Light management between plant models

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

Institutes : INRAE

Status : Python package

License : Cecill-C

URL : https://github.com/mwoussen/lightvegemanager

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

Overview

LightVegeManager is a Python package made for plant modeling and managing enlightment. It serves as an interface to merge several plant models and a light model. Applications involved by this tools are part of OpenAlea platform.

For pratical uses of this tool with mixed crops, see Plant Fusion

Required dependencies

• python 3
• numpy
• pandas

Geometric dependencies

• Openalea PlantGL
• Openalea MTG

Light Model dependencies

• CARIBU
• PyRATP (fork)
• RiRi5

Installing the tool

Targeted installation

1. Create a conda environment with miniconda3 and required dependencies

       conda create -n myenvname python=3 numpy=1.20.3 pandas -c conda-forge

2. Place yourself in your conda environment

       conda activate myenvname

3. Then install your preferred packages

   PlantGL

       conda install openalea.plantgl -c openalea3

   MTG

       conda install openalea.mtg -c openalea3

   CARIBU

       conda install alinea.caribu alinea.astk -c openalea3

   PyRATP

   1. Git console :

      git clone -b update_mobidiv https://github.com/mwoussen/PyRATP

   2. installation in the conda environment (in folder PyRATP)

      make mode=develop
      make clean

   RiRi5

   1. Git console :

      git clone https://github.com/glouarn/riri5

   2. installation in the conda environment (in folder riri5)

      python setup.py develop

   Development tools

       conda install pytest sphinx sphinx-rtd-theme -c conda-forge
       pip install nbsphinx nbsphinx_link pgljupyter

Complete installation

1. Create a conda environment with miniconda3

       conda create -n myenvname python=3 openalea.mtg openalea.plantgl alinea.caribu alinea.astk numpy=1.20.3 pandas pytest sphinx sphinx-rtd-theme -c conda-forge -c openalea3

2. Place yourself in your conda environment

       conda activate myenvname

3. Install PyRATP

   1. Git console :

      git clone -b update_mobidiv https://github.com/mwoussen/PyRATP

   2. installation in the conda environment (in folder PyRATP)

      make mode=develop
      make clean

4. Install RiRi5

   1. Git console :

      git clone https://github.com/glouarn/riri5

   2. installation in the conda environment (in folder riri5)

      python setup.py develop

5. Install LightVegeManager

   1. Git console :

      git clone https://github.com/mwoussen/lightvegemanager

   2. installation in the conda environment (in folder lightvegemanager)

      python setup.py develop

Contributing

The documentation is made with sphinx and unit testing with pytest.

Licence

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