Release for hydroroot paper

• Documentation: https://hydroroot.readthedocs.io
• OpenAlea.HydroRoot is a hydraulic root architecture modelling and a root architecture system generator package
• namespace is openalea.hydroroot

import openalea.hydroroot
from openalea.hydroroot import *

• Python 3: 3.10 to 3.13
• conda:
  • New Mac OS X architecture (M1, ...): support osx-arm64 on top of osx-64 architecture
  • package has a conda directory with meta.yaml using metadata from pyproject.toml for conda packaging and a environment.yml file
  • 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:
    • consistent continuous integration / deployment as been set up to using a dedicated github-action workflow
    • package is uploaded to openalea3 conda channel
  • installation via conda: mamba install openalea.visualea -c openalea3
• package is pip installable
  • package can be installed by running pip install . or in editable mode pip install -e . in root directory of the project

What's Changed

• fix issue #102 by @baugetfa in #103
• commented a call to plantgl viewer 3d and saved state of some nb by @baugetfa in #104
• [no ci] Add contributors section and badge to README by @pradal in #105
• WIP solver wrappers by @baugetfa in #98
• Post Release by @baugetfa in #101
• Paper hydroroot by @baugetfa in #107

Full Changelog: v2.1.0...v2.2.0

Release 2025

• 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 *

• Python 3: 3.10 to 3.13
• conda:
  • New Mac OS X architecture (M1, ...): support osx-arm64 on top of osx-64 architecture
  • package has a conda directory with meta.yaml using metadata from pyproject.toml for conda packaging and a environment.yml file
  • 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:
    • consistent continuous integration / deployment as been set up to using a dedicated github-action workflow
    • package is uploaded to openalea3 conda channel
  • installation via conda is now: mamba install openalea.visualea -c openalea3
• package is pip installable
  • setup.py is now 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

What's Changed

• update doc according to guidelines by @baugetfa in #18
• update doc according to guidelines II by @baugetfa in #19
• update version to 2.0.1 by @baugetfa in #20
• corrected error in conda-package-build by @baugetfa in #21
• forgot environment.yml for the doc by @baugetfa in #24
• forgot environment.yml, forgot sphynx pkg by @baugetfa in #25
• forgot environment.yml, the pb was in conf.py. by @baugetfa in #26
• still error in readthedocs by @baugetfa in #27
• still error in readthedocs by @baugetfa in #28
• still missing pkg in environment by @baugetfa in #29
• still missing pkg in environment by @baugetfa in #30
• Following guidelines and some correction on notebooks and scrips examples by @baugetfa in #31
• Add citation file by @pradal in #33
• correction no build with 3.8 by @baugetfa in #34
• Update environment.yml by @pradal in #36
• Fix citations by @pradal in #39
• corrected build number and ref to hydroshoot in pyproject by @baugetfa in #40
• test CI on 20-python-313-numpy by @baugetfa in #42
• test CI on 20-python-313-numpy 2 by @baugetfa in #43
• test CI with 3.13 by @baugetfa in #45
• undo previous modif test CI with 3.13 by @baugetfa in #46
• merge main into release2025 by @baugetfa in #47
• Release2025 by @baugetfa in #50
• doc by @baugetfa in #52
• Add oawidgets in dependances by @baugetfa in #53
• deleted environment.yml in doc by @baugetfa in #54
• deleted files by @baugetfa in #55
• doc, nbgallery by @baugetfa in #56
• update release2025 from main by @baugetfa in #57
• just change the size of the jupyter nb by @baugetfa in #59
• priority to openalea3/label/dev by @baugetfa in #61
• corrected docstring by @baugetfa in #63
• corrected visualea demo by @baugetfa in #64
• merged main by @baugetfa in #65
• Release2025 by @baugetfa in #66
• correction related to notebook by @baugetfa in #67
• getting the correct languages used in the repo by @baugetfa in #68
• Update CI by @baugetfa in #75
• use matlotlib-base, removed compiler in meat.yaml by @baugetfa in #76
• updated tool setuptools_scm in pyproject by @baugetfa in #77
• Update doc by @pradal in #78
• [openalea-bot] synced file(s) with openalea/.github by @christian34 in #81
• Documentation enhancement by @baugetfa in #80
• [no ci] pb csv visualea by @baugetfa in #82
• Fusion of millet with hydroroot by @baugetfa in #58
• deleted string: py{{ PY_VER }} as recommanded by @baugetfa in #83
• Update metainformation. When clicking on hydroroot in visualea, it op… by @baugetfa in #84
• #70 correction calculation by @baugetfa in #72
• update namespace oawidgets and rsml by @baugetfa in #85
• wrapper functions for cut and flow solvers by @baugetfa in #69
• [no ci] oawidgets to widgets by @baugetfa in #86
• [no ci] doc update by @baugetfa in #87
• Binder by @baugetfa in #89
• [no ci] removed symbolic link to real file by @baugetfa in #90
• Binder by @baugetfa in #91
• correction binder branch by @baugetfa in #93
• revert SSL env variable by @baugetfa in #94
• some last small things by @baugetfa in #95
• Fix syntax warnings due to backslash chars by @pradal in #96

New Contributors

• @christian34 made their first contribution in #81

Full Changelog: v2.0.0...v2.2.0

v2.0.0: Solute & Transport

What's Changed

• Solute and water transport, some miscellenous functions, partial reorganization of the example directory by @baugetfa in #13
• commit after conflict from branch documentation that was 5 commits behind the main. by @baugetfa in #15
• Visualea by @baugetfa in #17

Full Changelog: v1.0...v2.0.0

Hydroroot

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