1 of 57

1

An Introduction to Git and GitHub

#OpenScienceKE

2 of 57

2

Welcome & Intro
What GitHub is and how it’s used
Public vs Private repositories
Hands on README editing
Small Group Work
Projects & other “social” features

Outline

3 of 57

Git is a Version Control System.

Helps to keep track of the entire history of things that you are working on.
Facilitates collaboration on projects

GitHub is one of hosting services for Git Repositories

Web-based service for version control and online collaboration
The social networking site for developers
Used to manage projects and build a portfolio

Git and GitHub

4 of 57

4

Project Management

Open project: https://github.com/BioinfoNet/LowCostOpenAccess
Event: https://github.com/BioinfoNet/OpenScienceKEHackathon
Website Deve: https://github.com/mozilla/science.mozilla.org
All the Projects: https://github.com/daniellecrobinson/fellows-class-2016/projects/2

… And how it’s used

5 of 57

5

Websites

Organization: https://stephwright.github.io/PNWData/
Event: https://bioinfonet.github.io/OpenScienceKE/
Study Group: https://kipkurui.github.io/studyGroup/
Gitbook: https://mozilla.github.io/open-leadership-training-series/

… And how it’s used

6 of 57

6

Code documentation

Repository platform: https://github.com/Islandora/islandora
GitHub: https://github.com/github/

Open educational resources (OER)

Workshops: https://github.com/swcarpentry/swcarpentry
University course: https://github.com/cbahlai/OSRR_course

… And how it’s used

7 of 57

7

Open Data

Congressional data: https://github.com/unitedstates/congress-legislators
Global data: https://github.com/openaddresses/openaddresses
Data Catalogue: https://github.com/OpenExoplanetCatalogue/open_exoplanet_catalogue

… And how it’s used

8 of 57

8

So many things...

Dissertation: https://github.com/blahah/phd
CV: https://github.com/smythp/cv
To Do List: https://github.com/zee-moz/zannahplan
Trip Planning: https://github.com/stephwright/CampingWeekend

… And how it’s used

9 of 57

9

Sign up! (Have you already done this ?)

Sign up

10 of 57

10

First Repo

11 of 57

12 of 57

Cases:

snake_case
camelCase
train-case (kebab-case)
Pascal_Case

13 of 57

This is how you create a new repository. A repository (or repo) is GitHub lingo for a place to store your project files. Underneath where it says “Repository name” enter a name for your repo… it can be anything you want. Shorter is better. If you want a repo name with multiple words, you can either run all the words together, use hyphens between the words, or use underscores. If you use spaces, GitHub will automatically put hyphens in between your words.

Create a short description for your repo… again, it can be anything you want.

Make sure the Public radio button is selected. We’ll talk about Private repositories in a second.

And make sure to tick the box next to “Initialize this repository with a README”. We’ll discuss what that is in a bit.

When you have all that done, click the green “Create repository” button at the bottom and put a green sticky on your laptop. If you would like some help, place a red sticky on your laptop.

14 of 57

Free for personal use
Useful for handling sensitive information

Internal organization communication
Conference organization
1:1 consultations

Gateway for researchers uncomfortable with openness

Private Repositories

15 of 57

Back to our new repository. Once you click the green “Create repository” button, you should see a page similar to this.

Let’s talk about what we see here…. Top down…

Repository you’re in… path

Tabs… Code (where we are right now) . This tab shows you the folders and files in your repository.

Right now, you only have one file, README.md… because we initialized our repo w/ a README.

The .md stands for markdown. We’ll get to that in a minute.

Below your file list, you see your README displayed. It doesn’t say anything at the moment, except the title of your repository. The README file is the default file that will display when anyone comes to your repository.

This README is really boring, so we’re gonna fix that. To edit a file, click on the blue linked name of the file.

16 of 57

16

We are going to learn by doing

Go to: https://commonmark.org/

More resources:

GitHub md syntax: https://help.github.com/articles/basic-writing-and-formatting-syntax/
Emojis: https://www.webpagefx.com/tools/emoji-cheat-sheet/

Quick Intro to Markdown

17 of 57

18 of 57

Now that you’ve made some changes, we’re going to save those changes. In GitHub lingo, saving a change is called a “commit”. So down at the bottom of your README doc, you’ll see where it says “Commit changes”.

Write a VERY short phrase explaining what you did. They have one suggested for you there, which is fine, but in general, it’s better to be SLIGHTLY more descriptive because remember how we said GitHub was a version control platform? Well, it saves EVERY change you make and if you want to go back to a different version, it helps if you have enough of a description to know which version you want to go back to.

So the first box is for a brief description, the second box, you can add more detail.

When you’re done, click the green “Commit changes” button and ta da! You’ve just completed your first commit!

You will now see your markdown syntax as it will be viewed by others visiting your repo. Put up your green sticky when you’re done.

