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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
<meta charset="utf-8">
<meta name="generator" content="quarto-1.5.56">
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
<meta name="author" content="Sam Csik">
<meta name="author" content="Julien Brun">
<meta name="author" content="Ruth Oliver">
<meta name="author" content="Carmen Galaz Garcia">
<meta name="author" content="Max Czapanskiy">
<meta name="dcterms.date" content="2024-08-19">
<title>MEDS README Guidelines</title>
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<div id="quarto-sidebar-toc-left" class="sidebar toc-left">
<nav id="TOC" role="doc-toc" class="toc-active">
<h2 id="toc-title">Table of contents</h2>
<ul class="collapse">
<li><a href="#what-is-a-readme" id="toc-what-is-a-readme" class="nav-link active" data-scroll-target="#what-is-a-readme">What is a README?</a></li>
<li><a href="#repository-level-readmes" id="toc-repository-level-readmes" class="nav-link" data-scroll-target="#repository-level-readmes">Repository-level READMEs</a></li>
<li><a href="#wikis" id="toc-wikis" class="nav-link" data-scroll-target="#wikis">Wikis</a></li>
<li><a href="#organization-level-readmes" id="toc-organization-level-readmes" class="nav-link" data-scroll-target="#organization-level-readmes">Organization-level READMEs</a></li>
</ul>
</nav>
</div>
<div id="quarto-margin-sidebar" class="sidebar margin-sidebar zindex-bottom">
</div>
<main class="content" id="quarto-document-content">
<header id="title-block-header" class="quarto-title-block default">
<div class="quarto-title">
<h1 class="title">MEDS README Guidelines</h1>
<p class="subtitle lead">When and where to include a README, and what to talk about when you do</p>
</div>
<div class="quarto-title-meta">
<div>
<div class="quarto-title-meta-heading">Authors</div>
<div class="quarto-title-meta-contents">
<p><a href="https://samanthacsik.github.io/">Sam Csik</a> </p>
<p><a href="https://brunj7.github.io/about">Julien Brun</a> </p>
<p><a href="https://bren.ucsb.edu/people/ruth-oliver">Ruth Oliver</a> </p>
<p><a href="https://bren.ucsb.edu/people/carmen-galaz-garcia-0">Carmen Galaz Garcia</a> </p>
<p><a href="https://flukeandfeather.com/">Max Czapanskiy</a> </p>
</div>
</div>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">August 19, 2024</p>
</div>
</div>
<div>
<div class="quarto-title-meta-heading">Modified</div>
<div class="quarto-title-meta-contents">
<p class="date-modified">October 31, 2024</p>
</div>
</div>
</div>
</header>
<section id="what-is-a-readme" class="level2">
<h2 class="anchored" data-anchor-id="what-is-a-readme">What is a README?</h2>
<p><strong>A <a href="https://en.wikipedia.org/wiki/README">README</a> is a text file that lives in a project directory (often the <em>root</em> directory) and provides essential information about the software / product to users, developers, and / or contributors.</strong></p>
<p>The exact origin of the README isn’t totally clear, but they date back to <a href="https://medium.com/@NSomar/readme-md-history-and-components-a365aff07f10">at least 1974</a> with the invention of <a href="https://en.wikipedia.org/wiki/PDP-10">PDP-10</a>, an early <a href="https://en.wikipedia.org/wiki/Mainframe_computer">mainframe computer</a>. A README accompanied PDP-10 with information on how to operate some of its programs.</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">
<i class="callout-icon"></i>
</div>
<div class="callout-title-container flex-fill">
Why the all caps?
