October CodeRefinery HackMD, day 4

Icebreaker, day 4

The “helper” in the breakout rooms: what is a better name for their role?

How are the breakout rooms going in general?:

Intro questions:

Reproducible research

Break-out session 1

Reconvene at 9:35

Discuss with your neighbors or among all participants

Computer programs are expected to produce the same output for the same inputs. Is that true for research software? Can you give some examples? What can we do about it?

Word-count example

Let’s look at an example project which follows the project structure guidelines given above.

Since we’ll continue working with this repo, import it to your GitHub namespace by clicking “Use this template”. This generates a fresh repository from a template.

This project is about counting the frequency distribution of words in a given text, plotting results and testing Zipf’s law. We have subdirectories for raw data, source files, documentation, processsed data and results, and README and LICENSE files.

What are the requirements.txt, Dockerfile, and Snakefile files for? Do you think this project is reproducible?

Group 16

Research Software Problems:

What can we do about it?

Group 11

Group 4

Group 15

Group 8

Group 14

Compare requirements.txt:





E: What problems do you forsee when you write down minimal version constraints like scipy>=1.0?

Related questions:

Exercise: snakemake

20 minutes, until xx:37 https://coderefinery.github.io/reproducible-research/05-workflow-management/#exercise-using-snakemake

Breakout room status:

-> We can have a walk-through of the snakemake exercise after todays session (please stay in the main room after 12CET/13EET). Hope we can clear things up there :)

Fair software

How to make your software reproducible

What are the other alternatives for Zenodo?


:::danger Break until xx:03 :::

Social coding and open software

you can find the slides here: https://cicero.xyz/v3/remark/0.14.0/github.com/coderefinery/social-coding/master/talk.md/#1

Snakemake demonstration

:::danger Break until xx:45 :::

Feedback Day 4

Please write here something positive about today and something that we can improve on

Always ask questions at the very bottom of this document, right above this. Switch to view mode if you are only watching.

We are monitoring this hackMD, but we will reply every now and then so that you can focus on the speaker.