From 7aa30c3a67af64a897175b6be615d622bb320c64 Mon Sep 17 00:00:00 2001 From: baugetfa Date: Thu, 11 Sep 2025 10:57:24 +0200 Subject: [PATCH 1/4] deprecated alinea pyratp changed to openalea ratp --- doc/index.rst | 7 +------ doc/user/autosum.rst | 6 +++--- doc/user/ratp.rst | 2 +- 3 files changed, 5 insertions(+), 10 deletions(-) diff --git a/doc/index.rst b/doc/index.rst index 9fd408d8..d42223d9 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -36,11 +36,6 @@ Documentation - A `PDF <../latex/pyratp.pdf>`_ version of |pyratp| documentation is available. -.. seealso:: - - More documentation can be found on the - `openalea `__ wiki. - Authors ======= @@ -59,4 +54,4 @@ License .. note:: `Cecill-C `_ license is a LGPL compatible license. -.. |pyratp| replace:: Alinea.PyRATP +.. |pyratp| replace:: OpenAlea.PyRATP diff --git a/doc/user/autosum.rst b/doc/user/autosum.rst index 6e899f32..2419bd1e 100644 --- a/doc/user/autosum.rst +++ b/doc/user/autosum.rst @@ -7,12 +7,12 @@ Reference guide ################################### .. contents:: -.. currentmodule:: alinea.pyratp.__init__ +.. currentmodule:: openalea.ratp.__init__ -:mod:`alinea.pyratp` module +:mod:`openalea.ratp` module =============================================== -.. automodule:: alinea.pyratp.__init__ +.. automodule:: openalea.ratp.__init__ :members: :undoc-members: :inherited-members: diff --git a/doc/user/ratp.rst b/doc/user/ratp.rst index 5e5be5b3..1a5a5ffa 100644 --- a/doc/user/ratp.rst +++ b/doc/user/ratp.rst @@ -33,7 +33,7 @@ subroutines, which are all accessible in the OpenAlea environment. .. python:: - mamba install -c openalea3 -c conda-forge openalea.pyratp + mamba install -c openalea3 -c conda-forge openalea.ratp **RATP MODULES** From a5fc0704db1db777173ca8e4d73d667b47158491 Mon Sep 17 00:00:00 2001 From: baugetfa Date: Thu, 11 Sep 2025 11:17:28 +0200 Subject: [PATCH 2/4] DOC correction --- doc/user/ratp.rst | 50 +++++++++++++++++++++++++++++++---------------- 1 file changed, 33 insertions(+), 17 deletions(-) diff --git a/doc/user/ratp.rst b/doc/user/ratp.rst index 1a5a5ffa..6d138e79 100644 --- a/doc/user/ratp.rst +++ b/doc/user/ratp.rst @@ -1,10 +1,11 @@ -**RATP version 2 in OpenAlea environment** - -**User’s Guide** +================== +Model description +================== **H. Sinoquet, UMR PIAF, Clermont-Ferrand, France** -**INTRODUCTION** +INTRODUCTION +------------ The model **RATP** (Radiation Absorption, Transpiration and Photosynthesis) was designed to simulate the spatial distribution of @@ -29,13 +30,16 @@ modules, which can be used as a Python library in the OpenAlea environment. A Fortran90 module includes public variables and subroutines, which are all accessible in the OpenAlea environment. -**SOFTWARE INSTALLATION** +Software installation +--------------------- -.. python:: +.. code-block:: python mamba install -c openalea3 -c conda-forge openalea.ratp -**RATP MODULES** + +RATP modules +------------ Here is the list of RATP modules: @@ -59,7 +63,10 @@ Here is the list of RATP modules: - photosynthesis - 1. *module constant_values* + + +1. module constant_values +^^^^^^^^^^^^^^^^^^^^^^^^^ This module is aimed at setting values for physical constants. @@ -97,7 +104,8 @@ Syntax for calling subroutine **cv_set** in OpenAlea environment is: Ratp.constant_values.cv_set() -2. *module grid3D* +2. module grid3D +^^^^^^^^^^^^^^^^ This module is aimed at building a 3D grid, namely the spatial distribution of leaf area in the voxels. @@ -318,7 +326,8 @@ Syntax in OpenAlea environment is: Ratp.grid3d.g3d_destroy() -3. *module skyvault* +3. module skyvault +^^^^^^^^^^^^^^^^^^ This module is aimed at creating the skyvault, namely discretising the sky vault as a set of solid angles characterised by their central @@ -367,7 +376,8 @@ module **skyvault**. Syntax in OpenAlea environment is: Ratp.skyvault.sv_destroy() -4. *module vegetation_types* +4. module vegetation_types +^^^^^^^^^^^^^^^^^^^^^^^^^^ This