Version Control via Git and Github

June 2, 2015

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.

(includes git, cvs, svn, mercurial)



How do you record the history of your projects?

Bad

Piled Higher and Deeper by Jorge Cham, http://www.phdcomics.com

(http://www.phdcomics.com)

Good

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

RNeXML

https://github.com/ropensci/RNeXML

Code for RNeXML R package, plus RNeXML publication in RMarkdown


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.

Changes are saved sequentially

via Software carpentry

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

Different versions can be saved

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 navigatable 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

RNeXML

https://github.com/ropensci/RNeXML

Exercise: git via GitHub


  • create a git repository hosted at GitHub
  • record changes to files in the repository
  • history, diffs, and blame
  • two ways to collaborate on GitHub (aka 'Who are your collaborators?')
  • GitHub features: Issues and wikis