Version control with Git and R

Think holiday cheer and version control don’t go together? Think again! In this meetup we’ll introduce you to version controlling your R code with Git and RStudio and using browsing and collaboration features of GitHub.

All you need is a laptop, no worries if you don’t have git set up on your computer yet. However, if you get a chance before the meetup, write down your most (or least!) favourite R error that you encounter regularly and an emoji translation for it. During the workshop you’ll get a chance to submit a pull request to [errormoji](https://github.com/mine-cetinkaya-rundel/errormoji) with your translation.

Presented at R-Ladies LA: https://www.meetup.com/rladies-la/events/256976525/

Transcript

1. Photo by Julian Howard on Unsplash
   Version control with Git and R
   bit.ly/r-git-la
   December 17, 2018 - R-Ladies LA
   

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2. Meet & greet
   Associate Professor, Duke
   Statistical Science
   Data Scientist & Professional
   Educator, RStudio
   R-Ladies RTP Organizer
   Mine Çetinkaya-Rundel
   

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3. happygitwithr.com
   This is a very hands on,
   scraping the surface,
   introduction to version control with R and git.
   For a much more complete treatment, see
   

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4. Getting started
   ‣ Do you have latest versions R and RStudio installed?
   ‣ If not, install /update
   ‣ R: cran.r-project.org/
   ‣ RStudio: rstudio.com/products/rstudio/download/
   ‣ Or use RStudio Cloud: bit.ly/rladiesla
   ‣ Do you have a GitHub account?
   ‣ If not, create one at github.com (but wait for the next slide first!)
   

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5. What’s in a name?
   If you’re just about to choose a GitHub username…
   ‣ Incorporate your actual name
   ‣ Reuse username from other contexts, e.g., Twitter or Slack.
   ‣ Pick a username you’ll be comfortable revealing to your future boss.
   ‣ Shorter is better than longer.
   ‣ Be as unique as possible in as few characters as possible.
   ‣ Make it timeless — don’t highlight your current university, employer, or place of
   residence, e.g. JennyFromTheBlock.
   ‣ Avoid words laden with special meaning in programming, e.g. NA or …
   From http://happygitwithr.com/github-acct.html by Jenny Bryan
   

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6. A day
   in the life…
   

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7. Today I start a new
   project!
   So I’ll do the right thing and
   create a repo first.
   ‣ Step 1: Create a new repo on GitHub
   ‣ Step 2: Clone it locally using RStudio, and observe the
   literal creation of a directory on your computer
   ‣ Step 3: Make changes locally
   ‣ Step 4: Introduce yourself to Git
   ‣ Step 5: Commit and push to GitHub
   ‣ Step 6: Confirm your changes have propagated to GitHub
   DEMO
   1 YOUR
   TURN
   2
   

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8. DEMO
   1
   ‣ Step 1: Create a new repo on GitHub
   

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9. DEMO
   1
   ‣ Step 2: Clone it locally using RStudio, and observe the literal creation of a directory
   on your computer
   on Github…
   

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10. DEMO
    1
    ‣ Step 2: Clone it locally using RStudio, and observe the literal creation of a directory
    on your computer
    in RStudio…
    

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11. DEMO
    1
    ‣ Step 3: Make changes locally
    

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12. ‣ Step 3: Introduce yourself to Git
    git config !--global user.email "[YOUR EMAIL ADDRESS]"
    git config !--global user.name "[YOUR NAME]"
    DEMO
    1
    

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13. DEMO
    1
    ‣ Step 4: Commit and push to GitHub
    

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14. DEMO
    1
    ‣ Step 5: Confirm your changes have propagated to GitHub
    

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15. YOUR
    TURN
    2
    but first…
    and if one of these doesn’t work for you bit.ly/rladiesla for RStudio Cloud
    on Terminal (Mac) / Command / Git Bash (PC)
    which git
    git !--version
    

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16. Caching credentials
    ‣ Typing your username and password over and over will get old
    quickly
    ‣ Quick, short term fix:
    ‣ Run the following in the Terminal for caching password for 2 hours
    (60*60*2 = 7200 seconds)
    git config credential.helper 'cache !--timeout=7200'
    ‣ Longer term fix:
    ‣ HTTPS credential caching: happygitwithr.com/credential-caching.html
    ‣ Setting up SSH keys: happygitwithr.com/ssh-keys.html
    

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17. YOUR
    TURN
    2
    ‣ Step 1: Create a new repo on GitHub
    ‣ Step 2: Clone it locally using RStudio, and observe the literal creation of a
    directory on your computer
    ‣ Step 3: Make changes locally
    ‣ Step 4: Introduce yourself to Git
    ‣ Step 5: Commit and push to GitHub
    ‣ Step 6: Confirm your changes have propagated to GitHub
    ‣ Step 7 (new!): Make changes to the README by directly editing on GitHub
    and pull to see the changes reflected in your local project
    

