const result = await axe.run({
|
||||
exclude: [
|
||||
// https://github.com/microsoft/tabster/issues/288
|
||||
// MS has claimed they won't fix this, so we need to add an exclusion to
|
||||
// all tabster elements
|
||||
"[data-tabster-dummy]"
|
||||
],
|
||||
preload: { assets: ['cssom'], timeout: 50000 }
|
||||
});
|
||||
const reporter = this.options === true ? new QuartoAxeConsoleReporter(result) : new reporters[this.options.output](result, this.options);
|
||||
reporter.report();
|
||||
}
|
||||
}
|
||||
|
||||
export async function init() {
|
||||
const opts = document.querySelector("#quarto-axe-checker-options");
|
||||
if (opts) {
|
||||
const jsonOptions = JSON.parse(atob(opts.textContent));
|
||||
const checker = new QuartoAxeChecker(jsonOptions);
|
||||
await checker.init();
|
||||
}
|
||||
}
|
||||
+6
@@ -0,0 +1,6 @@
|
||||
/**
|
||||
* @popperjs/core v2.11.7 - MIT License
|
||||
*/
|
||||
|
||||
!function(e,t){"object"==typeof exports&&"undefined"!=typeof module?t(exports):"function"==typeof define&&define.amd?define(["exports"],t):t((e="undefined"!=typeof globalThis?globalThis:e||self).Popper={})}(this,(function(e){"use strict";function t(e){if(null==e)return window;if("[object Window]"!==e.toString()){var t=e.ownerDocument;return t&&t.defaultView||window}return e}function n(e){return e instanceof t(e).Element||e instanceof Element}function r(e){return e instanceof t(e).HTMLElement||e instanceof HTMLElement}function o(e){return"undefined"!=typeof ShadowRoot&&(e instanceof t(e).ShadowRoot||e instanceof ShadowRoot)}var i=Math.max,a=Math.min,s=Math.round;function f(){var e=navigator.userAgentData;return null!=e&&e.brands&&Array.isArray(e.brands)?e.brands.map((function(e){return e.brand+"/"+e.version})).join(" "):navigator.userAgent}function c(){return!/^((?!chrome|android).)*safari/i.test(f())}function p(e,o,i){void 0===o&&(o=!1),void 0===i&&(i=!1);var a=e.getBoundingClientRect(),f=1,p=1;o&&r(e)&&(f=e.offsetWidth>0&&s(a.width)/e.offsetWidth||1,p=e.offsetHeight>0&&s(a.height)/e.offsetHeight||1);var u=(n(e)?t(e):window).visualViewport,l=!c()&&i,d=(a.left+(l&&u?u.offsetLeft:0))/f,h=(a.top+(l&&u?u.offsetTop:0))/p,m=a.width/f,v=a.height/p;return{width:m,height:v,top:h,right:d+m,bottom:h+v,left:d,x:d,y:h}}function u(e){var n=t(e);return{scrollLeft:n.pageXOffset,scrollTop:n.pageYOffset}}function l(e){return e?(e.nodeName||"").toLowerCase():null}function d(e){return((n(e)?e.ownerDocument:e.document)||window.document).documentElement}function h(e){return p(d(e)).left+u(e).scrollLeft}function m(e){return t(e).getComputedStyle(e)}function v(e){var t=m(e),n=t.overflow,r=t.overflowX,o=t.overflowY;return/auto|scroll|overlay|hidden/.test(n+o+r)}function y(e,n,o){void 0===o&&(o=!1);var i,a,f=r(n),c=r(n)&&function(e){var t=e.getBoundingClientRect(),n=s(t.width)/e.offsetWidth||1,r=s(t.height)/e.offsetHeight||1;return 1!==n||1!==r}(n),m=d(n),y=p(e,c,o),g={scrollLeft:0,scrollTop:0},b={x:0,y:0};return(f||!f&&!o)&&(("body"!==l(n)||v(m))&&(g=(i=n)!==t(i)&&r(i)?{scrollLeft:(a=i).scrollLeft,scrollTop:a.scrollTop}:u(i)),r(n)?((b=p(n,!0)).x+=n.clientLeft,b.y+=n.clientTop):m&&(b.x=h(m))),{x:y.left+g.scrollLeft-b.x,y:y.top+g.scrollTop-b.y,width:y.width,height:y.height}}function g(e){var t=p(e),n=e.offsetWidth,r=e.offsetHeight;return Math.abs(t.width-n)<=1&&(n=t.width),Math.abs(t.height-r)<=1&&(r=t.height),{x:e.offsetLeft,y:e.offsetTop,width:n,height:r}}function b(e){return"html"===l(e)?e:e.assignedSlot||e.parentNode||(o(e)?e.host:null)||d(e)}function x(e){return["html","body","#document"].indexOf(l(e))>=0?e.ownerDocument.body:r(e)&&v(e)?e:x(b(e))}function w(e,n){var r;void 0===n&&(n=[]);var o=x(e),i=o===(null==(r=e.ownerDocument)?void 0:r.body),a=t(o),s=i?[a].concat(a.visualViewport||[],v(o)?o:[]):o,f=n.concat(s);return i?f:f.concat(w(b(s)))}function O(e){return["table","td","th"].indexOf(l(e))>=0}function j(e){return r(e)&&"fixed"!==m(e).position?e.offsetParent:null}function E(e){for(var n=t(e),i=j(e);i&&O(i)&&"static"===m(i).position;)i=j(i);return i&&("html"===l(i)||"body"===l(i)&&"static"===m(i).position)?n:i||function(e){var t=/firefox/i.test(f());if(/Trident/i.test(f())&&r(e)&&"fixed"===m(e).position)return null;var n=b(e);for(o(n)&&(n=n.host);r(n)&&["html","body"].indexOf(l(n))<0;){var i=m(n);if("none"!==i.transform||"none"!==i.perspective||"paint"===i.contain||-1!==["transform","perspective"].indexOf(i.willChange)||t&&"filter"===i.willChange||t&&i.filter&&"none"!==i.filter)return n;n=n.parentNode}return null}(e)||n}var D="top",A="bottom",L="right",P="left",M="auto",k=[D,A,L,P],W="start",B="end",H="viewport",T="popper",R=k.reduce((function(e,t){return e.concat([t+"-"+W,t+"-"+B])}),[]),S=[].concat(k,[M]).reduce((function(e,t){return e.concat([t,t+"-"+W,t+"-"+B])}),[]),V=["beforeRead","read","afterRead","beforeMain","main","afterMain","beforeWrite","write","afterWrite"];function q(e){var t=new Map,n=new Set,r=[];function o(e){n.add(e.name),[].concat(e.requires||[],e.requiresIfExists||[]).forEach((function(e){if(!n.has(e)){var r=t.get(e);r&&o(r)}})),r.push(e)}return e.forEach((function(e){t.set(e.name,e)})),e.forEach((function(e){n.has(e.name)||o(e)})),r}function C(e){return e.split("-")[0]}function N(e,t){var n=t.getRootNode&&t.getRootNode();if(e.contains(t))return!0;if(n&&o(n)){var r=t;do{if(r&&e.isSameNode(r))return!0;r=r.parentNode||r.host}while(r)}return!1}function I(e){return Object.assign({},e,{left:e.x,top:e.y,right:e.x+e.width,bottom:e.y+e.height})}function _(e,r,o){return r===H?I(function(e,n){var r=t(e),o=d(e),i=r.visualViewport,a=o.clientWidth,s=o.clientHeight,f=0,p=0;if(i){a=i.width,s=i.height;var u=c();(u||!u&&"fixed"===n)&&(f=i.offsetLeft,p=i.offsetTop)}return{width:a,height:s,x:f+h(e),y:p}}(e,o)):n(r)?function(e,t){var n=p(e,!1,"fixed"===t);return n.top=n.top+e.clientTop,n.left=n.left+e.clientLeft,n.bottom=n.top+e.clientHeight,n.right=n.left+e.clientWidth,n.width=e.clientWidth,n.height=e.clientHeight,n.x=n.lLine truncated
