Version control with git

Objective

• Understand the concept and motivation of version control
• Set up git on their machine (email address linked to their GH account; --global config)
• Understand that repos == folders =can= .Rproj.
• Initialize a git repo associated with an RStudio project called pilot-analyses.
• Understand the modify-add-commit progression. Apply this by making modifications to some R code and then committing it to the pilot-analyses repo (git commands: status, log, diff, add, commit)
• Use .gitignore to selectively exclude files from git.

Lesson outline

• Review of last week
  • Ask folks to share the diagram of their file system
  • Warm-up with review question from the slide deck
• Slides/lecture: Intro to version control with git
  • What is version control?
  • Why should I learn this? When will I need it?
• Live coding: git config
  • SW Carpentry Git lesson 2 https://swcarpentry.github.io/git-novice/02-setup
  • Setting up git using git config
    • Make sure participants use their GH email/intended GH email
    • git verb options
    • git config --global core.editor "vim"
    • git verb --help
• Live coding: git init
  • SW Carpentry Git lesson 3 https://swcarpentry.github.io/git-novice/03-create.html
  • Introduce the concept of a repository
  • Go over 3 ways to init a git repo and when to use each
  • Break to all create a project + repo called pilot-analyses
• Live coding: git status
  • Use git status to check that git init worked
  • Talk about git status as a bridge to tracking changes.
• Live coding: Tracking changes
  • SW Carpentry Git lesson 4 https://swcarpentry.github.io/git-novice/04-changes
  • Visualize in slides
  • Create a blank R file (using RStudio point and click)
  • Make comments/pseudocode changes.
  • git status
  • Go through git add/commit cycle
  • Repeat with additional changes, use git diff
  • Repeat with multiple files
  • Undo saved changes to a file using git restore
  • Use git reset HEAD~ to undo the git add and git commit commands
• Live coding: .gitignore
  • SW Carpentry Git lesson 6https://swcarpentry.github.io/git-novice/06-ignore
  • .gitignore:
    • DS_Store
    • Create a file and then ignore it.
• (Time permitting): SW Carpentry Git lesson 5
  • https://swcarpentry.github.io/git-novice/05-history
  • Navigating git history
• Homework:
  • Create a GitHub account if you don’t have one.
  • (Optional) identify an existing folder and turn it into a repository.

Installation & materials

1. Slides
2. Software Carpentry Version Control with Git episode #2
3. Software Carpentry Version Control with Git episode #3
4. Software Carpentry Version Control with Git episode #4
5. Software Carpentry Version Control with Git episode #6
6. (optional) Software Carpentry Version Control with Git episode #5

Citation

BibTeX citation:

@online{scott2023,
  author = {Scott, Eric and Diaz, Renata and Guo, Jessica and Riemer,
    Kristina},
  title = {Version Control with Git},
  date = {2023},
  url = {https://cct-datascience.github.io/repro-data-sci//lessons/3-git/notes.html},
  doi = {10.5281/zenodo.8411612},
  langid = {en}
}

For attribution, please cite this work as:

Scott, Eric, Renata Diaz, Jessica Guo, and Kristina Riemer. 2023. “Version Control with Git.” Reproducibility & Data Science in R. 2023. https://doi.org/10.5281/zenodo.8411612.