PyRATP (MobiDiv)

Fork from alinea.pyratp: https://github.com/openalea-incubator/PyRATP

RATP: Radiation Absorption, Transpiration and Photosynthesis

Dependencies

• make
• gcc 64 bits
• Python 3
• numpy
• pandas
• scipy
• openalea.plantgl
• openalea.mtg

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 example with conda

1. install gcc 64 bits (MinGW with Windows OS)
2. install miniconda 64 bits: https://docs.conda.io/en/latest/miniconda.html
3. Create a conda environment:

conda create -n myenvname openalea.mtg openalea.plantgl numpy=1.20.3 scipy pandas -c conda-forge -c fredboudon

4. set conda in the created environment: conda activate myenvname
5. download the repository:
   1. git clone git@github.com:mwoussen/PyRATP_MobiDiv.git or git clone https://github.com/mwoussen/PyRATP_MobiDiv.git
   2. cd PyRATP_MobiDiv
6. install the package: make if you want to edit the source files in the current folder : make mode=develop
7. clean the compilation step: make clean
8. test the package: python tests/smalltests.py

Troubleshootings

Installation under Windows OS

• PyRATP_Mobidiv works only in 64 bits
• It seems like the installation doesn't work with numpy >= 1.23
• Compilation error: undefined reference to __intrinsic_setjmpex l.3335 pyratpmodule.c
  1. replace #include<setjmp.h> with #include<setjmpex.h> in the file pyratpmodule.c (building folder)
  2. relauch the compilation f2py -c ... l.58 in the Makefile