Version Control

The Turing Way Community. This illustration is created by Scriberia with The Turing Way community, used under a CC-BY 4.0 licence. DOI: 10.5281/zenodo.3332807

All of us are probably familiar with some sort of version control, think of like Google Docs or track changes for a word document. It’s basically a history of all of the changes that have been made to the document you’re working on. With software like Google Docs that happens passively for you, it will automatically create backups every few minutes so you don’t have to think about saving a file. Today we’re going to be using software that we can apply the same idea but on a much larger and more controlled way. We are going to see how we can use those softwares to back up our work, share our work, and provide a clear, documented map of the developement of a project. So hopefully by the end of the next few days you will feel comfortable using GitHub for projects to make them more organized, transparent and colllaborative.

Git and GitHub

installed on local computer

tracks changes to files

separate versions

central, remote storage of files

everyone can contribute changes

changes can be combined and shared

We can leverage the interplay between both to help us share code and collaborate with others!

Basic Git/Github Workflow

Remote repository on Github

Where all of your code and related files lives online

Central location where everyone is sharing their changes

Connect the remote repository to the files on your local computer

git clone

git init

Local repository

Files kept on your local computer

Includes branches from the remote repository
- allows for different versions of the same file

Different from local working directory

Making changes locally

Commits

groups of small, meaningful changes

snapshots of your repository at that time

tell a story of the history of your repository

Commits

Make a commit in 2 stages:

save your changes locally and then stage the files you want to commit

git add <FILENAME>

commit your changes

git commit -m "descriptive commit message"

Push

To sync the changes you’ve made locally with the remote repository, you need to “PUSH” your commits

git push

Pull

To sync any changes that were made to the remote repository onto your local computer you need to “PULL” commits

2 ways:
1. git pull

git fetch, then eventually git merge

Branches

The default for all repositories is main

Pull Requests

Once you have finished development on your branch and want to add your changes to the main branch, you can submit a pull request

Live Demo

Let’s make our first commit!

Activity 1

Following the template provided here, create a new Markdown document with:

A list of everyone in your group, including:
- their affiliation
- their GitHub name
a picture of a species you work on
a code chunk with your most used function
a task list of three things you would like to learn from the workshop

Save the file with a new name.
Commit your file, and push to the repository.

Activity 2: Branches

Create a new branch from the main branch
Add your name to the list of participants.
Save your change, commit, and push to your branch.
Submit a Pull Request to merge your changes into main branch.