updated fork from openalea

.github/workflows/conda-package-build.yml

@@ -23,5 +23,5 @@ jobs:
       anaconda_token: ${{ secrets.ANACONDA_TOKEN }}
 
     with:
-      python-minor-version: '[10, 11, 12]'
-      operating-system: '["ubuntu-latest", "macos-13", "windows-latest"]'
+      force-channel-priority: conda-forge, openalea3/label/dev, openalea3
+      operating-system: '["ubuntu-latest", "macos-13", "windows-latest"]' # because of plantgl

.gitignore

@@ -73,4 +73,8 @@ nosetests.xml
 .DS_Store
 
 # Doc build
-doc/_build
+doc/_build
+
+# hydroroot
+example/test.rsml
+tmp*.*

README.md

@@ -0,0 +1,92 @@
+# HydroRoot
+
+[![CI status](https://github.com/openalea/hydroroot/actions/workflows/conda-package-build.yml/badge.svg)](https://github.com/openalea/hydroroot/actions/workflows/conda-package-build.yml)
+[![Documentation Status](https://readthedocs.org/projects/hydroroot/badge/?version=latest)](https://hydroroot.readthedocs.io/en/latest/?badge=latest)
+[![image](https://anaconda.org/openalea3/openalea.hydroroot/badges/version.svg)](https://anaconda.org/openalea3/openalea.hydroroot)
+
+## Software
+
+### Authors
+
+> -   Christophe Pradal
+> -   Yann Boursiac
+> -   Mikael Lucas
+> -   Fabrice Bauget
+> -   Christophe Godin
+> -   Christophe Maurel
+
+### Institutes
+
+CIRAD / INRAE / inria / CNRS
+
+### Status
+
+Python package
+
+### License
+
+CecILL-C
+
+**URL** : <https://hydroroot.rtfd.io>
+
+## About
+
+### Description
+
+OpenAlea.HydroRoot is a hydraulic root architecture modelling and a root
+architecture system generator package.
+
+### Content
+
+The OpenAlea.HydroRoot package contains a root architecture simulation
+model coupled with a water and solute transport solver. It contains a
+pure hydraulic solver that is solved using resistance network analogy.
+It also contains a water and solute transport solver that is more
+complex and see the root as a continuous medium.
+
+### Example
+
+Heat map representation of the incoming local radial flows on an
+arabidopsis root.
+
+![Alt Text](example/data/fig-6E.png)
+
+### Installation
+
+#### Conda Installation
+
+    conda create -n hydroroot -c conda-forge -c openalea3 openalea.hydroroot
+
+#### Requirements
+
+> -   openalea.mtg
+> -   openalea.plantgl
+> -   RSML
+> -   pandas \> 0.17
+> -   numpy
+> -   scipy
+
+#### Usage
+
+See notebook in example directory.
+
+## Documentation
+
+<https://hydroroot.rtfd.io>
+
+## Citations
+
+If you use Hydroroot for your research, please cite:
+
+1.  Yann Boursiac, Christophe Pradal, Fabrice Bauget, Mikaël Lucas,
+    Stathis Delivorias, Christophe Godin, Christophe Maurel, Phenotyping
+    and modeling of root hydraulic architecture reveal critical
+    determinants of axial water transport, Plant Physiology, Volume 190,
+    Issue 2, October 2022, Pages 1289--1306,
+    <https://doi.org/10.1093/plphys/kiac281>
+2.  Fabrice Bauget, Virginia Protto, Christophe Pradal, Yann Boursiac,
+    Christophe Maurel, A root functional--structural model allows
+    assessment of the effects of water deficit on water and solute
+    transport parameters, Journal of Experimental Botany, Volume 74,
+    Issue 5, 13 March 2023, Pages 1594--1608,
+    <https://doi.org/10.1093/jxb/erac471>

conda/meta.yaml

@@ -1,52 +1,69 @@
 {% set pyproject = load_file_data('../pyproject.toml', from_recipe_dir=True) %}
+{% set name = pyproject.get('project').get('name') %}
+{% set description = pyproject.get('project').get('description') %}
 {% set version = environ.get('SETUPTOOLS_SCM_PRETEND_VERSION', "0.0.0.dev") %}
+{% set license = pyproject.get('project').get('license') %}
+{% set home = pyproject.get('project', {}).get('urls', {}).get('Homepage', '') %}
+{% set build_deps = pyproject.get("build-system", {}).get("requires", []) %}
+{% set deps = pyproject.get('project', {}).get('dependencies', []) %}
+{% set conda_deps = pyproject.get('tool', {}).get('conda', {}).get('environment', {}).get('dependencies',[]) %}
+{% set test_deps = pyproject.get('project', {}).get('optional-dependencies', {}).get('test',[]) %}
 
 package:
-  name: {{ pyproject["project"]["name"] }}
+  name: {{ name }}
   version: {{ version }}
 
 source:
   path: ..
 
