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<!DOCTYPE html>
<html lang="en"><head>
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<meta name="generator" content="quarto-1.3.450">
<meta name="author" content="Researcher at the Macroecology workgroup">
<meta name="dcterms.date" content="2023-12-05">
<title> Introduction to Git and GitHub in RStudio</title>
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</head>
<body class="quarto-dark">
<div class="reveal">
<div class="slides">
<section id="title-slide" data-background-image="./images/ut_logo.svg, ./images/macroeco_logo.png" data-background-position="2% 2%, 98% 5%, center" data-background-size="120px, 300px, cover" class="quarto-title-block center">
<h1 class="title"><br><br><br>Introduction to Git and GitHub in RStudio</h1>
<p class="subtitle"><br>Diego P.F. Trindade</p>
<div class="quarto-title-authors">
<div class="quarto-title-author">
<div class="quarto-title-author-name">
Researcher at the Macroecology workgroup
</div>
</div>
</div>
<p class="date">December 5, 2023</p>
</section>
<section id="before-we-start" class="slide level2">
<h2>Before we start…</h2>
<ul>
<li><p>Everyone has a github account</p></li>
<li><p>RStudio and Git are connected</p></li>
</ul>
<div class="fragment">
<div style="font-size:46px">
<pre><code>- If not:
#install.packages("usethis")
usethis::use_git_config(user.name = "yourusername", user.email = "youremail@example.xx")
usethis::create_github_token()
#Copy your PAT
#Run the following line and paste it:
gitcreds::gitcreds_set()
</code></pre>
</div>
</div>
</section>
<section>
<section id="laelatu-meeting-macroecological-data-and-data-science" class="title-slide slide level1 center" data-background-image="./images/springWG.jpeg" data-background-opacity="0.3">
<h1><span style="color:#C8F526;font-size:86px">Laelatu meeting: <br>Macroecological data and data science</span></h1>
</section>
<section id="not-an-advanced-course" class="slide level2">
<h2>Not an advanced course</h2>
<p><img data-src="./images/gitmeme.png" class="absolute" style="top: 100px; left: 450px; width: 650px; height: 1800px; "></p>
</section>
<section id="github-in-a-nutshell" class="slide level2" data-background-image="./images/git-commit.png" data-background-opacity="0.15">
<h2>Git(Hub) in a nutshell</h2>
<div class="columns">
<div class="column" style="width:10%;">
<p><img data-src="https://git-scm.com/images/logos/downloads/Git-Logo-1788C.svg" class="absolute" style="top: 180px; left: 0px; width: 200px; height: 250px; "></p>
<p><img data-src="./images/github-mark-white.png" class="absolute" style="left: 40px; bottom: 250px; width: 150px; height: 150px; "></p>
</div><div class="column" style="width:7%;">
</div><div class="column" style="width:65%;">
<p><br><br><br></p>
<p>Git is a version control software that <strong>tracks changes</strong> to your files over time.</p>
<p><br><br><br></p>
<p>Github is a website for your git-versioned files.</p>
</div><div class="column" style="width:15%;">
<div class="footer">
<div style="text-align:right;">
<p><a href="https://allisonhorst.com/git-github">Illustration: Alisson Horst</a></p>
</div>
</div>
</div>
</div>
</section>
<section id="i-use-r-dropbox-why-should-i-care" class="slide level2">
<h2>I use R + DropBox, why should I care?</h2>
<div class="columns">
<div class="column" style="width:20%;">
</div><div class="column" style="width:80%;">
<p><br><br> <iframe src="https://giphy.com/embed/pPhyAv5t9V8djyRFJH" width="880" height="550" frameborder="1" class="giphy-embed" allowfullscreen=""></iframe></p>
<p>
<a href="https://giphy.com/gifs/wtf-obama-wth-pPhyAv5t9V8djyRFJH"></a>
</p>
</div>
</div>
</section>
<section id="something-like-this-can-happen" class="slide level2">
<h2>Something like this can happen</h2>
<p><img data-src="./images/files-comics.gif" class="absolute" style="top: 200px; left: 350px; width: 850px; height: 600px; "></p>
</section>
<section id="veryfinal_version2" class="slide level2">
<h2>Veryfinal_Version2</h2>
<p><br> <br></p>
<img data-src="./images/phd-comics-version-control.png" class="r-stretch quarto-figure-center"></section></section>
<section>
<section id="reproducibility-and-version-control" class="title-slide slide level1 center" data-background-image="./images/reprod.jpeg" data-background-opacity="0.2">
<h1><span style="color:yellow;">Reproducibility and Version Control</span></h1>
<div class="footer">
<div style="text-align:right;">
