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index.html
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<!DOCTYPE html>
<html lang="en"><head>
<script src="index_files/libs/clipboard/clipboard.min.js"></script>
<script src="index_files/libs/quarto-html/tabby.min.js"></script>
<script src="index_files/libs/quarto-html/popper.min.js"></script>
<script src="index_files/libs/quarto-html/tippy.umd.min.js"></script>
<link href="index_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="index_files/libs/quarto-html/light-border.css" rel="stylesheet">
<link href="index_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
<link href="index_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
<link href="index_files/libs/quarto-contrib/fontawesome6-0.1.0/all.css" rel="stylesheet">
<link href="index_files/libs/quarto-contrib/fontawesome6-0.1.0/latex-fontsize.css" rel="stylesheet"><meta charset="utf-8">
<meta name="generator" content="quarto-1.4.554">
<title>index</title>
<meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui">
<link rel="stylesheet" href="index_files/libs/revealjs/dist/reset.css">
<link rel="stylesheet" href="index_files/libs/revealjs/dist/reveal.css">
<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 */
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { 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;
color: #aaaaaa;
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode
{ color: #003b4f; background-color: #f1f3f5; }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span { color: #003b4f; } /* Normal */
code span.al { color: #ad0000; } /* Alert */
code span.an { color: #5e5e5e; } /* Annotation */
code span.at { color: #657422; } /* Attribute */
code span.bn { color: #ad0000; } /* BaseN */
code span.bu { } /* BuiltIn */
code span.cf { color: #003b4f; } /* ControlFlow */
code span.ch { color: #20794d; } /* Char */
code span.cn { color: #8f5902; } /* Constant */
code span.co { color: #5e5e5e; } /* Comment */
code span.cv { color: #5e5e5e; font-style: italic; } /* CommentVar */
code span.do { color: #5e5e5e; font-style: italic; } /* Documentation */
code span.dt { color: #ad0000; } /* DataType */
code span.dv { color: #ad0000; } /* DecVal */
code span.er { color: #ad0000; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #ad0000; } /* Float */
code span.fu { color: #4758ab; } /* Function */
code span.im { color: #00769e; } /* Import */
code span.in { color: #5e5e5e; } /* Information */
code span.kw { color: #003b4f; } /* Keyword */
code span.op { color: #5e5e5e; } /* Operator */
code span.ot { color: #003b4f; } /* Other */
code span.pp { color: #ad0000; } /* Preprocessor */
code span.sc { color: #5e5e5e; } /* SpecialChar */
code span.ss { color: #20794d; } /* SpecialString */
code span.st { color: #20794d; } /* String */
code span.va { color: #111111; } /* Variable */
code span.vs { color: #20794d; } /* VerbatimString */
code span.wa { color: #5e5e5e; font-style: italic; } /* Warning */
</style>
<link rel="stylesheet" href="index_files/libs/revealjs/dist/theme/quarto.css">
<link href="index_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/reveal-menu/menu.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/reveal-menu/quarto-menu.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/quarto-support/footer.css" rel="stylesheet">
<style type="text/css">
.callout {
margin-top: 1em;
margin-bottom: 1em;
border-radius: .25rem;
}
.callout.callout-style-simple {
padding: 0em 0.5em;
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
display: flex;
}
.callout.callout-style-default {
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
}
.callout .callout-body-container {
flex-grow: 1;
}
.callout.callout-style-simple .callout-body {
font-size: 1rem;
font-weight: 400;
}
.callout.callout-style-default .callout-body {
font-size: 0.9rem;
font-weight: 400;
}
.callout.callout-titled.callout-style-simple .callout-body {
margin-top: 0.2em;
}
.callout:not(.callout-titled) .callout-body {
display: flex;
}
.callout:not(.no-icon).callout-titled.callout-style-simple .callout-content {
padding-left: 1.6em;
}
.callout.callout-titled .callout-header {
padding-top: 0.2em;
margin-bottom: -0.2em;
}
.callout.callout-titled .callout-title p {
margin-top: 0.5em;
margin-bottom: 0.5em;
}
