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<!DOCTYPE html>
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<title>Use of GitHub in STAT545</title>
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<h1 class="title">Use of GitHub in STAT545</h1>
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<p><em>Mostly just notes for myself! Unconference talk at <a href="https://github.com/Reproducible-Science-Curriculum/Reproducible-Science-Hackathon-Dec-08-2014">#rrhack</a></em></p>
<p>Back story</p>
<ul>
<li>2013 no explicit usage of GitHub, yet vast majority of students elected to use for final project submission
<ul>
<li>What submission requirements induced this behavior?</li>
<li>no email attachments – email me a link to location on the web</li>
<li>I will not click on each file to download – must come in one bundle</li>
<li>course materials were on GitHub so they had been exposed</li>
</ul></li>
<li>2014 Jan - Apr used GitHub in another course (STAT 540 Stats for genomics)
<ul>
<li>students got educational GitHub accounts = 5 private repos</li>
<li>one public and one private repo per student</li>
<li>private repo used for homework submission and feedback</li>
<li>PAIN POINTS:</li>
<li>prof and TA made explicit collaborators on EACH private repo, by the student</li>
<li>students needed to submit link to their repo to prof</li>
<li>students cannot see each others work</li>
<li>internal matters handled in a private repo owned by me, with TAs added as collaborators</li>
<li>not easy to see all of these course-related repos as a collection</li>
</ul></li>
</ul>
<p>STAT 545 in 2014</p>
<ul>
<li><a href="http://stat545-ubc.github.io/git00_index.html">Explicit coverage of Git and GitHub</a> in the course</li>
<li><a href="https://help.github.com/categories/organizations/">GitHub Organization</a> Gold Account provided <em>gratis</em> by GitHub via their <a href="https://education.github.com">Education initiative</a></li>
<li>~50 private repos for free
<ul>
<li>one per student (team)</li>
<li>one for internal development by prof and TAs</li>
</ul></li>
<li>main course website is an <a href="https://help.github.com/articles/user-organization-and-project-pages/">Organization page</a>
<ul>
<li><a href="https://github.com/STAT545-UBC/STAT545-UBC.github.io">https://github.com/STAT545-UBC/STAT545-UBC.github.io</a></li>
<li><a href="http://stat545-ubc.github.io">http://stat545-ubc.github.io</a></li>
<li>inspired by back end of <a href="http://rmarkdown.rstudio.com">rmarkdown.rstudio.com</a> – see it in the <a href="https://github.com/rstudio/rmarkdown/tree/gh-pages">gh-pages branch of rmarkdown repo</a> and <a href="https://github.com/rstudio/rmarkdown/blob/gh-pages/Makefile">behold their Makefile</a></li>
</ul></li>
<li><a href="https://github.com/STAT545-UBC/Discussion/issues">Discussion repository’s issues</a> used as a class forum</li>
<li>Organization Teams give control over who can read, write, administer what
<ul>
<li><a href="https://help.github.com/articles/permission-levels-for-an-organization-repository/">chart</a> of repository access by team role</li>
<li>prof + TAs on Owners team</li>
<li>each student must be a singleton team :( (invisible to outside world)</li>
<li>all students belong to Students team (invisible to outside world)</li>
</ul></li>
<li>Teams and repos and permissions
<ul>
<li>Important: You cannot give an individual permission to do anything. Only a Team.</li>
<li>Each student is a team with one member. It is a “Write access” team on the student’s repository</li>
<li>The Students team is a “Read access” team on all student repositories.</li>
<li>The Owners team is omnipotent.</li>
<li>Tagging happy: <code>@STAT545-UBC/owners</code> works as a tag</li>
<li>Tagging sad: frustrated in our attempts to create a <code>@STAT545-UBC/markers</code> team – you can only <span class="citation">@mention</span> the Owners team, individual GitHub users or a team you are a member of</li>
</ul></li>
<li>Homework submission
<ul>
<li>student does work in her/his repo</li>
<li>opens an issue titled “Mark homework 11 of jenny_bryan”</li>
<li>puts SHA of relevant commit and tags <code>@STAT545-UBC/owners</code> in comment</li>
<li>marker puts comment in the issue, comments on commits, sends a pull request</li>
<li>marker closes issue when done</li>
</ul></li>
<li>Peer review
<ul>
<li>each assignment reviewed by two peers</li>
<li>issue titled “Peer review of jenny_bryan’s hwYY by karl_broman”</li>
<li>issue on jenny’s repo, formally assigned to karl</li>
<li>karl puts comments in the issue</li>
<li>karl indicates he is done but sadly cannot close the issue :( jenny or Owners must do that</li>
</ul></li>
<li>Programmatic interaction with GitHub is a MUST
<ul>
<li>started out using <a href="https://github.com/education/teachers_pet"><code>teachers_pet</code></a></li>
<li>created student teams, added students to singleton teams and the Students team</li>
<li>results were mixed, e.g. inflexibility of naming scheme, docs were uneven</li>
<li>regret over repo names :( <code>zz_</code> prefix did not have desired effect, delimiter chaos</li>
<li>added me to each repo for no reason?</li>
<li>supports a <em>very specific</em> <a href="https://education.github.com/guide">workflow</a>, e.g. one repository per student per assignment, seeded with boilerplate content</li>
<li>switched quickly to <a href="https://github.com/cscheid/rgithub"><code>github</code></a>, an R wrapper around <a href="http://developer.github.com/v3/">GitHub v3 API</a></li>
<li>once I figured out <a href="http://stat545-ubc.github.io/bit003_api-key-env-var.html">non-interactive authentication</a>, mostly success</li>
<li>excellent for creating ~100 issues each week</li>
<li>epic fail at adding new teams and repos mid-term; luckily volume small enough to do manually</li>
<li>fail not due to capability but lack of examples and, I think?, inconsistency about JSON-ification of inputs, i.e. whether user or wrapper function converts</li>
<li>documentation really doesn’t exist, no vignette</li>
</ul></li>
<li>Fake GitHub account and dummy repos and teams are a MUST
<ul>
<li>luckily I could create an account as my husband and hijack as needed</li>
<li>very hard to do “dry run” before you unleash your issue-creating script</li>
<li>Apparently someone’s GitHub handle is <a href="https://github.com/na"><code>NA</code></a>. Ask me how I know. Sorry about the issues, Nate Anderson!</li>
</ul></li>
<li>Other
<ul>
<li><a href="http://shinyapps.stat.ubc.ca/STAT545/peer-review/">Peer review Shiny app</a></li>
<li>any time spent configuring Git(Hub) and learning about usage patterns struck me as a valid pedagogical goal – so did not worry about the time spent on this</li>
<li>like Mine, harvesting the GitHub usernames is semi-painful; repo names however were within my control and I created them from official class registration list</li>
</ul></li>
</ul>
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