README.md

PyGMT paper figures

This repository contains the Jupyter notebooks and supporting data used to generate the figures presented in the PyGMT paper:

Dongdong Tian, Yvonne Fröhlich, Wei Ji Leong, Michael Grund, William Schlitzer, Max Jones, Leonardo Uieda, Joaquim Manuel Freire Luis

PyGMT: Bridging Python and the Generic Mapping Tools for Geospatial Visualization and Analysis

Submitted to Geochemistry, Geophysics, Geosystems

Files

• Fig1_PyGMT_GMT_comparison.ipynb: Example comparison of GMT CLI (Bash) and PyGMT (Python) scripts
• Fig2_PyGMT_ecosystem.ipynb: The PyGMT ecosystem
• Fig3_PyGMT_backgrounds.ipynb: Different types of geographic background basemaps of Iceland
• Fig4_PyGMT_pandas.ipynb: Seismicity along the Andaman-Sumatra-Java Subduction Zone
• Fig5_PyGMT_xarray.ipynb: Hemispherical views of long-wavelength Mars topography
• Fig6_PyGMT_geopandas.ipynb: Choropleth map of the population in the US
• Fig7_PyGMT_datetime.ipynb: GitHub star history of GMT and the wrappers
• star_history_github_*.csv: Cached GitHub stars data used by Figure 7

Environment setup

These notebooks require a development version of PyGMT. The environment definition in environment.yml currently installs PyGMT from TestPyPI:

• GMT: 6.6.0
• pygmt: 0.19.0.dev100

Create and activate the environment:

conda env create -f environment.yml
conda activate pygmt-paper-figures

Figure-specific note

Fig1_PyGMT_GMT_comparison.ipynb and Fig2_PyGMT_ecosystem.ipynb depend on PyGMT features that are available on specific development branches which are not merged into the main branch of PyGMT yet.

Install the matching branch before running each notebook:

• Fig1_PyGMT_GMT_comparison.ipynb: requires the feature/paragraph branch

pip install --force-reinstall "git+https://github.com/GenericMappingTools/pygmt.git@feature/paragraph"

• Fig2_PyGMT_ecosystem.ipynb: requires the code-pygmt-logo branch

pip install --force-reinstall "git+https://github.com/GenericMappingTools/pygmt.git@code-pygmt-logo"

Running the notebooks

Start JupyterLab inside the activated environment:

jupyter lab

Then open the notebooks and run them within the pygmt-paper-figures environment.

Notes

• The notebooks expect GMT to be available through the same environment.
• Some figures download remote resources or rely on online datasets.
• Figure outputs are typically saved as PNG files from within the notebooks.