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<!DOCTYPE html>
<html lang="en"><head>
<script src="cours_files/libs/clipboard/clipboard.min.js"></script>
<script src="cours_files/libs/quarto-html/tabby.min.js"></script>
<script src="cours_files/libs/quarto-html/popper.min.js"></script>
<script src="cours_files/libs/quarto-html/tippy.umd.min.js"></script>
<link href="cours_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="cours_files/libs/quarto-html/light-border.css" rel="stylesheet">
<link href="cours_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
<link href="cours_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles"><meta charset="utf-8">
<meta name="generator" content="quarto-1.4.552">
<meta name="author" content="Émilien Schultz - emilien.schultz@ensae.fr">
<title>Collaborative projects with Github</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="cours_files/libs/revealjs/dist/reset.css">
<link rel="stylesheet" href="cours_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;
}
</style>
<link rel="stylesheet" href="cours_files/libs/revealjs/dist/theme/quarto.css">
<link href="cours_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.css" rel="stylesheet">
<link href="cours_files/libs/revealjs/plugin/reveal-menu/menu.css" rel="stylesheet">
<link href="cours_files/libs/revealjs/plugin/reveal-menu/quarto-menu.css" rel="stylesheet">
<link href="cours_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;
}
div.callout-important .callout-icon::before {
background-image: url('data:image/png;base64,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');
}
div.callout-important.callout-style-default .callout-title {
background-color: #f7dddc
}
div.callout-warning {
border-left-color: #f0ad4e !important;
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</head>
<body class="quarto-light">
<div class="reveal">
<div class="slides">
<section id="title-slide" class="quarto-title-block center">
<h1 class="title">Collaborative projects with Github</h1>
<p class="subtitle">Introduction and good practices</p>
<div class="quarto-title-authors">
<div class="quarto-title-author">
<div class="quarto-title-author-name">
Émilien Schultz - emilien.schultz@ensae.fr
</div>
</div>
</div>
</section>
<section id="fist-who-are-we" class="slide level2">
<h2>Fist, who are we ?</h2>
<ul>
<li><strong>Me</strong> : somewhere in the computational social sciences</li>
<li><strong>You</strong> ?
<ul>
<li>What software/OS are you using ?</li>
<li>Do you know how to use command line interfaces ?</li>
<li>Have you heard about git/github a little ?</li>
</ul></li>
</ul>
</section>
<section id="starting-point" class="slide level2">
<h2>Starting point</h2>
<p><br></p>
<p><strong>You are going to carry out a collaborative project with programming & data</strong></p>
<p><br></p>
<p>How to ensure a collaborative project involving programming/data analysis runs smoothly?</p>
</section>
<section id="goals" class="slide level2">
<h2>Goals</h2>
<ul>
<li>Some best practices for collaboration around programming</li>
<li>Get familiar with GitHub</li>
<li>Start the structure of a project</li>
<li>Available resources</li>
<li>Discuss about coding practices</li>
</ul>
<p><em>This session will be language agnostique</em></p>
</section>
<section id="why-using-it-in-general" class="slide level2">
<h2>Why using it in general ?</h2>
<div title="Disclamer">
<div class="callout callout-warning callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Disclamer</strong></p>
</div>
<div class="callout-content">
<p>You don’t have to know everything</p>
<ul>
<li>There are numerous tutorials</li>
<li>The general philosophy comes first</li>
<li>Nevertheless, it can be very useful</li>
</ul>
</div>
</div>
</div>
</div>
</section>
<section id="what-does-it-mean-to-code-for-data-science" class="slide level2">
<h2>What does it mean to code for data science ?</h2>
<ul>
<li>A Set of Practices
