Why use version control?

Using Git

Using Git

Using Git

Using Git

Using branches

• Can maintain several parallel versions.
• Use one branch for the latest stable version (master).
• Other branches for development.
• Changes to one branch will not interfere with use of other branches.
• Different workflows use branches in variety of ways.

Cloud storage

GitHub hosts Git repositories. Great backup for source code and other documents (like this presentation).

Web interface

Social network

Create a repository

Create a new branch

Clone it

Two ways to access repositories on GitHub

1. HTTPS

   git clone https://github.com/jknightlab/git-tutorial.git

2. SSH

   git clone git@github.com:jknightlab/git-tutorial.git

Clone it

Two ways to access repositories on GitHub

1. HTTPS

   git clone https://github.com/jknightlab/git-tutorial.git

   • No additional setup required
   • Works from behind firewalls/proxies
   • Requires user name and password for every push, pull or fetch

   • Git can do this for you

     git config --global credential.helper 'cache --timeout=36000'

2. SSH

   git clone git@github.com:jknightlab/git-tutorial.git

Clone it

Two ways to access repositories on GitHub

1. HTTPS

   git clone https://github.com/jknightlab/git-tutorial.git

2. SSH

   git clone git@github.com:jknightlab/git-tutorial.git

   • Need to generate and deploy SSH keys
   • If private keys are password protected this has to be entered for each push, pull or fetch command.
   • Can use ssh-agent to take care of passwords.

Configure the repository

Tell Git your name and email address. These will be used to attribute commits.

git config --global user.name <your name>
git config --global user.email <your email>

git config --global core.autocrlf true

Switch branches

Currently we are using the master branch.

git status

git branch -a

git checkout data-collection

Add a file

Create a new file (using your favourite text editor).

git status

git add <your file>

Commit and push

Time to commit all staged changes (don't forget to add a descriptive commit message)

git commit -m "Added file with very important information"

git push

Pull

Before doing anything else, make sure your local repository is up to date.

git pull

Playing with the data

Create a new branch (off the data-collection branch).

git checkout -b analysis

files <- dir(pattern=".txt")
data <- lapply(files, read.table)
data <- do.call(rbind, data)
names(data) <- "value"
names <- lapply(files, strsplit, ".", fixed=TRUE)
data$name <- sapply(names, sapply, "[[", 1)
write.table(data, file="combined.tab", row.names=FALSE)

git add combined.tab
git rm *.txt
git commit -m "Combined data into single file"

Pushing the new branch to GitHub

When pushing a new branch for the first time we need to tell Git where it should go.

git push --set-upstream origin analysis

More fun with data

Let's plot the data

library(ggplot2)
data <- read.table("combined.tab", header=TRUE)
data$rank <- order(data$value)
ggplot(data, aes(y=value, x=rank)) + geom_point() + theme_bw()
ggsave("figure/combined.png")

git add figure/combined.png
git commit -m "added plot of data"
git push

The fun continues

Maybe that plot could be improved?

ggplot(data, aes(y=value, x=rank)) + geom_point() + 
        geom_text(aes(label=name), hjust=0, vjust=0) + 
        theme_bw()

git add figure/combined.png
git commit -m "Added labels to data points."
git push

Merging on GitHub

Clean-up

Branches that have been deleted on GitHub still exist in the local repository. Best to clean them up.

git pull
git branch --merged | grep -v "\*" | grep -v master | xargs -n 1 git branch -d
git pull --prune

Local merge

Can always merge locally and then push to GitHub.

Here we merge data-collection into master

git checkout master
git merge data-collection

git branch -d data-collection
git push

git push origin --delete data-collection

History and diffs

Common Git commands

git clone

Create a copy of a remote repository.

git add

Stage new or changed files for the next commit.

git commit

Commit a change set to the local repository.

git push

Push committed changes to the remote repository.

git pull

Get latest version of files from remote repository and merge them with the local copies.

git status

Show status of files in working directory relative to index.

Managing branches

git branch

Create a new branch or list existing branches. Can also delete local or remote branches (may want to merge into another branch first).

git checkout

Switch to a different branch.

git merge

Merge two branches.

More Git commands

git rm

Delete files from index and working directory.

git reset

Reset index and working directory to a previous commit.

git stash

Temporarily undo changes that you don't want to commit immediately.

Git and GitHub tutorials

• GitHub for Beginners part 1 and part 2
• Git: Your new best friend
• Git for Scientists
• Interactive online tutorial
• GitHub bootcamp
• Tutorials from Atlassian

Other Git resources

• Git documentation including installation instructions
• GitHub GUI for Windows and Mac
• GitHub workflow explained.
• Comparison of Git workflows.
• Detailed description of Git configuration.

Setting up ssh agent

If working on a Linux machine that isn't automatically starting an ssh-agent instance this can be achieved by adding the following code to .profile

SSH_ENV="$HOME/.ssh/environment"

function start_agent {
    echo "Initialising new SSH agent..."
    /usr/bin/ssh-agent -s | sed 's/^echo/#echo/' > "${SSH_ENV}"
    echo succeeded
    chmod 600 "${SSH_ENV}"
    . "${SSH_ENV}" > /dev/null
    /usr/bin/ssh-add;
}

# Source SSH settings, if applicable

if [ -f "${SSH_ENV}" ]; then
    . "${SSH_ENV}" > /dev/null
    ps -ef | grep ${SSH_AGENT_PID} | grep "$(whoami).*ssh-agent\s" > /dev/null || {
        start_agent;
    }
else
    start_agent;
fi

The ssh passphrase then only needs to be entered once when the ssh agent is started.