|
||||
|
||||
+236
@@ -0,0 +1,236 @@
|
||||
/* quarto syntax highlight colors */
|
||||
:root {
|
||||
--quarto-hl-ot-color: #003B4F;
|
||||
--quarto-hl-at-color: #657422;
|
||||
--quarto-hl-ss-color: #20794D;
|
||||
--quarto-hl-an-color: #5E5E5E;
|
||||
--quarto-hl-fu-color: #4758AB;
|
||||
--quarto-hl-st-color: #20794D;
|
||||
--quarto-hl-cf-color: #003B4F;
|
||||
--quarto-hl-op-color: #5E5E5E;
|
||||
--quarto-hl-er-color: #AD0000;
|
||||
--quarto-hl-bn-color: #AD0000;
|
||||
--quarto-hl-al-color: #AD0000;
|
||||
--quarto-hl-va-color: #111111;
|
||||
--quarto-hl-bu-color: inherit;
|
||||
--quarto-hl-ex-color: inherit;
|
||||
--quarto-hl-pp-color: #AD0000;
|
||||
--quarto-hl-in-color: #5E5E5E;
|
||||
--quarto-hl-vs-color: #20794D;
|
||||
--quarto-hl-wa-color: #5E5E5E;
|
||||
--quarto-hl-do-color: #5E5E5E;
|
||||
--quarto-hl-im-color: #00769E;
|
||||
--quarto-hl-ch-color: #20794D;
|
||||
--quarto-hl-dt-color: #AD0000;
|
||||
--quarto-hl-fl-color: #AD0000;
|
||||
--quarto-hl-co-color: #5E5E5E;
|
||||
--quarto-hl-cv-color: #5E5E5E;
|
||||
--quarto-hl-cn-color: #8f5902;
|
||||
--quarto-hl-sc-color: #5E5E5E;
|
||||
--quarto-hl-dv-color: #AD0000;
|
||||
--quarto-hl-kw-color: #003B4F;
|
||||
}
|
||||
|
||||
/* other quarto variables */
|
||||
:root {
|
||||
--quarto-font-monospace: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace;
|
||||
}
|
||||
|
||||
/* syntax highlight based on Pandoc's rules */
|
||||
pre > code.sourceCode > span {
|
||||
color: #003B4F;
|
||||
}
|
||||
|
||||
code.sourceCode > span {
|
||||
color: #003B4F;
|
||||
}
|
||||
|
||||
div.sourceCode,
|
||||
div.sourceCode pre.sourceCode {
|
||||
color: #003B4F;
|
||||
}
|
||||
|
||||
/* Normal */
|
||||
code span {
|
||||
color: #003B4F;
|
||||
}
|
||||
|
||||
/* Alert */
|
||||
code span.al {
|
||||
color: #AD0000;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* Annotation */
|
||||
code span.an {
|
||||
color: #5E5E5E;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* Attribute */
|
||||
code span.at {
|
||||
color: #657422;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* BaseN */
|
||||
code span.bn {
|
||||
color: #AD0000;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* BuiltIn */
|
||||
code span.bu {
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* ControlFlow */
|
||||
code span.cf {
|
||||
color: #003B4F;
|
||||
font-weight: bold;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* Char */
|
||||
code span.ch {
|
||||
color: #20794D;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* Constant */
|
||||
code span.cn {
|
||||
color: #8f5902;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* Comment */
|
||||
code span.co {
|
||||
color: #5E5E5E;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* CommentVar */
|
||||
code span.cv {
|
||||
color: #5E5E5E;
|
||||
font-style: italic;
|
||||
}
|
||||
|
||||
/* Documentation */
|
||||
code span.do {
|
||||
color: #5E5E5E;
|
||||
font-style: italic;
|
||||
}
|
||||
|
||||
/* DataType */
|
||||
code span.dt {
|
||||
color: #AD0000;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* DecVal */
|
||||
code span.dv {
|
||||
color: #AD0000;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* Error */
|
||||
code span.er {
|
||||
color: #AD0000;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* Extension */
|
||||
code span.ex {
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* Float */
|
||||
code span.fl {
|
||||
color: #AD0000;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* Function */
|
||||
code span.fu {
|
||||
color: #4758AB;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* Import */
|
||||
code span.im {
|
||||
color: #00769E;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* Information */
|
||||
code span.in {
|
||||
color: #5E5E5E;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* Keyword */
|
||||
code span.kw {
|
||||
color: #003B4F;
|
||||
font-weight: bold;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* Operator */
|
||||
code span.op {
|
||||
color: #5E5E5E;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* Other */
|
||||
code span.ot {
|
||||
color: #003B4F;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* Preprocessor */
|
||||
code span.pp {
|
||||
color: #AD0000;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* SpecialChar */
|
||||
code span.sc {
|
||||
color: #5E5E5E;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* SpecialString */
|
||||
code span.ss {
|
||||
color: #20794D;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* String */
|
||||
code span.st {
|
||||
color: #20794D;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* Variable */
|
||||
code span.va {
|
||||
color: #111111;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* VerbatimString */
|
||||
code span.vs {
|
||||
color: #20794D;
|
||||
font-style: inherit;
|
||||
}
|
||||
|
||||
/* Warning */
|
||||
code span.wa {
|
||||
color: #5E5E5E;
|
||||
font-style: italic;
|
||||
}
|
||||
|
||||
.prevent-inlining {
|
||||
content: "</";
|
||||
}
|
||||
|
||||
/*# sourceMappingURL=2dce1cc6c82594539e1579de68416b47.css.map */
|
||||
@@ -0,0 +1,847 @@
|
||||
import * as tabsets from "./tabsets/tabsets.js";
|
||||
import * as axe from "./axe/axe-check.js";
|
||||
|
||||
const sectionChanged = new CustomEvent("quarto-sectionChanged", {
|
||||
detail: {},
|
||||
bubbles: true,
|
||||
cancelable: false,
|
||||
composed: false,
|
||||
});
|
||||
|
||||
const layoutMarginEls = () => {
|
||||
// Find any conflicting margin elements and add margins to the
|
||||
// top to prevent overlap
|
||||
const marginChildren = window.document.querySelectorAll(
|
||||
".column-margin.column-container > *, .margin-caption, .aside"
|
||||
);
|
||||
|
||||
let lastBottom = 0;
|
||||
for (const marginChild of marginChildren) {
|
||||
if (marginChild.offsetParent !== null) {
|
||||
// clear the top margin so we recompute it