</div>
</div>
<div class="callout-body-container callout-body">
<p>The <a href="https://en.wikipedia.org/wiki/ASCII">ASCII</a> (American Standard Code for Information Interchange) system sorts uppercase letters before lowercase ones. Running <code>ls</code> (to list files) in the command line will list the README near the top, making it one of the first files a user will encounter (ideal for a file that’s meant to contain critical information about how to use / engage with directory content!).</p>
</div>
</div>
<p>Platforms like <a href="https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-readmes">GitHub</a> heavily encourage the use of README files (you can just check a box to add one when creating a new repository on GitHub). The contents of a README that lives in a repo’s root directory are automatically displayed on the repo’s landing page (but note that you can also include READMEs in subdirectories as well). GitHub supports the use of <code>README.md</code> files, which are written in <a href="https://en.wikipedia.org/wiki/Markdown">Markdown</a>.</p>
</section>
<section id="repository-level-readmes" class="level2">
<h2 class="anchored" data-anchor-id="repository-level-readmes">Repository-level READMEs</h2>
<p><strong>You should always include a <a href="https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-readmes">README</a> in the root directory of your GitHub repositories.</strong> A README is typically the first item that visitors will see when they arrive at your repository. This makes them the perfect place to tell people what your project is, why its useful, and how to get started using it. What you include in a given README will look different depending on the project, but here are some guidelines for getting started:</p>
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<div class="callout-title-container flex-fill">
How to add a repository-level README:
</div>
<div class="callout-btn-toggle d-inline-block border-0 py-1 ps-1 pe-0 float-end"><i class="callout-toggle"></i></div>
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<div class="callout-body-container callout-body">
<p><em>There are a number of different ways:</em></p>
<p><strong>From GitHub:</strong></p>
<ol type="a">
<li>Check the <strong>Add a README file</strong> box when creating a repository from GitHub, or</li>
<li>Click the green <strong>Add a README</strong> button that appears below your files on a GitHub repository that does not yet have a README</li>
<li>Click the <strong>Add file</strong> button at the top of a repository’s landing page (next to the green <strong>Code</strong> button) > select <strong>+ Create new file</strong> > name it <code>README.md</code> and add content > click <strong>Commit changes…</strong></li>
</ol>
<p><strong>From RStudio (GUI):</strong></p>
<ol start="4" type="a">
<li>Use the <strong>Files pane</strong> to click <strong>Blank File</strong> > select <strong>Text File</strong> > type <code>README.md</code></li>
</ol>
<p><strong>From the command line:</strong></p>
<ol start="5" type="a">
<li>Navigate to your repository’s root directory using <code>cd</code> (use <code>pwd</code> to verify / check your location) > type <code>touch README.md</code></li>
</ol>
</div>
</div>
</div>
<section id="always-include" class="level3">
<h3 class="anchored" data-anchor-id="always-include">Things you should <em>always</em> include in your GitHub repository READMEs:</h3>
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<div class="callout-title-container flex-fill">
Important
</div>
</div>
<div class="callout-body-container callout-body">
<p>These core elements are required for <em>all</em> MEDS-related homework assignments and projects.</p>
</div>
</div>
<ul class="task-list">
<li><label><input type="checkbox"><span class="teal-text"><strong>A short, but descriptive title</strong></span></label>
<ul>
<li>A README’s title is set to the repository name by default - change this!</li>
</ul></li>
<li><label><input type="checkbox"><span class="teal-text"><strong>A brief explanation of the repository’s purpose</strong></span></label>
<ul>
<li>Paragraphs or a bulleted list are both acceptable options</li>
<li>You may include an image or logo that represents the project</li>
</ul></li>
<li><label><input type="checkbox"><span class="teal-text"><strong>A concise description of what’s housed in the repository</strong></span></label>
<ul>
<li>This includes information about the repository structure or file organization</li>
</ul></li>
<li><label><input type="checkbox"><span class="teal-text"><strong>Details regarding data access</strong></span></label>
<ul>
<li>Any necessary information on where data lives (e.g. is it housed in the repo, on a server, in a library / package etc.) and how to access it in order to run the code</li>
</ul></li>
<li><label><input type="checkbox"><span class="teal-text"><strong>A list of authors or current contributors (for collaborative work)</strong></span></label>
<ul>
<li>Consider hyperlinking collaborators’ GitHub profiles or other professional profile</li>
</ul></li>
<li><label><input type="checkbox"><span class="teal-text"><strong>References and / or Acknowledgements</strong></span></label>
<ul>
<li>In an appropriate, consistent format, including links</li>
<li>Provide reference to any other individuals or sources that supported the development of the repository. For example, did you fork an existing repository? Did the work have any funding sources? Were there individuals you consulted with or were inspired by?</li>
<li>Don’t forget to add references for data sets too</li>
</ul></li>
</ul>
</section>
<section id="consider-including" class="level3">
<h3 class="anchored" data-anchor-id="consider-including">Things you should consider including, but may vary depending on the goals and complexity of the project:</h3>
