Pythonic-dockers for geosciences

Dockerfile(s) for running various pygplates and geosciency codes

• Dockerfile-20.04: For DockerDesktop 2.2, an old version of docker and using Ubuntu 20.04 (Focal Fossa). This includes an older version of GDAL, as well as pygplates, many other python packages, and GMT 6.4.
• Dockerfile-22.04: recommended version to use, using Ubuntu 22.04 (Jammy Jellyfish). This includes pygplates, GMT (v6.4), gplately (v1.0) and all its trimmings, pygmt (v0.9), shapely (v2.0.1), and many many other useful modules!
• Dockerfile-22.10: does not include pygplates

How-to

• docker pull nickywright/geo-python: this will download the docker container image created using Dockerfile-22.04
• For systems that can only use an older version of Docker Desktop (~2.2), use the Dockerfile-20.04 image using docker pull nickywright/geo-docker

Build instructions

For the Dockerfiles, you might need to have pygplates downloaded and in the same directory.

Dockerfile-20.04:

• to build: docker build -f Dockerfile-20.04 . -t geodoc
• to run as user: docker run -it geodoc bash
• to run with ports (e.g. for JupyterLab): docker run -p 8888:8888 geodoc

Dockerfile-22.04:

Note: this will not work with DockerDesktop 2.2 (an old version).

We need to do this on two machines: an arm64 (e.g. M1/M2 Macs) and an intel machine, so that we get docker containers compatible with both.

• to build: docker build -f Dockerfile-22.04 . -t geodoc

• Tag: docker tag geodoc nickywright/geo-python:22.04-arm64 (on arm64) or docker tag geodoc nickywright/geo-python:22.04-x86 (on x86)

• Push to dockerhub: docker push nickywright/geo-python:22.04-arm64 or docker push nickywright/geo-python:22.04-x86

• Manifest step so that everything is under a single 'latest' tag:

  • docker manifest create nickywright/geo-python:latest --amend nickywright/geo-python:22.04-arm64 --amend nickywright/geo-python:22.04-x86
  • docker manifest push nickywright/geo-python:latest

• To get: docker pull nickywright/geo-python

• To run: Put relevant files into a folder, navigate to that folder in terminal, and then do:

  • docker run -v $PWD:/home/jovyan/workspace -p 8888:8888 nickywright/geo-python
  • Copy the last JupyterLab URL into a web browser, where you can then run the notebooks and scripts!

Other helpful tips:

If you modify a text file on windows, you might need to fix so the docker (unix system) can read it. In a terminal (via the JupyterLab interface, once the docker is launched, you can do:

• tr -d '\15\32' < windows_compatible_file.txt > unix_compatible_file.txt