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Pangeo Docker Images

Build Status Publish Status DockerHub Version

Latest DockerHub Images: https://hub.docker.com/orgs/pangeo/repositories

Image Description Size Pulls
base-image Foundational Dockerfile for builds
base-notebook minimally functional image for pangeo hubs
pangeo-notebook above + core earth science analysis packages
ml-notebook above + GPU-enabled tensorflow2

Click on the image name in the table above for a current list of installed packages and versions

Image tagging and "continuous building"

This repository uses GitHub Actions to build images, run tests, and push images to DockerHub.

  • Pull requests from forks trigger rebuilding all images

  • pangeo/base-notebook:master corresponds to current "staging" image in sync with master branch. Built with every commit to master. Also tagged with short GitHub short SHA pangeo/base-notebook:2639bd3.

  • Tags pushed to GitHub manually represent "production" releases with corresponding tags on DockerHub pangeo/pangeo-notebook:2020.03.11. The latest tag also corresponds to the most recent GitHub tag.

How to build images through CI

A common need is to update conda package versions in these images. To do so simply, 1) Fork this repo, 2) edit pangeo-notebook/environment.yml on your fork, 3) create a PR. Compatible packages versions with conda-lock and a lock file is automatically committed added as a commit in your PR.

How to build images locally

You'll need at least Conda installed, and Docker if you want to build and test locally.

# create a fork of this repo and clone it locally
git clone https://github.com/mygithub/pangeo-docker-images
cd pangeo-docker-images
# Install conda-lock
conda env create -f environment-condalock.yml
git checkout -b change-pangeo-notebook

Edit pangeo-notebook/environment.yml to change packages! Note that make pangeo-notebook is a convenient shortcut to build and test. See the Makefile for specific commands that are run. For example, you can just run conda-lock and don't have to run Docker to build and test locally.

make pangeo-notebook
git commit -a -m "added x packages, changed x version"
git push
# go to github to create PR, or use github cli https://cli.github.com

How to use the base-image with a Pangeo Binder

https://github.com/pangeo-data/pangeo-binder-template

How to launch jupyterlab locally with one of these images

docker run -it --rm -p 8888:8888 pangeo/base-notebook:latest jupyter lab --ip 0.0.0.0

Design:

Goals:
  1. compatible with Pangeo BinderHubs and JupyterHubs
  2. compatible with Repo2Docker Python configuration files
  3. reproducible build process and explicit conda package lists
  4. small size, fast build
  5. easy to customize

Everything stems from the Dockerfile in the base-image folder. The base-image configures default settings for Conda and Dask with condarc.yml and dask_config.yml files. The base-image is not meant to run on its own, it is the common foundation for -notebook images that install Python packages including JupyerLab and lab extensions. Lists of Conda packages for each image are specified in an environment.yml in each -notebook folder, and compatible Dask and Jupyter packages are guaranteed by specifying the pangeo-notebook conda metapackage.

You can pre-solve for compatible environments locally with conda-lock to convert the environment.yml file to a conda-linux-64.lock file which is an explicit list of compatible packages solved by Conda. The major advantage of doing this is that if you rebuild at a later date the resulting Conda environment is identical, which improves reproducibility. For this reason, when building off of the base-image, any existing conda-linux-64.lock file takes precedence over the environment.yml file.

Environment

The runtime environment sets two variables by default

  1. $PANGEO_ENV: name of the conda environment.
  2. $PANGEO_SCRATCH: a URL like gcs://pangeo-scratch/username/ that points to a cloud storage bucket for temporary storage. This is set if the variable $PANGEO_SCRATCH_PREFIX and JUPYTERHUB_USER are detected. The prefix should be like s3://pangeo-scratch

Other notes