<p><a href="https://www.science.org/doi/10.1126/science.354.6308.142">Illustration: Robert Neubecker</a></p>
</div>
</div>
</section>
<section id="how-does-git-work" class="slide level2">
<h2>How does Git work?</h2>
<p><br> <br></p>
<img data-src="./images/basic-git.jpeg" class="r-stretch quarto-figure-center"></section>
<section id="how-does-git-work-1" class="slide level2">
<h2>How does Git work?</h2>
<p><br> <br></p>
<img data-src="./images/versions.png" class="r-stretch quarto-figure-center"></section>
<section class="slide level2">
<iframe data-external="1" src="https://www.youtube.com/embed/s3JldKoA0zw?start=4" width="100%" height="100%" title="" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen=""></iframe>
</section>
<section id="why-using-git" class="slide level2">
<h2>Why using Git?</h2>
<ul>
<li><p>Several backups of your work!</p></li>
<li><p>Keep track of all changes, and go back in time if necessary;</p></li>
<li><p>Easy to share your work with others (papers, analyses, functions, packages);</p></li>
<li><p>Work in collaboration (branches, issues, pull requests).</p></li>
</ul>
</section>
<section id="why-git-rstudio" class="slide level2">
<h2>Why Git + RStudio?</h2>
<ul>
<li><p>Most ecologists use R;</p></li>
<li><p>RStudio has an easy and well-connected interface with GitHub;</p></li>
<li><p>Repository/Projects;</p></li>
<li><p>GitHub act as a “preprint” for R packages or functions.</p></li>
</ul>
</section>
<section id="potential-drawbacks" class="slide level2">
<h2>Potential drawbacks</h2>
<ul>
<li><p>Allows files up to 100mb;</p></li>
<li><p>Simultaneous changes can be problematic;</p></li>
<li><p>GitHub demons are always awaiting to be summoned.</p></li>
</ul>
</section></section>
<section>
<section id="git-can-be-used-by-yourself-or-as-a-team" class="title-slide slide level1 center">
<h1>Git can be used by yourself or as a team</h1>
</section>
<section id="introvert-git-user" class="slide level2">
<h2>Introvert git user</h2>
<ul>
<li><p>You manage your projects alone (on one or multiple machines);</p></li>
<li><p>You commit, push and pull your own changes (keep track of your changes);</p></li>
<li><p>It is still fun and safe!</p></li>
</ul>
<img data-src="./images/basic-git.jpeg" class="r-stretch quarto-figure-center"></section></section>
<section>
<section id="lets-make-a-quick-tour" class="title-slide slide level1 center" data-background-image="./images/workflow.png" data-background-opacity="0.3">
<h1><span style="color:#C8F526;">Let’s make a quick tour</span></h1>
<div class="footer">
<div style="text-align:right;">
<p><a href="https://allisonhorst.com/git-github">Illustration: Alisson Horst</a></p>
</div>
</div>
</section>
<section id="lets-see-how-it-works-in-practice" class="slide level2">
<h2>Let’s see how it works in practice</h2>
<ul>
<li><p>Creating a new repository;</p></li>
<li><p>Connecting this repository to RStudio</p></li>
</ul>
</section>
<section id="lets-see-how-it-works-in-practice-1" class="slide level2">
<h2>Let’s see how it works in practice</h2>
<ul>
<li><p>From GitHub to RStudio</p></li>
<li><p>From local computer to GitHub</p></li>
<li><p>Using command line</p></li>
</ul>
</section>
<section id="lets-see-how-it-works-in-practice-2" class="slide level2">
<h2>Let’s see how it works in practice</h2>
<ul>
<li><p><span style="color:#F4BA02;">From GitHub to RStudio</span>;</p></li>
<li><p>From local computer to GitHub;</p></li>
<li><p>Using command line.</p></li>
</ul>
</section>
<section id="st-task---lets-create-our-first-repository" class="slide level2">
<h2>1<sup>st</sup> task - let’s create our first repository</h2>
<ul>
<li><p>Creating a new repository on GitHub;</p></li>
<li><p>Creating a new project in RStudio using version control;</p></li>
<li><p>Cloning your GitHub repository and connecting it to RStudio.</p></li>
</ul>
<div class="fragment">
<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>Warning</strong></p>
</div>
<div class="callout-content">
<ul>
<li><strong>Let’s work locally</strong>. Don’t use DropBox, Onedrive, GoogleDrive.</li>
</ul>
</div>
</div>
</div>
</div>
<aside class="notes">
<ul>
<li>README, gitignore,</li>
</ul>
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</section>
<section id="from-the-command-line" class="slide level2">
<h2>From the command line</h2>
<div style="font-size:48px;">
<pre><code>create a repository on github
go to the terminal and choose your folder (cd path)
echo "# My project's README" >> README.md
git init
git add .
