previous episode

Introduction to Git and GitHub

next episode

Getting started with GitHub

Overview

Teaching: 25 min
Exercises: 0 min
Questions

  • What is a remote repository?

  • How can I use GitHub to work from multiple locations?

Objectives

  • Understand how to set up remote repository

  • Understand how to push local changes to a remote repository

  • Understand how to clone a remote repository

We’re going to set up a remote repository that we can use from multiple locations. The remote repository can also be shared with colleagues, if we want to.

GitHub

GitHub is a company which provides remote repositories for Git and a range of functionalities supporting their use. GitHub allows users to set up their private and public source code Git repositories. It provides tools for browsing, collaborating on and documenting code. GitHub, like other services such as GitLab and Bitbucket, supports a wealth of resources to support projects including:

GitHub for research

GitHub isn’t the only remote repositories provider. It is very popular, however, particularly within the open source communities.

Also, GitHub has functionality which is particularly useful for researchers such as making code citable!

Get an account

Let’s get back to our tutorial. We’ll first need a GitHub account.

Sign up or sign in if you already have an account.

Create a new repository

Now, we can create a repository on GitHub,

You’ll get a page with new information about your repository. We already have our local repository and we will be pushing it to GitHub, so we can do the following:

$ git remote add origin https://github.com/<USERNAME>/git-papers.git

This line sets up an alias origin, to correspond to the URL of our new repository on GitHub.

Generating an ssh key for access to GitHub:

To be able to push changes to GitHub, you will need to generate an ssh key and upload the public part of that key to GitHub. This will allow your computer and GitHub to recognize each other.

Start by generating a key:

ssh-keygen -t ed25519 -C "your_email@example.com"

Save the file to its default location and protect it with a password. Then:

eval "$(ssh-agent -s)"
ssh-add ~/.ssh/id_ed25519

To add this key to your ssh configuration.

Next, we go to GitHub to add this key to your account, proceed to https://github.com/settings/keys.

We copy the contents of the public key: less ~/.ssh/id_ed25519.pub into a new ssh key entry (name it so we remember it). Now, we are ready to push our work to a remote repository.

Push locally tracked files to a remote repository

Now we can execute the following:

$ git push -u origin master

Counting objects: 32, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (28/28), done.
Writing objects: 100% (32/32), 3.29 KiB | 0 bytes/s, done.
Total 32 (delta 7), reused 0 (delta 0)
To https://github.com/emdupre/git-papers.git
 * [new branch]      master -> master
Branch master set up to track remote branch master from origin.

This pushes our master branch to the remote repository, (named via the alias origin) and creates a new master branch in the remote repository.

Now, on GitHub, we should see our code, and if we click the Commits tab we should see our complete history of commits.

Our local repository is now available on GitHub. This means that anywhere we can access GitHub, we can access our repository!

Push other local branches to a remote repository

Let’s push each of our local branches into our remote repository:

$ git push origin branch_name

The branch should now be created in our GitHub repository.

To list all branches (local and remote):

$ git branch -a

Deleting branches (for information only)

Don’t do this now. This is just for information. To delete branches, use the following syntax:

$ git branch -d <branch_name>			# For local branches
$ git push origin --delete <branch_name>	# For remote branches

Cloning a remote repository

Now, let’s do something drastic! But before that step, make sure that you pushed all your local branches into the remote repository!

$ cd ..
$ rm -rf git-papers

Gulp! We’ve just wiped our local repository! But, because we’ve pushed to GitHub, we have still have a copy! We can just copy the repository down using git clone:

$ git clone https://github.com/<USERNAME>/git-papers.git

Cloning into 'git-papers'...
remote: Counting objects: 32, done.
remote: Compressing objects: 100% (21/21), done.
remote: Total 32 (delta 7), reused 32 (delta 7), pack-reused 0
Unpacking objects: 100% (32/32), done.
Checking connectivity... done.

Cloning creates an exact copy of the repository. By default it creates a directory with the same name as the name of the repository.

Now, if we change into git-papers we can see that we have our repository,

$ cd git-papers
$ git log

and we can see our Git configuration files too:

$ ls -A

In order to see the other branches locally, we can check them out as before:

$ git branch -r					# Show remote branches
$ git checkout paperWJohn			# Check out the paperWJohn branch

Push changes to a remote repository

We can use our cloned repository just as if it were the original, local repository ! So, let’s make some changes to our files and commit these.

$ git checkout master				# We'll continue working on the master branch
$ nano journal.md				# Add results section
$ git add journal.md				# Stage changes
$ git commit

Having done that, how do we send our changes back to the remote repository? We can do this by pushing our changes:

$ git push origin master

If we now check our GitHub page we should be able to see our new changes under the Commit tab.

To see all configured remotes for this repository (we can have multiple!), type:

$ git remote -v

Key Points

  • Git is the version control system: GitHub is a remote repositories provider.

  • git clone to make a local copy of a remote repository

  • git push to send local changes to remote repository

previous episode

next episode