|
||||
marginChild.style.marginTop = null;
|
||||
const top = marginChild.getBoundingClientRect().top + window.scrollY;
|
||||
if (top < lastBottom) {
|
||||
const marginChildStyle = window.getComputedStyle(marginChild);
|
||||
const marginBottom = parseFloat(marginChildStyle["marginBottom"]);
|
||||
const margin = lastBottom - top + marginBottom;
|
||||
marginChild.style.marginTop = `${margin}px`;
|
||||
}
|
||||
const styles = window.getComputedStyle(marginChild);
|
||||
const marginTop = parseFloat(styles["marginTop"]);
|
||||
lastBottom = top + marginChild.getBoundingClientRect().height + marginTop;
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
window.document.addEventListener("DOMContentLoaded", function (_event) {
|
||||
// Recompute the position of margin elements anytime the body size changes
|
||||
if (window.ResizeObserver) {
|
||||
const resizeObserver = new window.ResizeObserver(
|
||||
throttle(() => {
|
||||
layoutMarginEls();
|
||||
if (
|
||||
window.document.body.getBoundingClientRect().width < 990 &&
|
||||
isReaderMode()
|
||||
) {
|
||||
quartoToggleReader();
|
||||
}
|
||||
}, 50)
|
||||
);
|
||||
resizeObserver.observe(window.document.body);
|
||||
}
|
||||
|
||||
const tocEl = window.document.querySelector('nav.toc-active[role="doc-toc"]');
|
||||
const sidebarEl = window.document.getElementById("quarto-sidebar");
|
||||
const leftTocEl = window.document.getElementById("quarto-sidebar-toc-left");
|
||||
const marginSidebarEl = window.document.getElementById(
|
||||
"quarto-margin-sidebar"
|
||||
);
|
||||
// function to determine whether the element has a previous sibling that is active
|
||||
const prevSiblingIsActiveLink = (el) => {
|
||||
const sibling = el.previousElementSibling;
|
||||
if (sibling && sibling.tagName === "A") {
|
||||
return sibling.classList.contains("active");
|
||||
} else {
|
||||
return false;
|
||||
}
|
||||
};
|
||||
|
||||
// dispatch for htmlwidgets
|
||||
// they use slideenter event to trigger resize
|
||||
function fireSlideEnter() {
|
||||
const event = window.document.createEvent("Event");
|
||||
event.initEvent("slideenter", true, true);
|
||||
window.document.dispatchEvent(event);
|
||||
}
|
||||
|
||||
const tabs = window.document.querySelectorAll('a[data-bs-toggle="tab"]');
|
||||
tabs.forEach((tab) => {
|
||||
tab.addEventListener("shown.bs.tab", fireSlideEnter);
|
||||
});
|
||||
|
||||
// dispatch for shiny
|
||||
// they use BS shown and hidden events to trigger rendering
|
||||
function distpatchShinyEvents(previous, current) {
|
||||
if (window.jQuery) {
|
||||
if (previous) {
|
||||
window.jQuery(previous).trigger("hidden");
|
||||
}
|
||||
if (current) {
|
||||
window.jQuery(current).trigger("shown");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// tabby.js listener: Trigger event for htmlwidget and shiny
|
||||
document.addEventListener(
|
||||
"tabby",
|
||||
function (event) {
|
||||
fireSlideEnter();
|
||||
distpatchShinyEvents(event.detail.previousTab, event.detail.tab);
|
||||
},
|
||||
false
|
||||
);
|
||||
|
||||
// Track scrolling and mark TOC links as active
|
||||
// get table of contents and sidebar (bail if we don't have at least one)
|
||||
const tocLinks = tocEl
|
||||
? [...tocEl.querySelectorAll("a[data-scroll-target]")]
|
||||
: [];
|
||||
const makeActive = (link) => tocLinks[link].classList.add("active");
|
||||
const removeActive = (link) => tocLinks[link].classList.remove("active");
|
||||
const removeAllActive = () =>
|
||||
[...Array(tocLinks.length).keys()].forEach((link) => removeActive(link));
|
||||
|
||||
// activate the anchor for a section associated with this TOC entry
|
||||
tocLinks.forEach((link) => {
|
||||
link.addEventListener("click", () => {
|
||||
if (link.href.indexOf("#") !== -1) {
|
||||
const anchor = link.href.split("#")[1];
|
||||
const heading = window.document.querySelector(
|
||||
`[data-anchor-id="${anchor}"]`
|
||||
);
|
||||
if (heading) {
|
||||
// Add the class
|
||||
heading.classList.add("reveal-anchorjs-link");
|
||||
|
||||
// function to show the anchor
|
||||
const handleMouseout = () => {
|
||||
heading.classList.remove("reveal-anchorjs-link");
|
||||
heading.removeEventListener("mouseout", handleMouseout);
|
||||
};
|
||||
|
||||
// add a function to clear the anchor when the user mouses out of it
|
||||
heading.addEventListener("mouseout", handleMouseout);
|
||||
}
|
||||
}
|
||||
});
|
||||
});
|
||||
|
||||
const sections = tocLinks.map((link) => {
|
||||
const target = link.getAttribute("data-scroll-target");
|
||||
if (target.startsWith("#")) {
|
||||
return window.document.getElementById(decodeURI(`${target.slice(1)}`));
|
||||
} else {
|
||||
return window.document.querySelector(decodeURI(`${target}`));
|
||||
}
|
||||
});
|
||||
|
||||
const sectionMargin = 200;
|
||||
let currentActive = 0;
|
||||
// track whether we've initialized state the first time
|
||||
let init = false;
|
||||
|
||||
const updateActiveLink = () => {
|
||||
// The index from bottom to top (e.g. reversed list)
|
||||
let sectionIndex = -1;
|
||||
if (
|
||||
window.innerHeight + window.pageYOffset >=
|
||||
window.document.body.offsetHeight
|
||||
) {
|
||||
// This is the no-scroll case where last section should be the active one
|
||||
sectionIndex = 0;
|
||||
} else {
|
||||
// This finds the last section visible on screen that should be made active
|
||||
sectionIndex = [...sections].reverse().findIndex((section) => {
|
||||
if (section) {
|
||||
return window.pageYOffset >= section.offsetTop - sectionMargin;
|
||||
} else {
|
||||
return false;
|
||||
}
|
||||
});
|
||||
}
|
||||
if (sectionIndex > -1) {
|
||||
const current = sections.length - sectionIndex - 1;
|
||||
if (current !== currentActive) {
|
||||
removeAllActive();
|
||||
currentActive = current;
|
||||
makeActive(current);
|
||||
if (init) {
|
||||
window.dispatchEvent(sectionChanged);
|