.callout.callout-titled.callout-style-simple .callout-content p {
margin-top: 0;
}
.callout.callout-titled.callout-style-default .callout-content p {
margin-top: 0.7em;
}
.callout.callout-style-simple div.callout-title {
border-bottom: none;
font-size: .9rem;
font-weight: 600;
opacity: 75%;
}
.callout.callout-style-default div.callout-title {
border-bottom: none;
font-weight: 600;
opacity: 85%;
font-size: 0.9rem;
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-default div.callout-content {
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-simple .callout-icon::before {
height: 1rem;
width: 1rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 1rem 1rem;
}
.callout.callout-style-default .callout-icon::before {
height: 0.9rem;
width: 0.9rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 0.9rem 0.9rem;
}
.callout-title {
display: flex
}
.callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
.callout.no-icon::before {
display: none !important;
}
.callout.callout-titled .callout-body > .callout-content > :last-child {
padding-bottom: 0.5rem;
margin-bottom: 0;
}
.callout.callout-titled .callout-icon::before {
margin-top: .5rem;
padding-right: .5rem;
}
.callout:not(.callout-titled) .callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
/* Callout Types */
div.callout-note {
border-left-color: #4582ec !important;
}
div.callout-note .callout-icon::before {
background-image: url('data:image/png;base64,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');
}
div.callout-note.callout-style-default .callout-title {
background-color: #dae6fb
}
div.callout-important {
border-left-color: #d9534f !important;
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<div class="column logo" style="width:30%;">
<!--  -->
<p><img data-src="img/git-logo.png"></p>
</div><div class="column" style="width:70%;">
<div class="title">
<p>Version control</p>
</div>
<div class="subtitle">
<p>Introduction to git & GitHub</p>
</div>
<div class="date">
<p>May 2024</p>
</div>
<div class="columns">
<div class="column author" style="width:45%;">
<p>Nicolas Casajus<br> <a href="mailto:[email protected]"><i class="fa-solid fa-paper-plane" aria-label="paper-plane"></i></a> <a href="https://github.com/ahasverus"><i class="fa-brands fa-github" aria-label="github"></i></a> <a href="https://nicolascasajus.fr"><i class="fa-solid fa-globe" aria-label="globe"></i></a></p>
<div class="affiliation">
<p><i class="fa-solid fa-house" aria-label="house"></i> <a href="https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/">FRB-CESAB</a></p>
</div>
</div><!--
::: {.column .author width="45%"}
Camille Coux<br/>
[](mailto:[email protected])
[](https://github.com/camillecoux)
[](https://www.fondationbiodiversite.fr/en/membre/camille-coux/)
::: {.affiliation}
[https://github.com/frbcesab](https://github.com/frbcesab)
:::
:::
-->
</div>
</div>
</div>
</div>
</div>
</section>
<section>
<section id="introduction" class="title-slide slide level1 center">
<h1>Introduction</h1>
</section>
<section id="motivations" class="slide level2">
<h2>Motivations</h2>
<div class="columns">
<div class="column" data-align="left" style="width:50%;">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/folder_without_git.png"></p>
<figcaption>Project content (without <code>git</code>)</figcaption>
</figure>
</div>
</div><div class="column" style="width:50%;">
</div>
</div>
</section>
<section id="motivations-1" class="slide level2">
<h2>Motivations</h2>
<div class="columns">
<div class="column" data-align="left" style="width:50%;">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/folder_without_git.png"></p>
<figcaption>Project content (without <code>git</code>)</figcaption>
</figure>
</div>
</div><div class="column" style="width:50%;">
<p><strong>Questions</strong></p>
<ul>
<li>Which version of <code>analyses.R</code> is the final one?</li>
<li>What about <code>data.csv</code>?</li>
<li>What are the differences between versions?</li>
<li>Who have contributed to these versions? When?</li>
</ul>
</div>
</div>
</section>
<section id="motivations-2" class="slide level2">
<h2>Motivations</h2>
<div class="columns">
<div class="column" data-align="left" style="width:50%;">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/folder_without_git.png"></p>