<ul>
<li>From script to software</li>
<li>From data scientist to computer scientist</li>
</ul></li>
<li>A Set of Technologies
<ul>
<li>Different languages, software, etc.</li>
</ul></li>
<li>A Set of More or Less Interdependent Artifacts
<ul>
<li>Files, texts, folders, application</li>
<li>Intermediate, final</li>
</ul></li>
</ul>
</section>
<section id="with-the-challenge-of-working-together" class="slide level2">
<h2>With the challenge of working together</h2>
<ul>
<li>Sharing storage</li>
<li>Communicating over various channels</li>
<li>Keeping track of various versions</li>
<li>…</li>
</ul>
</section>
<section id="so-what-possibily-could-go-wrong" class="slide level2">
<h2>So, what possibily could go wrong ?</h2>
<ul>
<li>Different coding styles leading to chaos</li>
<li>Asynchronous contributions : conflicts …</li>
<li>Profusion of versions</li>
<li>Increased likelihood of errors</li>
<li>…</li>
</ul>
<p><strong>How to avoid problems (at least some) ?</strong></p>
</section>
<section id="a-classic-situation" class="slide level2" style="text-align: center;">
<h2>A classic situation</h2>
<img data-src="./img/finalfinal.png" class="quarto-figure quarto-figure-center r-stretch" width="600"><p>There are solutions against that…</p>
</section>
<section id="first-rule-structuring-a-project" class="slide level2">
<h2>First rule : Structuring a Project</h2>
<ul>
<li>Separate code from data
<ul>
<li>Different logic</li>
<li>Different tools</li>
</ul></li>
<li>Document / Comment your productions
<ul>
<li>Be explicit</li>
</ul></li>
<li>Modularize : create distinct elements</li>
</ul>
</section>
<section id="second-rule-a-common-file-system" class="slide level2">
<h2>Second rule : a common file system</h2>
<ul>
<li>data in a data directory</li>
<li>scripts in a script directory</li>
<li>…</li>
</ul>
<p><strong>What are the other elements of a project ?</strong></p>
</section>
<section>
<section id="next-step-code-management" class="title-slide slide level1 center">
<h1>Next step : code management</h1>
</section>
<section id="what-is-code-versionning" class="slide level2">
<h2>What is code versionning ?</h2>
<ul>
<li><em>Option 1</em> : there is only one document and you send each version by email
<ul>
<li>slow and a lots of version</li>
</ul></li>
<li><em>Option 2</em> : there is only one document online on the cloud and you work on it
<ul>
<li>difficulty to keep track of the versions</li>
<li>can be chaos</li>
</ul></li>
<li><em>Option 3</em> : each contribution is clearly identified in a shared file system with clear rules of addition</li>
</ul>
<p><strong>Entering Git & Github</strong></p>
</section>
<section id="code-versioning-is-old" class="slide level2">
<h2>Code versioning is old</h2>
<ul>
<li>Tools like RCS, CVS, or Subversion around since the early 1980s
<ul>
<li>Some readings : <a href="https://journals.openedition.org/sdt/33283">Industrial public goods: A genesis of the insertion of free software in Silicon Valley, Gabriel Alcaras, Sociologie du travail, 2020</a></li>
</ul></li>
<li>Leading the way to distributed tools</li>
</ul>
<p><strong>Somehow, it is a meta file organisation that keeps track of contributions and force you to (some) good practices</strong></p>
</section>
<section id="git-and-the-linux-history" class="slide level2">
<h2>Git and the Linux history</h2>
<ul>
<li>An history born from the free software movement</li>
<li>A bazar of contribution
<ul>
<li>No vertical integration</li>
</ul></li>
<li>Linux Torvald benevolent dictator
<ul>
<li><a href="https://blog.brachiosoft.com/en/posts/git/">Obligatory point of passage</a></li>
</ul></li>
<li>The big question :
<ul>
<li>How to collabore on code</li>
</ul></li>
</ul>
</section>
<section id="git" class="slide level2" style="text-align: center;">
<h2>Git</h2>
<img data-src="./img/gitxkcd.png" class="r-stretch"><p><a href="https://xkcd.com/1597/">Credits : xkcd</a></p>
</section>
