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Use of GitHub in STAT545

Mostly just notes for myself! Unconference talk at #rrhack

Back story

  • 2013 no explicit usage of GitHub, yet vast majority of students elected to use for final project submission
    • What submission requirements induced this behavior?
    • no email attachments -- email me a link to location on the web
    • I will not click on each file to download -- must come in one bundle
    • course materials were on GitHub so they had been exposed
  • 2014 Jan - Apr used GitHub in another course (STAT 540 Stats for genomics)
    • students got educational GitHub accounts = 5 private repos
    • one public and one private repo per student
    • private repo used for homework submission and feedback
    • PAIN POINTS:
    • prof and TA made explicit collaborators on EACH private repo, by the student
    • students needed to submit link to their repo to prof
    • students cannot see each others work
    • internal matters handled in a private repo owned by me, with TAs added as collaborators
    • not easy to see all of these course-related repos as a collection

STAT 545 in 2014

  • Explicit coverage of Git and GitHub in the course
  • GitHub Organization Gold Account provided gratis by GitHub via their Education initiative
  • ~50 private repos for free
    • one per student (team)
    • one for internal development by prof and TAs
  • main course website is an Organization page
  • Discussion repository's issues used as a class forum
  • Organization Teams give control over who can read, write, administer what
    • chart of repository access by team role
    • prof + TAs on Owners team
    • each student must be a singleton team :( (invisible to outside world)
    • all students belong to Students team (invisible to outside world)
  • Teams and repos and permissions
    • Important: You cannot give an individual permission to do anything. Only a Team.
    • Each student is a team with one member. It is a "Write access" team on the student's repository
    • The Students team is a "Read access" team on all student repositories.
    • The Owners team is omnipotent.
    • Tagging happy: @STAT545-UBC/owners works as a tag
    • Tagging sad: frustrated in our attempts to create a @STAT545-UBC/markers team -- you can only @mention the Owners team, individual GitHub users or a team you are a member of
  • Homework submission
    • student does work in her/his repo
    • opens an issue titled "Mark homework 11 of jenny_bryan"
    • puts SHA of relevant commit and tags @STAT545-UBC/owners in comment
    • marker puts comment in the issue, comments on commits, sends a pull request
    • marker closes issue when done
  • Peer review
    • each assignment reviewed by two peers
    • issue titled "Peer review of jenny_bryan's hwYY by karl_broman"
    • issue on jenny's repo, formally assigned to karl
    • karl puts comments in the issue
    • karl indicates he is done but sadly cannot close the issue :( jenny or Owners must do that
  • Programmatic interaction with GitHub is a MUST
    • started out using teachers_pet
    • created student teams, added students to singleton teams and the Students team
    • results were mixed, e.g. inflexibility of naming scheme, docs were uneven
    • regret over repo names :( zz_ prefix did not have desired effect, delimiter chaos
    • added me to each repo for no reason?
    • supports a very specific workflow, e.g. one repository per student per assignment, seeded with boilerplate content
    • switched quickly to github, an R wrapper around GitHub v3 API
    • once I figured out non-interactive authentication, mostly success
    • excellent for creating ~100 issues each week
    • epic fail at adding new teams and repos mid-term; luckily volume small enough to do manually
    • 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
    • documentation really doesn't exist, no vignette
  • Fake GitHub account and dummy repos and teams are a MUST
    • luckily I could create an account as my husband and hijack as needed
    • very hard to do "dry run" before you unleash your issue-creating script
    • Apparently someone's GitHub handle is NA. Ask me how I know. Sorry about the issues, Nate Anderson!
  • Other
    • Peer review Shiny app
    • 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
    • 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