<figcaption>Project content (without <code>git</code>)</figcaption>
</figure>
</div>
</div><div class="column" style="width:50%;">
<p><strong>Questions</strong></p>
<ul>
<li>Which version of <code>analyses.R</code> is the final one?</li>
<li>What about <code>data.csv</code>?</li>
<li>What are the differences between versions?</li>
<li>Who have contributed to these versions? When?</li>
</ul>
</div>
</div>
<p><i class="fa-solid fa-hand-point-right" aria-label="hand-point-right"></i> We need a tool that deals with versions for us</p>
</section>
<section id="motivations-3" class="slide level2">
<h2>Motivations</h2>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/git-logo-long.png" class="quarto-figure quarto-figure-center" style="width:15.0%"></p>
</figure>
</div>
<div class="columns">
<div class="column" data-align="left" style="width:50%;">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/folder_without_git.png"></p>
<figcaption>Project content (without <code>git</code>)</figcaption>
</figure>
</div>
</div><div class="column" data-align="left" style="width:50%;">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/folder_with_git.png"></p>
<figcaption>Project content (with <code>git</code>)</figcaption>
</figure>
</div>
</div>
</div>
</section>
<section id="presentation-of-git" class="slide level2">
<h2>Presentation of <code>git</code></h2>
<p><code>git</code> is a <strong>Version Control System</strong> (VCS).</p>
</section>
<section id="presentation-of-git-1" class="slide level2">
<h2>Presentation of <code>git</code></h2>
<p><code>git</code> is a <strong>Version Control System</strong> (VCS). With <code>git</code> you can:</p>
<div class="columns">
<div class="column" data-align="left" style="width:60%;">
<ul>
<li>keep your working copy clean</li>
<li>make contributions transparent <br>(what | who | when | why)</li>
<li>keep the entire history of a file (and project)</li>
<li>inspect a file throughout its life time</li>
<li>revert back to a previous version</li>
<li>handle multiple versions (branches)</li>
<li>facilitate collaborations w/ code hosting platforms <br>(GitHub, GitLab, Bitbucket, etc.)</li>
<li>backup your project</li>
</ul>
</div><div class="column" style="width:40%;">
<p><br> <br> <img data-src="img/git-logo-long.png"></p>
</div>
</div>
</section>
<section id="a-word-of-warning" class="slide level2">
<h2>A word of warning</h2>
<p><strong><code>git</code></strong> and <strong><code>GitHub</code></strong> are <strong>not the same thing</strong></p>
<ul>
<li><code>git</code> is a free and open-source <strong>software</strong></li>
<li><code>GitHub</code> (and co) is a <strong>web platform</strong> to host and share projects tracked by <code>git</code></li>
</ul>
<div class="fragment">
<p><br></p>
<p>In other words:</p>
<blockquote>
<p>You do not need <code>GitHub</code> to use <code>git</code> but you cannot use <code>GitHub</code> without using <code>git</code></p>
</blockquote>
</div>
</section>
<section id="git-as-a-cli" class="slide level2">
<h2>git as a CLI</h2>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/git-cli.png" class="quarto-figure quarto-figure-center" style="width:60.0%"></p>
</figure>
</div>
</section>
<section id="rstudio-and-git" class="slide level2">
<h2>RStudio and git</h2>
<div class="columns">
<div class="column" style="width:100%;">
<p><strong>Git main panel</strong></p>
<p><img data-src="img/git-rstudio.png" style="width:80.0%"></p>
</div><div class="column" style="width:0%;">
</div>
</div>
</section>
<section id="rstudio-and-git-1" class="slide level2">
<h2>RStudio and git</h2>
<div class="columns">
<div class="column" style="width:50%;">
<p><strong>Stage files, view differences and commit changes</strong></p>
<p><img data-src="img/rstudio-change.png" style="width:100.0%"></p>
</div><div class="column" style="width:50%;">
<p><strong>View history and versions</strong></p>
<p><img data-src="img/rstudio-history.png" style="width:100.0%"></p>
</div>
</div>
</section></section>
<section>
<section id="using-git" class="title-slide slide level1 center">
<h1>Using <code>git</code></h1>
</section>
<section id="how-does-git-work" class="slide level2">
<h2>How does <code>git</code> work?</h2>
<ul>
<li><code>git</code> takes a sequence of <strong>snapshots</strong></li>
