Version control with git

Git and Github

In this lesson we will setup and use git to track changes and recover earlier states in a project. We will link our local git project to github to create a long-lasting and sharable record of the project.

Terminology

• git - a software system to track changes locally on your computer. Usually used to track text-based files like computer code.
  
• github - a free, public website where you can host git tracked projects.
  
• repository - (repo) - a collection of project files tracked together with git
  
• commit (noun) - a snapshot of the tracked project at a specific point in time
• commit (verb) - the act of capturing a snapshot of your project with git
• push - copying changes from local project up to github
• pull - copying changes from github to your local project

Setting up a new Github repository

• Log into your github account
• Select the repositories tab and click the “new” button
• Name the repository
• fill in a short description
• add a readme file
• and select a license (I use MIT)
• all other options, accept the defaults
• create!

Start a linked project on your local computer

• select “new project” from the file menu
• select “version controlled”
• select “git”
• you will be asked for the repository URL
  • through your browser, go to the github repository you just created
  • click the “clone” button
  • copy the repository url and paste into Rstudio
• If this is your first time linking to github through Rstudio, you will need to provide log in details for your github account (see Installation Instructions).

Make a webpage for your repository

• select “new file” > “R markdown” from the file menu
• Provide a title for your page
• Save this file as “index”
• Click the “knit” button at the top of the markdown editor window

Commit the changes to project and push to Github

• click over to the terminal
  • if you are on a windows PC set the options so that the terminal opens with git bash
    
• run the following commands
• git status
• git add -A
• git commit -am 'initial commit'
• git push

Host your “index” on Github pages

• return to your repository of Github
• open the “Settings and go to”Pages"
• scroll to “Source” and change from “None” to “master branch”
• Refresh page and you should see a message informing you of the web address for your page.
• For example mine is https://mbtoomey.github.io/Biol_7263/

Git workflow

All of these commands are implemented in the terminal

Check the status of your project and make sure you are up-to-date with the remote repository

• git status- provides details of the current project status
• git pull - pulls down any changes from the github repository – Note that you can work on the same project on different computers, as long as you are careful to push and pull changes throught your github repository.

Do some work and commit it to the timeline

• Do your actual work and make changes to files through Rstudio, text editors, or other specific software
• git status - git will report that the files differ from the repository
• git add -A - stage the changes
• git commit -am 'informative comment'
  • this will commit and log the changes you have made in git
  • comments should:
    • start with an active verb
    • all lower case
    • no punctuation
• You can then add these changes to your Github repository
  • git push

Reviewing the commits in your repro

• git log - full list with details of each commit
• git log --oneline - a concise list of the commits
• git log -2 - shows the last two commits
  • you can vary the parameter to see more or less
• git log -1 -p HEAD - see details of all the changes in the last commit

Amending a commit

For small changes

• make changes
• stage the changes
• git commit --amend -C Head
  • This will amend the changes you have made to the last commit

Change the git message

• git commit --amend -m '<revised message>'
• revises message on last commit

Delete a commit

• git reset --hard HEAD^
  • ^ indicates a single step backward
  • this will get rid of all changes in the last commit
  • be careful, this can’t be undone

Recover a file from an earlier commit

• first find it in your commits
• git log --oneline -- <file name>
  • only shows commits where your file was modified
• git checkout <hashcode of last commit where file was present> -- <file name>

Branching

• git branch
  • shows all branches and currently active branch
    
• git branch <name of new branch>
  • adds a new branch
    
• git checkout <name of new branch>
  • switches to the new branch
• git merge --log <name of branch to be merged into current>
  • first switch to branch you want to merge into
  • merges working branch back into main with commit comments
• git branch -d <name>
  • deletes branches that have been merged to master
• git branch -D <name>
  • deletes branches without merging
  • good if you do not want to keep changes