Jupyter Notebooks

Jupyter Notebooks are documents which can contain live (Python) code, equations, visualizations and narrative text and can be used as an intuitive interface for OGS projects. The following video gives an introduction to using OpenGeoSys with Jupyter Notebooks:

Jupyter Notebooks container environments

You can start with pre-defined container environment from one of the images

Usage

With Docker:

docker run --rm -p 8888:8888 -v $PWD:/home/jovyan/work --user `id -u $USER` \
    --group-add users quay.io/jupyter/scipy-notebook

This mounts your current directory into ~/work inside the container.

Windows notes

The above command only works when you run Docker from within a WSL2 Linux shell!

  • Install Docker Desktop on Windows, it automatically configures WSL2.
  • Install a Linux distribution from the Microsoft App Store. We recommend Ubuntu 22.04.
  • In the Docker Desktop application under Settings / Resources / WSL integration add your Linux distribution.
  • Open a command prompt in your Linux distribution (At the start menu type the name of the distribution) and run the container.
    • If your current working contains spaces write out $PWD, e.g.:

      ... -v /c/Users/My\ Name/working/directory:/home/jovyan/work ...

With Singularity:

singularity run docker://quay.io/jupyter/scipy-notebook

Open the specified URL shown in the command output in your browser, e.g.

http://127.0.0.1:8888/lab?token=xxx

You may have to modify the IP address if this is running on a remote machine.

Install ogs

Click on Terminal and install OGSTools (which also installs ogs itself):

pip install ogstools

You install other Python packages too. Please note that this is a temporary installation. If you stop the container the manually installed packages will be deleted.


This article was written by Lars Bilke. If you are missing something or you find an error please let us know.
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