||||
}
|
||||
init = true;
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
const inHiddenRegion = (top, bottom, hiddenRegions) => {
|
||||
for (const region of hiddenRegions) {
|
||||
if (top <= region.bottom && bottom >= region.top) {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
return false;
|
||||
};
|
||||
|
||||
const categorySelector = "header.quarto-title-block .quarto-category";
|
||||
const activateCategories = (href) => {
|
||||
// Find any categories
|
||||
// Surround them with a link pointing back to:
|
||||
// #category=Authoring
|
||||
try {
|
||||
const categoryEls = window.document.querySelectorAll(categorySelector);
|
||||
for (const categoryEl of categoryEls) {
|
||||
const categoryText = categoryEl.textContent;
|
||||
if (categoryText) {
|
||||
const link = `${href}#category=${encodeURIComponent(categoryText)}`;
|
||||
const linkEl = window.document.createElement("a");
|
||||
linkEl.setAttribute("href", link);
|
||||
for (const child of categoryEl.childNodes) {
|
||||
linkEl.append(child);
|
||||
}
|
||||
categoryEl.appendChild(linkEl);
|
||||
}
|
||||
}
|
||||
} catch {
|
||||
// Ignore errors
|
||||
}
|
||||
};
|
||||
function hasTitleCategories() {
|
||||
return window.document.querySelector(categorySelector) !== null;
|
||||
}
|
||||
|
||||
function offsetRelativeUrl(url) {
|
||||
const offset = getMeta("quarto:offset");
|
||||
return offset ? offset + url : url;
|
||||
}
|
||||
|
||||
function offsetAbsoluteUrl(url) {
|
||||
const offset = getMeta("quarto:offset");
|
||||
const baseUrl = new URL(offset, window.location);
|
||||
|
||||
const projRelativeUrl = url.replace(baseUrl, "");
|
||||
if (projRelativeUrl.startsWith("/")) {
|
||||
return projRelativeUrl;
|
||||
} else {
|
||||
return "/" + projRelativeUrl;
|
||||
}
|
||||
}
|
||||
|
||||
// read a meta tag value
|
||||
function getMeta(metaName) {
|
||||
const metas = window.document.getElementsByTagName("meta");
|
||||
for (let i = 0; i < metas.length; i++) {
|
||||
if (metas[i].getAttribute("name") === metaName) {
|
||||
return metas[i].getAttribute("content");
|
||||
}
|
||||
}
|
||||
return "";
|
||||
}
|
||||
|
||||
async function findAndActivateCategories() {
|
||||
// Categories search with listing only use path without query
|
||||
const currentPagePath = offsetAbsoluteUrl(
|
||||
window.location.origin + window.location.pathname
|
||||
);
|
||||
const response = await fetch(offsetRelativeUrl("listings.json"));
|
||||
if (response.status == 200) {
|
||||
return response.json().then(function (listingPaths) {
|
||||
const listingHrefs = [];
|
||||
for (const listingPath of listingPaths) {
|
||||
const pathWithoutLeadingSlash = listingPath.listing.substring(1);
|
||||
for (const item of listingPath.items) {
|
||||
const encodedItem = encodeURI(item);
|
||||
if (
|
||||
encodedItem === currentPagePath ||
|
||||
encodedItem === currentPagePath + "index.html"
|
||||
) {
|
||||
// Resolve this path against the offset to be sure
|
||||
// we already are using the correct path to the listing
|
||||
// (this adjusts the listing urls to be rooted against
|
||||
// whatever root the page is actually running against)
|
||||
const relative = offsetRelativeUrl(pathWithoutLeadingSlash);
|
||||
const baseUrl = window.location;
|
||||
const resolvedPath = new URL(relative, baseUrl);
|
||||
listingHrefs.push(resolvedPath.pathname);
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Look up the tree for a nearby linting and use that if we find one
|
||||
const nearestListing = findNearestParentListing(
|
||||
offsetAbsoluteUrl(window.location.pathname),
|
||||
listingHrefs
|
||||
);
|
||||
if (nearestListing) {
|
||||
activateCategories(nearestListing);
|
||||
} else {
|
||||
// See if the referrer is a listing page for this item
|
||||
const referredRelativePath = offsetAbsoluteUrl(document.referrer);
|
||||
const referrerListing = listingHrefs.find((listingHref) => {
|
||||
const isListingReferrer =
|
||||
listingHref === referredRelativePath ||
|
||||
listingHref === referredRelativePath + "index.html";
|
||||
return isListingReferrer;
|
||||
});
|
||||
|
||||
if (referrerListing) {
|
||||
// Try to use the referrer if possible
|
||||
activateCategories(referrerListing);
|
||||
} else if (listingHrefs.length > 0) {
|
||||
// Otherwise, just fall back to the first listing
|
||||
activateCategories(listingHrefs[0]);
|
||||
}
|
||||
}
|
||||
});
|
||||
}
|
||||
}
|
||||
if (hasTitleCategories()) {
|
||||
findAndActivateCategories();
|
||||
}
|
||||
|
||||
const findNearestParentListing = (href, listingHrefs) => {
|
||||
if (!href || !listingHrefs) {
|
||||
return undefined;
|
||||
}
|
||||
// Look up the tree for a nearby linting and use that if we find one
|
||||
const relativeParts = href.substring(1).split("/");
|
||||
while (relativeParts.length > 0) {
|
||||
const path = relativeParts.join("/");
|
||||
for (const listingHref of listingHrefs) {
|
||||
if (listingHref.startsWith(path)) {
|
||||
return listingHref;
|
||||
}
|
||||
}
|
||||
relativeParts.pop();
|
||||
}
|
||||
|
||||
return undefined;
|
||||
};
|
||||
|
||||
const manageSidebarVisiblity = (el, placeholderDescriptor) => {
|
||||
let isVisible = true;
|
||||
let elRect;
|
||||
|
||||
return (hiddenRegions) => {
|
||||
if (el === null) {
|
||||
return;
|
||||
}
|
||||
|
||||
// Find the last element of the TOC
|
||||
const lastChildEl = el.lastElementChild;
|
||||
|
||||
if (lastChildEl) {
|
||||
// Converts the sidebar to a menu
|
||||
const convertToMenu = () => {
|
||||
for (const child of el.children) {
|
||||
child.style.opacity = 0;
|
||||
child.style.overflow = "hidden";
|
||||
child.style.pointerEvents = "none";
|
||||
}
|
||||
|
||||
nexttick(() => {
|
||||
const toggleContainer = window.document.createElement("div");
|
||||
toggleContainer.style.width = "100%";
|
||||
toggleContainer.classList.add("zindex-over-content");
|
||||
