Release 2025 notes

Openalea Improvements

• OpenAlea Guidelines: guide lines for all the OpenAlea packages

  • openalea namespace is now consistent across packages: openalea/pkg_name replace alinea/pkg_name (modelers)

  • conda packaging:

    • New Mac OS X architecture (M1, …): support osx-arm64 on top of osx-64 architecture (user)

    • all packages have a conda directory with meta.yaml using metadata from pyproject.toml for conda packaging and a environment.yml file (developers)

    • environment.yml is used to build documentation and also to install locally package in development mode

      mamba env create -f conda/environment.yml
      

    • continuous integration (developers):

      • consistent continuous integration / deployment as been set up for all packages using a dedicated github-action workflow

      • all packages are now automatically uploaded to openalea3 conda channel

    • installation via conda is now for all packages in the release:

      mamba install openalea.pkg_name -c openalea3
      

  • all packages but openalea.plantgl are locally pip installable

    • setup.py is replaced by pyproject.toml

    • package can be installed by running pip install . or in editable mode pip install -e . in root directory of the project

    • openalea.ratp is not working in editable mode

  • all packages have documentation (user and reference)

Release Packages

The foolowing packages are part of the 2025 release.

FSPM formalism and data structure

• openalea.plantgl: 3D Plant Geometric Library

• openalea.lpy: L-System Plant Simulation Environment

• openalea.mtg: Multiscale Tree Graph datastructure and algorithms

• openalea.rsml: Data format for Root System, compatible with MTG

Software Platform and Scientific Workflow System

• openalea.core: Main Component software formalisms and implementation

• openalea.visualea: Visual Programming Environment

• openalea.grapheditor: Generic Graph Edition, interaction and Visualisation with OpenAlea/VisuAlea

• openalea.scipack: Scientific Python Stack for VisuAlea

• openalea.oalab: Make your application reusable!

• openalea.widgets: Jupyter Widgets for MTG, PlantGL, and LPy

Light Interception & Ecophysiology

• openalea.caribu: Light Intercetion by Plants

• openalea.ratp: Radiation, Absorption, Transpiration, and Photosynthesis

• openalea.spice: Fast Path Tracer for Light Interception

• openalea.astk: Sky luminance and sky sources from Weather data

FunctionalStructural Plant Models aka FSPM

• openalea.hydroroot: Simulating and phenotyping Root Hydraulic Architecture

• openalea.hydroshoot: Simulating Shoot Hydraulic Transport, Leaf Energy budget, and Gas Exchange Fluxes.

Plant simulation and 3D reconstruction

• openalea.adel: 3D reconstruction of Maize and Wheat

• openalea.weberpenn: 3D Generation of Trees from Parameters

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Main changes, GitHub and documentation link are listed for each packages below.

openalea.plantgl 3.22.3

• https://github.com/openalea/plantgl

• Documentation: https://plantgl.rtfd.io

• OpenAlea.PlantGL provides light interception methods comparable to openalea.caribu

• support c++17 and numpy 2

openalea.lpy 3.15.4

• https://github.com/openalea/lpy

• Documentation: https://lpy.readthedocs.io

• OpenAlea.L-Py is a simulation software that mixes L-systems construction with the Python high-level modeling language.

• support c++17 and numpy 2

openalea.core 2.5.0

• https://github.com/openalea/core

• OpenAlea.Core implements the components and workflows execution

openalea.mtg 2.3.0

• https://github.com/openalea/mtg

• Documentation: https://mtg.rtfd.io

• Visualisation of MTG in the Notebook is provided by the package openalea.widgets

openalea.widgets 1.1.2

• https://github.com/openalea/oawidgets

• Documentation: https://oawidgets.readthedocs.io

• Set of jupyter notebook widgets dedicated to OpenAlea.

• namespace changed from oawidgets to openalea.widgets instead of

import oawidgets
from oawidgets import *

do

import openalea.widgets
from openalea.widgets import *

openalea.scipack 2.5.2

• https://github.com/openalea/scipack

• Documentation: https://scipack.readthedocs.io

• openalea.scipack replaces the meta-package openalea.components a set of wrappers of standard Python packages for openalea.visualea

• It regroups: openalea.stdlib, openalea.pylab, openalea.numpy and openalea.image, but calls did not change.

openalea.grapheditor 2.5.0

• https://github.com/openalea/grapheditor

• Documentation: https://grapheditor.readthedocs.io

• OpenAlea.GraphEditor is a base package for editing graph with various graph data structures.

• This package is used by openalea.visualea

openalea.oalab 2.5.0

• https://github.com/openalea/oalab

• OpenAlea.OaLab is another end user application.

openalea.visualea 2.5.0

• https://github.com/openalea/visualea

• Documentation: https://visualea.readthedocs.io

• OpenAlea.VisuAlea has been resurrected

• All the workflows are not fully functional but the software is functional

openalea.weberpenn 2.5.0

• https://github.com/openalea/weberpenn

• OpenAlea.WeberPenn is a simple model to build trees from parameters.