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18. RStudio / Git
    

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20. ‣ View options
    ‣ Staging and committing all changes in a
    document at once
    ‣ Staging and committing various
    changes within a document one by one
    ‣ Commit messages
    ‣ Amending a previous commit
    ‣ Pushing
    

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21. ‣ History of commits
    ‣ What is HEAD?
    ‣ Filtering history of commits by File
    or Directory
    

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22. ‣ Branching
    ‣ Switching between branches
    ‣ Dropbox / backup caution
    

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23. What if…
    

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24. I have been working on a
    project for a while, and now I’m
    realizing I should have been
    tracking it with git.
    ‣ Step 0: Create an RStudio Project from existing directory (if
    an .Rproj file doesn’t already exist)
    ‣ Step 1: usethis!::use_git() and follow instructions
    ‣ Step 2: Create a new repo on GitHub without a README
    ‣ Step 3: Add remote via on RStudio
    ‣ Click Add remote and paste the URL, and pick a remote
    name (origin), then Add.
    ‣ Back in the New Branch dialog enter master as the
    branch name and make sure Sync branch with remote is
    checked, then Create. “Create.
    ‣ In the next dialog, choose overwrite.
    For more, see happygitwithr.com/existing-github-last.html
    DEMO
    

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25. Collaboration
    

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26. Fork and a pull request
    ‣ If you just want a copy of someone’s repo, clone it
    ‣ If you might propose changes to that repo, fork it
    ‣ Let’s give it a try at github.com/mine-cetinkaya-rundel/errormoji
    ‣ Fork the repo, then add your emoji error translation
    ‣ You can do this by directly editing in GitHub or by cloning your
    fork and editing in RStudio / local text editor
    ‣ Then submit a pull request
    ‣ Not feeling inspired: Submit a PR that says so!
    YOUR
    TURN
    

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27. Merge conflicts
    ‣ Merge conflicts are one of the biggest challenges of collaborating
    on GitHub
    ‣ A good way of avoiding them (or at least making them less of an
    annoyance) is to commit and push/pull often
    ‣ Another tip for dealing with them is to learn to appreciate them as a
    toll that prevent unwanted changes making their way into your
    code, analysis, report, etc.
    2
    YOUR
    TURN
    ‣ Now you will cause a merge conflict and we’ll resolve it together!
    ‣ I will cause a merge conflict and resolve it
    DEMO
    1
    

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28. Miscalleny
    

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29. ghpages
    ‣ You can get a webpage for your project for free with GitHub
    ‣ To set up, go to Settings, and then scroll down to GitHub Pages
    ‣ Easiest option is to link everything you want exposed from your
    README
    ‣ Alternatively you can host files for the web in a docs folder, see
    more at bookdown.org/yihui/blogdown/ on this
    github.com/rstudio-education/shiny-wsds18
    

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30. R Markdown
    ‣ Want GitHub to display your rendered R Markdown file? Use
    output: github_document in your YAML
    ‣ Make sure to commit and push all figures you want displayed
    ‣ Label your R chunks informatively for informatively named figure
    files
    ‣ And be careful about changing the label of R chunks that
    generate plots — figures saved under the old name won’t
    automatically disappear
    

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31. Deleting repos
    ‣ Deleting locally is just like deleting any other folder
    ‣ Deleting on GitHub requires going into the DANGER ZONE!
    

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32. Private repos
    ‣ Why private repos?
    ‣ Teaching — FERPA!
    ‣ Keeping projects on the DL during development
    ‣ Data privacy — but this may not address this issue
    ‣ Getting private repos for free
    ‣ Students, faculty, and educational/research staff via GitHub Education
    ‣ Find out more at help.github.com/articles/about-github-education-for-educators-
    and-researchers/
    ‣ Apply for free repositories for a GitHub Organization for courses or research/lab
    groups
    ‣ Official nonprofit organizations and charities via GitHub for Good: github.com/
    nonprofit
    ‣ Everyone else can pay for some private repos, see github.com/pricing for more info
    

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33. GitHub for teaching
    ‣ You can use GitHub as your course LMS!
    ‣ Each class is an Organization (where you can request unlimited private
    repositories by showing GitHub that you’re using it for teaching)
    ‣ One repo per student / per project
    ‣ GitHub Classroom offers some functionality for repository creation for
    students
    ‣ ghclass package allows you to do everything from R!
    ‣ rundel.github.io/ghclass/articles/ghclass.html
    
    

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34. Photo by Julian Howard on Unsplash
    Slides at bit.ly/r-git-la
    mine-cetinkaya-rundel
    cetinkaya.mine@gmail.com
    @minebocek
    

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