19 of 57

20 of 57

20

Interface Tour & Jargon Busting

Fork
README
Issue
Main
Branch
Collaborator vs Contributor

21 of 57

21

Make your own copy of the entire repository

22 of 57

22

Ways to get all the files from the web to your computer

23 of 57

23

Make your own copy of the entire repository

When you Fork a repository, you make your own copy that lives online on your GitHub account. When you Clone, you are copying the version controlled files to your computer. Changes you make won’t affect the original in either case.

Ways to get all the files from the web to your computer

24 of 57

24

Create, assign & manage Issues by clicking on this tab

25 of 57

25

Create, assign & manage Issues by clicking on this tab

26 of 57

26

Your default branch is the Master - but you can switch or add branches here

27 of 57

27

Your default branch is the Main - but you can switch or add branches here

If your collaborators suggest changes, as we will all do later, their changes go onto a new Branch until you accept them and Merge their changes into the Main.

28 of 57

28

The README is automatically rendered when you visit a repo

29 of 57

29

Upload files from your computer to this repo

30 of 57

30

Create a new file

31 of 57

31

Settings - add collaborators here

32 of 57

32

Settings - add collaborators here

Collaborators have permission to make changes to files in your repository without your approval (they are the inner circle). Anyone can be a Contributor via Pull Requests (though you don’t need to accept their contributions).

33 of 57

33

The README is automatically rendered when you visit a repo

Create, assign & manage Issues by clicking on this tab

Your default branch is the Master - but you can switch or add branches here

Create a new file

Upload files

Ways to get all the files from the web to your computer

Settings - add collaborators here

Make your own copy of the entire repository

34 of 57

34

Jargon Busting!

Fork - A copy on GitHub
Clone - A copy on your computer
README - First thing you see in a repo
Issue - A way to manage, assign tasks
Main - The default “main” branch
Branch - An alternate version of the file
Collaborator vs Contributor

35 of 57

35

GitHub

:tada: = 🎉

36 of 57

36

https://github.com/BioinfoNet/MyFirstFork
Fork!
Open README.md
Click the pen to edit
Personalize the README
Commit changes!
Send a pull request

Hands On Forking & README Editing!

🎉

37 of 57

37

Checkpoint

How did that go?
Where did you get stuck?
What was intuitive?
What was not?

38 of 57

38

Part 2

39 of 57

39

In Depth GitHub Functionality

Issue Tracking
Branching and Merging
Forking and Pull Requests

40 of 57

40

Issues Tracking

41 of 57

41

Issues

Issues are your “to-do’s” - they are the tasks you need to perform, the bugs you need to fix, and things you want to accomplish.

You can “label” issues and “assign” them to collaborators (or yourself) to do.

https://github.com/tiimgreen/github-cheat-sheet

42 of 57

42

Creating Issues:

43 of 57

43

Issue Tracking!

44 of 57

44

Branching and Merging

45 of 57

45

Creating a branch:

Notice when we create a branch - we can jump back and forth between our “READMEs” and see the different content. - <<quick demo! >>

46 of 57

46

Merging a branch into “master”:

You decide you like what you’ve done and want to merge those changes into your master branch. - <<mini demo >>

47 of 57

47

Creating a branch:

Notice when we create a branch - we can jump back and forth between our “READMEs” and see the different content. - <<quick demo! >>

48 of 57

48

Merging a branch into “master”:

You decide you like what you’ve done and want to merge those changes into your master branch. - <<mini demo >>

49 of 57

49

Forks & Pull Requests

50 of 57

50

Fork

VERB: To fork

you copy someone else’s repo with the intention to build on it/improve it and contribute back changes using “pull requests” - You are not a collaborator, but you may become a contributor.

You just did this!

NOUN: A fork

A copy of someone else’s project where you can make changes.

51 of 57

51

Pull Request

Make a pull request when you’ve made changes (commits) to a project.

Changes can be on a forked repo or a branch of your repo.

Merging these changes into the project either in the “master” branch or branch of interest. It is a “hey, pull these changes into the project”.

52 of 57

52

Hands on Exercise!

Fork a repo or become a collaborator
Make changes by writing in Markdown
Merge your changes with pull requests
Make something wonderful together!

53 of 57

53

Checkpoint

How did that go?
Where did you get stuck?
What was intuitive?
What was not?

54 of 57

54

Projects and other “Social” Features

Wiki
Projects
Watch/Start/etc.
Pulse and Graphs

55 of 57

55

Advanced GitHub

GH Pages
GitBook
Continuous Integration (Travis)

56 of 57

56

clone to local and demo from there
add vs. commit allows staging multiple files for single commit
allows local version control without cloud storage
reproducible research
resolve conflicts

Git command line demo

57 of 57

Danielle Robinson Jessica Gallinger

Steph Wright Steve Van Tuyl

These slides have been edited for OpenScienceKE and East Africa Open Science Tour workshop by Caleb

57

Slides Attributions