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RLadiesBergen_ReproducibleBookClubNumber2.html
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<div class="slides">
<section id="title-slide" data-background-image="img/branches.jpg" class="quarto-title-block center">
<h1 class="title">Version Control with Git</h1>
<p class="subtitle">Reproducible Book Club #2</p>
<div class="quarto-title-authors">
<div class="quarto-title-author">
<div class="quarto-title-author-name">
Turkuler Ozgumus
</div>
</div>
</div>
<p class="date">2023-11-07</p>
</section>
<section class="slide level2">
<h3 id="outline">Outline</h3>
<p>Chapter 4 of Building reproducible analytical pipelines with R</p>
<ul>
<li>Version control</li>
<li>Git</li>
<li>Github</li>
<li>Use of Git and Github</li>
</ul>
</section>
<section class="slide level2">
<h3 id="version-control">Version control</h3>
<ul>
<li>Keep track of changes on text files</li>
<li>It is possible to see
<ul>
<li>how the file changed,</li>
<li>who made the changes and,</li>
<li>when these are made.</li>
</ul></li>
</ul>
</section>
<section class="slide level2">
<h3 id="so-what">So what?</h3>
<ul>
<li>Easy collaboration</li>
<li>Safe backup</li>
<li>Adding/not adding new features</li>
</ul>
</section>
<section class="slide level2">
<h3 id="git">Git</h3>
<ul>
<li>Git is a tool to be used to control the version.</li>
<li>It should be installed on the computer before usage.</li>
</ul>
</section>
<section class="slide level2">
<h3 id="github">Github</h3>
<ul>
<li>Is an online service to host project repositories.</li>
<li>One should have an account to be able to use it.</li>
<li>Pros:
<ul>
<li>Large community</li>
<li>Continuous integration via Github Actions<br>
</li>
</ul></li>
<li>Cons:
<ul>
<li>Owned by Microsoft (privacy issues)</li>
<li>Not possible to self-host an instance of Github</li>
</ul></li>
<li>There are alternatives: Gitlab, Bitbucket…</li>
</ul>
</section>
<section class="slide level2">
<h3 id="some-notes">Some notes!</h3>
<ul>
<li>Do not put git repositories into cloud services like Dropbox and Onedrive: <img data-src="https://media.makeameme.org/created/conflicts-conflicts-everywhere-5ab1de.jpg"></li>
<li>Public repository does not mean that everyone can make changes on the files.</li>
</ul>
</section>
<section class="slide level2">
<h3 id="installing-git">Installing Git</h3>
<ul>
<li>open terminal ( <img data-src="img/linux.png" style="width:3.0%"> , <img data-src="img/white_mac.png" style="width:3.0%"> ) or command prompt (<img data-src="img/Windows_logo_-_2021.svg.png" style="width:3.0%">)</li>
<li>run</li>
</ul>
<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="fu">which</span> git</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>or</p>
<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> <span class="at">--version</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
<section class="slide level2">
<h3 id="installing-git-1">Installing Git</h3>
<ul>
<li><img data-src="img/linux.png" style="width:12.0%"></li>
</ul>
<div class="sourceCode" id="cb3"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">sudo</span> apt-get update</span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="fu">sudo</span> apt-get install git</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>or https://git-scm.com/download/linux</p>
<ul>
<li><img data-src="img/white_mac.png" style="width:12.0%"></li>
</ul>
<p>https://git-scm.com/download/mac</p>
<ul>
<li><img data-src="img/Windows_logo_-_2021.svg.png" style="width:2.0%"></li>
</ul>
<p>https://git-scm.com/download/win</p>
</section>
<section class="slide level2">
<h3 id="opening-a-github-account">Opening a Github account</h3>
<ul>
<li>Open https://github.com</li>
</ul>
<div class="fragment">
<p><img data-src="https://media.makeameme.org/created/yeah-if-you-7tjfok.jpg"></p>
</div>
</section>
<section class="slide level2">
<h3 id="git-superbasics">Git superbasics</h3>
<ul>
<li>Create a folder called <em>housing</em></li>
<li>Save below scripts under this folder
<ul>
<li>save_data.R: https://is.gd/7PhUjd<br>
</li>
<li>analysis.R: https://is.gd/qCJEbi</li>
</ul></li>
</ul>
</section>
<section class="slide level2">
<h3 id="git-superbasics-1">Git superbasics</h3>
<ul>
<li>On terminal, go to <em>housing</em> folder by using</li>
</ul>
<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="bu">cd</span> /path/to/folder/housing</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>or</p>
<ul>
<li>Open the folder on file explorer
<ul>
<li><img data-src="img/linux.png" style="width:3.0%">, right-click inside the folder and select “Open Terminal here” or similar</li>
<li><img data-src="img/Windows_logo_-_2021.svg.png" style="width:3.0%">, right-click inside the folder and select “Open Git Bash here” or similar</li>
<li><img data-src="img/white_mac.png" style="width:3.0%">, activate this option by using google search results for “open terminal at folder macOS”</li>
</ul></li>
</ul>
</section>
<section class="slide level2">
<h3 id="git-superbasics-2">Git superbasics</h3>
<ul>
<li>Use ls om terminal/Git bash and check folder contents</li>
</ul>
<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="fu">ls</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<ul>
<li>We will use terminal/Git bash for the rest</li>
</ul>
</section>
<section class="slide level2">
<h3 id="git-superbasics-3">Git superbasics</h3>
<div class="sourceCode" id="cb6"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></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>
<img data-src="img/output.png" class="r-stretch"></section>