toggleContainer.classList.add("quarto-sidebar-toggle");
|
||||
toggleContainer.classList.add("headroom-target"); // Marks this to be managed by headeroom
|
||||
toggleContainer.id = placeholderDescriptor.id;
|
||||
toggleContainer.style.position = "fixed";
|
||||
|
||||
const toggleIcon = window.document.createElement("i");
|
||||
toggleIcon.classList.add("quarto-sidebar-toggle-icon");
|
||||
toggleIcon.classList.add("bi");
|
||||
toggleIcon.classList.add("bi-caret-down-fill");
|
||||
|
||||
const toggleTitle = window.document.createElement("div");
|
||||
const titleEl = window.document.body.querySelector(
|
||||
placeholderDescriptor.titleSelector
|
||||
);
|
||||
if (titleEl) {
|
||||
toggleTitle.append(
|
||||
titleEl.textContent || titleEl.innerText,
|
||||
toggleIcon
|
||||
);
|
||||
}
|
||||
toggleTitle.classList.add("zindex-over-content");
|
||||
toggleTitle.classList.add("quarto-sidebar-toggle-title");
|
||||
toggleContainer.append(toggleTitle);
|
||||
|
||||
const toggleContents = window.document.createElement("div");
|
||||
toggleContents.classList = el.classList;
|
||||
toggleContents.classList.add("zindex-over-content");
|
||||
toggleContents.classList.add("quarto-sidebar-toggle-contents");
|
||||
for (const child of el.children) {
|
||||
if (child.id === "toc-title") {
|
||||
continue;
|
||||
}
|
||||
|
||||
const clone = child.cloneNode(true);
|
||||
clone.style.opacity = 1;
|
||||
clone.style.pointerEvents = null;
|
||||
clone.style.display = null;
|
||||
toggleContents.append(clone);
|
||||
}
|
||||
toggleContents.style.height = "0px";
|
||||
const positionToggle = () => {
|
||||
// position the element (top left of parent, same width as parent)
|
||||
if (!elRect) {
|
||||
elRect = el.getBoundingClientRect();
|
||||
}
|
||||
toggleContainer.style.left = `${elRect.left}px`;
|
||||
toggleContainer.style.top = `${elRect.top}px`;
|
||||
toggleContainer.style.width = `${elRect.width}px`;
|
||||
};
|
||||
positionToggle();
|
||||
|
||||
toggleContainer.append(toggleContents);
|
||||
el.parentElement.prepend(toggleContainer);
|
||||
|
||||
// Process clicks
|
||||
let tocShowing = false;
|
||||
// Allow the caller to control whether this is dismissed
|
||||
// when it is clicked (e.g. sidebar navigation supports
|
||||
// opening and closing the nav tree, so don't dismiss on click)
|
||||
const clickEl = placeholderDescriptor.dismissOnClick
|
||||
? toggleContainer
|
||||
: toggleTitle;
|
||||
|
||||
const closeToggle = () => {
|
||||
if (tocShowing) {
|
||||
toggleContainer.classList.remove("expanded");
|
||||
toggleContents.style.height = "0px";
|
||||
tocShowing = false;
|
||||
}
|
||||
};
|
||||
|
||||
// Get rid of any expanded toggle if the user scrolls
|
||||
window.document.addEventListener(
|
||||
"scroll",
|
||||
throttle(() => {
|
||||
closeToggle();
|
||||
}, 50)
|
||||
);
|
||||
|
||||
// Handle positioning of the toggle
|
||||
window.addEventListener(
|
||||
"resize",
|
||||
throttle(() => {
|
||||
elRect = undefined;
|
||||
positionToggle();
|
||||
}, 50)
|
||||
);
|
||||
|
||||
window.addEventListener("quarto-hrChanged", () => {
|
||||
elRect = undefined;
|
||||
});
|
||||
|
||||
// Process the click
|
||||
clickEl.onclick = () => {
|
||||
if (!tocShowing) {
|
||||
toggleContainer.classList.add("expanded");
|
||||
toggleContents.style.height = null;
|
||||
tocShowing = true;
|
||||
} else {
|
||||
closeToggle();
|
||||
}
|
||||
};
|
||||
});
|
||||
};
|
||||
|
||||
// Converts a sidebar from a menu back to a sidebar
|
||||
const convertToSidebar = () => {
|
||||
for (const child of el.children) {
|
||||
child.style.opacity = 1;
|
||||
child.style.overflow = null;
|
||||
child.style.pointerEvents = null;
|
||||
}
|
||||
|
||||
const placeholderEl = window.document.getElementById(
|
||||
placeholderDescriptor.id
|
||||
);
|
||||
if (placeholderEl) {
|
||||
placeholderEl.remove();
|
||||
}
|
||||
|
||||
el.classList.remove("rollup");
|
||||
};
|
||||
|
||||
if (isReaderMode()) {
|
||||
convertToMenu();
|
||||
isVisible = false;
|
||||
} else {
|
||||
// Find the top and bottom o the element that is being managed
|
||||
const elTop = el.offsetTop;
|
||||
const elBottom =
|
||||
elTop + lastChildEl.offsetTop + lastChildEl.offsetHeight;
|
||||
|
||||
if (!isVisible) {
|
||||
// If the element is current not visible reveal if there are
|
||||
// no conflicts with overlay regions
|
||||
if (!inHiddenRegion(elTop, elBottom, hiddenRegions)) {
|
||||
convertToSidebar();
|
||||
isVisible = true;
|
||||
}
|
||||
} else {
|
||||
// If the element is visible, hide it if it conflicts with overlay regions
|
||||
// and insert a placeholder toggle (or if we're in reader mode)
|
||||
if (inHiddenRegion(elTop, elBottom, hiddenRegions)) {
|
||||
convertToMenu();
|
||||
isVisible = false;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
};
|
||||
};
|
||||
|
||||
const tabEls = document.querySelectorAll('a[data-bs-toggle="tab"]');
|
||||
for (const tabEl of tabEls) {
|
||||
const id = tabEl.getAttribute("data-bs-target");
|
||||
if (id) {
|
||||
const columnEl = document.querySelector(
|
||||
`${id} .column-margin, .tabset-margin-content`
|
||||
);
|
||||
if (columnEl)
|
||||
tabEl.addEventListener("shown.bs.tab", function (event) {
|
||||
const el = event.srcElement;
|
||||
if (el) {
|
||||
const visibleCls = `${el.id}-margin-content`;
|
||||
// walk up until we find a parent tabset
|
||||
let panelTabsetEl = el.parentElement;
|
||||
while (panelTabsetEl) {
|
||||
if (panelTabsetEl.classList.contains("panel-tabset")) {
|
||||
break;
|
||||
}
|
||||
panelTabsetEl = panelTabsetEl.parentElement;
|
||||
}
|
||||
|
||||
if (panelTabsetEl) {
|
||||
const prevSib = panelTabsetEl.previousElementSibling;
|
||||
if (
|
||||
prevSib &&
|
||||
prevSib.classList.contains("tabset-margin-container")
|
||||
) {
|
||||
const childNodes = prevSib.querySelectorAll(
|
||||
".tabset-margin-content"
|
||||
);
|
||||
