Version Control via Git and Github

Overview

Teaching: 30 min
Exercises: 10 min

Questions

• How do you record the history of your projects?

• What is version control?

Objectives

• Present overview of version control.

Prerequisites

Installation of git:

• On mac and Linux git comes installed.
• On Windows PC, install git for Windows
• Create GitHub account

Recording the history of your projects

What is version control?

Version control is a system that records changes to a file or set of files over time so that you can recall specific versions later.

Question?

How do you record the history of your projects?

Bad - Run on file names

PhD Comics

Good - Informatively named files

   2013-10-14_manuscriptFish.doc
   2013-10-30_manuscriptFish.doc
   2013-11-05_manusctiptFish_intitialRyanEdits.doc
   2013-11-10_manuscriptFish.doc
   2013-11-11_manuscriptFish.doc
   2013-11-15_manuscriptFish.doc
   2013-11-30_manuscriptFish.doc
   2013-12-01_manuscriptFish.doc
   2013-12-02_manuscriptFish_PNASsubmitted.doc
   2014-01-03_manuscriptFish_PLOSsubmitted.doc
   2014-02-15_manuscriptFish_PLOSrevision.doc
   2014-03-14_manuscriptFish_PLOSpublished.doc

Better - Saving everything together at once

Everytime you make a save, you zip the entire directory that your project files are in and save it with a date.

Best - Version Control

Code for RNeXML R package, plus RNeXML publication in RMarkdown

How does a version control system work?

• Version control systems start with a base version of the document and then save just the changes you made at each step of the way.
• You can think of it as a tape: if you rewind the tape and start at the base document, then you can play back each change and end up with your latest version.

Software Carpentry

• You can then think about “playing back” different sets of changes onto the base document and getting different versions of the document.

Software Carpentry

Why use Git and GitHub

Why use Git?

• Makes you fearless
• Easy to set up
• Allows you to take a snapshot of every stage of your project history
• Takes up minimal space
• Creates a easy navigable map to the history of all changes made

Features of using a Hosting Service Like GitHub

• Backup of your project
• No need for a server: easy to set up
• GitHub’s strong community: your colleagues are probably already there
• Provides tools to help enhance collaboration
• A common location to share off your work

Example

Code for RNeXML R package, plus RNeXML publication in RMarkdown

Key Points

• Version control is an integral part of reproducible research

• Manipulate data in a reproducible manner