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@@ -1 +1 @@
-cc8e168b
+5057411d

basics.html

@@ -247,14 +247,16 @@ <h1 class="title"><span class="chapter-number">1</span>&nbsp; <span class="chapt
 <h2 data-number="1.1" class="anchored" data-anchor-id="getting-started"><span class="header-section-number">1.1</span> Getting started</h2>
 <section id="installing-git" class="level3" data-number="1.1.1">
 <h3 data-number="1.1.1" class="anchored" data-anchor-id="installing-git"><span class="header-section-number">1.1.1</span> Installing Git</h3>
+<p><a href="https://github.com/git-guides/install-git">Here</a> is a general guide for installing git for the different operating software.</p>
 <ul>
 <li>for windows</li>
 <li>for MacOS</li>
+<li>for Linux</li>
 </ul>
 </section>
 <section id="setting-up" class="level3" data-number="1.1.2">
 <h3 data-number="1.1.2" class="anchored" data-anchor-id="setting-up"><span class="header-section-number">1.1.2</span> Setting up</h3>
-<p>GitHub account</p>
+<p>If you don’t already have one create a <a href="https://github.com/">GitHub</a> account.</p>
 <div class="callout callout-style-default callout-note callout-titled">
 <div class="callout-header d-flex align-content-center">
 <div class="callout-icon-container">
@@ -268,15 +270,23 @@ <h3 data-number="1.1.2" class="anchored" data-anchor-id="setting-up"><span class
 <p>If you are a university student you qualify for a <a href="https://education.github.com/pack">free pro account</a></p>
 </div>
 </div>
-<p>Authorisations/configuring to github</p>
 </section>
 <section id="talking-to-git" class="level3 page-columns page-full" data-number="1.1.3">
 <h3 data-number="1.1.3" class="anchored" data-anchor-id="talking-to-git"><span class="header-section-number">1.1.3</span> Talking to git</h3>
-<ul>
-<li>Linking with RStudio</li>
-<li>VSCode</li>
-<li>Terminal</li>
-</ul>
+<p>Now that you have installed <code>git</code> you need to link it to your GitHub account and make sure that the two are able to ‘talk’ to each other. Again there are many ways to set this up. We will discuss some of these approaches below.</p>
+<section id="linking-with-rstudio" class="level4" data-number="1.1.3.1">
+<h4 data-number="1.1.3.1" class="anchored" data-anchor-id="linking-with-rstudio"><span class="header-section-number">1.1.3.1</span> Linking with RStudio</h4>
+<ol type="1">
+<li><strong>Tell RStudio where to find the git programme</strong>: Under the Tools menu, open Global Options and go to the Git/SVN section. Then enable the version control interface and make sure RStudio knows where to find git. For MacOS, enter the path (which you can find by typing <code>which git</code> into your terminal), for Windows, find the git program in your Program Files.</li>
+<li><strong>Configure Git</strong>: The easiest way to do this is in <code>R</code> through the {usethis} package (so install that if you don’t have it - install.packages(“usethis”)). and you can just run usethis::use_git_config(user.name=“Jane Doe”, user.email=“jane@example.org”) in your R console. Replace with your name and the email that is linked to your GitHub account</li>
+<li><strong>Link your GitHub account</strong>: Now you need to link your GitHub account/credentials. The path of least resistance is going the HTTPS, personal access token (PAT) route. <a href="https://happygitwithr.com/https-pat">{usethis}</a> package, which outlines how to get a PAT and link that to your git credentials.</li>
+</ol>
+</section>
+<section id="linking-with-vscode" class="level4" data-number="1.1.3.2">
+<h4 data-number="1.1.3.2" class="anchored" data-anchor-id="linking-with-vscode"><span class="header-section-number">1.1.3.2</span> Linking with VSCode</h4>
+</section>
+<section id="linking-with-terminal" class="level4 page-columns page-full" data-number="1.1.3.3">
+<h4 data-number="1.1.3.3" class="anchored" data-anchor-id="linking-with-terminal"><span class="header-section-number">1.1.3.3</span> Linking with Terminal</h4>
 
 <div class="no-row-height column-margin column-container"><div class="">
 <div class="quarto-figure quarto-figure-center">
@@ -287,12 +297,19 @@ <h3 data-number="1.1.3" class="anchored" data-anchor-id="talking-to-git"><span c
 </div>
 </div></div></section>
 </section>
+</section>
 <section id="understanding-the-version-control-workflow" class="level2" data-number="1.2">
 <h2 data-number="1.2" class="anchored" data-anchor-id="understanding-the-version-control-workflow"><span class="header-section-number">1.2</span> Understanding the version control workflow</h2>
 <section id="key-terms" class="level3" data-number="1.2.1">
 <h3 data-number="1.2.1" class="anchored" data-anchor-id="key-terms"><span class="header-section-number">1.2.1</span> Key terms</h3>
 <p>repo - short for repository repository - the directory or folder that is under version control local - the repository on your computer remote - the repository on GitHub commit - take a snapshot of one or more files in the repository push - send commits from the local repo to the remote repo pull - retrieve commits from the remote repo to the local repo .gitignore a file that tells git which files or types of files you don’t want to commit</p>
 <p>Let’s start by briefly explaining the basic workflow. On GitHub you can make repositories, which is a kind of project. Your online repository, or short repo, is called remote. To use your repository, you need to clone it locally onto your computer and it is then called local. You can write and edit R code locally on your computer. The new code is then committed and pushed back to the remote. If you follow this workflow consistently, GitHub will keep track of all the changes you make.</p>
+<div class="quarto-figure quarto-figure-center">
+<figure class="figure">
+<p><img src="assets/workflows/github_basic.png" class="img-fluid figure-img"></p>
+<figcaption>This is the basic github workflow. First we need to retrieve the remote version of repository. We now have an exact copy of the online repository locally. We are then free to work on and develop the files that are in the repository. Once we have made our changes we need to send these back to the remote repository.</figcaption>
+</figure>
+</div>
 </section>
 </section>
 <section id="references" class="level2 unnumbered">