<li>Each snapshot can contain changes for one or many file(s)</li>
<li>User chooses which files to <em>‘save’</em> in a snapshot and when <br>(<code>!=</code> file hosting services like Dropbox, Google Drive, etc.)</li>
</ul>
<div class="fragment">
<p><br></p>
<p><i class="fa-solid fa-hand-point-right" aria-label="hand-point-right"></i> In the <code>git</code> universe, a snapshot is a <strong>version</strong>, i.e. the state of the whole project at a specific point in time</p>
</div>
<div class="fragment">
<p><br></p>
<p>A snapshot is a two-step process:</p>
<ul>
<li><strong>Stage files</strong>: select which files to add to the version</li>
<li><strong>Commit changes</strong>: save the version and add metadata (<code>commit message</code>)</li>
</ul>
</div>
</section>
<section id="basic-workflow" class="slide level2">
<h2>Basic workflow</h2>
<p><i class="fa-solid fa-hand-point-right" aria-label="hand-point-right"></i> Initialize <code>git</code> in a (empty) folder (<code>repository</code>)</p>
<div class="columns">
<div class="column" style="width:60%;">
<p><img data-src="img/git-workflow-0.png" style="width:100.0%"></p>
</div><div class="column" style="width:40%;">
<p><br></p>
<div class="sourceCode" id="cb1"><pre class="sourceCode numberSource bash number-lines code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href=""></a><span class="fu">git</span> init</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p><br> The <strong>three areas</strong> of a <code>git</code> <code>repository</code>:</p>
<ul>
<li><strong><code>working copy</code></strong>: current state of the directory (what you actually see)</li>
<li><strong><code>staging area</code></strong>: selected files that will be added to the next version</li>
<li><strong><code>repository</code></strong>: area w/ all the versions<br>(the <code>.git/</code> subdirectory)</li>
</ul>
</div>
</div>
</section>
<section id="basic-workflow-1" class="slide level2">
<h2>Basic workflow</h2>
<p><i class="fa-solid fa-hand-point-right" aria-label="hand-point-right"></i> Add new files in the <code>repository</code></p>
<div class="columns">
<div class="column" style="width:60%;">
<p><img data-src="img/git-workflow-1.png" style="width:100.0%"></p>
</div><div class="column" style="width:40%;">
<p><br></p>
<div class="sourceCode" id="cb2"><pre class="sourceCode numberSource bash number-lines code-with-copy"><code class="sourceCode bash"><span id="cb2-1"><a href=""></a><span class="fu">git</span> status</span>
<span id="cb2-2"><a href=""></a></span>
<span id="cb2-3"><a href=""></a><span class="co"># On branch main</span></span>
<span id="cb2-4"><a href=""></a><span class="co"># </span></span>
<span id="cb2-5"><a href=""></a><span class="co"># No commits yet</span></span>
<span id="cb2-6"><a href=""></a><span class="co"># </span></span>
<span id="cb2-7"><a href=""></a><span class="co"># Untracked files:</span></span>
<span id="cb2-8"><a href=""></a><span class="co"># README.md</span></span>
<span id="cb2-9"><a href=""></a><span class="co"># analyses.R</span></span>
<span id="cb2-10"><a href=""></a><span class="co"># data.csv</span></span>
<span id="cb2-11"><a href=""></a><span class="co"># </span></span>
<span id="cb2-12"><a href=""></a><span class="co"># Nothing added to commit but untracked files present</span></span>
<span id="cb2-13"><a href=""></a><span class="co"># Use "git add <file>..." to track</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</section>
<section id="basic-workflow-2" class="slide level2">
<h2>Basic workflow</h2>
<p><i class="fa-solid fa-hand-point-right" aria-label="hand-point-right"></i> <code>Stage</code> (select) one file</p>
<div class="columns">
<div class="column" style="width:60%;">
<p><img data-src="img/git-workflow-2.png" style="width:100.0%"></p>
</div><div class="column" style="width:40%;">
<p><br></p>
<div class="sourceCode" id="cb3"><pre class="sourceCode numberSource bash number-lines code-with-copy"><code class="sourceCode bash"><span id="cb3-1"><a href=""></a><span class="fu">git</span> add data.csv</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p><br></p>
<div class="sourceCode" id="cb4"><pre class="sourceCode numberSource bash number-lines code-with-copy"><code class="sourceCode bash"><span id="cb4-1"><a href=""></a><span class="fu">git</span> status</span>