<section id="how-does-it-work" class="slide level2">
<h2>How does it work</h2>
<ul>
<li>A base unit : the repository containing everything</li>
<li>A network of contribution with a unique id</li>
<li>Everything recorded</li>
<li>Possibility to have parallel versions</li>
</ul>
<img data-src="./img/branches.png" data-weight="500" class="r-stretch quarto-figure-center"><p class="caption"><a href="https://lutece.paris.fr/support/jsp/site/Portal.jsp?page=wiki&view=page&page_name=git&language=fr">Source : Lutece.paris.fr</a></p><p><strong>A world in itself…</strong></p>
</section>
<section id="what-is-git-exactly" class="slide level2">
<h2>What is Git exactly ?</h2>
<p>Git is a command line tool which allow to :</p>
<ul>
<li>add modifications to this structure</li>
<li>manage changes (back, forward, fusions)</li>
<li>natively installed on unix systems</li>
</ul>
<p>Over time</p>
<ul>
<li>embedded in other tools (VS code)
<ul>
<li><a href="https://git-scm.com/downloads/guis">There are GUI</a></li>
</ul></li>
<li>became an infrastructure of programming practices & OS</li>
</ul>
<pre><code>$ git</code></pre>
</section>
<section id="workflow" class="slide level2" style="text-align: center;">
<h2>Workflow</h2>
<img data-src="./img/git-committing.svg" class="r-stretch"></section>
<section id="small-demo-with-the-slides" class="slide level2">
<h2>Small demo with the slides</h2>
<ul>
<li><a href="https://swcarpentry.github.io/git-novice/02-setup.html">First configure git</a></li>
<li>Then, initializing a git repo (CLI is useful)
<ul>
<li><code>git init</code> => a .git directory</li>
<li><code>git status</code></li>
<li><code>git add FILE</code> => staging area</li>
<li><code>git diff</code></li>
<li><code>git commit</code> -m “MESSAGE”</li>
<li><code>git log</code></li>
</ul></li>
</ul>
</section>
<section id="git-messages" class="slide level2" style="text-align: center;">
<h2>Git messages</h2>
<p>Clear messages if possible…</p>
<img data-src="./img/git_commit_2x.png" class="r-stretch"><p><a href="https://xkcd.com/1296/">Credit: xkcd</a></p>
</section>
<section id="possibility-to-see-the-diff" class="slide level2">
<h2>Possibility to see the diff</h2>
<ul>
<li>with specific commits</li>
<li>with specific files
<ul>
<li><code>git diff IDCOMIT FILE</code></li>
</ul></li>
</ul>
</section>
<section id="possibility-to-restore" class="slide level2">
<h2>Possibility to restore</h2>
<ul>
<li><code>git restore FILE</code></li>
<li><code>git reset --hard</code></li>
</ul>
</section>
<section id="section" class="slide level2">
<h2></h2>
<div title="Code & Data">
<div class="callout callout-important callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Code & Data</strong></p>
</div>
<div class="callout-content">
<p>Git is not designed to version data</p>
<p>Other solutions as <a href="https://git-lfs.com/">Git LFS</a> or <a href="https://zenodo.org/">Zenodo</a> for research.</p>
</div>
</div>
</div>
</div>
</section></section>
<section>
<section id="from-local-to-cloud" class="title-slide slide level1 center">
<h1>From local to cloud</h1>
</section>
<section id="github-genesis" class="slide level2">
<h2>Github genesis</h2>
<div class="columns">
<div class="column" style="width:70%;">
<ul>
<li>A company built on git in 2008
<ul>
<li>Bought by Microsoft in 2018 (mutation of OS)</li>
</ul></li>
<li>Basically : Git on cloud plus services
<ul>
<li>Centralized repository</li>
</ul></li>
<li>A system of rights to access (maintainer, contributor, etc.)</li>
<li>A new grammar of how to contribute
<ul>
<li>push, pull, pull request, etc.</li>
</ul></li>
</ul>
</div><div class="column" style="width:30%;">
<p><img data-src="./img/octocat.jpg"> <a href="https://myoctocat.com/build-your-octocat/">Build your octocat</a></p>
</div>
</div>
</section>
<section id="a-plateforme-for-projects" class="slide level2">
<h2>A plateforme for projects</h2>
<ul>
<li>A central repository that connect developers and users
<ul>
