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REPRODUCING.md

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Reproducing our results

You can download a copy of all the files in this repository by cloning the git repository:

git clone https://github.com/compgeolab/NAME_OF_THIS_REPOSITORY

or downloading a zip archive from the provided DOI in the README.md.

All source code used to generate the results and figures in the paper are in the code folder. There you can find the Jupyter notebooks and .py modules that perform the calculations and generate the figures and results presented in the paper.

The LaTeX sources for the manuscript text and figures are in paper.

Setting up your environment

You'll need a working Python 3 environment with all the standard scientific packages installed (numpy, pandas, scipy, matplotlib, etc). The easiest (and recommended) way to get this is to download and install the Mambaforge Python distribution. This will give you access to a Python 3 environment and the excellent mamba package manager (a drop-in replacement for conda).

Besides the standard scientific packages, you'll also need to install some extra libraries like: Numba for just-in-time compilation; Harmonica, Verde, Boule and Pooch from the Fatiando a Terra project; PyGMT for generating maps and more.

Instead of manually installing them, they can all be automatically installed using a conda environment.

  1. Inside the cloned repository (or an unzipped version), create a new virtual environment from the environment.yml file by running: 
    mamba env create -f environment.yml
  2. Check the environment name in the environment.yml file.
  3. Activate the new environment by running: 
    mamba activate ENVIRONMENT_NAME

Generating the results from the paper

All results and their associated figures are created by the notebooks in the code folder. To fully reproduce them, run each notebook from top to bottom following the numerical order of notebook file names.

With the environment activated, start a JupyterLab server by running:

jupyter lab

Once in JupyterLab, open each notebook in turn and run them from top to bottom.

Some notebooks might take several minutes to run, depending on the resources of your system.

Generating the preprint PDF

The paper folder provides a Makefile that includes commands that automatically build the preprint PDF from the LaTeX source files using Tectonic. GNU Make should be installed in your conda environment from above.

Inside the paper folder, run the make command to generate preprint.pdf.