<ul class="task-list">
<li><label><input type="checkbox"><span class="teal-text"><strong>How to install or where to start</strong></span></label>
<ul>
<li>Does your repository contain software that users will need to download or install? Do users access your software via a web browser? Do they need to install any dependencies? Do users need to clone your repository? etc.</li>
</ul></li>
<li><label><input type="checkbox"><span class="teal-text"><strong>A quick demo</strong></span></label>
<ul>
<li>Related to #1, above. Its important to keep this concise! You may include images. Any long-form instructional documentation is best moved to the repository’s wiki</li>
</ul></li>
<li><label><input type="checkbox"><span class="teal-text"><strong>What do do if a bug is spotted</strong></span></label>
<ul>
<li>Make mention of GitHub issues and what information a user should include in an issue</li>
</ul></li>
<li><label><input type="checkbox"><span class="teal-text"><strong>Contributing</strong></span></label>
<ul>
<li>Do you welcome contributions from others? If so, its important to explain how one might contribute (e.g. fork & pull request, open an issue, both?)</li>
</ul></li>
<li><label><input type="checkbox"><span class="teal-text"><strong>License</strong></span></label>
<ul>
<li>Important for allowing others to reuse your work (which is copyrighted, by default; <a href="https://choosealicense.com/no-permission/">read about what it means when no license is available</a>)</li>
<li>What license you choose depends on what type of work you are trying to license. There are different licenses used for code / software, content, and data. Some helpful resources for getting started:
<ol type="a">
<li><em>Licensing code / software:</em> check out this page, <a href="https://choosealicense.com/">Choose an open source license</a>, by GitHub. A couple popular options for software include <a href="https://choosealicense.com/licenses/mit/">MIT License</a> and <a href="https://choosealicense.com/licenses/gpl-3.0/">GNU GPLv3</a></li>
<li><em>Licensing content (i.e. non-software):</em> check out this page, <a href="https://creativecommons.org/share-your-work/cclicenses/">About CC Licenses</a>, by Creative Commons. A few good CC options for non-software content include <a href="https://creativecommons.org/licenses/by/4.0/?ref=chooser-v1">CC BY</a>, <a href="https://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a>, and <a href="https://creativecommons.org/licenses/by-nc/4.0/">CC BY-NC</a>.</li>
<li><em>Licensing data:</em> You’ll chat more about this in <a href="https://bren.ucsb.edu/courses/eds-213">EDS 213 (Databases and Data Management)</a>!</li>
</ol></li>
</ul></li>
</ul>
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<div class="callout-header d-flex align-content-center">
<div class="callout-icon-container">
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<div class="callout-title-container flex-fill">
Keep READMEs concise
</div>
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<div class="callout-body-container callout-body">
<p>While it may be tempting to provide as much information as you possibly can into your README, it might not necessarily be the right home for <em>everything</em> (see the <a href="#wikis">Wikis</a> section, below). I find this advice from <a href="https://github.com/hackergrrl">Kira Oakley</a> in her article, <a href="https://github.com/hackergrrl/art-of-readme?tab=readme-ov-file#readme">Art of README</a> to be a helpful reminder:</p>
<blockquote class="blockquote">
<p>“The lack of a README is a powerful red flag, but even a lengthy README is not indicative of there being high quality. The ideal README is as short as it can be without being any shorter. Detailed documentation is good – make separate pages for it! – but keep your README succinct.”</p>
</blockquote>
</div>
</div>
</section>
<section id="example-repo-readmes" class="level3">
<h3 class="anchored" data-anchor-id="example-repo-readmes">Example GitHub repository READMEs:</h3>
<p>Each project is different and so is its README. As you browse through different repositories you will see that not all of them have the same sections. However, they all offer a clear starting point for a newcomer to understand what the project is about. Here are some GitHub repositories with READMEs we like:</p>
<ul>
<li><strong><a href="https://github.com/samanthacsik/strava-dashboard">strava-dashboard</a></strong>, by Samantha Csik - code for a Shiny dashboard</li>
<li><strong><a href="https://github.com/samanthacsik/EDS-240-data-viz">EDS-240-data-viz</a></strong>, by Samantha Csik - code for a course website</li>
<li><strong><a href="https://github.com/annaramji/thomas-fire">thomas-fire</a></strong>, by Anna Ramji - a MEDS student project</li>
<li><strong><a href="https://github.com/pydata/xarray">xarray</a></strong> - a Python package for working with multidimensional arrays and datasets</li>
<li><strong><a href="https://github.com/allisonhorst/palmerpenguins/">palmerpenguins</a></strong> - an R package that contains teaching data</li>
<li><strong><a href="https://github.com/NCEAS/metajam">metajam</a></strong> - an R package for downloading and reading in metadata from repositories in the DataONE network</li>
<li><strong><a href="https://github.com/matiassingers/awesome-readme">awesome-readme</a></strong>, by Matias Singers - a curated list of awesome READMEs</li>
</ul>
<div class="callout callout-style-default callout-tip callout-titled">
<div class="callout-header d-flex align-content-center">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<div class="callout-title-container flex-fill">
Don’t forget to update your repo’s “About” section as well!
