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CLI

The VeRCYe CLI (command line interface), simplifies data ingestion and execution of yield studies.

Usage

Make sure you have folled the setup instructions and have installed vercye with pip install -e . in this project's root directory and have activated your virtual environment.

Optional: Set up environemental defaults

If you have a system wide installation and want all studies to be saved in the same directory, copy the .env_example file to .env in the projects root. And set the paths to your shared storage and cache directories. Then, you will not have to provide the --dir option in the following instructions.

  1. Activate your virtual environment with the vercye instalation (depending on your venv setup). E.g:
conda activate vercye
  1. Initialize a new yield study.
vercye init --name your-study-name --dir /path/to/study/store

  1. [Optional] Download remotely sensed imagery & create LAI.

  2. Only required if the LAI data for your region of interest is not yet available locally.

  3. Fill in the lai configuration under /path/to/study/store/lai_config.yaml.
  4. Run the following command to download the imagery:
vercye lai --name your-study-name --dir /path/to/study/store

  1. Prepare your study

  2. Fill in the run congfiguration under /path/to/study/store/setup_config.yaml.

  3. Run the following command to create your study directory and config template.
vercye prep --name your-study-name --dir /path/to/study/store

  1. Set your run options

  2. Fill in the run congfiguration under /path/to/study/store/study/config.yaml.

  3. If you already had the LAI data available locally, ensure to adapt the lai_dir, lai_region and lai_resolution.

  4. [Optional] Download the chirps data.

  5. Only required if chirps data is not yet downloaded for the complete study range.

  6. Ensure you have completed step 4, and have set apsim_params.chirps_dir correctly in /path/to/study/store/study/config.yaml.
vercye chirps --name your-study-name --dir /path/to/study/store

  1. [Optional] Authenticate with EarthEngine

  2. Only required if using ERA5 meteorological data.

  3. Requires authenticating with your earth engine account to submit jobs.
earthengine authenticate

Run this command and follow the promtes in the terminal.

  1. Run your study

  2. You might want to adapt the number of cores to use in /path/to/study/store depending on your system.

vercye run --name your-study-name --dir /path/to/study/store/profile/config.yaml