• The model is available through VisuAlea

openalea.rsml 1.5.0

• https://github.com/openalea/rsml

• Documentation: https://rsml.readthedocs.io

• OpenAlea package managing the RootSystemML file format that represents root architectural data

• namespace changed from rsml to openalea.rsml instead of

import rsml
from rsml import *

do

import openalea.rsml
from openalea.rsml import *

openalea.caribu 8.2.1

• https://github.com/openalea/caribu

• Documentation: https://caribu.readthedocs.io

• Caribu is a modelling suite for lighting 3D virtual scenes, especially designed for the illumination of virtual plant canopies such as virtual crop fields.

• Caribu has been split in two packages: openalea.caribu pure python and openalea.libcaribu with c++ code.

• namespace changed from alinea.caribu to openalea.caribu instead of

import alinea.caribu
from alinea.caribu.caribu import radiosity

do

import openalea.caribu
from openalea.caribu.caribu import radiosity

openalea.astk 3.1.0

• https://github.com/openalea/astk

• Documentation: https://openalea-astk.readthedocs.io

• Astk allows to calculate sky luminance and sky sources to be used with FSPM light models from weather data.

• namespace changed from alinea.astk to openalea.astk instead of

import alinea.astk
from alinea.astk.Weather import Weather

do

import openalea.astk
from openalea.astk.Weather import Weather

openalea.adel 2.1.1

• https://github.com/openalea/adel/

• Documentation: https://adel.readthedocs.io

• OpenAlea.Adel (Architectural model of DEvelopment based on L-systems) allows to simulate the 3D architectural development of the shoot of gramineaous plant.

• namespace changed from alinea.adel to openalea.adel instead of

import alinea.adel
from alinea.adel import *

do

import openalea.adel
from openalea.adel import *

openalea.ratp 2.2.0

• https://github.com/openalea/pyratp

• Documentation: https://pyratp.rtfd.io

• RATP: Radiation Absorption, Transpiration and Photosynthesis.

• namespace changed from alinea.pyratp to openalea.ratp instead of

import alinea.pyratp
from alinea.pyratp.skyvault import Skyvault

do

import openalea.ratp
from openalea.ratp.skyvault import Skyvault

openalea.spice 1.1.0

• https://github.com/openalea/spice

• Documentation: https://openalea-spice.readthedocs.io

• Spice (Spectral Photon Interception in Controlled Environment) : New package for light simulation in controlled environments based on photon mapping.

openalea.hydroroot 2.1.0

• https://github.com/openalea/hydroroot

• Documentation: https://hydroroot.readthedocs.io

• OpenAlea.HydroRoot is a hydraulic root architecture modelling and a root architecture system generator package

• namespace changed from hydroroot to openalea.hydroroot instead of

import hydroroot
from hydroroot import *

do

import openalea.hydroroot
from openalea.hydroroot import *

openalea.hydroshoot 5.3.0

• https://github.com/openalea/hydroshoot

• Documentation: https://hydroshoot.readthedocs.io

• Hydroshoot provides a grapevine-specific module (architecture) which builds plant shoot structure for potted of trained grapevines

• namespace changed from hydroshoot to openalea.hydroshoot instead of

import hydroshoot
from hydroshoot import *

do

import openalea.hydroshoot
from openalea.hydroshoot import *

openalea.wheatfspm

• https://github.com/openalea/WheatFspm

• Documentation: https://wheatfspm.readthedocs.io

• WheatFspm is a Functional Structural Plant Model (FSPM) of wheat which fully integrates shoot morphogenesis and the metabolism of carbon (C) and nitrogen (N) at organ scale within a 3D representation of plant architecture.

• It now regroups in one model: CN-Wheat, Elong-Wheat, fspm-wheat, Growth-Wheat, Farquhar-Wheat, Respi-Wheat, Senesc-Wheat

• namespace changed from fspmwheat to openalea.fspmwheat, idem for cnwheat, elongwheat, farquharwheat, growthwheat, respiwheat, senescwheat instead of

from fspmwheat import *
from cnwheat import *
from elongwheat import *
from farquharwheat import *
from growthwheat import *
from respiwheat import *
from senescwheat import *

do

from openalea.fspmwheat import *
from openalea.cnwheat import *
from openalea.elongwheat import *
from openalea.farquharwheat import *
from openalea.growthwheat import *
from openalea.respiwheat import *
from openalea.senescwheat import *

openalea.phenomenal 1.10.4

• https://github.com/openalea/phenomenal

• Documentation: https://phenomenal.readthedocs.io

• An automatic open source library for 3D shoot architecture reconstruction and analysis for image-based plant phenotyping

• optional package openalea.phenotyping_data provides Data from plant phenotyping platform primarly aimed at desmonstrating/testing openalea.phenomenal, needed to run some of the tutorials

• Calibration has been extented to n-cameras n-calibration targets cases, and with simpler parameterisation