Plant Fusion: API for mixed crop modelling

Authors : Maurane Woussen, Romain Barillot, Didier Combes, Gaëtan Louarn

Institutes : INRAE

Status : Python package

License : Cecill-C

URL : https://github.com/openalea-incubator/plantfusion

Documentation : https://plantfusion.readthedocs.io/en/latest/

Overview

This package provides an API for modelling mixing crops involving several functional-structural plant models (FSPM). Its aim is to simplify the building of such simulations. It takes place through the MobiDiv research project, especially in the modelling of mixed crops with wheat and alfafa.

Currently, this API recognizes two FSPM, CN-Wheat and l-egume.

Modules required

Main packages used for the simulations:

• CN-Wheat: wheat modelling
• l-egume: legume modelling
• CARIBU: light modelling through surfacic meshes*
• PyRATP: light modelling through volumic meshes
• RiRi5: compact version of RATP
• LightVegeManager: Tool for managing lighting for plant modelling
• soil3ds

Their dependencies:

• openalea.mtg
• openalea.plantgl
• openalea.lpy
• Adel wheat
• numpy
• pandas
• scipy
• gcc
• gfortran
• make

Installation

We use conda for managing our python environment.

Note: git commands must be run in a git bash terminal (or linux terminal) and python, conda, mamba, in a powershell terminal (or linux terminal).

0. Recommended step: install mamba in your base conda environment:

conda install mamba 

1. Create your conda environment (replace conda with mamba if installed):

conda create -n myenvname openalea.mtg openalea.plantgl openalea.deploy openalea.lpy openalea.sconsx alinea.caribu alinea.astk numpy=1.22.4 pandas pytest sphinx sphinx-rtd-theme xlrd coverage nose statsmodels scipy=1.7.3 scons zipp=3.15.0 m2w64-gcc-fortran -c conda-forge -c openalea3

2. Convert CARIBU and Astk namespace in PEP 420. This step is required for installing other packages in the alinea namespace. To do so, you need to delete the __init__.py file in the alinea folder. For example, on a Windows computer, you could use this command:

del C:\Users\username\AppData\Local\miniconda3\envs\myenvname\Lib\site-packages\alinea.astk-2.3.2-py3.9.egg\alinea\__init__.py
del C:\Users\username\AppData\Local\miniconda3\envs\myenvname\Lib\site-packages\alinea.caribu-8.0.10-py3.9-win-amd64.egg\alinea\__init__.py

/!\ For all the following steps, run the commands inside the downloaded folders (commands after git clone).

3. Installation of Adel

   1. git clone -b python3 https://github.com/rbarillot/adel

   2. Convert the namespace package to PEP 420:

      1. Delete the __init__.py in alinea folder

         del src/alinea/__init__.py

      2. Replace the setup.py with setup_adel.py in plantfusion/installation_ressources. Rename it setup.py.

   3. Installation : python setup.py develop

4. Installation of PyRATP. For this step, you need to have gcc, gfortran and make installed

   1. Download the package: git clone -b update_mobidiv https://github.com/mwoussen/PyRATP

   2. Installation:

      make mode=develop
      make clean

   Note: make will compile the fortran part, then run the package installation with pip.

5. Installation of WheatFspm

   1. Create a WheatFspm folder and copy the clone_wheatfspm.sh and setup_wheatfspm.py files in it.

   2. Run clone_wheatfspm.sh in a git bash terminal. This step will download all the wheatfspm submodules.

   3. Rename setup_wheatfspm.py to setup.py and install the package with python setup.py develop

6. Installation of l-egume

   1. Download the package: git clone -b Develop https://github.com/glouarn/l-egume

   2. Install: python setup.py develop

7. Installation of LightVegeManager

   1. Download the package: git clone https://github.com/mwoussen/lightvegemanager

   2. Install: python setup.py develop

8. Installation of soil3ds

   1. Download the package: git clone https://github.com/glouarn/soil3ds

   2. Install: python setup.py develop

9. Installation of riri5

   1. Download the package: git clone https://github.com/glouarn/riri5

   2. Install: python setup.py develop

Simulation Examples

• copy of l-egume default simulation with the API
• copy of fspmwheat default simulation with the API
• compare l-egume default with l-egume + RATP
• compare l-egume default with l-egume + CARIBU
• compare fspmwheat default with fspmwheat + RATP
• soil coupling fspmwheat + soil3ds
• light coupling l-egume + fspmwheat + CARIBU
• full coupling l-egume + fspmwheat + CARIBU + soil3ds

Usage

In your conda environment run one the simulation scripts in simulations:

python simulations/simulation_name.py

Licence

This project is licensed under the CeCILL-C License - see file LICENSE for details