<section class="slide level2">
<h3 id="git-superbasics-4">Git superbasics</h3>
<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="fu">git</span> status</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<img data-src="img/output2.png" class="r-stretch"></section>
<section class="slide level2">
<h3 id="git-superbasics-5">Git superbasics</h3>
<div class="sourceCode" id="cb8"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></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>
<div class="fragment">
<p><em>git add</em> needs file(s) to be specified</p>
</div>
<div class="fragment">
<div class="sourceCode" id="cb9"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></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>
</div>
<div class="fragment">
<div class="sourceCode" id="cb10"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> status</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section class="slide level2">
<h3 id="git-superbasics-6">Git superbasics</h3>
<div class="sourceCode" id="cb11"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> commit <span class="at">-m</span> <span class="st">"Project start"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="fragment">
<div class="sourceCode" id="cb12"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> status</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section class="slide level2">
<h3 id="git-superbasics-7">Git superbasics</h3>
<p>Make a change from</p>
<p><img data-src="img/script1.png"></p>
<p>to</p>
<p><img data-src="img/script2.png"></p>
</section>
<section class="slide level2">
<h3 id="git-superbasics-8">Git superbasics</h3>
<div class="sourceCode" id="cb13"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> status</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="fragment">
<div class="sourceCode" id="cb14"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></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>
</div>
<div class="fragment">
<div class="sourceCode" id="cb15"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> commit <span class="at">-m</span> <span class="st">"Added a comment to analysis.R"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section class="slide level2">
<h3 id="git-superbasics-9">Git superbasics</h3>
<p><em>how to recover a deleted file before committing the change</em></p>
<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="fu">rm</span> analysis.R</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="fragment">
<div class="sourceCode" id="cb17"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb17-1"><a href="#cb17-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> status</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="fragment">
<div class="sourceCode" id="cb18"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb18-1"><a href="#cb18-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> stash</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="fragment">
<div class="sourceCode" id="cb19"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb19-1"><a href="#cb19-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="fragment">
<div class="sourceCode" id="cb20"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> stash drop</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section class="slide level2">
<h3 id="git-superbasics-10">Git superbasics</h3>
<p><em>how to recover a deleted file after committing the change</em></p>
<div class="sourceCode" id="cb21"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb21-1"><a href="#cb21-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rm</span> analysis.R</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="fragment">
<div class="sourceCode" id="cb22"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb22-1"><a href="#cb22-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> status</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="fragment">
<div class="sourceCode" id="cb23"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb23-1"><a href="#cb23-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> add .</span>
<span id="cb23-2"><a href="#cb23-2" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> commit <span class="at">-m</span> <span class="st">"Removed analysis.R"</span></span>
<span id="cb23-3"><a href="#cb23-3" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> status</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section class="slide level2">
<h3 id="git-superbasics-11">Git superbasics</h3>
<p><em>how to recover a deleted file after committing the change</em></p>
<div class="sourceCode" id="cb24"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb24-1"><a href="#cb24-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> log</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<img data-src="img/gitlog1.png" class="r-stretch"><div class="fragment">
<div class="sourceCode" id="cb25"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb25-1"><a href="#cb25-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> revert ab43b4b1069cd98768..HEAD</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section class="slide level2">
<h3 id="git-superbasics-12">Git superbasics</h3>
<p><em>how to recover a deleted file after committing the change</em></p>
<div class="sourceCode" id="cb26"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb26-1"><a href="#cb26-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> log</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<img data-src="img/gitlog2.png" class="r-stretch"></section>
