Introduction to Git for (Data) Scientists

KAUST Visualization Core Lab

5 October 2021

1:00 pm - 5:00 pm

Instructors: Dr. David R. Pugh

Helpers: TBD

General Information

The Visualization Core Lab will host a Version Control using Git for (Data) Scientists workshop. Visualization lab staff will provide an introduction to version control using Git designed for learners with little or no previous experience working with automated version control.

Version control is the lab notebook of the digital world: it’s what professionals use to keep track of what they’ve done and to collaborate with other people. Every large software development project relies on it, and most programmers use it for their small jobs as well. And it isn’t just for software: books, papers, small data sets, and anything that changes over time or needs to be shared can and should be stored in a version control system.

In this workshop we will be using Git from the Unix shell. Some previous experience with the shell is expected.

Topics covered will include the following.

This hands-on lesson is part of the Introduction to Data Science Workshop Series being offered by KVL as part of our on-going efforts to build capacity in core data science skills both at KAUST and within the Kingdom of Saudi Arabia (KSA).

The workshop curriculum largely follows the curriculum developed by Software Carpentry, a volunteer project dedicated to helping researchers get their work done in less time and with less pain by teaching them basic research computing skills.

This is a live-coding based workshop and learners are expected to work along with the instructor using freely available cloud resources provided by the Binder project.

For more information on what Software Carpentry teaches and why, please see their paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students (MSc and PhD), post-docs, scientists, faculty, and industry researchers and practioners at KAUST and within the Kingdom of Saudi Arabia (KSA).

When: 5 October 2021. Add to your Google Calendar.

Registration: Register Now!

Course Materials: Introduction to Version Control using Git for (Data) Scientists

Contact: Please email help@vis.kaust.edu.sa for more information.


Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct.This document also outlines how to report an incident if needed.


Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Schedule

Before Pre-workshop Survey
13:00 Introduction to Version Control with Git
15:00 Afternoon break
15:15 Introduction to GitHub
16:00 Basics of Open Science
16:30 Wrap up
17:00 END
After Post-workshop Survey

Syllabus

Version Control with Git

  • Creating a Repository
  • Recording Changes to Files: add, commit, ...
  • Viewing Changes: status, diff, ...
  • Ignoring Files
  • Working on the Web: clone, pull, push, ...
  • Resolving Conflicts
  • Open Licenses
  • Where to Host Work, and Why
  • Reference...

Setup

To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. Select "Use the nano editor by default" and click on "Next".
    3. Keep "Use Git from the Windows Command Prompt" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Select "Use Windows' default console window" and click on "Next".
    7. Click on "Install".
    8. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

The default shell in all versions of macOS is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Git should be installed on your computer as part of your Bash install (described above).

Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.