Swarm_quicklooks

Notebooks run automatically to display recent Swarm data at https://quicklooks.swarmdisc.org

Interact with them yourself on the VRE using the nbgitpuller link above. You won't get exact reproducibility - the software is not fixed the same, and the data is in flux.

Run locally with Podman / Docker

Requires: Podman. Will need to edit the scripts to make them work with Docker.

git clone https://github.com/Swarm-DISC/Swarm_quicklooks
cd Swarm_quicklooks

• build-book.sh: Executes the notebooks with nbmake and builds the html with jupyter-book
• build-and-deploy.sh: Runs the above, plus deploys that book to netlify. Requires netlify cli
• run-lab.sh: Run a JupyterLab where the notebooks can be edited.

Development

• This repo holds the docker build config in ./docker/, made available at <ghcr.io/swarm-disc/swarm_quicklooks>
  • Based on jupyter/minimal-notebook
  • Adds two extra conda environments which can be updated independently:
    • swarmpal-runner: Environment containing SwarmPAL, used to reliably run the notebooks. Notebooks should select this kernel.
    • jupyterbook: Minimal environment with pytest, nbmake, jupyter-book. This is used to execute the notebooks (using the swarmpal-runner kernel) and build the pretty html.
  • Use the uploaded Docker image directly, or build one locally
• Update notebooks within ./jupyterbook/notebooks/