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Version control with Git and R

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/

Mine Cetinkaya-Rundel

December 18, 2018
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  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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  19. ‣ 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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  20. ‣ History of commits
    ‣ What is HEAD?
    ‣ Filtering history of commits by File
    or Directory

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

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  22. 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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  23. Collaboration

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  24. 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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  25. 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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  26. 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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  27. 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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  28. Deleting repos
    ‣ Deleting locally is just like deleting any other folder
    ‣ Deleting on GitHub requires going into the DANGER ZONE!

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  29. 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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  30. 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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  31. Photo by Julian Howard on Unsplash
    Slides at bit.ly/r-git-la
    mine-cetinkaya-rundel
    [email protected]
    @minebocek

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