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.
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-bookbuild-and-deploy.sh
: Runs the above, plus deploys that book to netlify. Requires netlify clirun-lab.sh
: Run a JupyterLab where the notebooks can be edited.
- 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 theswarmpal-runner
kernel) and build the pretty html.
- Use the uploaded Docker image directly, or build one locally
- Update notebooks within
./jupyterbook/notebooks/