<span id="cb4-2"><a href=""></a></span>
<span id="cb4-3"><a href=""></a><span class="co"># On branch main</span></span>
<span id="cb4-4"><a href=""></a><span class="co"># </span></span>
<span id="cb4-5"><a href=""></a><span class="co"># No commits yet</span></span>
<span id="cb4-6"><a href=""></a><span class="co"># </span></span>
<span id="cb4-7"><a href=""></a><span class="co"># Changes to be committed:</span></span>
<span id="cb4-8"><a href=""></a><span class="co"># (use "git rm --cached <file>..." to unstage)</span></span>
<span id="cb4-9"><a href=""></a><span class="co"># new file: data.csv</span></span>
<span id="cb4-10"><a href=""></a><span class="co"># </span></span>
<span id="cb4-11"><a href=""></a><span class="co"># Untracked files:</span></span>
<span id="cb4-12"><a href=""></a><span class="co"># (use "git add <file>..." to track)</span></span>
<span id="cb4-13"><a href=""></a><span class="co"># README.md</span></span>
<span id="cb4-14"><a href=""></a><span class="co"># analyses.R</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</section>
<section id="basic-workflow-3" class="slide level2">
<h2>Basic workflow</h2>
<p><i class="fa-solid fa-hand-point-right" aria-label="hand-point-right"></i> <code>Stage</code> (select) several files</p>
<div class="columns">
<div class="column" style="width:60%;">
<p><img data-src="img/git-workflow-3.png" style="width:100.0%"></p>
</div><div class="column" style="width:40%;">
<p><br></p>
<div class="sourceCode" id="cb5"><pre class="sourceCode numberSource bash number-lines code-with-copy"><code class="sourceCode bash"><span id="cb5-1"><a href=""></a><span class="fu">git</span> add data.csv analyses.R</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p><br></p>
<div class="sourceCode" id="cb6"><pre class="sourceCode numberSource bash number-lines code-with-copy"><code class="sourceCode bash"><span id="cb6-1"><a href=""></a><span class="fu">git</span> status</span>
<span id="cb6-2"><a href=""></a></span>
<span id="cb6-3"><a href=""></a><span class="co"># On branch main</span></span>
<span id="cb6-4"><a href=""></a><span class="co"># </span></span>
<span id="cb6-5"><a href=""></a><span class="co"># No commits yet</span></span>
<span id="cb6-6"><a href=""></a><span class="co"># </span></span>
<span id="cb6-7"><a href=""></a><span class="co"># Changes to be committed:</span></span>
<span id="cb6-8"><a href=""></a><span class="co"># (use "git rm --cached <file>..." to unstage)</span></span>
<span id="cb6-9"><a href=""></a><span class="co"># new file: analyses.R</span></span>
<span id="cb6-10"><a href=""></a><span class="co"># new file: data.csv</span></span>
<span id="cb6-11"><a href=""></a><span class="co"># </span></span>
<span id="cb6-12"><a href=""></a><span class="co"># Untracked files:</span></span>
<span id="cb6-13"><a href=""></a><span class="co"># (use "git add <file>..." to track)</span></span>
<span id="cb6-14"><a href=""></a><span class="co"># README.md</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</section>
<section id="basic-workflow-4" class="slide level2">
<h2>Basic workflow</h2>
<p><i class="fa-solid fa-hand-point-right" aria-label="hand-point-right"></i> <code>Stage</code> (select) all files</p>
<div class="columns">
<div class="column" style="width:60%;">
<p><img data-src="img/git-workflow-4.png" style="width:100.0%"></p>
</div><div class="column" style="width:40%;">
<p><br></p>
<div class="sourceCode" id="cb7"><pre class="sourceCode numberSource bash number-lines code-with-copy"><code class="sourceCode bash"><span id="cb7-1"><a href=""></a><span class="fu">git</span> add .</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p><br></p>
<div class="sourceCode" id="cb8"><pre class="sourceCode numberSource bash number-lines code-with-copy"><code class="sourceCode bash"><span id="cb8-1"><a href=""></a><span class="fu">git</span> status</span>
<span id="cb8-2"><a href=""></a></span>
<span id="cb8-3"><a href=""></a><span class="co"># On branch main</span></span>
<span id="cb8-4"><a href=""></a><span class="co"># </span></span>
<span id="cb8-5"><a href=""></a><span class="co"># No commits yet</span></span>
<span id="cb8-6"><a href=""></a><span class="co"># </span></span>
<span id="cb8-7"><a href=""></a><span class="co"># Changes to be committed:</span></span>