for (const childEl of childNodes) {
|
||||
if (childEl.classList.contains(visibleCls)) {
|
||||
childEl.classList.remove("collapse");
|
||||
} else {
|
||||
childEl.classList.add("collapse");
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
layoutMarginEls();
|
||||
});
|
||||
}
|
||||
}
|
||||
|
||||
// Manage the visibility of the toc and the sidebar
|
||||
const marginScrollVisibility = manageSidebarVisiblity(marginSidebarEl, {
|
||||
id: "quarto-toc-toggle",
|
||||
titleSelector: "#toc-title",
|
||||
dismissOnClick: true,
|
||||
});
|
||||
const sidebarScrollVisiblity = manageSidebarVisiblity(sidebarEl, {
|
||||
id: "quarto-sidebarnav-toggle",
|
||||
titleSelector: ".title",
|
||||
dismissOnClick: false,
|
||||
});
|
||||
let tocLeftScrollVisibility;
|
||||
if (leftTocEl) {
|
||||
tocLeftScrollVisibility = manageSidebarVisiblity(leftTocEl, {
|
||||
id: "quarto-lefttoc-toggle",
|
||||
titleSelector: "#toc-title",
|
||||
dismissOnClick: true,
|
||||
});
|
||||
}
|
||||
|
||||
// Find the first element that uses formatting in special columns
|
||||
const conflictingEls = window.document.body.querySelectorAll(
|
||||
'[class^="column-"], [class*=" column-"], aside, [class*="margin-caption"], [class*=" margin-caption"], [class*="margin-ref"], [class*=" margin-ref"]'
|
||||
);
|
||||
|
||||
// Filter all the possibly conflicting elements into ones
|
||||
// the do conflict on the left or ride side
|
||||
const arrConflictingEls = Array.from(conflictingEls);
|
||||
const leftSideConflictEls = arrConflictingEls.filter((el) => {
|
||||
if (el.tagName === "ASIDE") {
|
||||
return false;
|
||||
}
|
||||
return Array.from(el.classList).find((className) => {
|
||||
return (
|
||||
className !== "column-body" &&
|
||||
className.startsWith("column-") &&
|
||||
!className.endsWith("right") &&
|
||||
!className.endsWith("container") &&
|
||||
className !== "column-margin"
|
||||
);
|
||||
});
|
||||
});
|
||||
const rightSideConflictEls = arrConflictingEls.filter((el) => {
|
||||
if (el.tagName === "ASIDE") {
|
||||
return true;
|
||||
}
|
||||
|
||||
const hasMarginCaption = Array.from(el.classList).find((className) => {
|
||||
return className == "margin-caption";
|
||||
});
|
||||
if (hasMarginCaption) {
|
||||
return true;
|
||||
}
|
||||
|
||||
return Array.from(el.classList).find((className) => {
|
||||
return (
|
||||
className !== "column-body" &&
|
||||
!className.endsWith("container") &&
|
||||
className.startsWith("column-") &&
|
||||
!className.endsWith("left")
|
||||
);
|
||||
});
|
||||
});
|
||||
|
||||
const kOverlapPaddingSize = 10;
|
||||
function toRegions(els) {
|
||||
return els.map((el) => {
|
||||
const boundRect = el.getBoundingClientRect();
|
||||
const top =
|
||||
boundRect.top +
|
||||
document.documentElement.scrollTop -
|
||||
kOverlapPaddingSize;
|
||||
return {
|
||||
top,
|
||||
bottom: top + el.scrollHeight + 2 * kOverlapPaddingSize,
|
||||
};
|
||||
});
|
||||
}
|
||||
|
||||
let hasObserved = false;
|
||||
const visibleItemObserver = (els) => {
|
||||
let visibleElements = [...els];
|
||||
const intersectionObserver = new IntersectionObserver(
|
||||
(entries, _observer) => {
|
||||
entries.forEach((entry) => {
|
||||
if (entry.isIntersecting) {
|
||||
if (visibleElements.indexOf(entry.target) === -1) {
|
||||
visibleElements.push(entry.target);
|
||||
}
|
||||
} else {
|
||||
visibleElements = visibleElements.filter((visibleEntry) => {
|
||||
return visibleEntry !== entry;
|
||||
});
|
||||
}
|
||||
});
|
||||
|
||||
if (!hasObserved) {
|
||||
hideOverlappedSidebars();
|
||||
}
|
||||
hasObserved = true;
|
||||
},
|
||||
{}
|
||||
);
|
||||
els.forEach((el) => {
|
||||
intersectionObserver.observe(el);
|
||||
});
|
||||
|
||||
return {
|
||||
getVisibleEntries: () => {
|
||||
return visibleElements;
|
||||
},
|
||||
};
|
||||
};
|
||||
|
||||
const rightElementObserver = visibleItemObserver(rightSideConflictEls);
|
||||
const leftElementObserver = visibleItemObserver(leftSideConflictEls);
|
||||
|
||||
const hideOverlappedSidebars = () => {
|
||||
marginScrollVisibility(toRegions(rightElementObserver.getVisibleEntries()));
|
||||
sidebarScrollVisiblity(toRegions(leftElementObserver.getVisibleEntries()));
|
||||
if (tocLeftScrollVisibility) {
|
||||
tocLeftScrollVisibility(
|
||||
toRegions(leftElementObserver.getVisibleEntries())
|
||||
);
|
||||
}
|
||||
};
|
||||
|
||||
window.quartoToggleReader = () => {
|
||||
// Applies a slow class (or removes it)
|
||||
// to update the transition speed
|
||||
const slowTransition = (slow) => {
|
||||
const manageTransition = (id, slow) => {
|
||||
const el = document.getElementById(id);
|
||||
if (el) {
|
||||
if (slow) {
|
||||
el.classList.add("slow");
|
||||
} else {
|
||||
el.classList.remove("slow");
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
manageTransition("TOC", slow);
|
||||
manageTransition("quarto-sidebar", slow);
|
||||
};
|
||||
const readerMode = !isReaderMode();
|
||||
setReaderModeValue(readerMode);
|
||||
|
||||
// If we're entering reader mode, slow the transition
|
||||
if (readerMode) {
|
||||
slowTransition(readerMode);
|
||||
}
|
||||
highlightReaderToggle(readerMode);
|
||||
hideOverlappedSidebars();
|
||||
|
||||
// If we're exiting reader mode, restore the non-slow transition
|
||||
if (!readerMode) {
|
||||
slowTransition(!readerMode);
|
||||
}
|
||||
};
|
||||
|
||||
const highlightReaderToggle = (readerMode) => {
|
||||
const els = document.querySelectorAll(".quarto-reader-toggle");
|
||||
if (els) {
|
||||
els.forEach((el) => {
|
||||
if (readerMode) {
|
||||
el.classList.add("reader");
|
||||
} else {
|
||||
el.classList.remove("reader");
|
||||
}
|
||||
});
|
||||
}
|
||||
};
|
||||
|
||||
const setReaderModeValue = (val) => {
|
||||
if (window.location.protocol !== "file:") {
|
||||
window.localStorage.setItem("quarto-reader-mode", val);
|
||||
} else {
|
||||
localReaderMode = val;
|
||||
}
|
||||
};
|
||||
