The second part of the CodeRefinery workshop focuses on reproducible software. You will learn about how to make software FAIR and how you make your software available to peers and reviewers during the publication process, using Snakemake. We will continue to learn how to build documentation with the documentation generator Sphinx (and compare it with others) and how to deploy it to Read the Docs, a service which hosts open documentation for free. The lesson about Jupyter and JupyterLab will provide insights towards good practices for reproducibility, collaboration, and reusability. On the last day we will discuss why testing often needs to be part of the software development cycle and how such a cycle can be implemented. We will see automated testing works and practice designing and writing tests. Lastly we will learn about the advantages of modular code development by type-along lessons.

For who

The workshop is useful for everyone working with software (e.g. writing scripts or changing scripts written by colleagues) that would like to learn

• how to make code available and understandable to others and your future self;
• how to generate software documentation for your code;
• how to increase software quality by implementing tests;
• how you can make your coding life easier by modular code development.

Prerequisites

• The workshop does not teach participants how to program. Ideally you already have some experience with writing or editing code, in any programming language.
• Experience with using the command line. No expertise is required, but the lesson will be mostly taken from the command line. We will help each other, but basic knowledge may help you.
• Participants should be familiar with using a text editor on their system (Nano, Notepad, Emacs, Vim etc.)
• Basic knowledge of Git.
• You need to install Git, Python, Snakemake, Sphinx, a recent version of Jupyter and JupyterLab, and pytest prior to the workshop.

How

This workshop will follow the official CodeRefinery lesson stream via Twitch. The CodeRefinery is a Nordic project to teach basic scientific computing tools, funded by the Nordic e-Infrastructure Collaboration.

As VU team, we will listen to the instructors and discuss the lessons in our local Zoom room. We will do all exercises together and help each other. Our helpers will provide expertise and context information specific for the VU.

This workshop consists of 3 half days: Tue-Thu, September 26h-28th, 08:50 - 13:30 each day.

Schedule

More information about the CodeRefinery workshop can be found here: https://coderefinery.github.io/2023-09-19-workshop/

EC for Students

You can obtain an edubadge that proves an investment of 28 hours of study if you follow both parts of the CodRefinery workshop. The edubadge can be uploaded into Hora Finita to claim 1 EC for this workshop. The ist part of the CodeRefinery workshop takes place September 19th-21st, 08:50 - 13:30 each day.

You can register for the 1st half of the workshop here: https://vu-nl.libcal.com/event/4070499