MSD-LIVE Statemodify Notebook

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This repo contains the Dockerfile to build the notebook image as well as the notebooks used in the MSD-LIVE deployment. It will rebuild the image and redeploy the notebooks whenever changes are pushed to the main branch.

The data folder is too big, so we are not checking this into github. You will have to pull from s3 if you want to test locally

Testing the notebook locally

1. Get the data

   # make sure you are in the jupyter-notebook-xanthos folder
   mkdir data
   cd data
   aws s3 cp s3://xanthos-notebook-bucket/data . --recursive
   

2. Start the notebook via docker compose

   # make sure you are in the jupyter-notebook-xanthos folder
   docker compose up

Testing a dev deployment notebook in the cloud

Zoe does this when debugging the base notebook:

1. Build a new base notebook image:

   ~/msdlive/jupyter/jupyter-stacks/images/hub-notebook$ docker compose build

2. Retag the base notebook image with 'dev':

   ~/msdlive/jupyter/jupyter-stacks/images/hub-notebook$ docker tag ghcr.io/msd-live/jupyter/python-notebook:latest notebook:dev

3. Build the xanthos image to use 'dev' tag:

   Edit Dockerfile to use

   FROM ghcr.io/msd-live/jupyter/python-notebook:dev AS build-image

   build and publish the dev image:

   ~/msdlive/jupyter/notebook_repos/jupyter-notebook-xanthos$ docker build -t ghcr.io/msd-live/jupyter/xanthos-notebook:dev -f Dockerfile .
   ~/msdlive/jupyter/notebook_repos/jupyter-notebook-xanthos$ docker push ghcr.io/msd-live/jupyter/xanthos-notebook:dev

4. You might need to update the xanthos stack deployment if it was deployed to use 'latest' instead of 'dev':

   Edit jupyter-stack/deployments/xanthos/config.dev.yaml to have

   notebook_image: ghcr.io/msd-live/jupyter/xanthos-notebook:dev

   Redeploy the stack:

   ~/msdlive/jupyter/jupyter-stacks/stacks$ ./stack.sh run_deployment deploy xanthos dev

MSD-LIVE customization via plugin:

Input data dir needed to be writable so removed symlink from user's home dir that points to /data (was read only) and copies from /data to user's home dir