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arnaou committed Sep 25, 2024
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8 changes: 8 additions & 0 deletions _sources/notebooks.ipynb
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"There is a lot more that you can do with outputs (such as including interactive outputs)\n",
"with your book. For more information about this, see [the Jupyter Book documentation](https://jupyterbook.org)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"```{tableofcontents}\n",
"```"
]
}
],
"metadata": {
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8 changes: 4 additions & 4 deletions genindex.html
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</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction to Python</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="markdown.html">Markdown Files</a></li>
<li class="toctree-l1"><a class="reference internal" href="notebooks.html">Content with notebooks</a></li>
<li class="toctree-l1 has-children"><a class="reference internal" href="markdown-notebooks.html">Notebooks with MyST Markdown</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l2"><a class="reference internal" href="mymarkdownfile.html">Here’s my sample title</a></li>
<li class="toctree-l1"><a class="reference internal" href="markdown.html">1. Alternative name</a></li>
<li class="toctree-l1"><a class="reference internal" href="notebooks.html">2. Content with notebooks</a></li>
<li class="toctree-l1 has-children"><a class="reference internal" href="markdown-notebooks.html">3. Notebooks with MyST Markdown</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l2"><a class="reference internal" href="mymarkdownfile.html">3.4. Here’s my sample title</a></li>
</ul>
</details></li>
</ul>
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18 changes: 9 additions & 9 deletions index.html
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<script>DOCUMENTATION_OPTIONS.pagename = 'index';</script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Markdown Files" href="markdown.html" />
<link rel="next" title="1. Markdown Files" href="markdown.html" />
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<meta name="docsearch:language" content="en"/>
</head>
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</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction to Python</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="markdown.html">Markdown Files</a></li>
<li class="toctree-l1"><a class="reference internal" href="notebooks.html">Content with notebooks</a></li>
<li class="toctree-l1 has-children"><a class="reference internal" href="markdown-notebooks.html">Notebooks with MyST Markdown</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l2"><a class="reference internal" href="mymarkdownfile.html">Here’s my sample title</a></li>
<li class="toctree-l1"><a class="reference internal" href="markdown.html">1. Alternative name</a></li>
<li class="toctree-l1"><a class="reference internal" href="notebooks.html">2. Content with notebooks</a></li>
<li class="toctree-l1 has-children"><a class="reference internal" href="markdown-notebooks.html">3. Notebooks with MyST Markdown</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l2"><a class="reference internal" href="mymarkdownfile.html">3.4. Here’s my sample title</a></li>
</ul>
</details></li>
</ul>
Expand Down Expand Up @@ -405,9 +405,9 @@ <h1>Welcome to your Jupyter Book<a class="headerlink" href="#welcome-to-your-jup
<div class="toctree-wrapper compound">
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction to Python</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="markdown.html">Markdown Files</a></li>
<li class="toctree-l1"><a class="reference internal" href="notebooks.html">Content with notebooks</a></li>
<li class="toctree-l1"><a class="reference internal" href="markdown-notebooks.html">Notebooks with MyST Markdown</a></li>
<li class="toctree-l1"><a class="reference internal" href="markdown.html">1. Alternative name</a></li>
<li class="toctree-l1"><a class="reference internal" href="notebooks.html">2. Content with notebooks</a></li>
<li class="toctree-l1"><a class="reference internal" href="markdown-notebooks.html">3. Notebooks with MyST Markdown</a></li>
</ul>
</div>
</section>
Expand Down Expand Up @@ -447,7 +447,7 @@ <h1>Welcome to your Jupyter Book<a class="headerlink" href="#welcome-to-your-jup
title="next page">
<div class="prev-next-info">
<p class="prev-next-subtitle">next</p>
<p class="prev-next-title">Markdown Files</p>
<p class="prev-next-title"><span class="section-number">1. </span>Markdown Files</p>
</div>
<i class="fa-solid fa-angle-right"></i>
</a>
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38 changes: 19 additions & 19 deletions markdown-notebooks.html
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<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />

<title>Notebooks with MyST Markdown &#8212; DIG4BIO-workshops</title>
<title>3. Notebooks with MyST Markdown &#8212; DIG4BIO-workshops</title>



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<script>DOCUMENTATION_OPTIONS.pagename = 'markdown-notebooks';</script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Here’s my sample title" href="mymarkdownfile.html" />
<link rel="prev" title="Content with notebooks" href="notebooks.html" />
<link rel="next" title="3.4. Here’s my sample title" href="mymarkdownfile.html" />
<link rel="prev" title="2. Content with notebooks" href="notebooks.html" />
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<meta name="docsearch:language" content="en"/>
</head>
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</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction to Python</span></p>
<ul class="current nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="markdown.html">Markdown Files</a></li>
<li class="toctree-l1"><a class="reference internal" href="notebooks.html">Content with notebooks</a></li>
<li class="toctree-l1 current active has-children"><a class="current reference internal" href="#">Notebooks with MyST Markdown</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l2"><a class="reference internal" href="mymarkdownfile.html">Here’s my sample title</a></li>
<li class="toctree-l1"><a class="reference internal" href="markdown.html">1. Alternative name</a></li>
<li class="toctree-l1"><a class="reference internal" href="notebooks.html">2. Content with notebooks</a></li>
<li class="toctree-l1 current active has-children"><a class="current reference internal" href="#">3. Notebooks with MyST Markdown</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l2"><a class="reference internal" href="mymarkdownfile.html">3.4. Here’s my sample title</a></li>
</ul>
</details></li>
</ul>
Expand Down Expand Up @@ -382,9 +382,9 @@ <h2> Contents </h2>
</div>
<nav aria-label="Page">
<ul class="visible nav section-nav flex-column">
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#an-example-cell">An example cell</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#create-a-notebook-with-myst-markdown">Create a notebook with MyST Markdown</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#quickly-add-yaml-metadata-for-myst-notebooks">Quickly add YAML metadata for MyST Notebooks</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#an-example-cell">3.1. An example cell</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#create-a-notebook-with-myst-markdown">3.2. Create a notebook with MyST Markdown</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#quickly-add-yaml-metadata-for-myst-notebooks">3.3. Quickly add YAML metadata for MyST Notebooks</a></li>
</ul>
</nav>
</div>
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<article class="bd-article">

