Coding workshop 1: toward sharing Python code

about

This workshop aims to offer means to re-use Python code written by colleagues and to prepare and share code with colleagues. The advocated practices, also, help to make scientific results reproducible. The workshop is contained in the files starting with a number and ending in .ipynb (jupyter notebooks). The number is used to order the workshop material. It is work-in-progress - please file issues or talk to your colleagues if things should be changed or advanced.

prerequisites

We use GitHub to share the code, because it is basically accessible everywhere. Some of the Boku-Met repositories are not public. To access those, you need to become a member of Boku-Met. Ask any of your colleagues for an invitation. Further, you will need to get git to authenticate at GitHub. There are many options available, see the docs on git's credential helpers. The simplest way is using the GitHub command line tool gh. After installation, do gh auth login whenever you want to install some repository with anything similar to pip install git+https://github.com/boku-met/.... This will save an authentication token into your local environment¹. You will be asked to provide this token. It can be obtained in the "developer settings" of your GitHub account. Please find detailed instructions online, for example, in the GitHub docs. To verify that you are good to go, try running the below:

conda create -n tmp pip
pip install "git+https://github.com/boku-met/data-utils"
conda env remove -n tmp

Finally, prepare the means to view and execute Jupyter Notebooks. All modern integrated development environments (IDEs) can do that. However, you can also use a conda environment with Jupyter installed and a browser. In that case, run jupyter lab or jupyter notebook <notebook>.ipynb and follow the instructions to access it in your browser.

Footnotes

1. The token is saved as plain text. This is a security risk. That is why it makes sense to limit its life time and restrict it to the resource you need to have access to. You will be asked to make these choices when creating it. However, try to balance the risk of someone obtaining the token (and having access to our shared GitHub account) and the hassle of overly tight restrictions. ↩