SimPEG User Tutorials

A set of user tutorials for SimPEG.

Website of the tutorials: https://simpeg.xyz/user-tutorials.

How to build the website locally

The SimPEG User Tutorials were created using Myst. Myst is capable of building the website from content stored in Jupyter Notebooks.

We can build the website from the current content in the Jupyter Notebooks. This can be done in a few seconds with very slim resource requirements.

Rerunning the notebooks is a more intensive task that will require significant amount of memory (specially for the computationally intensive notebooks) and it will take some time.

Here you'll find instructions to:

• Build and the website locally
• Rerun notebooks in the repo

Build and serve the website locally

Start by cloning this repository:

git clone https://github.com/simpeg/user-tutorials
cd user-tutorials

To build the website you'll need to install mystmd. Alternatively, you can create a conda environment using the environment.yml file:

conda env create -f environment.yml

Once you have mystmd installed, we can now build the website from its sources.

Build and serve

The following command will build the website and serve it locally, so you can preview it. Follow the instructions that will be prompted by the command to see the website:

myst start

Build only

The following command will build the website and store the HTML files in a new _build folder:

myst build --html

Clean cached builds

myst clean --all

Rerun notebooks

Start by cloning this repository:

git clone https://github.com/simpeg/user-tutorials
cd user-tutorials

And create a conda environment using the provided environment.yml file:

conda env create -f environment.yml

We can use nbconvert to rerun a notebook and overwrite its output cells in place. To rerun a single notebook, use:

jupyter nbconvert --to notebook --execute --inplace notebook.ipynb

To rerun all notebooks, use:

Caution

Rerunning all notebooks is a computationally intensive task. Some notebooks require significant amount of memory to allocate large sensitivity matrices.

Important

If you are using bash as your shell, make sure to run shopt -s globstar to enable the globstar feature that allows the use of ** for filename expansion.

jupyter nbconvert --to notebook --execute --inplace notebooks/**/*.ipynb

Check style of notebooks

We can check the code style of our notebooks using ruff. Simply run the following command to check the style of the notebooks:

ruff check notebooks

You can run the following that the notebooks are correctly formatted:

ruff format --check notebooks

And run this to autoformat them:

ruff format --fix notebooks

Alternatively, you can use the targets we have in the Makefile, like make check and make format. Read more information about the available targets by running make help.

License

All text and figures are licensed under a Creative Commons Attribution 4.0 International License, except where explicitly expressed. A copy of this license is provided in LICENSE-CC-BY.

All code in this repository is free software: you can redistribute it and/or modify it under the terms of the MIT License. A copy of this license is provided in LICENSE.