Everyday Reproducibility

Welcome to everyday computational reproducibility.

Here, you will find the material for and some other helpful links.

Slides

In order, our slides may be found at the following links:

1. intro
2. notebooks
3. programming
4. version control
5. containers
6. conclusion

as well as some exercises to go along

1. notebook ex
2. prog ex
3. container ex

Notebook Software

Before our course, we highly recommend that participants download and have installed some type of notebook writing software. For example, either:

1. jupyter lab, or,
2. RStudio

In particular, we really recommend using jupyter lab and will be using it in the course.

In lieu of downloading these, one may use them on the web:

1. Google colab for jupyter-like notebooks: https://colab.research.google.com/
2. Posit cloud for RStudio: posit.cloud

Installation guides:

Jupyter

• General instructions: https://jupyter.org/install
• Windows specifically: https://crib.utwente.nl/manual/pages/jupyterlab-install-guide/index.pdf

rstudio

• General instructions: https://rstudio-education.github.io/hopr/starting.pdf
• Windows specifically: https://www.stat.colostate.edu/~jah/talks_public_html/isec2020/installRStudio.pdf

Containerization Software

For those wishing to follow along with the containerization software, we recommend that users install either:

1. podman, or,
2. docker

N.B. installing this more advanced software may be more challenging. Some helpful links follow:

WSL For windows users, having windows subsystem for linux (WSL) is required for using either podman or docker.

• Official windows instructions for installing WSL: https://learn.microsoft.com/en-us/windows/wsl/install

podman

• Official website: https://podman.io/
• Windows instructions: https://www.redhat.com/sysadmin/run-podman-windows

docker

• Linux intructions: https://docs.docker.com/desktop/install/linux-install/
• Windows instructions: https://docs.docker.com/desktop/install/windows-install/

Once one of the containerization software choices has been installed, one may try pulling one of our images below.

Images

• A basic reproducibility image: hub.docker.com/r/gjhunt/repro

One may pull this using podman as

podman run -it --rm -p 8888:8888 -p 8787:8787 gjhunt/repro

or with docker as

docker run -it --rm -p 8888:8888 -p 8787:8787 gjhunt/repro