Best Practices for Writing Reproducible Code

Thanks:

To you for being here!
To the Open Science Community Utrecht (OSCU) and Research Data Management Support (RDM Support) for supporting the development of this workshop
To Armel Lefebvre, Bianca Kramer, Cedric Thieulot, Erik van Sebille, Jeroen Bosman, Jeroen Ooms, Jonathan de Bruin, Lukas van de Wiel, Mateusz Kuzak, Menno Fraters, Neha Moopen, Philippe Delandmeter, and Renato Alves, for helping develop this workshop
To your teachers and helpers today!

Who are you? What brings you here?

E.g. your name, pronouns, background, and motivation for this workshop.

General guidelines (and advice!)

Ask for help when you need it!
- Raise your hand
- Use a sticky note
Our helpers can help you with technical issues
Take a computer break when we take a break!

Please open the workshop site

You can find all workshop information at tinyurl.com/repcopilot.

Being reproducible

Is this enough?

Access to the code
Access to the data
(And let’s assume we can replicate the enviroment)

How confident do you feel?

This code is a kludgly, ugly, inefficient mess. (…) It is probably riddled with problems, mistakes, bugs, inefficiencies, vestigial code stubs, etc etc. (…) I am as confident as I am capable of being that all of the factual claims that were made in the manuscript are accurate.

We need to do more: we need to inspire trust.

The code is correct (and I have made it easy for you/someone to check);
My workflow is robust;
My workflow itself is accessible, and I will be guiding you through it.

The Four Facets of Reproducibility

Documentation

What do you need to execute this project? Where do you start?

Organization

Demonstrate a trustworthy workflow.

Dissemination

Share your data, release your code, publish your findings.

Automation

Automated analyses trace your steps, and prevent human error (or at the very least: document it).

What will we do in this workshop?

We will take you through a workflow (in a broad sense!)

Setting up a project
Establishing a robust backup / version control system
Writing good code
Writing documentation
Making your project accessible

We will end by trying to reproduce each others’ projects!

What do we expect from you?

Our group has many different abilities and experiences. We hope you will value this as much as we do!
We have done our best to make the workshop asynchronous so you can work at your own pace.
However, we have incorporated several moments for shared discussion and questions. Use them!
Feel free and safe to share your expertise and experiences.

Our objectives for you

We want to teach you good habits that will make your work more accessible, trustworthy, and reproducible by others. In doing so, we have tried to identify those habits that are a good return on investment: meaning, they save you time in the not-so-long run.

Welcome!