I’m looking for real-world examples of repro-packs or research compendiums: bundles of code, figure plotting scripts, data, and whatever else is needed to reproduce the results in a computational paper.
Reproducibility packages AKA repro-packs is the term Lorena Barba’s group uses (http://blogs.nature.com/naturejobs/2017/04/17/techblog-my-digital-toolbox-lorena-barba/).
As an example, here’s a link to a GitHub repository that houses code for one of their papers (https://github.com/barbagroup/pygbe_lspr_paper) – there’s a link in the README poining to the final repro-pack on Figshare.
Research compendium is another name for this practice that I know from hearing Karthik Ram talk about it at. Slides from a talk he gave here https://github.com/karthik/rstudio2019 with links to several real-world examples.
I’m specifically looking for examples that use Python (obvs), and from as many different research areas as possible.
Mainly what I’d like to see is how people structure code across research domains.
Recently I led a session on “Python 102” about the basics of organizing code (https://python-102.readthedocs.io/en/latest/packaging.html#), and I couldn’t find a lot of different examples, but maybe that’s because I don’t know where to look.
So I’m hoping to crowdsource those examples.
My idea is to maybe make them part of a blog post for pyOpenSci, not the end-all be-all on the subject but maybe like a mini-review that a student could at least look at to get ideas on how to package their code and share their results in a reproducible way.
What I am not looking for is source code for libraries, tools, etc., even though that is of course the scope of PyOpenSci. Fairly simple examples without a ton of development-related cruft (docker/travis/environment.yml etc) in the root of the repository would be great.
Of course I love to see a beautifully organized codebase for libraries but the idea here is to show someone a real-world example from their field what simulation / analysis / figure scripts etc for their papers might look like. Like a bunch of concrete examples of the structure suggested in “Good Enough Practices for Scientific Computing” (https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510). Plus some inspiration for the whole repro-pack itself (figures are def field specific too!)
Thanks, looking forward to seeing what people share and hearing any comments