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Building, starting, and stopping a container

Assumptions:

  • Docker is running
  • You have a terminal session
  • Your current working directory is set to the main project directory.

Containers must be built if:

  • you are using the environment for the first time
  • you have made changes to any of the DS environment files listed below

Otherwise, you may proceed to Starting a stopped container

Building a container

At the command line:

docker compose -f environment/compose.yml build
docker compose -f environment/compose.yml up -d

When you bring up JupyterLab, you may see this warning. That's okay, you can ignore it.

WARN[0000] Found orphan containers ([<some_container_name>]) for this project. If you removed or renamed this service in your compose file, you can run this command with the --remove-orphans flag to clean it up.

Starting a stopped container

To start the JupyterLab Docker container, at the command line:

docker compose -f environment/compose.yml start

Accessing JupyterLab

When it's done spinning up, the container will be accessible via any webbrowser on the host machine at http://localhost:PORT_NUMBER/ (eg. http://localhost:10000).

Stopping a container

To stop the JupyterLab Docker container, at the command line:

docker compose -f environment/compose.yml stop

Structure

Docker elements

Dockerfile

This file defines the basic configuration for the Docker part of the environment. The container it uses is based on pinned version of the jupyter/datascience-notebook image, and it finishes by installing the configured packages.

compose.yml

This file uses the Dockerfile for most configuration, but additionally configures the container ports and maps the project directories on your host machine to /home/jovyan in the container.

DS environment files

requirements.txt

Additional Python packages to be installed when the container is built.

r-packages.R

Additional R packages to be installed when the container is built.

jupyter-extensions.csv

Additional JupyterLab extensions to be installed when the container is built.

Supporting files

install-jupyter-extensions.sh

This script installs the JupyterLab extensions, and is run by the Dockerfile.

jupyter_server_config.py

This is where you can make changes to the Jupyter server configuration. By default, it sets the JupyterLab UI to launch in the jupyterlab folder of the main project and removes server authentication since this project is only meant to be run on a researcher's computer and not in a shared or production environment.