What stood out to you when (if) you diagrammed your file system?
Review
If your current working directory is Users/kristinariemer/Dropbox/Documents, what command could be used to change directory into the local Documents folder?
Learning objectives
Understand the what and why of version control
Set up git on your computer
Create a git repository associated with an R project
Use git to track and record changes to a git repository
Use .gitignore to selectively exclude files from git.
Version Control
Semi-automated system for tracking changes with unlimited “undo”
Why Learn Version Control?
Track development of research projects like a lab notebook
Keep project in sync across computers including HPC
Share and collaborate on projects in a clear and manageable way
Git and GitHub for version control
Git: version control on your computer.
GitHub: connects your local Git to the cloud.
Project management
Collaboration
Visual interface
Optional!
Coding time: Git Setup
We installed git last week, so you should be ready to set it up!
Shell
git config --global user.name "Your Name"git config --global user.email "youremail@arizona.edu"# Use your GitHub associated email
Coding time
General syntax: gitverboptions
Set up text editor choice:
git config --global core.editor "vim"
Use the --help flag to see options
Git repositories
Git works with the unit of the repository
Repositories are folders
Good practice: repositories == .Rprojects
Creating a git repository
You have options:
RStudio Wizard when creating an R project
git init in an existing directory/R Project
usethis::use_git in an existing R Project
RStudio New Project Wizard
Before you create the directory…
File > New R Project…
RStudio New Project Wizard
git init
Create a new directory (or R project) on your computer
git init
git init
Navigate to it on the command line
Run git init from the command line
git init
usethis::use_git()
Create a new R Project
usethis::use_git()
usethis::use_git()
Open the R Project
From inside the R project, run…
usethis::use_git()
Coding time
Create a new R project and initialize it as a git repo.
Use any of the 3 approaches we’ve just gone over.
Report back: how did it go?
Coding time
Introduce git status
Coding time
Introduce modifications to this repository
Try git status again
Saving modifications: a two-step process
Coding time
git add
git commit --m "foo"
Adding multiple files to same commit
Coding time
Modify-add-commit cycle
git diff
git restore to reset saved changes to the last commit
git reset HEAD\~ to (effectively) undo an add-commit cycle
Coding time
Ignore files with .gitignore
Takeaways
git handles keeping track of versions and changes
Initialize a git repo 3 ways, depending on the current state of your project
The core git workflow is the modify-add-commit cycle