<li>a “community”</li>
</ul></li>
<li>Allow contributions to be visible</li>
<li>Allow discussions</li>
</ul>
<p>Why to use it ?</p>
<ul>
<li>Reproducibility</li>
<li>Transparency</li>
<li>Ease of collaboration</li>
<li>Communicating your work</li>
<li>Never lose a file</li>
<li>Work from multiple machines seemlessly</li>
</ul>
</section>
<section id="github-a-social-media" class="slide level2">
<h2>Github : a social media</h2>
<ul>
<li>A showcase of projects
<ul>
<li>Stars</li>
</ul></li>
<li>A platform to stay updated
<ul>
<li>Versions & contributions</li>
</ul></li>
<li>A space for socializing & exchanging
<ul>
<li>Issues</li>
<li>Communities</li>
</ul></li>
</ul>
</section>
<section id="lets-have-a-look-the-most-famous-repository" class="slide level2">
<h2>Let’s have a look : the most famous repository</h2>
<ul>
<li><a href="https://github.com/EvanLi/Github-Ranking">Most famous repository</a></li>
<li><a href="https://anvaka.github.io/map-of-github/#2/0/0">Map of Github</a></li>
</ul>
<!-- Would be interesting to dig in the existing map of github -->
</section>
<section id="a-lot-of-services" class="slide level2">
<h2>A lot of services</h2>
<ul>
<li>Actions (Continuous integrations)</li>
<li>Github pages</li>
<li>Wiki</li>
<li>…</li>
</ul>
</section>
<section id="github-is-not-alone" class="slide level2">
<h2>Github is not alone</h2>
<p>Other open-source code-sharing platform (“forges” in French)</p>
<ul>
<li>SourceForge</li>
<li>Bitbucket</li>
<li>Gitlab</li>
<li>Gitti</li>
</ul>
</section>
<section id="diversity-of-uses" class="slide level2">
<h2>Diversity of uses</h2>
<ul>
<li>CLI</li>
<li>In other tools
<ul>
<li>VS Code</li>
<li>R Studio</li>
<li>Jupyter</li>
</ul></li>
<li>GUI
<ul>
<li>Github Desktop</li>
</ul></li>
</ul>
</section>
<section id="lets-have-a-look-with-cli" class="slide level2">
<h2>Let’s have a look with CLI</h2>
<p>Let’s put our slides on Github</p>
<ul>
<li>git init / git clone</li>
<li><strong>git pull</strong></li>
<li>git status</li>
<li>git remote -v</li>
<li>git add</li>
<li>git commit</li>
<li><strong>git push</strong></li>
<li>…</li>
</ul>
</section>
<section id="complete-worklow" class="slide level2" style="text-align: center;">
<h2>Complete worklow</h2>
<img data-src="./img/githubflow.png" class="r-stretch"></section>
<section id="authentification" class="slide level2">
<h2>Authentification</h2>
<p>It can sometime be tricky…</p>
<ul>
<li>HTTPS</li>
<li>SSH</li>
</ul>
<p><a href="https://swcarpentry.github.io/git-novice/07-github.html">How to setup SSH keys</a></p>
</section>
<section id="initialize-your-github-repository" class="slide level2">
<h2>Initialize your Github repository</h2>
<p>Hands one : create your first repository</p>
<ul>
<li>create one from Github</li>
<li>modify the github README</li>
<li>clone it on your computer</li>
<li>make a modification + push</li>
</ul>
</section>
<section id="give-permission" class="slide level2">
<h2>Give permission</h2>
<ul>
<li>Give permission to a colleague to modify your repository</li>
<li>Make him/her do a change</li>
<li>Then, try yourself to make a change</li>
</ul>
</section>
<section id="advanced-point-how-to-resolve-conflicts" class="slide level2">
<h2>[Advanced point] How to resolve conflicts</h2>
<p>When the history of different versions of a repository diverge, there are solutions;</p>
<ul>
<li>merge/rebase strategies : keep the modifications and arbitrate on conflicts</li>
<li>brute force : you can erase (not advised)</li>
</ul>
<p><strong>Sometime, it can be trick</strong></p>
</section>
<section id="ways" class="slide level2" style="text-align: center;">
<h2>2 ways</h2>
<img data-src="./img/rebasemerge.png" class="r-stretch"></section>
<section id="it-can-be-messy" class="slide level2" style="text-align: center;">
<h2>It can be messy</h2>
<img data-src="./img/git-merge.gif" class="r-stretch"></section>
<section id="advanced-point-.gitignore-file" class="slide level2">