</div>
</div>
<div class="callout-body-container callout-body">
<p>To the right of every GitHub repository lives an “About” section, where visitors can find some brief but helpful information about the project. For example, take a look at Allison Horst’s <a href="https://github.com/allisonhorst/palmerpenguins/">palmerpenguins</a> repository:</p>
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<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="images/palmerpenguins.png" class="img-fluid quarto-figure quarto-figure-center figure-img" style="width:100.0%"></p>
</figure>
</div>
</div>
</div>
<p><strong>Click on the gear icon to update your repo’s About section.</strong> You should always include a short description of the project. It can be super helpful to also add relevant links (e.g. package documentation, a report, a hosted GitHub Page, etc.)</p>
</div>
</div>
</section>
</section>
<section id="wikis" class="level2">
<h2 class="anchored" data-anchor-id="wikis">Wikis</h2>
<p>While READMEs are used to provide a quick overview of what your project is / does, wikis should be used to provide additional documentation. From <a href="https://docs.github.com/en/communities/documenting-your-project-with-wikis/about-wikis">GitHub Docs</a>:</p>
<blockquote class="blockquote">
<p>“You can use your repository’s wiki to share long-form content about your project, such as how to use it, how you designed it, or its core principles”</p>
</blockquote>
<p>A great way to streamline a repository’s README is to move any documentation-style information to a wiki, and then link to the appropriate wiki page from your README. Each wiki page should focus on a single topic.</p>
<div class="callout callout-style-default callout-tip callout-titled">
<div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-6-contents" aria-controls="callout-6" aria-expanded="false" aria-label="Toggle callout">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<div class="callout-title-container flex-fill">
How to add a wiki:
</div>
<div class="callout-btn-toggle d-inline-block border-0 py-1 ps-1 pe-0 float-end"><i class="callout-toggle"></i></div>
</div>
<div id="callout-6" class="callout-6-contents callout-collapse collapse">
<div class="callout-body-container callout-body">
<ol type="1">
<li>Navigate to your repository’s landing page > click <strong>Wiki</strong> (top menu)</li>
<li>Click the green <strong>Create the first page</strong> button to create your wiki’s landing page > add content > click <strong>Save page</strong></li>
<li>To add additional pages, click the green <strong>New page button</strong> (top right corner when you’re on your wiki’s home page) > provide a title / content > click <strong>Save page</strong></li>
</ol>
</div>
</div>
</div>
<section id="example-github-repository-wikis" class="level3">
<h3 class="anchored" data-anchor-id="example-github-repository-wikis">Example GitHub repository wikis:</h3>
<ul>
<li><a href="https://github.com/Openscapes/website-new/wiki">Openscapes website wiki</a>, by Openscapes (a user-guide of sorts; notes and conventions for Openscapes website maintainers and contributors)</li>
<li><a href="https://github.com/samanthacsik/cute-cats-dogs/wiki">NCEAS Roundtable (August 2023) workshop materials wiki</a>, by Samantha Csik (setup instructions for workshop participants)</li>
<li><a href="https://github.com/yihui/xaringan/wiki"><code>{xaringan}</code> wiki</a>, by Yihui Xie (includes tips and further customizations that aren’t covered in the official R package documentation)</li>
</ul>
</section>
</section>
<section id="organization-level-readmes" class="level2">
<h2 class="anchored" data-anchor-id="organization-level-readmes">Organization-level READMEs</h2>
<p><a href="https://docs.github.com/en/organizations/collaborating-with-groups-in-organizations/about-organizations">GitHub organizations</a> are shared accounts, that comprise members (each with their own <em>personal</em> GitHub account) who can collaborate across many projects at once.</p>
<p><strong>You have the option to add both public (visible to anyone) and private (visible only to organization members) profile READMEs to separately serve each of those communities.</strong> The content you choose to include in an organization profile README is quite flexible, but it’s often valuable to add the purpose of the organization, any high-level summary information, and links to important websites / external resources / specific repositories within the organization.</p>
<div class="callout callout-style-default callout-tip callout-titled">
<div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-7-contents" aria-controls="callout-7" aria-expanded="false" aria-label="Toggle callout">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<div class="callout-title-container flex-fill">
How to add an organization-level README:
</div>
<div class="callout-btn-toggle d-inline-block border-0 py-1 ps-1 pe-0 float-end"><i class="callout-toggle"></i></div>
</div>
<div id="callout-7" class="callout-7-contents callout-collapse collapse">
<div class="callout-body-container callout-body">
