This code recreates the figures from Segmental retention models for representing the hydraulic properties of evolving structured soils. It consists of the following files

• README.md -- this file.
• LICENSE.txt -- text of the MIT licence, applicable to the code (not to the data) contained in this repository.
• ruff.toml -- configuration file for the Ruff Python formatter.
• segmental_models.yaml -- specification of the Python packages necessary to run the code, in YAML format.
• vangenuchten.py -- a simple Python implementation of the Van Genuchten soil water retention curve.
• MJGCB2020_PoSD.csv -- A comma-separated values file containing the time-dependent porosities for the compaction example, based on A framework for modelling soil structure dynamics induced by biological activity.
• MJB2020_PoSD.csv -- As above, but for the organic amendment example, based on Modelling dynamic interactions between soil structure and the storage and turnover of soil organic matter.
• segmental_models.py -- the main Python file implementing the segmental retention models and the conductivity estimate.
• segmental_models.ipynb -- A Jupyter notebook recreating Figs. 1 and 2.
• segmental_models_compaction.ipynb -- A Jupyter notebook recreating Fig. 3.
• segmental_models_amendment.ipynb -- A Jupyter notebook recreating Fig. 4.

Follow the instructions below to set up and run the code.

Download or clone the repository

To download the latest version, click the green <> Code button and Download ZIP.

If you're using git, you can alternatively clone the entire repository using

git clone <url of this repository> segmental-retention-models && cd segmental-retention-models

Set up the environment

If you don't have conda or mamba installed, install the Miniforge3 distribution following the instructions in its readme. Then create and activate the environment using

mamba env create -f segmental_models.yaml && conda activate segmental_models

Start the notebook server

Start the notebook server

jupyter notebook

In the browser window that opens, open the .ipynb files and use Run All Cells from the Run menu to run them.