glouarn / l-egume

L-egume is an individual-based model for the simulation of populaton dynamics in herbaceous legume species. It is part of the Virtual GrassLand model (VGL) developed on the OpenAlea platfom.

========================= README for L-egume

This is L-egume model, a generic model of forage legume morphogenesis.

See Louarn, G., Faverjon, L. (2018). A generic individual-based model to simulate morphogenesis, C–N acquisition and population dynamics in contrasting forage legumes. Annals of botany, 121(5), 875-896. Faverjon, L. (2018). Calibration et evaluation d’un modele individu-centre generique de morphogenese des legumineuses fourrageres – Application a la prediction des equilibres inter-specifiques dans des communautes prairiales experimentales. PhD Thesis. Univ. Poitiers.

1. Getting Started

These instructions will get you a copy of L-egume up and running on your local machine.

1.1 Prerequisites

To install and use L-egume, you need first to install the dependencies.

L-egume has been tested on Windows 10 64bit.

1.1.1 Install the dependencies on Windows 10 64 bit

1. Install Python 3.7 or 3.9 using Anaconda

   • go to https://www.anaconda.com/download/
   • click on "64-Bit Graphical Installer",
   • download "Anaconda3-2020.02-Windows-x86_64.exe" and install it selecting the following options:
     • install for all users,
     • default destination directory,
     • install all subfeatures, including subfeature "Add python.exe to Path".

2. Create and Activate a conda environment using 'Anaconda Prompt':

   • Open an 'Anaconda Prompt' console

   • Create a new environment (e.g. envtest) using the following command lines:

      conda create -n envtest python=3.9 xlrd=2.0.1 numpy=1.20.3 scipy=1.7.3 pandas=1.3.4 openalea.lpy openalea.mtg alinea.caribu -c conda-forge -c fredboudon

   • Activate the new environment using the following command line:

      activate *envtest*

1.2 Installing VGL submodels

Note: We suppose you already installed the dependencies for your operating system. Otherwise follow these instructions.

1.2.1 Install riri5 and soil3ds environmental models

To install riri5 :

• open and activate the envtest conda environment with installed dependencies ,
• go to your local copy of project riri5 (from https://github.com/glouarn/riri5),
• or get a copy of the latest model version (from a Git console: git clone -b Develop https://github.com/glouarn/riri5.git)
• run command:

   python setup.py develop

To install soil3ds :

• open and activate the envtest conda environment with installed dependencies ,
• go to your local copy of project soil3ds (from https://github.com/glouarn/soil3ds),
• or get a copy of the latest model version (from a Git console: git clone -b Develop https://github.com/glouarn/soil3ds.git)
• run command:

   python setup.py develop

1.2.2 Install L-egume plant model in "develop" mode (recommended: will handle shortcuts)

Install L-egume in "develop" mode if you want to get L-egume installed and then be able to frequently edit the code and not have to re-install L-egume to have the changes to take effect immediately.

To install L-egume in "develop" mode:

• open and activate a conda environment with installed dependencies,
• go to your local copy of project L-egume (you can get the latest version from https://github.com/glouarn/l-egume/),
• or get a copy of the latest model version (from a Git console: git clone -b Develop https://github.com/glouarn/l-egume.git)
• run command:

   python setup.py develop

1.3 Running

• open and activate the envtest conda environment with installed models

To run a simulation example, three options:

• 1. Run l-egume from the L-py GUI, launch 'lpy' from the envtest conda environment open/load 'l-egume.lpy' file from l-egume folder, Use Run or Animate button to launch a simulation from within L-py GUI

  2. Run l-egume from the command line:

     • default example:

       python run_legume_usm.py

     • run of a specific Unit of Simulation (USM):

       python run_legume_usm.py -f 'usm_xlsfile' -i 'inputs_folder' -b 'usm_spreasheet_name' -u 'usmID' -o 'outputs_folder'

  3. Run multiple simulations: see l-egume_batch.py in multisim folder for an example (require mutiprocessing)

See the user guide for a step by step explanation of how to set and run model L-egume (https://github.com/glouarn/TD_VGL).

[AFTER: TO BE COMPLETED!!!]

2. Reading the docs

To build the user and reference guides:

• install the model (see Installation of the model),
• open and activate the envtest conda environment
• to install sphinx, run command:

   conda install pytest sphinx sphinx-rtd-theme -c conda-forge

• move to the docs folder within l-egume project
• run command:

   make html

• and direct your browser to file docs/_build/html/index.html.
• (To be done...`),

3. Testing

The test allows to verify that the model implementation accurately represents the developer’s conceptual description of the model and its solution.

To run the test :

• install the model (see Installation of the model),
• open a command line interpreter,
• go to the directory test of your local copy of the project,
• (To be done: and run this command: python test_legume.py).

Built With

• Python, NumPy, SciPy,
• Sphinx: building of the documentation,

Contact

For any question, send an email to <gaetan.louarn @ inrae.fr>.

Versioning

We use a Git repository of OpenAlea on GitHub for versioning: https://github.com/openalea-incubator/l-egume
If you need an access to the current development version of the model, please send an email to <gaetan.louarn @ inrae.fr>. For versionning, use a git client and get git clone [email protected]:openalea-incubator/l-egume.git SSH will is required

Authors

Gaetan LOUARN, Lucas FAVERJON - see file AUTHORS for details

License

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