index.html

@@ -8,7 +8,7 @@
 
 <meta name="author" content="Xiaoxiao Li">
 <meta name="author" content="Tanya Strydom">
-<meta name="dcterms.date" content="2025-01-13">
+<meta name="dcterms.date" content="2025-01-14">
 
 <title>Using Github for Scientific Collaboration</title>
 <style>
@@ -221,7 +221,7 @@ <h1 class="title">Using Github for Scientific Collaboration</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">January 13, 2025</p>
+      <p class="date">January 14, 2025</p>
     </div>
   </div>
 

search.json

@@ -45,7 +45,7 @@
     "href": "basics.html#getting-started",
     "title": "1  The basics of GitHub",
     "section": "",
-    "text": "1.1.1 Installing Git\n\nfor windows\nfor MacOS\n\n\n\n1.1.2 Setting up\nGitHub account\n\n\n\n\n\n\nNote\n\n\n\nIf you are a university student you qualify for a free pro account\n\n\nAuthorisations/configuring to github\n\n\n1.1.3 Talking to git\n\nLinking with RStudio\nVSCode\nTerminal\n\n\n\n\n\n\n#94: professortocat_v2 © GitHub, Inc.",
+    "text": "1.1.1 Installing Git\nHere is a general guide for installing git for the different operating software.\n\nfor windows\nfor MacOS\nfor Linux\n\n\n\n1.1.2 Setting up\nIf you don’t already have one create a GitHub account.\n\n\n\n\n\n\nNote\n\n\n\nIf you are a university student you qualify for a free pro account\n\n\n\n\n1.1.3 Talking to git\nNow that you have installed git you need to link it to your GitHub account and make sure that the two are able to ‘talk’ to each other. Again there are many ways to set this up. We will discuss some of these approaches below.\n\n1.1.3.1 Linking with RStudio\n\nTell RStudio where to find the git programme: Under the Tools menu, open Global Options and go to the Git/SVN section. Then enable the version control interface and make sure RStudio knows where to find git. For MacOS, enter the path (which you can find by typing which git into your terminal), for Windows, find the git program in your Program Files.\nConfigure Git: The easiest way to do this is in R through the {usethis} package (so install that if you don’t have it - install.packages(“usethis”)). and you can just run usethis::use_git_config(user.name=“Jane Doe”, user.email=“jane@example.org”) in your R console. Replace with your name and the email that is linked to your GitHub account\nLink your GitHub account: Now you need to link your GitHub account/credentials. The path of least resistance is going the HTTPS, personal access token (PAT) route. {usethis} package, which outlines how to get a PAT and link that to your git credentials.\n\n\n\n1.1.3.2 Linking with VSCode\n\n\n1.1.3.3 Linking with Terminal\n\n\n\n\n\n#94: professortocat_v2 © GitHub, Inc.",
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@@ -56,7 +56,7 @@
     "href": "basics.html#understanding-the-version-control-workflow",
     "title": "1  The basics of GitHub",
     "section": "1.2 Understanding the version control workflow",
-    "text": "1.2 Understanding the version control workflow\n\n1.2.1 Key terms\nrepo - short for repository repository - the directory or folder that is under version control local - the repository on your computer remote - the repository on GitHub commit - take a snapshot of one or more files in the repository push - send commits from the local repo to the remote repo pull - retrieve commits from the remote repo to the local repo .gitignore a file that tells git which files or types of files you don’t want to commit\nLet’s start by briefly explaining the basic workflow. On GitHub you can make repositories, which is a kind of project. Your online repository, or short repo, is called remote. To use your repository, you need to clone it locally onto your computer and it is then called local. You can write and edit R code locally on your computer. The new code is then committed and pushed back to the remote. If you follow this workflow consistently, GitHub will keep track of all the changes you make.",
+    "text": "1.2 Understanding the version control workflow\n\n1.2.1 Key terms\nrepo - short for repository repository - the directory or folder that is under version control local - the repository on your computer remote - the repository on GitHub commit - take a snapshot of one or more files in the repository push - send commits from the local repo to the remote repo pull - retrieve commits from the remote repo to the local repo .gitignore a file that tells git which files or types of files you don’t want to commit\nLet’s start by briefly explaining the basic workflow. On GitHub you can make repositories, which is a kind of project. Your online repository, or short repo, is called remote. To use your repository, you need to clone it locally onto your computer and it is then called local. You can write and edit R code locally on your computer. The new code is then committed and pushed back to the remote. If you follow this workflow consistently, GitHub will keep track of all the changes you make.\n\n\n\nThis is the basic github workflow. First we need to retrieve the remote version of repository. We now have an exact copy of the online repository locally. We are then free to work on and develop the files that are in the repository. Once we have made our changes we need to send these back to the remote repository.",
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