Making Code Ready for Publication

Description

Code is an important product to share for publication. There are numerous benefits to sharing your code, including for your career and because publications now require it.

In this workshop, we will discuss ways to share analysis code in your publication, from sharing scripts and notebooks on github, to making your code executable via systems such as binder.org, to packaging your code to share with others as a software package.

Learning Objectives

Explore examples of code in repositories being submitted with a paper (https://github.com/KarstensLab/igaseq example; https://github.com/laderast/ExonModelStrain example)
Explain what kinds of files in a minimum set to include to share code and analyses in Python and R
Utilize systems such as mybinder.org or GitHub codespaces to make your code runnable from your GitHub repository
Discuss the benefits of packaging and submitting your code to package repositories such as CRAN or PyPi

Audience

Majority of us want to share analyses, not software
Leverage some principles from software packaging to share scripts and notebooks
Software packaging is its own topic

Slides

Prerequisite

Intro to Git/GitHub highly suggested