module is aimed at defining physical and physiological properties of each vegetation type included in the 3D scene. This includes leaf @@ -559,7 +569,8 @@ module **vegetation_types**. Syntax in OpenAlea environment is: Ratp.vegetation_types.vt_destroy() -5. *module micrometeo* +5. module micrometeo +^^^^^^^^^^^^^^^^^^^^ This module is aimed at setting the micrometeorological environment experienced by the 3D scene. @@ -620,7 +631,8 @@ is: Ratp.micrometeo.mm_destroy() -6. *module dir_interception* +6. module dir_interception +^^^^^^^^^^^^^^^^^^^^^^^^^^ This module is aimed at computing directional radiation interception in a vegetated 3D grid where several vegetation types are included. This @@ -734,7 +746,8 @@ the OpenAlea environment is: Ratp.dir_interception.di_destroy() -7. *module hemi_interception* +7. module hemi_interception +^^^^^^^^^^^^^^^^^^^^^^^^^^^ This module is aimed at computing hemispherical radiation interception in a vegetated 3D grid where several vegetation types are included, by @@ -812,7 +825,8 @@ Subroutine **hi_destroy** deallocates allocatable arrays of module Ratp.hemi_interception.hi_destroy() -8. *module shortwave_balance* +8. module shortwave_balance +^^^^^^^^^^^^^^^^^^^^^^^^^^^ Module **shortwave_balance** computes radiation balance from: @@ -902,7 +916,8 @@ is: Ratp.shortwave_balance.swrb_destroy() -9. *module energy_balance* +9. module energy_balance +^^^^^^^^^^^^^^^^^^^^^^^^^ Module **energy_balance** computes transpiration rates, stomatal conductance and leaf temperature, in a 3D scene including one or several @@ -984,7 +999,8 @@ is: Ratp.energy_balance.eb_destroy() -10. *module photosynthesis* +10. module photosynthesis +^^^^^^^^^^^^^^^^^^^^^^^^^ Module **photosynthesis** computes assimilation rates by using Farquhar’s model in a 3D scene including one or several vegetation types From 4d3b91d733a659b4652f3994307d55540506304e Mon Sep 17 00:00:00 2001 From: baugetfa Date: Thu, 11 Sep 2025 11:40:16 +0200 Subject: [PATCH 3/4] update readme with authors --- README.md | 27 ++++++++++++++++++++++----- 1 file changed, 22 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 4c12a8e7..f4f9ade8 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,32 @@ -# Package Name +# PyRATP [![Docs](https://readthedocs.org/projects/pyratp/badge/?version=latest)](https://pyratp.readthedocs.io/) [![Build Status](https://github.com/openalea/PyRatp/actions/workflows/conda-package-build.yml/badge.svg?branch=master)](https://github.com/openalea/PyRatp/actions/workflows/conda-package-build.yml?query=branch%3Amaster) [![Python Version](https://img.shields.io/badge/python-3.10%20%7C%203.11%20%7C%203.12-blue)](https://www.python.org/downloads/) [![License](https://img.shields.io/badge/License--CeCILL-C-blue)](https://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html) [![Anaconda-Server Badge](https://anaconda.org/openalea3/pyratp/badges/version.svg)](https://anaconda.org/openalea3/pyratp) -## Description -# PyRATP +## Software + +### Authors +> - Herve Sinoquet +> - Marc Saudreau +> - Jerome Ngao +> - Boris Adam +> - Christophe Pradal +> - Christian Fournier +> - Fabrice Bauget + +### Description RATP: Radiation Absorption, Transpiration and Photosynthesis -## Dependencies +### Status +Python package + +### License +CecILL-C +**URL** : + +### Dependencies - meson-python - numpy - pandas @@ -18,7 +35,7 @@ RATP: Radiation Absorption, Transpiration and Photosynthesis - openalea.mtg - QtPy -## Modifications +### 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 From c50596f6581fe66cf9276580075141a1f08452aa Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Thu, 11 Sep 2025 12:17:45 +0200 Subject: [PATCH 4/4] Update README.md Fix doc weblink --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index f4f9ade8..59391a8c 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,7 @@ Python package ### License CecILL-C -**URL** : +**URL** : ### Dependencies - meson-python