Soils Revealed Data

This folder outlines data processes for the Soils Revealed project.

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Setup

The environment

To run the notebooks you need to create an environment with the dependencies. There are two options:

Docker

If you have docker in your system, you run a jupyter lab server with:

docker compose up --build

And if you want to get into the container, use a terminal in jupyter lab, vscode remote development or run this command:

docker exec -it soils_revealed_notebooks /bin/bash

Conda environment

Create the environment with:

mamba env create -n soils-revealed -f environment.yml

This will create an environment called soils-revealed with a common set of dependencies.

git (if needed) and pre-commit hooks

If this project is a new and standalone (not a module in a bigger project), you need to initialize git:

git init

If the project is already in a git repository, you can skip this step.

To install the pre-commit hooks, with the environment activated and in the project root directory, run:

pre-commit install

Update the environment

If you need to update the environment installing a new package, you simply do it with:

mamba install [package]  # or `pip install [package]` if you want to install it via pip

then update the environment.yml file so others can clone your environment with:

mamba env export --no-builds -f environment.yml

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Datasets

• Space-time statistical modelling of soil organic carbon concentration and stocks
• Soil carbon debt of 12,000 years of human land use

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Processing

This doc explains how to go from raw data to the final precalculations. It consists of 2 scripts located in the processing folder:

1. from_GeoTIFFs_to_Zarr.py which transform raw GeoTIFFs located in Google Cloud bucket into Zarrs in a local or remote (S3) directory.
2. compute_precalculations.py It takes the raster (as Zarr) and vector data and computes the precalculations.

First! transform all raw data from GeoTIFFs to Zarrs.

python from_GeoTIFFs_to_Zarr.py experimental,global,scenarios

Second! Compute precalculations

python compute_precalculations.py \
experimental,global,scenarios \
political_boundaries,hydrological_basins,biomes,landforms