porous_media: python utilities for SBML

porous_media is a collection of python utilities for working with porous media simulation results and meshes with source code available from https://github.com/matthiaskoenig/porous_media.

Features include among others

• Visualization of VTK results
• Image processing
• Mesh manipulation
• FEBio helpers

If you have any questions or issues please open an issue.

How to cite

License

• Source Code: MIT
• Documentation: CC BY-SA 4.0

Installation

Dependencies

porous_media depends on ffmpeg for creation of the videos which can be installed via on linux via

sudo apt -y install ffmpeg

Make sure you can execute the following successfully from the command line:

ffmpeg

pip

porous_media is available from pypi and can be installed via

pip install porous_media

The develop version can be installed via

pip install git+https://github.com/matthiaskoenig/porous_media.git@develop

Development

Setup develop environment

uv sync --group dev

Setup pre-commit

pre-commit install
pre-commit run

Testing

Run all tests in parallel

tox run-parallel

Run single target

tox r -e py314

Funding

Matthias König is supported and by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 "QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection - A Systems Medicine Approach)" by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA).

© 2023-2026 Matthias König