|
||||
const isReaderMode = () => {
|
||||
if (window.location.protocol !== "file:") {
|
||||
return window.localStorage.getItem("quarto-reader-mode") === "true";
|
||||
} else {
|
||||
return localReaderMode;
|
||||
}
|
||||
};
|
||||
let localReaderMode = null;
|
||||
|
||||
const tocOpenDepthStr = tocEl?.getAttribute("data-toc-expanded");
|
||||
const tocOpenDepth = tocOpenDepthStr ? Number(tocOpenDepthStr) : 1;
|
||||
|
||||
// Walk the TOC and collapse/expand nodes
|
||||
// Nodes are expanded if:
|
||||
// - they are top level
|
||||
// - they have children that are 'active' links
|
||||
// - they are directly below an link that is 'active'
|
||||
const walk = (el, depth) => {
|
||||
// Tick depth when we enter a UL
|
||||
if (el.tagName === "UL") {
|
||||
depth = depth + 1;
|
||||
}
|
||||
|
||||
// It this is active link
|
||||
let isActiveNode = false;
|
||||
if (el.tagName === "A" && el.classList.contains("active")) {
|
||||
isActiveNode = true;
|
||||
}
|
||||
|
||||
// See if there is an active child to this element
|
||||
let hasActiveChild = false;
|
||||
for (const child of el.children) {
|
||||
hasActiveChild = walk(child, depth) || hasActiveChild;
|
||||
}
|
||||
|
||||
// Process the collapse state if this is an UL
|
||||
if (el.tagName === "UL") {
|
||||
if (tocOpenDepth === -1 && depth > 1) {
|
||||
// toc-expand: false
|
||||
el.classList.add("collapse");
|
||||
} else if (
|
||||
depth <= tocOpenDepth ||
|
||||
hasActiveChild ||
|
||||
prevSiblingIsActiveLink(el)
|
||||
) {
|
||||
el.classList.remove("collapse");
|
||||
} else {
|
||||
el.classList.add("collapse");
|
||||
}
|
||||
|
||||
// untick depth when we leave a UL
|
||||
depth = depth - 1;
|
||||
}
|
||||
return hasActiveChild || isActiveNode;
|
||||
};
|
||||
|
||||
// walk the TOC and expand / collapse any items that should be shown
|
||||
if (tocEl) {
|
||||
updateActiveLink();
|
||||
walk(tocEl, 0);
|
||||
}
|
||||
|
||||
// Throttle the scroll event and walk peridiocally
|
||||
window.document.addEventListener(
|
||||
"scroll",
|
||||
throttle(() => {
|
||||
if (tocEl) {
|
||||
updateActiveLink();
|
||||
walk(tocEl, 0);
|
||||
}
|
||||
if (!isReaderMode()) {
|
||||
hideOverlappedSidebars();
|
||||
}
|
||||
}, 5)
|
||||
);
|
||||
window.addEventListener(
|
||||
"resize",
|
||||
throttle(() => {
|
||||
if (tocEl) {
|
||||
updateActiveLink();
|
||||
walk(tocEl, 0);
|
||||
}
|
||||
if (!isReaderMode()) {
|
||||
hideOverlappedSidebars();
|
||||
}
|
||||
}, 10)
|
||||
);
|
||||
hideOverlappedSidebars();
|
||||
highlightReaderToggle(isReaderMode());
|
||||
});
|
||||
|
||||
tabsets.init();
|
||||
axe.init();
|
||||
|
||||
function throttle(func, wait) {
|
||||
let waiting = false;
|
||||
return function () {
|
||||
if (!waiting) {
|
||||
func.apply(this, arguments);
|
||||
waiting = true;
|
||||
setTimeout(function () {
|
||||
waiting = false;
|
||||
}, wait);
|
||||
}
|
||||
};
|
||||
}
|
||||
|
||||
function nexttick(func) {
|
||||
return setTimeout(func, 0);
|
||||
}
|
||||
@@ -0,0 +1,95 @@
|
||||
// grouped tabsets
|
||||
|
||||
export function init() {
|
||||
window.addEventListener("pageshow", (_event) => {
|
||||
function getTabSettings() {
|
||||
const data = localStorage.getItem("quarto-persistent-tabsets-data");
|
||||
if (!data) {
|
||||
localStorage.setItem("quarto-persistent-tabsets-data", "{}");
|
||||
return {};
|
||||
}
|
||||
if (data) {
|
||||
return JSON.parse(data);
|
||||
}
|
||||
}
|
||||
|
||||
function setTabSettings(data) {
|
||||
localStorage.setItem(
|
||||
"quarto-persistent-tabsets-data",
|
||||
JSON.stringify(data)
|
||||
);
|
||||
}
|
||||
|
||||
function setTabState(groupName, groupValue) {
|
||||
const data = getTabSettings();
|
||||
data[groupName] = groupValue;
|
||||
setTabSettings(data);
|
||||
}
|
||||
|
||||
function toggleTab(tab, active) {
|
||||
const tabPanelId = tab.getAttribute("aria-controls");
|
||||
const tabPanel = document.getElementById(tabPanelId);
|
||||
if (active) {
|
||||
tab.classList.add("active");
|
||||
tabPanel.classList.add("active");
|
||||
} else {
|
||||
tab.classList.remove("active");
|
||||
tabPanel.classList.remove("active");
|
||||
}
|
||||
}
|
||||
|
||||
function toggleAll(selectedGroup, selectorsToSync) {
|
||||
for (const [thisGroup, tabs] of Object.entries(selectorsToSync)) {
|
||||
const active = selectedGroup === thisGroup;
|
||||
for (const tab of tabs) {
|
||||
toggleTab(tab, active);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
function findSelectorsToSyncByLanguage() {
|
||||
const result = {};
|
||||
const tabs = Array.from(
|
||||
document.querySelectorAll(`div[data-group] a[id^='tabset-']`)
|
||||
);
|
||||
for (const item of tabs) {
|
||||
const div = item.parentElement.parentElement.parentElement;
|
||||
const group = div.getAttribute("data-group");
|
||||
if (!result[group]) {
|
||||
result[group] = {};
|
||||
}
|
||||
const selectorsToSync = result[group];
|
||||
const value = item.innerHTML;
|
||||
if (!selectorsToSync[value]) {
|
||||
selectorsToSync[value] = [];
|
||||
}
|
||||
selectorsToSync[value].push(item);
|
||||
}
|
||||
return result;
|
||||
}
|
||||
|
||||
function setupSelectorSync() {
|
||||
const selectorsToSync = findSelectorsToSyncByLanguage();
|
||||
Object.entries(selectorsToSync).forEach(([group, tabSetsByValue]) => {
|
||||
Object.entries(tabSetsByValue).forEach(([value, items]) => {
|
||||
items.forEach((item) => {
|
||||
item.addEventListener("click", (_event) => {
|
||||
setTabState(group, value);
|
||||
toggleAll(value, selectorsToSync[group]);
|
||||
});
|
||||
});
|
||||
});
|
||||
});
|
||||
return selectorsToSync;
|
||||
}
|
||||
|
||||
const selectorsToSync = setupSelectorSync();
|
||||
for (const [group, selectedName] of Object.entries(getTabSettings())) {
|
||||
const selectors = selectorsToSync[group];
|
||||
// it's possible that stale state gives us empty selections, so we explicitly check here.
