PyRATP

Software

Authors

• Herve Sinoquet
• Marc Saudreau
• Jerome Ngao
• Boris Adam
• Christophe Pradal
• Christian Fournier
• Fabrice Bauget

Description

RATP: Radiation Absorption, Transpiration and Photosynthesis

Status

Python package

License

CecILL-C URL : https://pyratp.rtfd.io

Dependencies

• meson-python
• numpy
• pandas
• scipy
• openalea.plantgl
• openalea.mtg
• QtPy

Modifications

• Installation with make: it compiles fortran part with f2py then installs the package with setuptools and pip
• Compute transmitted radiation for each voxel
• Intercepted and transmitted radiation among the output results
• leaf angle distribution for each voxel
• Local or solar hour option for computing sun position
• Possibility for external use of the sun computation routine

Installation

for user

1. Install Miniforge: https://github.com/conda-forge/miniforge
2. Create a conda environment:

mamba create -n pyratp openalea.ratp -c conda-forge -c openalea3

3. activate the environment: mamba activate pyratp

The user has the possibility to install the package from a candicate release channel of the conda repository of openalea as follows:

mamba create -n pyratp openalea.ratp -c conda-forge -c openalea3/label/rc

The rc channel corresponds to the latest build of PyRatp when the main channel is the stable release.

For developpers Linux (python modification only)

Editable install with conda/environment.yml is not functionning because of namespace conflict. A workaround is as follow:

1. download the repository and change to the root directory:

   git clone https://github.com/openalea/PyRATP.git
   cd PyRATP

2. Create a conda environment with dependencies manually with:

mamba create -n pyratp  -c openalea3 -c conda-forge  openalea.plantgl openalea.mtg qtpy compilers meson-python gfortran scipy pytest jupyter

3. activate the environment: mamba activate pyratp

4. Build the fortran library:

meson setup builddir
meson compile -C builddir
cp builddir/src/openalea/ratp/pyratp.cpython-31*.so src/openalea/ratp

5. modify the Python path: via the environment variable

export PYTHONPATH="$PWD/src":$PYTHONPATH

For developpers (python and fortran modifications)

Editable installation with conda/environment.yml is not functioning because of namespace conflict. A workaround is as follows:

1. download the repository and change to the root directory:

   git clone https://github.com/openalea/PyRATP.git
   cd PyRATP

2. Create a conda environment with dependencies manually:

Using MAC and Linux:

mamba create -n pyratp_dev -c conda-forge -c openalea3 openalea.plantgl openalea.mtg qtpy compilers meson-python scipy pytest jupyter

Using Windows:

mamba create -n pyratp_dev -c conda-forge -c openalea3 openalea.plantgl openalea.mtg qtpy m2w64-toolchain meson-python scipy pytest gfortran jupyter

4. activate the environment: mamba activate pyratp_dev

5. Compile everything:

pip install ."[test]"

and after each modification of the python or Fortran part, run

pip install .

then restart your kernel (when using IPython) for your modifications to be taken into account.

6. Have a look at the notebooks and scripts in example/!