git commit -m "first commit"
git branch -M main
git remote add origin <repolink>
git push -u origin main
</code></pre>
</div>
</section></section>
<section>
<section id="first-githubs-power---version-control" class="title-slide slide level1 center">
<h1>First GitHub’s power - Version control</h1>
</section>
<section id="version-control" class="slide level2">
<h2>Version control</h2>
<ul>
<li><p>Let’s create some scripts, edit and save them, commit and push;</p></li>
<li><p>Repeat this process and check what happens.</p></li>
</ul>
</section>
<section id="git-pannel-anatomy" class="slide level2">
<h2>Git pannel anatomy</h2>
<p><br></p>
<img data-src="./images/git_tab.png" class="r-stretch quarto-figure-center"><div class="footer">
<div style="text-align:right;">
<p><a href="https://oliviergimenez.github.io/reproducible-science-workshop/slides/1_github.html#13">Image: Olivier Gimenez</a></p>
</div>
</div>
</section>
<section id="nd-task---create-a-project-you-are-currently-working-on" class="slide level2">
<h2>2<sup>nd</sup> task - Create a project you are currently working on</h2>
<ul>
<li><p>Create a repository on GitHub;</p></li>
<li><p>Clone it and make a new project in RStudio;</p></li>
<li><p>Copy and paste your folders/scripts into this new projects’ folder.</p></li>
</ul>
<div class="fragment">
<ul>
<li><p><span style="font-size:38px; color:red">If you have large data files (>100mb):</span></p>
<ul>
<li><p><span style="font-size:32px">You can try using .RData, .RDS or zip files instead (if they don’t exceed 100mb);</span></p></li>
<li><p><span style="font-size:32px">Or even, you can use large files locally and .gitignore them!</span></p></li>
</ul></li>
</ul>
</div>
</section>
<section id="cloning-public-repositories" class="slide level2">
<h2>Cloning public repositories</h2>
<ul>
<li><p>Public GitHub repositories can also be cloned;</p></li>
<li><p>A nice strategy to learn new things;</p></li>
<li><p>Very convenient when reviewing papers that use GitHub!</p></li>
</ul>
</section>
<section id="rd-task---cloning-a-repository" class="slide level2">
<h2>3<sup>rd</sup> task - Cloning a repository</h2>
<ul>
<li>Let’s try to Clone a nice repository on GitHub.</li>
</ul>
<div class="fragment">
<ul>
<li>Now, make any change to this project, commit and try to push it.</li>
</ul>
</div>
<div class="fragment">
<div style="font-size:48px">
<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>Warning</strong></p>
</div>
<div class="callout-content">
<p>I hope that a wild error appeared!</p>
</div>
</div>
</div>
</div>
</div>
</section>
<section id="clone-and-fork" class="slide level2">
<h2>Clone and Fork</h2>
<ul>
<li><p>Clone: creates a local version of the original repository;</p></li>
<li><p>Fork: creates a copy of the repository on your GitHub (which you can then clone);</p></li>
<li><p>More advanced users use that approach to improve someone’s package/functions.</p></li>
</ul>
<div class="fragment">
<ul>
<li>Let’s now try to fork and then clone the same repository.</li>
</ul>
</div>
</section></section>
<section>
<section id="how-to-collaborate-using-git" class="title-slide slide level1 center">
<h1>How to collaborate using git</h1>
</section>
<section id="collaborative-git" class="slide level2">
<h2>Collaborative git</h2>
<div class="fragment">
<!-- -->
<h4 id="always-pull-first">“Always PULL first!”</h4>
</div>
<img data-src="./images/GitHub-diagram.jpeg" class="r-stretch quarto-figure-center"><aside class="notes">
<ul>
<li>Workgroup example</li>
</ul>
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</section>
<section id="issues-canwill-appear" class="slide level2">
<h2>Issues can/will appear!</h2>
<iframe src="https://giphy.com/embed/MCZ39lz83o5lC" width="1080" height="850" frameborder="0" class="giphy-embed" allowfullscreen="">
</iframe>
<p>
<a href="https://giphy.com/gifs/MCZ39lz83o5lC"></a>
</p>
</section>
<section id="dealing-with-some-simplecommon-issues" class="slide level2">
<h2>Dealing with some simple/common issues</h2>
<p><br></p>
<h3 id="st-issue">1st issue:</h3>
