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<html>
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Git Basics
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GitHub Basics
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More Git Skills
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RStudio Cloud 1
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RStudio Cloud 2
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More Resources
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<h1 class="title toc-ignore">GitHub Basics</h1>
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<table class="table" style="margin-left: auto; margin-right: auto;">
<tbody>
<tr>
<td style="text-align:left;color: white !important;background-color: blue !important;width: 20%; ">
Compartmentalized
</td>
<td style="text-align:left;color: white !important;background-color: blue !important;width: 20%; ">
Documented
</td>
<td style="text-align:left;color: white !important;background-color: blue !important;width: 20%; ">
Extendible
</td>
<td style="text-align:left;color: white !important;background-color: blue !important;width: 20%; ">
Reproducible
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<td style="text-align:left;color: white !important;background-color: blue !important;width: 20%; ">
Robust
</td>
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<div id="overview" class="section level1">
<h1>Overview</h1>
<p>Key GitHub.com skills.</p>
<ul>
<li>How to use issues.</li>
<li>How to use releases.</li>
<li>A production workflow (what I do).</li>
<li>How to use organizations—for yourself or a team.</li>
<li>How to set things up in your shared repository in order to work as a small team.</li>
</ul>
</div>
<div id="key-github-skills" class="section level1">
<h1>Key GitHub skills</h1>
<div id="issues" class="section level2">
<h2>Issues</h2>
<ul>
<li>Use the Issues in GitHub to enter any issues (bugs, feature changes, notes).</li>
</ul>
<p><img src="images/issues.png" /></p>
<p><img src="images/issues2.png" /></p>
<ul>
<li>Add code to your issue so you can easily recreate the problem.</li>
</ul>
<p><img src="images/code-issues.png" /></p>
<ul>
<li>You can reference issues in your commits with #<num of the issue></li>
</ul>
</div>
<div id="releases" class="section level2">
<h2>Releases</h2>
<ul>
<li>The release or tag feature in GitHub will help you go back in time and document working states</li>
<li>Use a NEWS file to keep a notebook of all your major changes.</li>
</ul>
<p><em>Pro tip</em> checkout the state of the repository at the time of a release. From the terminal:</p>
<pre><code>git checkout v1.0</code></pre>
<p>When done:</p>
<pre><code>git switch -</code></pre>
<p><strong>Warning <code>git checkout ...</code> will change all your time stamps.</strong></p>
</div>
<div id="my-production-workflows" class="section level2">
<h2>My production workflows</h2>
<p><a href="https://atsa-es.github.io/MARSS/">MARSS R package</a></p>
<p>I develop on the main branch as long as I can break work into small tasks. The versions that users use are either CRAN releases or GitHub releases. I warn them that the main branch is a development branch and might be broken.</p>
<div id="workflow-with-small-tasks" class="section level3">
<h3>Workflow with small tasks</h3>
<p><img src="images/marss-workflow-1.png" /></p>
</div>
<div id="workflow-when-i-might-break-things" class="section level3">
<h3>Workflow when I might break things</h3>
<p>A major re-organization or new functionality that has the potential to break things is done on a branch.</p>
<p><img src="images/marss-workflow-2.png" /></p>
</div>
</div>
<div id="organizations" class="section level2">
<h2>Organizations</h2>
<p>I use this to organize collections of repositories. Example: <a href="https://github.com/eeholmes" class="uri">https://github.com/eeholmes</a></p>
<ul>
<li>Share access to repos across a team</li>
<li>Have team discussions</li>
<li>Have a organization landing page</li>
</ul>
</div>
<div id="pro-tip-using-github-actions" class="section level2">
<h2>Pro tip: Using GitHub Actions</h2>
<ul>
<li><a href="https://github.com/nmfs-openscapes/12-07-21-GitHub-Actions">Eli’s NMFS R UG presentation on GitHub Actions</a></li>
</ul>
<p>You may have heard about them. Let’s see it in action. We make a GitHub Action that will update our Readme file whenever a relevant change happens. We’ll see a bigger example next week with RMarkdown reports.</p>
<p>To set up our action:</p>
<ul>
<li>Create a .github folder in our repo</li>
<li>Create a workflows folder in the .github folder</li>
<li>Create a file <code>render-readme.yml</code> with the instructions for what to do to make the Readme.md file.</li>
</ul>
<p>Our yml file has a set of instructions to the server that is going to do the work.</p>
<pre><code>on:
push:
paths:
- README.Rmd
- test.csv
name: Render README
jobs:
render:
name: Render README
runs-on: macOS-latest
steps:
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-r@v1
- uses: r-lib/actions/setup-pandoc@v1
- name: Install packages
run: Rscript -e 'install.packages(c("rmarkdown", "knitr"))'
- name: Render README
run: Rscript -e 'rmarkdown::render("README.Rmd", output_format = "md_document")'
- name: Commit results
run: |
git commit README.md -m 'Re-build README.Rmd' || echo "No changes to commit"
git push origin || echo "No changes to commit"</code></pre>
</div>
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<hr>
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<i class="fas fa-cubes"></i> NWFSC Math Bio Program <i class="fas fa-cubes"></i>
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