Jupyter Notebook Scientific Python Stack

NSLS-II Quickstart

If using docker-machine:

docker-machine start default
eval $(docker-machine env default)

Then:

make proxy
make tmpnb
make open

What it Gives You

• Jupyter Notebook server (v4.0.x or v3.2.x, see tag)
• Conda Python 3.5.x environment
• Latest stable release of scientific Python packages and the bleeding-edge master of NSLS-II data collection and analysis packages
• Unprivileged user jovyan (uid=1000, configurable, see options) in group users (gid=100) with ownership over /home/jovyan and /opt/conda
• (v4.0.x) tini as the container entrypoint and start-notebook.sh as the default command
• Options for HTTPS, password auth, and passwordless sudo

Basic Use

The following command starts a container with the Notebook server listening for HTTP connections on port 8888 without authentication configured.

docker run -d -p 8888:8888 jupyter/nsls2-tutorial

Docker Options

You may customize the execution of the Docker container and the Notebook server it contains with the following optional arguments.

• -e PASSWORD="YOURPASS" - Configures Jupyter Notebook to require the given password. Should be conbined with USE_HTTPS on untrusted networks.
• -e USE_HTTPS=yes - Configures Jupyter Notebook to accept encrypted HTTPS connections. If a pem file containing a SSL certificate and key is not found in /home/jovyan/.ipython/profile_default/security/notebook.pem, the container will generate a self-signed certificate for you.
• (v4.0.x) -e NB_UID=1000 - Specify the uid of the jovyan user. Useful to mount host volumes with specific file ownership.
• -e GRANT_SUDO=yes - Gives the jovyan user passwordless sudo capability. Useful for installing OS packages. You should only enable sudo if you trust the user or if the container is running on an isolated host.
• -v /some/host/folder/for/work:/home/jovyan/work - Host mounts the default working directory on the host to preserve work even when the container is destroyed and recreated (e.g., during an upgrade).
• (v3.2.x) -v /some/host/folder/for/server.pem:/home/jovyan/.ipython/profile_default/security/notebook.pem - Mounts a SSL certificate plus key for USE_HTTPS. Useful if you have a real certificate for the domain under which you are running the Notebook server.
• (v4.0.x) -v /some/host/folder/for/server.pem:/home/jovyan/.local/share/jupyter/notebook.pem - Mounts a SSL certificate plus key for USE_HTTPS. Useful if you have a real certificate for the domain under which you are running the Notebook server.
• -e INTERFACE=10.10.10.10 - Configures Jupyter Notebook to listen on the given interface. Defaults to '*', all interfaces, which is appropriate when running using default bridged Docker networking. When using Docker's --net=host, you may wish to use this option to specify a particular network interface.
• -e PORT=8888 - Configures Jupyter Notebook to listen on the given port. Defaults to 8888, which is the port exposed within the Dockerfile for the image. When using Docker's --net=host, you may wish to use this option to specify a particular port.

Conda Environments

The default Python 3.x Conda environment resides in /opt/conda. A second Python 2.x Conda environment exists in /opt/conda/envs/python2. You can switch to the python2 environment in a shell by entering the following:

source activate python2

You can return to the default environment with this command:

source deactivate

The commands ipython, python, pip, easy_install, and conda (among others) are available in both environments.