<ul>
<li><p>Go to GitHub, create a new repository, connect it to RStudio and invite a collaborator (person next to you);</p></li>
<li><p><strong>Ask him/her to change a file and push it.</strong></p></li>
<li><p>Now, don’t pull the changes and try to make new changes to the same file and commit/push it yourself.</p></li>
</ul>
<div class="fragment">
<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>Warning</strong></p>
</div>
<div class="callout-content">
<p>I hope that a wild error appeared!</p>
</div>
</div>
</div>
</div>
</section>
<section id="why" class="slide level2">
<h2>Why?</h2>
<p><br></p>
<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>Important</strong></p>
</div>
<div class="callout-content">
<div style="font-size:42px">
<p><strong>Always PULL first!</strong></p>
</div>
</div>
</div>
</div>
</section>
<section id="nd-issue" class="slide level2">
<h2>2nd issue:</h2>
<ul>
<li><p><strong>Ask your collaborator to change a file and “forget” to commit or push it</strong>;</p></li>
<li><p>Change the same file yourself (either add or remove anything), commit and push it;</p></li>
<li><p>Ask your collaborator to commit and push his/her changes.</p></li>
</ul>
</section>
<section id="most-simple-issues-can-be-solved-with-pull" class="slide level2">
<h2>Most simple issues can be solved with “Pull”</h2>
<ul>
<li><p>Sometimes not though;</p></li>
<li><p><a href="https://ohshitgit.com/">Oh Shit Git!</a>, <a href="https://stackoverflow.com/">StackOverflow</a> and <a href="https://openai.com/blog/chatgpt">ChatGPT</a> are our friends</p></li>
</ul>
</section></section>
<section>
<section id="git-allow-us-to-test-new-things-safely-branches" class="title-slide slide level1 center">
<h1>Git allow us to test new things safely: <span style="color:red;">Branches!</span></h1>
</section>
<section id="lets-try-some-branch-approaches" class="slide level2">
<h2>Let’s try some branch approaches</h2>
<ul>
<li><p>Branches can be viewed as experiments;</p></li>
<li><p>Useful when working in collaboration but also alone;</p></li>
</ul>
<img data-src="./images/git-branches.png" class="r-stretch quarto-figure-center"></section>
<section id="working-as-a-team-with-branches" class="slide level2">
<h2>Working as a team with branches</h2>
<ul>
<li><p>Pull the changes;</p></li>
<li><p>Create a new branch;</p></li>
<li><p>Create a new script inside of this branch and work on it;</p></li>
<li><p>Push the changes and check your repository on GitHub;</p></li>
</ul>
<div class="fragment">
<ul>
<li>New Feature: <span style="color:red;">Pull request</span></li>
</ul>
</div>
</section>
<section id="mergin-conflicts" class="slide level2">
<h2>Mergin conflicts</h2>
<ul>
<li><p>When two people work in separate branches but in the same file, conflicts will happen.</p>
<ul>
<li><p>You and your colleague will create a new branch;</p></li>
<li><p>You both will work on the same script but in separate branches;</p></li>
<li><p>Push the changes and check your repository on GitHub;</p></li>
</ul></li>
</ul>
</section>
<section id="working-alone-with-branches" class="slide level2">
<h2>Working alone with branches</h2>
<ul>
<li>The same can be done when working alone</li>
</ul>
<img data-src="./images/git-branches.png" class="r-stretch quarto-figure-center"></section>
<section id="issues-pull-request" class="slide level2">
<h2>Issues + Pull request</h2>
<ul>
<li><p>This is how data science is being pushed forward;</p></li>
<li><p>Great feature when working as a team;</p></li>
<li><p>Let’s try to create some issues and solve them.</p></li>
</ul>
</section></section>
<section id="thats-it-the-basic-toolkit-to-start-using-git-is-ready" class="title-slide slide level1 center">
<h1>That’s it! The basic toolkit to start using git is ready</h1>
</section>
<section>
<section id="additional-tips" class="title-slide slide level1 center">
<h1>Additional tips</h1>
</section>
<section id="a-few-commands-that-can-save-us" class="slide level2">
<h2>A few commands that can save us</h2>
<div class="fragment">
<!-- -->