<span id="cb8-8"><a href=""></a><span class="co"># (use "git rm --cached <file>..." to unstage)</span></span>
<span id="cb8-9"><a href=""></a><span class="co"># new file: analyses.R</span></span>
<span id="cb8-10"><a href=""></a><span class="co"># new file: data.csv</span></span>
<span id="cb8-11"><a href=""></a><span class="co"># new file: README.md</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</section>
<section id="basic-workflow-5" class="slide level2">
<h2>Basic workflow</h2>
<p><i class="fa-solid fa-hand-point-right" aria-label="hand-point-right"></i> <code>Commit</code> changes to create a new version</p>
<div class="columns">
<div class="column" style="width:60%;">
<p><img data-src="img/git-workflow-5.png" style="width:100.0%"></p>
</div><div class="column" style="width:40%;">
<p><br></p>
<div class="sourceCode" id="cb9"><pre class="sourceCode numberSource bash number-lines code-with-copy"><code class="sourceCode bash"><span id="cb9-1"><a href=""></a><span class="fu">git</span> commit <span class="at">-m</span> <span class="st">"a good commit message"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</section>
<section id="basic-workflow-6" class="slide level2">
<h2>Basic workflow</h2>
<p><i class="fa-solid fa-hand-point-right" aria-label="hand-point-right"></i> Now we are <code>up-to-date</code></p>
<div class="columns">
<div class="column" style="width:60%;">
<p><img data-src="img/git-workflow-6.png" style="width:100.0%"></p>
</div><div class="column" style="width:40%;">
<p><br></p>
<div class="sourceCode" id="cb10"><pre class="sourceCode numberSource bash number-lines code-with-copy"><code class="sourceCode bash"><span id="cb10-1"><a href=""></a><span class="fu">git</span> status</span>
<span id="cb10-2"><a href=""></a></span>
<span id="cb10-3"><a href=""></a><span class="co"># On branch main</span></span>
<span id="cb10-4"><a href=""></a><span class="co"># nothing to commit, working tree clean</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</section>
<section id="the-status-of-a-file" class="slide level2">
<h2>The status of a file</h2>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/git-file-lifecycle-0.png" class="quarto-figure quarto-figure-center" style="width:50.0%"></p>
</figure>
</div>
<p>With <code>git</code> a file can be <strong>untracked</strong> or <strong>tracked</strong><sup>1</sup>. If it’s <strong>tracked</strong>, it can be:</p>
<ul>
<li>unmodified</li>
<li>modifed and unstaged</li>
<li>modified and staged</li>
</ul>
<aside><ol class="aside-footnotes"><li id="fn1"><p><a href="https://git-scm.com/book/en/v2/Git-Basics-Recording-Changes-to-the-Repository" class="uri">https://git-scm.com/book/en/v2/Git-Basics-Recording-Changes-to-the-Repository</a></p></li></ol></aside></section>
<section id="the-status-of-a-file-1" class="slide level2">
<h2>The status of a file</h2>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/git-file-lifecycle-1.png" class="quarto-figure quarto-figure-center" style="width:50.0%"></p>
</figure>
</div>
<p>When you create a new file, by default it’s <strong>untracked</strong>.</p>
</section>
<section id="the-status-of-a-file-2" class="slide level2">
<h2>The status of a file</h2>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/git-file-lifecycle-2.png" class="quarto-figure quarto-figure-center" style="width:50.0%"></p>
</figure>
</div>
<p>To tell <code>git</code> to <strong>track</strong> this new file, you have to <strong>stage</strong> it.</p>
</section>
<section id="the-status-of-a-file-3" class="slide level2">
<h2>The status of a file</h2>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/git-file-lifecycle-3.png" class="quarto-figure quarto-figure-center" style="width:50.0%"></p>
</figure>
</div>
<p>After <strong>commiting</strong> your changes, the file becomes <strong>unmodified</strong> (up-to-date with the latest version).</p>
</section>
<section id="the-status-of-a-file-4" class="slide level2">
<h2>The status of a file</h2>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/git-file-lifecycle-4.png" class="quarto-figure quarto-figure-center" style="width:50.0%"></p>
</figure>
</div>
<p>If you edit <strong>tracked file</strong>, it becomes <strong>modified</strong>.</p>
</section>
