githubr: making it easy to talk to GitHub from R | #mozsprint 2016

Brian Bot is principal scientist and community manager at Sage Bionetworks. Brian is a longtime open science advocate and has brought several projects to Mozilla Science. When I finally met Brian at our first Working Open Workshop, I was blown away by his passion and ability to bring the right groups together to promote an open research ecosystem.

Since then, I learned about githubr, a package used internally at Sage written by Brian. We decided that adding githubr to CRAN would be a perfect project for the Global Sprint. I interviewed Brian to learn more about githubr and how you can help June 2-3 at #mozsprint.


What is githubr?

githubr is a lightweight R package which allows analysts to leverage github as a source code repository for versioning their code.

How does githubr make it easy to use GitHub for version control?

githubr focuses on enabling researchers to ‘source’ in code directly from a GitHub repo and record the specific version / hash of that script as part of their analytical processing (e.g. include in a provenance record).

How has githubr helped you with your research?

githubr is used extensively by Sage researchers to record and share their analysis scripts through GitHub repos and the Synapse provenance APIs – allowing further transparency into what exact code was run against what data to produce a specific output.

How can others help you during the Mozilla Science Global Sprint, June 2-3?

The goal of the githubr Global Sprint is to get the package in a CRAN-ready state. Specific things that need to be done include porting of tests from RUnit to the testthat framework, adding examples to the documentation files, and other small enhancements. Issues for the Global Spring will be tracked here.

What kind of skills do I need to help you work on githubr?

Basic knowledge of R package development and/or experiencing with unit and integration testing. Familiarity with the GitHub APIs is nice, but not necessary.

Any other contributions that you think would be useful?

YES! Feedback / suggestions for future directions or improvements to the packages are always welcome!


Come join us wherever you are June 2-3 at the Mozilla Science Global Sprint to work on githubr and many other projects! Have your own project? Submissions are open for new project ideas.