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Version control with Git

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Working from multiple locations with a remote repository

Overview

Teaching: 30 min
Exercises: 5 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 Bitbucket and GitLab supports a wealth of resources to support projects including:

Note GitHub’s free repositories have public licences by default. If you don’t want to share (in the most liberal sense) your stuff with the world and you want to use GitHub, you can create a private repository, which is limited to 3 collaborators for a free GitHub account.

Are you already using GitHub?

  • If you’re not already using GitHub (or similar) for your research code what is holding you back? What concerns do you have?
  • If you’ve already taken the plunge, how did you overcome any concerns?

Some thoughts

  • Your code isn’t ‘good enough’ yet
    • Getting your code shared online is one of the best ways to improve it.
    • GitHub has some great tools for collaboration which will make it easier to get help from others (e.g. code review from a colleague) and
    • Having the history of changes and discussions all in one place makes it easier for someone else to build on your code (or vice versa)
    • The reality is code is nearly always a work-in-progress, so it’s best to just get started wherever you’re currently up to
  • Who owns code in a public repo?
    • Keeping your code in a private repo will ensure that no-one can view it or use it
    • Even a public repo without a licence is covered by default copyright laws
    • However, adding a licence e.g. MIT and making a release means others can use it but you would retain copyright for your work
    • https://choosealicense.com/ is a good tool for deciding which licence is appropriate for you
    • You can also release code with a DOI so that people can cite it in papers.

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 using SSH, so this is the option we will use:

ssh-address

$ git remote add origin git@github.com:<USERNAME>/paper.git
$ git push -u origin master

Authentication Errors

If you get a warning that HTTPS access is deprecated, or a token is required, then you accidentally cloned the repository using HTTPS and not SSH. You can fix this from the command line by resetting the remote repository URL setting on your local repo:

$ git remote set-url origin git@github.com:<YOUR_GITHUB_USERNAME>/paper.git

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

Push locally tracked files to a remote repository

Now copy and paste the second line,

$ 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 github.com:gcapes/paper
 * [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. So, 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

Automatically enter your ssh passphrase with the ssh agent

If your ssh key has a passphrase and you don’t want to enter it every time, you can add your key to the ssh agent which manages your keys and remembers your passphrase.

Be sure to follow the correct instructions for your operating system at the link above!

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 that we have a copy of the repo on GitHub, we can download or git clone a fresh copy to work on from another computer.

So let’s pretend that the repo we’ve been working on so far is on a PC in the office, and you want to do some work on your laptop at home in the evening.

Before we clone the repo, we’ll navigate up one directory so that we’re not already in a git repo.

cd ..

Then to clone the repo into a new directory called laptop_paper

$ git clone git@github.com:<USERNAME>/paper.git laptop_paper

Cloning into 'laptop_paper'...
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 deafult it creates a directory with the same name as the name of the repository. However, we already have a paper dircectory, so have specified that we want to clone into a new directory laptop_paper.

Now, if we cd into laptop_paper we can see that we have our repository,

$ cd laptop_paper
$ 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 switch simulations			# Check out the simulations branch

Push changes to a remote repository

We can use our cloned repository just as if it was a local repository so let’s add a results section and commit the changes.

$ git switch master			# We'll continue working on the master branch
$ nano paper.md				# Add results section
$ git add paper.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 remote repositories (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

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