<section id="the-status-of-a-file-5" class="slide level2">
<h2>The status of a file</h2>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/git-file-lifecycle-5.png" class="quarto-figure quarto-figure-center" style="width:50.0%"></p>
</figure>
</div>
<p>When you decide to create a new version, <strong>stage</strong> the <strong>modified</strong> file.</p>
</section>
<section id="the-status-of-a-file-6" class="slide level2">
<h2>The status of a file</h2>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/git-file-lifecycle-6.png" class="quarto-figure quarto-figure-center" style="width:50.0%"></p>
</figure>
</div>
<p>After <strong>commiting</strong> your changes, the file becomes <strong>unmodified</strong> (up-to-date with the latest version).</p>
</section>
<section id="the-.gitignore" class="slide level2">
<h2>The <code>.gitignore</code></h2>
<p><i class="fa-solid fa-hand-point-right" aria-label="hand-point-right"></i> We can also tell <code>git</code> to <strong>ignore specific files</strong>: it’s the purpose of the <code>.gitignore</code> file</p>
<div class="fragment">
<p><br></p>
<div class="columns">
<div class="column" style="width:50%;">
<p>Which files? For instance:</p>
<ul>
<li>passwords, tokens and other secrets</li>
<li>temporary files</li>
<li>large files</li>
</ul>
</div><div class="column" style="width:50%;">
</div>
</div>
</div>
</section>
<section id="the-.gitignore-1" class="slide level2">
<h2>The <code>.gitignore</code></h2>
<p><i class="fa-solid fa-hand-point-right" aria-label="hand-point-right"></i> We can also tell <code>git</code> to <strong>ignore specific files</strong>: it’s the purpose of the <code>.gitignore</code> file</p>
<p><br></p>
<div class="columns">
<div class="column" style="width:50%;">
<p>Which files? For instance:</p>
<ul>
<li>passwords, tokens and other secrets</li>
<li>temporary files</li>
<li>large files</li>
</ul>
</div><div class="column" style="width:50%;">
<p>The syntax is simple:</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode numberSource txt number-lines code-with-copy"><code class="sourceCode default"><span id="cb11-1"><a href=""></a># Ignore a specific file</span>
<span id="cb11-2"><a href=""></a>README.html</span>
<span id="cb11-3"><a href=""></a></span>
<span id="cb11-4"><a href=""></a># Ignore all PDF</span>
<span id="cb11-5"><a href=""></a>*.pdf</span>
<span id="cb11-6"><a href=""></a></span>
<span id="cb11-7"><a href=""></a># Ignore a folder</span>
<span id="cb11-8"><a href=""></a>data/</span>
<span id="cb11-9"><a href=""></a></span>
<span id="cb11-10"><a href=""></a># Ignore a subfolder</span>
<span id="cb11-11"><a href=""></a>data/raw-data/</span>
<span id="cb11-12"><a href=""></a></span>
<span id="cb11-13"><a href=""></a># Ignore a specific file in a subfolder</span>
<span id="cb11-14"><a href=""></a>data/raw-data/raw-data.csv</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
<p><br></p>
<div class="fragment">
<p><i class="fa-solid fa-hand-point-right" aria-label="hand-point-right"></i> Template for <i class="fa-brands fa-r-project" aria-label="r-project"></i> projects available <a href="https://github.com/github/gitignore/blob/main/R.gitignore">here</a></p>
</div>
</section>
<section id="commits" class="slide level2">
<h2>Commits</h2>
<div class="columns">
<div class="column" style="width:50%;">
<p>When committing a new version (w/ <code>git commit</code>), the following information must be added:</p>
<ul>
<li><strong><code>WHO</code></strong> - the person who has made the changes <br>(automatically added by <code>git</code>)</li>
<li><strong><code>WHEN</code></strong> - the date of the commit <br>(automatically added by <code>git</code>)</li>
<li><strong><code>WHAT</code></strong> - the files that have been modified <br>(selected by the user w/ <code>git add</code>)</li>
<li><strong><code>WHY</code></strong> - the reason of the commit, i.e. what has been done compared to the previous version <br>(added by the user w/ <code>git commit</code>)</li>
</ul>
</div><div class="column" style="width:50%;">
</div>
</div>
</section>
<section id="commits-1" class="slide level2">
<h2>Commits</h2>
<div class="columns">
<div class="column" style="width:50%;">
<p>When committing a new version (w/ <code>git commit</code>), the following information must be added:</p>
