Git for research

L. Collado-Torres
2014-04-03

View this presentation

http://lcolladotor.github.io/git-for-research/

or

http://bit.ly/GitResearch

Version control

How do you version control?

  • Do nothing, hope for the best!
  • Mark them as old, new
  • Store files in a different directory
  • Append a _v1, _v2, etc to the file name
  • Add the date, for example: 2012_9_11_class.pdf
  • Use Dropbox, Google Drive, Google Docs, ShareLatex or something else to manage the files.

Why use a version control system?

  • Good organization can save a lot of time!
  • Clean directory
  • Best for collaborating with others: specially if you are working on the same file
  • Good project development practice
  • Helps share & reproduce

Git

  • It's a distributed version control system (DVCS)
  • The most used system: subversion uses git for their code!
  • Highly popular thanks to GitHub

Git basics

git init

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git clone

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git config

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git add

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git commit

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git status

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git log

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Using git

SourceTree

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Get it from http://www.sourcetreeapp.com/

Central workflow

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Fork + pull request

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Example: HopStat post

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Branches for features

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Example: derfinder

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GitHub

Overview

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Share code

Via a repository

  • One or more authors
  • Issues and bug tracking
  • Allows multiple branches

Via a gist

  • One author
  • Very quick: copy and paste

Both allow forking + comments

Issues and bug tracking

knitrBootstrap example

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rMaps example

Great way to figure out how to do something with other great people!

  • 28 comments + 4 people involved

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A gist example

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A gist example: revisions

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Host your R package

devtools makes it easy to share code via GitHub (and others)

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Open source report card

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How to get started

Where to host?

  • GitHub offers 5 private repos to .edu accounts
  • Bitbucket offers unlimited private repos to .edu accounts
  • Can use GitHub login info for Bitbucket (including ssh keys)

Code for this presentation

https://github.com/lcolladotor/git-for-research

Thank you!