========================= 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 7/10 64bit.

1.1.1 Install the dependencies on Windows 10 64 bit

1. Install Python 3.6 using Anaconda

   • go to https://www.anaconda.com/download/
   • click on "64-Bit Graphical Installer",
   • download "Anaconda2-2018.12-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. py37_64) using the following command lines: conda create -n py37_64 -c fredboudon -c conda-forge openalea.lpy openalea.mtg openalea.plantscan3D conda install openalea.lpy -c fredboudon -c conda-forge
   • Activate the new environment using the following command line: activate py37_64

3. Install scipy package (v1.1.0):

   • in your acivated conda environment, install successively : conda install -c anaconda scipy

4. Install xlrd package (v1.2.0):

   • in your acivated conda environment, install successively : conda install -c conda-forge xlrd

5. Install OpenAlea L-py:

   • go to https://github.com/openalea/lpy to check latest install recommendations for PlantGL

   • To correct lpy console display bug: (not required anymore after python 3)

     • go to envs\nom_environnement\library\bin
     • create a new file 'mylpy.bat'
     • write inside the following command line: python -c "from openalea.lpy.gui.lpystudio import main ; main()"
     • you can now launch lpy studio from your acivated conda environment using “mylpy”

1.2 Installing

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

You can install L-egume either in "install" or "develop" mode.

1.2.1 Install L-egume in "install" mode

Install L-egume in "install" mode if you're not going to develop, edit or debug it, i.e. you just want to used it as third party package.

To install L-egume in "end-user" 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://sourcesup.renater.fr/projects/l-egume/),
• run command: python setup.py install --user.

1.2.2 Install L-egume 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://sourcesup.renater.fr/projects/l-egume/),
• run command: python setup.py develop --user.

1.3 Running

To run a simulation example, two options:

• 1. open Lpy platform, load l-egume.lpy file from legume folder, Use Run or animate button to launch a simulation
  2. Run l-egume from a python script (see l-egume_batch_mixture8.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.

[AFTER: TO BE COMPLETED!!!]

2. Reading the docs

To build the user and reference guides:

• install the model (see Installation of the model),
• open a command line interpreter,
• go to the top directory of your local copy of the project,
• run this command: python setup.py build_sphinx,
• and direct your browser to file doc/_build/html/index.html.

3. Testing

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

The test:

• runs the model on 200 steps,
• concatenates the outputs of the model in pandas dataframes,
• writes the outputs dataframes to CSV files,
• compares actual to expected outputs,
• raises an error if actual and expected outputs are not equal up to a given tolerance.

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,
• and run this command: python test_lgrass.py.

Built With

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

Contributing

First, send an email to lgrass-request@groupes.renater.fr to be added to the project.

Then,

• check for open issues or open a fresh issue to start a discussion around a feature idea or a bug: https://sourcesup.renater.fr/tracker/?group_id=3957.
• If you feel uncomfortable or uncertain about an issue or your changes, feel free to email lgrass@groupes.renater.fr.

Contact

For any question, send an email to lgrass-request@groupes.renater.fr.

Versioning

We use a Git repository on SourceSup for versioning: https://sourcesup.renater.fr/projects/l-egume
If you need an access to the current development version of the model, please send an email to lgrass-request@groupes.renater.fr. For versionning, use a git client and get git clone git+ssh://glouarn@git.renater.fr:2222/scmrepos/git/l-egume/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