Version control & Automation

In this 2h. session we introduce the concepts of version control and automation of tasks. The first relates to keeping track of changes as they occur throughout the proccess, while the second one allows us to break up the different components of an analysis and have them automatically run, when needed, in the correct sequence.

Requirements

The two tools with which we will play to explore these ideas practically are git and make. You will need to have them installed on your machine to follow along in your laptop. Head over to the Requirements page to see how to install them if you haven’t yet.

Basic understanding of what a terminal client/command-line is and how to interact with it at a very basic level is required to follow along this session.

Outcomes

This session will provide you with the following skills:

• An understanding of what version control is and why it is important to include in your workflow
• Enough knowledge of git, as a particular version control software, to be able to:
  • Initiate a project
  • Track changes as you work
  • Examine the history of changes you have made to the project
  • Compare different versions
  • Revert to previous versions of a file
  • Ignore some files inside a project folder
• An understanding of what task automation is and why it is important in a good workflow
• General understanding of how make, a powerful tool to automate processes, works and how it can be used to sequentially connect very complex workflows
• Enough knowledge to make a very simple Makefile and run it on your machine

Slides

• git (html, pdf)
• make (html, pdf)

References

Git:

• Chacon, Scott (2009). Pro Git. Apress; 1 edition.
• Software carpentry.Version control with git. Online resource.

Make:

• Bostock, Mike (2013). Why Use Make. Blog post.
• Jones, Zachary. GNU Make for Reproducible Data Analysis. Blog post.