<h4 id="always-pull-first-1">“Always PULL first!”</h4>
</div>
<ul>
<li><p>I committed something that should not be committed:</p>
<ul>
<li>git HEAD~soft</li>
</ul></li>
<li><p>How to go back in time?</p>
<ul>
<li>git revert <sha> or make a new branch on GitHub page using SHA</sha></li>
</ul></li>
</ul>
</section></section>
<section>
<section id="group-task" class="title-slide slide level1 center">
<h1>Group task</h1>
</section>
<section id="lets-create-small-groups" class="slide level2">
<h2>Let’s create small groups</h2>
<ul>
<li><p>Group 1: Survey of birds that visit backyards, nature centers, community areas, and other locales in North America;</p></li>
<li><p>Group 2: Erasmus student data;</p></li>
<li><p>Group 3: Bee colonies in the US;</p></li>
<li><p>Group 4: Baby names over time;</p></li>
<li><p>Group 5: Palmer penguins data.</p></li>
</ul>
</section>
<section id="st-group-task" class="slide level2">
<h2>1<sup>st</sup> Group task:</h2>
<ul>
<li><p>Let’s explore the data/scripts, make changes, commit and push</p></li>
<li><p>Each person changes a specific file (no overlap!)</p></li>
<li><p>You can either communicate saying when you pushed so the other person can pull the changes</p></li>
<li><p>You can also choose not saying anything. Your teammates will receive an error, but since you are working on different files they just need to pull the changes and everything will be fine;</p></li>
<li><p>All collaborators change, commit and push their changes and solve the conflicts (which will be solved simply by clicking pull - I hope)</p></li>
</ul>
</section>
<section id="nd-group-task" class="slide level2">
<h2>2<sup>nd</sup> Group task:</h2>
<ul>
<li><p>Let’s continue making changes but now using branches.</p></li>
<li><p>Each person creates a branch (maybe using his/her name)</p></li>
<li><p>Let’s keep working each person in a different script</p></li>
<li><p>Make changes and pull requests</p></li>
</ul>
</section>
<section id="rd-group-task" class="slide level2">
<h2>3<sup>rd</sup> Group task:</h2>
<ul>
<li><p>Let’s try to create some conflicts and learn how to solve them.</p></li>
<li><p>Now, two persons will work on the same script</p></li>
<li><p>To make things less complicated, each person changes a simple thing (e.g. the label of a plot)</p></li>
<li><p>They push and try to pull request their changes (and solve the conflicts that will appear)</p></li>
</ul>
</section>
<section id="th-group-task" class="slide level2">
<h2>4<sup>th</sup> Group task</h2>
<ul>
<li><p>Let’s create issues and ask collaborators to solve them.</p></li>
<li><p>Remember to use the # linked to the issue</p></li>
</ul>
</section>
<section id="take-home-messages" class="slide level2">
<h2>Take-home messages</h2>
<ul>
<li><p>I hope you agree that git is a great tool for both using it alone or as a team;</p></li>
<li><p>When used in collaborations, communication is key;</p></li>
<li><p>All git issues can be solved;</p></li>
<li><p>If not, or too complicated, just burn it down and continue from where it was working previously.</p></li>
</ul>
</section>
<section class="slide level2">
<div class="column" style="width:15%;">
</div>
<iframe src="https://giphy.com/embed/xUPOqo6E1XvWXwlCyQ" width="1080" height="870" frameborder="0" class="giphy-embed" allowfullscreen="">
</iframe>
<p>
<a href="https://giphy.com/gifs/spacejam-space-jam-movie-xUPOqo6E1XvWXwlCyQ"></a>
</p>
</section>
<section id="sources" class="slide level2">
<h2>Sources</h2>
<ul>
<li><p>How to connect Git and RStudio, and more complex stuff: <a href="https://happygitwithr.com/index.html">Happy Git With R</a></p></li>
<li><p>How to solve the most common issues: <a href="https://ohshitgit.com/">Oh Shit Git!</a></p></li>
<li><p>Important notes: <a href="https://raw.githack.com/uo-ec607/lectures/master/02-git/02-Git.html#1">click here</a></p></li>
<li><p>Tips on how to collaborate on Rstudio with Git: <a href="https://jtr13.github.io/cc21/collaborating-on-rstudio-with-github.html">click here</a></p></li>
</ul>
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