<section class="slide level2">
<h3 id="git-superbasics-13">Git superbasics</h3>
<p><em>how to recover a deleted file after committing the change</em></p>
<div class="sourceCode" id="cb27"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb27-1"><a href="#cb27-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> revert 8e51867dc5</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
<section class="slide level2">
<h3 id="git-and-github">Git and Github</h3>
<p><strong>Push</strong> -> uploading the changes we did on our local repository to GitHub</p>
</section>
<section class="slide level2">
<h3 id="git-and-github-1">Git and Github</h3>
<ul>
<li>Create a new repository with following:
<ul>
<li>Repository name: housing</li>
<li>Public</li>
<li>No README file</li>
</ul></li>
</ul>
</section>
<section class="slide level2">
<h3 id="git-and-github-2">Git and Github</h3>
<img data-src="img/git_new_repo.png" class="r-stretch"></section>
<section class="slide level2">
<h3 id="git-and-github-3">Git and Github</h3>
<img data-src="img/git_new_repo_2.png" class="r-stretch"></section>
<section class="slide level2">
<h3 id="git-and-github-4">Git and Github</h3>
<img data-src="img/git_repo_start.png" class="r-stretch"></section>
<section class="slide level2">
<h3 id="git-and-github-5">Git and Github</h3>
<img data-src="img/git_repo_start_ssh.png" class="r-stretch"></section>
<section class="slide level2">
<h3 id="git-and-github-6">Git and Github</h3>
<div class="sourceCode" id="cb28"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb28-1"><a href="#cb28-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> remote add origin [email protected]:turkulerc/housing.git</span>
<span id="cb28-2"><a href="#cb28-2" aria-hidden="true" tabindex="-1"></a><span class="co"># if you would like to rename the branch from "master" to "main"</span></span>
<span id="cb28-3"><a href="#cb28-3" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> branch <span class="at">-M</span> main </span>
<span id="cb28-4"><a href="#cb28-4" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> push <span class="at">-u</span> origin main</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="fragment">
<p><img data-src="img/error.jpg"></p>
</div>
</section>
<section class="slide level2">
<h3 id="git-and-github-7">Git and Github</h3>
<div class="fragment">
<ul>
<li>Generate a public/private RSA key pair<br>
</li>
</ul>
</div>
<div class="fragment">
<div class="sourceCode" id="cb29"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb29-1"><a href="#cb29-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ssh-keygen</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="fragment">
<p><img data-src="img/sshkey1.png"></p>
<ul>
<li>Leave this empty and press enter</li>
</ul>
</div>
</section>
<section class="slide level2">
<h3 id="git-and-github-8">Git and Github</h3>
<div class="fragment">
<p><img data-src="img/sshkey2.png"></p>
<ul>
<li>Leave this empty, too</li>
</ul>
</div>
<div class="fragment">
<p><img data-src="img/sshkey3.png"> - Confirm empty passphase by pressing enter again!</p>
</div>
</section>
<section class="slide level2">
<h3 id="git-and-github-9">Git and Github</h3>
<img data-src="img/sshkey4.png" class="r-stretch"></section>
<section class="slide level2">
<h3 id="git-and-github-10">Git and Github</h3>
<p>We need to copy the contents of the id_rsa.pub file to Github</p>
<ul>
<li>go to <a href="https://github.com">https://github.com</a></li>
<li>go to your profile settings</li>
<li>select <em>SSH and GPG keys</em><br>
</li>
<li>select <em>New SSH key</em></li>
<li>Name this key and paste the contents of id_rsa.pub in the text box and click on “add SSH key”</li>
</ul>
</section>
<section class="slide level2">
<h3 id="git-and-github-11">Git and Github</h3>
<img data-src="img/github_add_ssh.png" class="r-stretch"></section>
<section class="slide level2">
<h3 id="git-and-github-12">Git and Github</h3>
<p>Back to the terminal/Git bash</p>
<div class="sourceCode" id="cb30"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb30-1"><a href="#cb30-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> push <span class="at">-u</span> origin master</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="fragment">
<p><img data-src="img/git_push_success.png"></p>
</div>
<div class="fragment">
<p><img data-src="img/git_push_success2.png"></p>
</div>
</section>
<section class="slide level2">
<h3 id="getting-to-know-github">Getting to know Github</h3>
<p><a href="https://github.com">https://github.com</a></p>
</section>
<section class="slide level2">
<h3 id="getting-to-know-github-1">Getting to know Github</h3>
<img data-src="img/github_new_issue2.png" class="r-stretch"></section>
<section class="slide level2">
<h3 id="minimal-reproducible-example-mre">Minimal, reproducible example (MRE)</h3>
<ul>
<li>The code needs to be self-contained</li>
<li>Required packages to run the code should be listed –> sessionInfo()</li>
<li>Provide code to create any object that the code snippet requires</li>
</ul>
<div class="fragment">
<ul>
<li>{reprex}</li>
</ul>
</div>
</section>
<section class="slide level2">
<h3 id="some-additional-resources">Some additional resources</h3>
<ul>
<li>https://happygitwithr.com/</li>
<li>https://ohshitgit.com/</li>
</ul>
</section>
<section id="thanks" class="title-slide slide level1 center" data-background-image="img/bw_branches.jpg">
<h1>THANKS!</h1>
<div class="footer footer-default">
</div>
</section>
</div>
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