|
||||
if (selectors) {
|
||||
toggleAll(selectedName, selectors);
|
||||
}
|
||||
}
|
||||
});
|
||||
}
|
||||
@@ -0,0 +1 @@
|
||||
.tippy-box[data-animation=fade][data-state=hidden]{opacity:0}[data-tippy-root]{max-width:calc(100vw - 10px)}.tippy-box{position:relative;background-color:#333;color:#fff;border-radius:4px;font-size:14px;line-height:1.4;white-space:normal;outline:0;transition-property:transform,visibility,opacity}.tippy-box[data-placement^=top]>.tippy-arrow{bottom:0}.tippy-box[data-placement^=top]>.tippy-arrow:before{bottom:-7px;left:0;border-width:8px 8px 0;border-top-color:initial;transform-origin:center top}.tippy-box[data-placement^=bottom]>.tippy-arrow{top:0}.tippy-box[data-placement^=bottom]>.tippy-arrow:before{top:-7px;left:0;border-width:0 8px 8px;border-bottom-color:initial;transform-origin:center bottom}.tippy-box[data-placement^=left]>.tippy-arrow{right:0}.tippy-box[data-placement^=left]>.tippy-arrow:before{border-width:8px 0 8px 8px;border-left-color:initial;right:-7px;transform-origin:center left}.tippy-box[data-placement^=right]>.tippy-arrow{left:0}.tippy-box[data-placement^=right]>.tippy-arrow:before{left:-7px;border-width:8px 8px 8px 0;border-right-color:initial;transform-origin:center right}.tippy-box[data-inertia][data-state=visible]{transition-timing-function:cubic-bezier(.54,1.5,.38,1.11)}.tippy-arrow{width:16px;height:16px;color:#333}.tippy-arrow:before{content:"";position:absolute;border-color:transparent;border-style:solid}.tippy-content{position:relative;padding:5px 9px;z-index:1}
|
||||
@@ -0,0 +1,2 @@
|
||||
!function(e,t){"object"==typeof exports&&"undefined"!=typeof module?module.exports=t(require("@popperjs/core")):"function"==typeof define&&define.amd?define(["@popperjs/core"],t):(e=e||self).tippy=t(e.Popper)}(this,(function(e){"use strict";var t={passive:!0,capture:!0},n=function(){return document.body};function r(e,t,n){if(Array.isArray(e)){var r=e[t];return null==r?Array.isArray(n)?n[t]:n:r}return e}function o(e,t){var n={}.toString.call(e);return 0===n.indexOf("[object")&&n.indexOf(t+"]")>-1}function i(e,t){return"function"==typeof e?e.apply(void 0,t):e}function a(e,t){return 0===t?e:function(r){clearTimeout(n),n=setTimeout((function(){e(r)}),t)};var n}function s(e,t){var n=Object.assign({},e);return t.forEach((function(e){delete n[e]})),n}function u(e){return[].concat(e)}function c(e,t){-1===e.indexOf(t)&&e.push(t)}function p(e){return e.split("-")[0]}function f(e){return[].slice.call(e)}function l(e){return Object.keys(e).reduce((function(t,n){return void 0!==e[n]&&(t[n]=e[n]),t}),{})}function d(){return document.createElement("div")}function v(e){return["Element","Fragment"].some((function(t){return o(e,t)}))}function m(e){return o(e,"MouseEvent")}function g(e){return!(!e||!e._tippy||e._tippy.reference!==e)}function h(e){return v(e)?[e]:function(e){return o(e,"NodeList")}(e)?f(e):Array.isArray(e)?e:f(document.querySelectorAll(e))}function b(e,t){e.forEach((function(e){e&&(e.style.transitionDuration=t+"ms")}))}function y(e,t){e.forEach((function(e){e&&e.setAttribute("data-state",t)}))}function w(e){var t,n=u(e)[0];return null!=n&&null!=(t=n.ownerDocument)&&t.body?n.ownerDocument:document}function E(e,t,n){var r=t+"EventListener";["transitionend","webkitTransitionEnd"].forEach((function(t){e[r](t,n)}))}function O(e,t){for(var n=t;n;){var r;if(e.contains(n))return!0;n=null==n.getRootNode||null==(r=n.getRootNode())?void 0:r.host}return!1}var x={isTouch:!1},C=0;function T(){x.isTouch||(x.isTouch=!0,window.performance&&document.addEventListener("mousemove",A))}function A(){var e=performance.now();e-C<20&&(x.isTouch=!1,document.removeEventListener("mousemove",A)),C=e}function L(){var e=document.activeElement;if(g(e)){var t=e._tippy;e.blur&&!t.state.isVisible&&e.blur()}}var D=!!("undefined"!=typeof window&&"undefined"!=typeof document)&&!!window.msCrypto,R=Object.assign({appendTo:n,aria:{content:"auto",expanded:"auto"},delay:0,duration:[300,250],getReferenceClientRect:null,hideOnClick:!0,ignoreAttributes:!1,interactive:!1,interactiveBorder:2,interactiveDebounce:0,moveTransition:"",offset:[0,10],onAfterUpdate:function(){},onBeforeUpdate:function(){},onCreate:function(){},onDestroy:function(){},onHidden:function(){},onHide:function(){},onMount:function(){},onShow:function(){},onShown:function(){},onTrigger:function(){},onUntrigger:function(){},onClickOutside:function(){},placement:"top",plugins:[],popperOptions:{},render:null,showOnCreate:!1,touch:!0,trigger:"mouseenter focus",triggerTarget:null},{animateFill:!1,followCursor:!1,inlinePositioning:!1,sticky:!1},{allowHTML:!1,animation:"fade",arrow:!0,content:"",inertia:!1,maxWidth:350,role:"tooltip",theme:"",zIndex:9999}),k=Object.keys(R);function P(e){var t=(e.plugins||[]).reduce((function(t,n){var r,o=n.name,i=n.defaultValue;o&&(t[o]=void 0!==e[o]?e[o]:null!=(r=R[o])?r:i);return t}),{});return Object.assign({},e,t)}function j(e,t){var n=Object.assign({},t,{content:i(t.content,[e])},t.ignoreAttributes?{}:function(e,t){return(t?Object.keys(P(Object.assign({},R,{plugins:t}))):k).reduce((function(t,n){var r=(e.getAttribute("data-tippy-"+n)||"").trim();if(!r)return t;if("content"===n)t[n]=r;else try{t[n]=JSON.parse(r)}catch(e){t[n]=r}return t}),{})}(e,t.plugins));return n.aria=Object.assign({},R.aria,n.aria),n.aria={expanded:"auto"===n.aria.expanded?t.interactive:n.aria.expanded,content:"auto"===n.aria.content?t.interactive?null:"describedby":n.aria.content},n}function M(e,t){e.innerHTML=t}function V(e){var t=d();return!0===e?t.className="tippy-arrow":(t.className="tippy-svg-arrow",v(e)?t.appendChild(e):M(t,e)),t}function I(e,t){v(t.content)?(M(e,""),e.appendChild(t.content)):"function"!=typeof t.content&&(t.allowHTML?M(e,t.content):e.textContent=t.content)}function S(e){var t=e.firstElementChild,n=f(t.children);return{box:t,content:n.find((function(e){return e.classList.contains("tippy-content")})),arrow:n.find((function(e){return e.classList.contains("tippy-arrow")||e.classList.contains("tippy-svg-arrow")})),backdrop:n.find((function(e){return e.classList.contains("tippy-backdrop")}))}}function N(e){var t=d(),n=d();n.className="tippy-box",n.setAttribute("data-state","hidden"),n.setAttribute("tabindex","-1");var r=d();function o(n,r){var o=S(t),i=o.box,a=o.content,s=o.arrow;r.theme?i.setAttribute("data-theme",r.theme):i.removeAttribute("data-theme"),"string"==typeof r.animation?i.setAttribute("data-animation",r.animation):i.removeAttribute("data-animation"),r.inertia?i.setAttribute("data-inertia",""):i.removeAttribute("data-inertia"),i.style.maxWidth="number"==tyLine truncated
|
||||
|
||||
File diff suppressed because it is too large.
Load diff
File diff suppressed because it is too large.
Load diff
File renamed without changes.
|
500 Internal Server Error
An error occurred: An error occurred Gitea Version: 28.0.0 |