========================= README for L-Grass

This is L-Grass model, a model of rye grass morphogenesis.

See Migault V. 2015. Insertion de la morphogenèse racinaire dans L grass, un modèle structure-fonction de graminées fourragères. Verdenal A. 2009. De la simulation de la morphogénèse de l’appareil aérien du ray-grass anglais (Lolium perenne L.). Exploration d’un schéma cybernétique inspiré du concept d’auto-organisation et applications. Verdenal A, Combes D, Escobar-Gutiérrez AJ. 2008. A study of ryegrass architecture as a self-regulated system, using functional-structural plant modelling. Functional Plant Biology 35: 911–924.

1. Getting Started

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

1.1 Prerequisites

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

L-grass has been tested on Windows.

1.1.1 Install the dependencies on Windows 10 64 bit

1. Install Python

   • go to https://www.python.org/downloads/windows/download,
   • click on "Latest Python 2 Release [...]",
   • download "Windows x86-64 MSI installer" 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. Install OpenAlea Vplants:

   • go to http://openalea.gforge.inria.fr/dokuwiki/doku.php?id=download:windows,
   • download OpenAlea 1.2 and Vplants 1.2,
   • install both installers:

3. Install NumPy:

   • go to http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy,
   • download NumPy+MKL for Python 2 64 bit,
   • install it using pip installer:
     • open a command line interpreter,
     • go to the directory where you saved NumPy+MKL for Python 2 64 bit,
     • install NumPy+MKL from the downloaded wheel file.
       For example, if you downloaded file "numpy-1.13.1+mkl-cp27-cp27m-win_amd64.whl", type: pip install "numpy-1.13.1+mkl-cp27-cp27m-win_amd64.whl".

4. Install Pandas

   • go to http://www.lfd.uci.edu/~gohlke/pythonlibs/#pandas,
   • download Pandas for Python 2 64 bit,
   • install it using pip installer:
     • open a command line interpreter,
     • go to the directory where you saved Pandas for Python 2 64 bit,
     • install Pandas from the downloaded wheel file.
       For example, if you downloaded file "pandas-0.20.3-cp27-cp27m-win_amd64.whl", type: pip install "pandas-0.20.3-cp27-cp27m-win_amd64.whl".

5. Install Sphinx

   • go to http://www.lfd.uci.edu/~gohlke/pythonlibs/#misc,
   • download Sphinx for Python 2,
   • install it using pip installer:
     • open a command line interpreter,
     • go to the directory where you saved Sphinx for Python 2,
     • install Sphinx from the downloaded wheel file.
       For example, if you downloaded file "Sphinx-1.6.3-py2.py3-none-any.whl", type: pip install "Sphinx-1.6.3-py2.py3-none-any.whl".

1.2 Installing

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

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

1.2.1 Install L-grass in "install" mode

Install L-grass 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-grass in "end-user" mode:

• open a command line interpreter,
• go to your local copy of project L-grass,
• run command: python setup.py install --user.

1.2.2 Install L-grass in "develop" mode

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

To install L-grass in "develop" mode:

• open a command line interpreter,
• go to your local copy of project L-grass,
• run command: python setup.py develop --user.

1.3 Running

To run a simulation example, two options:

• 1. open Lpy platform, load lgrass.lpy file from lgrass folder, Use Run or animate button to launch a simulation
  2. Run lgrass from a python script (see main.py in test folder for an example)

See the user guide for a step by step explanation of how to set and run model L-grass.

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 [email protected] 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 [email protected].

Contact

For any question, send an email to [email protected].

Versioning

We use a Git repository on SourceSup for versioning: https://sourcesup.renater.fr/projects/lgrass/.
If you need an access to the current development version of the model, please send an email to [email protected]. For versionning, use a git client and get git clone git+ssh://[email protected]:2222/lgrass.git. SSH will is required

Authors

Alban VERDENAL, Didier COMBES and Vincent MIGAULT - see file AUTHORS for details

License

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