<p><strong>README that’s visible to the public:</strong></p>
<ol type="1">
<li>Create a <em>public</em> repository within your organization and name it <code>.github</code></li>
<li>Add a folder named <code>profile</code> to your <code>.github</code> repository, then add a <code>README.md</code> file inside <code>profile/</code> (i.e. <code>.github/profile/README.md</code>)</li>
</ol>
<p><strong>README that’s visible to members only:</strong></p>
<ol type="1">
<li>Create a <em>private</em> repository within your organization and name it <code>.github-private</code></li>
<li>Add a folder named <code>profile</code> to your <code>.github-private</code> repository, then add a <code>README.md</code> file inside <code>profile/</code> (i.e. <code>.github-private/profile/README.md</code>)</li>
</ol>
</div>
</div>
</div>
<p><strong>Alternatively (or in addition to), you can update your organization’s profile information, including a title and description, as well as relevant links – these will appear across the top of your organization’s landing page.</strong></p>
<div class="callout callout-style-default callout-tip callout-titled">
<div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-8-contents" aria-controls="callout-8" aria-expanded="false" aria-label="Toggle callout">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<div class="callout-title-container flex-fill">
How to update an organization’s profile information
</div>
<div class="callout-btn-toggle d-inline-block border-0 py-1 ps-1 pe-0 float-end"><i class="callout-toggle"></i></div>
</div>
<div id="callout-8" class="callout-8-contents callout-collapse collapse">
<div class="callout-body-container callout-body">
<p>Click on the Settings tab (top menu) to update your organization’s profile picture, description, add URLs, etc.</p>
</div>
</div>
</div>
<p>For example, see <a href="https://github.com/lter">LTER’s GitHub organization</a>, which includes both updated profile information <em>and</em> a public README:</p>
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="images/lter-org.png" class="img-fluid quarto-figure quarto-figure-center figure-img" style="width:100.0%"></p>
</figure>
</div>
</div>
</div>
<div class="callout callout-style-default callout-note callout-titled">
<div class="callout-header d-flex align-content-center">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<div class="callout-title-container flex-fill">
You’ll be asked to create an organization-level READMEs for your Capstone work
</div>
</div>
<div class="callout-body-container callout-body">
<p>In <a href="https://bren.ucsb.edu/courses/eds-411b">EDS 411 (Capstone Project)</a>, you’ll create a GitHub organization to house all your Capstone-related repositories and code. You’ll also be required to include specific information in your organization’s README (you’ll talk much more about the <a href="https://docs.google.com/document/d/10d9-h8UBC1JwZ08MdxI-WJhxfc7DnUolXjgBV1N-pJA/edit">required checklist</a> in EDS 411). In the meantime, check out a few examples GitHub organizations and their associated README information.</p>
</div>
</div>
<section id="example-github-organizations-with-added-profile-information" class="level3">
<h3 class="anchored" data-anchor-id="example-github-organizations-with-added-profile-information">Example GitHub organizations with added profile information:</h3>
<ul>
<li><strong><a href="https://github.com/UCSB-MEDS">UCSB MEDS</a></strong>, by the Master of Environmental Data Science program (a place where MEDS admin organize teaching materials and other related content)</li>
<li><strong><a href="https://github.com/thenatureconservancy">The Nature Conservancy</a></strong>, by TNC (scripts and apps from TNC scientists and geologists)</li>
<li><strong><a href="https://github.com/NCAR">NCAR</a></strong>, by the NSF National Center for Atmospheric Research (a home for NCAR software and projects)</li>
</ul>
</section>
<section id="example-public-github-organization-readmes" class="level3">
<h3 class="anchored" data-anchor-id="example-public-github-organization-readmes">Example (public) GitHub organization READMEs:</h3>
<ul>
<li><strong><a href="https://github.com/outdoor-equity">Outdoor Equity</a></strong>, by Halina Do-Linh & Clarissa Boyajian (MEDS 2022 Capstone project)</li>
<li><strong><a href="https://github.com/CASAschools">CASAschools</a></strong>, by Liane Chen, Charlie Curtin, Kristina Glass & Hazel Vaquero (MEDS 2024 Capstone project)</li>
<li><strong><a href="https://github.com/nmfs-opensci">NMFS Open Science</a></strong>, by the National Marine Fisheries Service (contains work which supports open science and open data literacy across NOAA fisheries)</li>
<li><strong><a href="https://github.com/NASA-GISS">NASA Goddard Institute for Space Studies</a></strong>, by NASA (laboratory in the Earth Sciences Division of NASA’s Goddard Space Flight Center)</li>
<li><strong><a href="https://github.com/github">GitHub</a></strong>, by GitHub (yes, GitHub is built on GitHub!)</li>
</ul>
</section>
</section>
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