<section class="tex2jax_ignore mathjax_ignore" id="notebooks-with-myst-markdown">
<h1>Notebooks with MyST Markdown<a class="headerlink" href="#notebooks-with-myst-markdown" title="Link to this heading">#</a></h1>
<h1><span class="section-number">3. </span>Notebooks with MyST Markdown<a class="headerlink" href="#notebooks-with-myst-markdown" title="Link to this heading">#</a></h1>
<p>Jupyter Book also lets you write text-based notebooks using MyST Markdown.
See <a class="reference external" href="https://jupyterbook.org/file-types/myst-notebooks.html">the Notebooks with MyST Markdown documentation</a> for more detailed instructions.
This page shows off a notebook written in MyST Markdown.</p>
<section id="an-example-cell">
<h2>An example cell<a class="headerlink" href="#an-example-cell" title="Link to this heading">#</a></h2>
<h2><span class="section-number">3.1. </span>An example cell<a class="headerlink" href="#an-example-cell" title="Link to this heading">#</a></h2>
<p>With MyST Markdown, you can define code cells with a directive like so:</p>
<div class="cell docutils container">
<div class="cell_input docutils container">
Expand All @@ -425,7 +425,7 @@ <h2>An example cell<a class="headerlink" href="#an-example-cell" title="Link to
</div>
</section>
<section id="create-a-notebook-with-myst-markdown">
<h2>Create a notebook with MyST Markdown<a class="headerlink" href="#create-a-notebook-with-myst-markdown" title="Link to this heading">#</a></h2>
<h2><span class="section-number">3.2. </span>Create a notebook with MyST Markdown<a class="headerlink" href="#create-a-notebook-with-myst-markdown" title="Link to this heading">#</a></h2>
<p>MyST Markdown notebooks are defined by two things:</p>
<ol class="arabic simple">
<li><p>YAML metadata that is needed to understand if / how it should convert text files to notebooks (including information about the kernel needed).
Expand All @@ -435,7 +435,7 @@ <h2>Create a notebook with MyST Markdown<a class="headerlink" href="#create-a-no
<p>That’s all that is needed to get started!</p>
</section>
<section id="quickly-add-yaml-metadata-for-myst-notebooks">
<h2>Quickly add YAML metadata for MyST Notebooks<a class="headerlink" href="#quickly-add-yaml-metadata-for-myst-notebooks" title="Link to this heading">#</a></h2>
<h2><span class="section-number">3.3. </span>Quickly add YAML metadata for MyST Notebooks<a class="headerlink" href="#quickly-add-yaml-metadata-for-myst-notebooks" title="Link to this heading">#</a></h2>
<p>If you have a markdown file and you’d like to quickly add YAML metadata to it, so that Jupyter Book will treat it as a MyST Markdown Notebook, run the following command:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">jupyter</span><span class="o">-</span><span class="n">book</span> <span class="n">myst</span> <span class="n">init</span> <span class="n">path</span><span class="o">/</span><span class="n">to</span><span class="o">/</span><span class="n">markdownfile</span><span class="o">.</span><span class="n">md</span>
</pre></div>
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<i class="fa-solid fa-angle-left"></i>
<div class="prev-next-info">
<p class="prev-next-subtitle">previous</p>
<p class="prev-next-title">Content with notebooks</p>
<p class="prev-next-title"><span class="section-number">2. </span>Content with notebooks</p>
</div>
</a>
<a class="right-next"
href="mymarkdownfile.html"
title="next page">
<div class="prev-next-info">
<p class="prev-next-subtitle">next</p>
<p class="prev-next-title">Here’s my sample title</p>
<p class="prev-next-title"><span class="section-number">3.4. </span>Here’s my sample title</p>
</div>
<i class="fa-solid fa-angle-right"></i>
</a>
Expand All @@ -509,9 +509,9 @@ <h2>Quickly add YAML metadata for MyST Notebooks<a class="headerlink" href="#qui
</div>
<nav class="bd-toc-nav page-toc">
<ul class="visible nav section-nav flex-column">
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#an-example-cell">An example cell</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#create-a-notebook-with-myst-markdown">Create a notebook with MyST Markdown</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#quickly-add-yaml-metadata-for-myst-notebooks">Quickly add YAML metadata for MyST Notebooks</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#an-example-cell">3.1. An example cell</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#create-a-notebook-with-myst-markdown">3.2. Create a notebook with MyST Markdown</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#quickly-add-yaml-metadata-for-myst-notebooks">3.3. Quickly add YAML metadata for MyST Notebooks</a></li>
</ul>
</nav></div>

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