<ul>
<li><strong><code>WHO</code></strong> - the person who has made the changes <br>(automatically added by <code>git</code>)</li>
<li><strong><code>WHEN</code></strong> - the date of the commit <br>(automatically added by <code>git</code>)</li>
<li><strong><code>WHAT</code></strong> - the files that have been modified <br>(selected by the user w/ <code>git add</code>)</li>
<li><strong><code>WHY</code></strong> - the reason of the commit, i.e. what has been done compared to the previous version <br>(added by the user w/ <code>git commit</code>)</li>
</ul>
</div><div class="column" style="width:50%;">
<p>A commit message has a title line, and an optional body</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode numberSource bash number-lines code-with-copy"><code class="sourceCode bash"><span id="cb12-1"><a href=""></a><span class="co"># Commit message w/ title</span></span>
<span id="cb12-2"><a href=""></a><span class="fu">git</span> commit <span class="at">-m</span> <span class="st">"title"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p><br></p>
<p><strong>What is a good commit message?</strong></p>
<p>A good commit title:</p>
<ul>
<li>should be <strong>short</strong> (less than 50 characters)</li>
<li>should be <strong>informative</strong> and <strong>unambiguous</strong></li>
<li>should use <strong>active voice</strong> and <strong>present tense</strong></li>
</ul>
</div>
</div>
<div class="fragment">
<p><br></p>
<p>An <strong>optional body</strong> can be added to provide <strong>detailed information</strong> and to link <strong>external references</strong> (e.g. issue, pull request, etc.)</p>
</div>
</section>
<section id="when-should-you-commit" class="slide level2">
<h2>When should you commit?</h2>
<div class="columns">
<div class="column" style="width:50%;">
<p><img data-src="img/in-case-of-fire.png" style="width:90.0%"></p>
</div><div class="column" style="width:50%;">
</div>
</div>
</section>
<section id="when-should-you-commit-1" class="slide level2">
<h2>When should you commit?</h2>
<div class="columns">
<div class="column" style="width:50%;">
<p><img data-src="img/in-case-of-fire.png" style="width:90.0%"></p>
</div><div class="column" style="width:50%;">
<p><br></p>
<ul>
<li>Commit a new version when you reach a <strong>milestone</strong></li>
<li>Create <strong>small</strong> and atomic commits</li>
<li>Commit a state that is actually <strong>working</strong></li>
</ul>
</div>
</div>
</section></section>
<section>
<section id="using-github" class="title-slide slide level1 center">
<h1>Using GitHub</h1>
</section>
<section id="code-hosting-platforms" class="slide level2">
<h2>Code hosting platforms</h2>
<p>GitHub and co are <strong>cloud-based git repository hosting services</strong></p>
<p><i class="fa-solid fa-hand-point-right" aria-label="hand-point-right"></i> Perfect solutions to collaborate on projects tracked by <code>git</code></p>
<div class="fragment">
<p><br></p>
<p><strong>Services</strong></p>
<ul>
<li>Full integration of version control (commits, history, differences)</li>
<li>Easy collaboration w/ branches, forks, pull requests</li>
<li>Issues tracking system</li>
<li>Enhanced documentation rendering (README, Wiki)</li>
<li>Static website hosting</li>
<li>Automation & monitoring (CI/CD)</li>
</ul>
</div>
</section>
<section id="main-platforms" class="slide level2">
<h2>Main platforms</h2>
<div class="columns">
<div class="column center" style="width:50%;">
<p><img data-src="img/github-logo.png" style="width:25.0%"> <br> <a href="https://github.com/"><strong>GitHub</strong></a></p>
<p><br> <img data-src="img/bitbucket-logo.png" style="width:25.0%"> <br> <a href="https://bitbucket.org/"><strong>BitBucket</strong></a></p>
</div><div class="column center" style="width:50%;">
<p><img data-src="img/gitlab-logo.png" style="width:25.0%"> <br> <a href="https://gitlab.com/"><strong>GitLab</strong></a></p>
<p><br> <img data-src="img/sourceforge-logo.png" style="width:25.0%"> <br> <a href="https://sourceforge.net/"><strong>SourceForge</strong></a></p>
</div>
</div>
</section>
<section id="presentation-of-github" class="slide level2">
<h2>Presentation of GitHub</h2>
<div class="columns">
<div class="column" style="width:50%;">
<p><strong>Overview</strong></p>
<ul>
<li>Created in 2008</li>