<h2>[Advanced point] .gitignore file</h2>
<p>Possibility to exclude files from the tracking</p>
<ul>
<li>Data</li>
<li>Config files</li>
<li>Private information</li>
</ul>
<p>Add them in a file called .gitignore</p>
</section>
<section id="advanced-point-branches" class="slide level2">
<h2>[Advanced point] branches</h2>
<ul>
<li>Not only one succession of commits</li>
<li>But different series in parallel</li>
<li>And the possibility to merge from one branch to another</li>
</ul>
<p>Why ? Test things without modifying the principal branch for instance</p>
</section>
<section id="advanced-point-pull-requests" class="slide level2">
<h2>[Advanced point] pull requests</h2>
<p>It is a proposed change to a codebaseWhen a pull request is created</p>
<ul>
<li>Made on an independant branch</li>
<li>Proposed to review for the repository</li>
<li>Possibility to discuss on it</li>
</ul>
</section></section>
<section>
<section id="your-project" class="title-slide slide level1 center">
<h1>Your project</h1>
</section>
<section id="how-to-prepare-your-project" class="slide level2">
<h2>How to prepare your project</h2>
<ul>
<li>Choose a file system easy to use
<ul>
<li>Adapt it if needed</li>
</ul></li>
<li>Set up a repository</li>
<li>Discuss on how you want to work
<ul>
<li>Every one can modify</li>
<li>Choose a maintainer</li>
</ul></li>
</ul>
</section>
<section id="our-cookie-cutter-for-the-project" class="slide level2">
<h2>Our cookie-cutter for the project</h2>
<ul>
<li>A Github organisation</li>
<li>A blank repository playing the part of a <a href="https://github.com/policyinaction/cookiecutter-project">cookiecutter</a></li>
</ul>
</section>
<section id="create-a-fork-of-the-repository" class="slide level2">
<h2>Create a fork of the repository</h2>
<ul>
<li>Fork the repository</li>
<li>Give it a name</li>
<li>Change the readme with your name</li>
</ul>
</section></section>
<section>
<section id="other-aspects" class="title-slide slide level1 center">
<h1>Other aspects</h1>
</section>
<section id="use-onyxia" class="slide level2">
<h2>Use Onyxia</h2>
<ul>
<li><a href="https://onyxia.lab.groupe-genes.fr/account/user-interface">GENES Data Lab</a>, based on a plateforme developed by INSEE</li>
<li>Possibility to create temporary services</li>
<li>Triple separation
<ul>
<li>Code</li>
<li>Computation</li>
<li>Data (S3)</li>
</ul></li>
<li>Add a token in Onyxia
<ul>
<li><em>small demo with Jupyter</em></li>
</ul></li>
</ul>
</section>
<section id="style" class="slide level2">
<h2>Style</h2>
<ul>
<li>“Code is read more often than it is written. Code should always be written in a way that promotes readability.”</li>
</ul>
<p><em>Guido von Rossum - PEP8 Python</em></p>
</section>
<section id="data" class="slide level2">
<h2>Data</h2>
<ul>
<li>Where to store them ?</li>
<li>What are the best format ?</li>
<li>What is a good metadata ?</li>
</ul>
</section>
<section id="software" class="slide level2">
<h2>Software</h2>
<ul>
<li>How to choose between open and commercial software ?</li>
<li>How to keep track of the versions ?</li>
</ul>
</section>
<section id="advanced-virtual-environment" class="slide level2">
<h2>[Advanced] Virtual environment</h2>
<ul>
<li>conda / venv for Python</li>
<li>renv pour R</li>
</ul>
</section></section>
<section id="ressources" class="title-slide slide level1 center">
<h1>Ressources</h1>
<ul>
<li><a href="https://swcarpentry.github.io/git-novice/">Version control with Git - Software Carpentry</a></li>
<li><a href="https://inseefrlab.github.io/formation-bonnes-pratiques-git-R">Good practices for statistical projects with R & Git (INSEE)</a></li>
<li><a href="https://git-scm.com/book/en/v2">Git Reference guidelines</a></li>
<li><a href="https://programminghistorian.org/en/lessons/retired/getting-started-with-github-desktop">An Introduction to Version Control Using GitHub Desktop</a></li>
</ul>
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