 build:
   noarch: python
-  string: py{{ PY_VER }}
-  preserve_egg_dir: True
   number: 0
-  script: {{PYTHON}} -m pip install . -vv
+  preserve_egg_dir: True
+  string: py{{ PY_VER }}
+  script:
+    - {{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-build-isolation -vv
 
 requirements:
+  host:
+    - python
+    {% for dep in build_deps %}
+    - {{ dep }}
+    {% endfor  %}
+
   build:
-    - python {{ pyproject["project"]["requires-python"] }}
-    {% for dep in pyproject["build-system"]["requires"] %}
-    - {{ dep.lower() }}
-    {% endfor %}
+    - {{ compiler("cxx") }}
 
   run:
-    - python {{ pyproject["project"]["requires-python"] }}
-    {% for dep in pyproject["project"]["dependencies"] %}
-    - {{ dep.lower() }}
-    {% endfor %}
-    {% for dep in pyproject["tool"]["conda"]["environment"]["dependencies"] %}
-    - {{ dep.lower() }}
+    - python
+    {% for dep in deps + conda_deps %}
+    - {{ dep }}
     {% endfor %}
 
+
 test:
   requires:
-    - pytest
+    {% for dep in test_deps %}
+    - {{ dep }}
+    {% endfor %}
 
   imports:
     - openalea.hydroroot
 
   source_files:
     - test/**
     - test/data/**
+
   commands:
     - cd test
     - pytest -v
 
 about:
-  summary: {{ pyproject["project"]["description"] }}
-  license: {{ pyproject["project"]["license"] }}
-  home: {{ pyproject["project"]["urls"]["Homepage"] }}
+  home: {{ home }}
+  summary: {{ description }}
+  license: {{ license }}
 
+extra:
+  recipe-maintainers:
+    - baugetfa
+    - pradal

example/Boursiac2022/boursiac2022.ipynb

@@ -42,7 +42,7 @@
     "# to display inline plots in the notebook\n",
     "%matplotlib inline\n",
     "# to be able to use the plantGL viewer in 3D\n",
-    "%gui qt"
+    "# %gui qt"
    ]
   },
   {
@@ -1718,7 +1718,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "version": "3.12.11"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

example/Boursiac2022/simulation_fig-1B-3C-6E-7B.py

@@ -9,15 +9,14 @@
 
 import glob
 import argparse
-import tempfile, os
 
+from openalea.plantgl.algo.view import view
 import openalea.plantgl.all as pgl
 from openalea.mtg import turtle as turt
-from IPython.display import Image, display
 
 from openalea.hydroroot.main import hydroroot_flow
 from openalea.hydroroot.init_parameter import Parameters
-from openalea.hydroroot.display import get_root_visitor, plot
+from openalea.hydroroot.display import get_root_visitor, mtg_scene
 from openalea.hydroroot import radius
 from openalea.hydroroot.generator.markov import my_seed,generate_g
 from openalea.hydroroot.generator.measured_root import mtg_from_aqua_data
@@ -102,9 +101,7 @@ def plot_order(g1, has_radius=True, r_base=1.e-4, r_tip=5e-5, prune=None, name=N
                 sh.appearance =pgl.Material(colors[vid])
     scene = pgl.Scene([sh for shid in shapes.values() for sh in shid ])
 
-    pgl.Viewer.display(scene)
-    if name is not None:
-            pgl.Viewer.frameGL.saveImage(name)
+    return scene
 
 if __name__ == '__main__':
 
@@ -161,15 +158,9 @@ def plot_order(g1, has_radius=True, r_base=1.e-4, r_tip=5e-5, prune=None, name=N
                 alpha = 0.2 # radius in millimeter identical for all orders
                 gcopy = g.copy() # copy because we change the radius property in plot below
                 if prop != 'order':
-                    plot(gcopy, has_radius=False, r_base = alpha * 1.e-3, r_tip = alpha * 9.9e-4, prop_cmap = prop)
+                    s = mtg_scene(gcopy, has_radius=False, r_base = alpha * 1.e-3, r_tip = alpha * 9.9e-4, prop_cmap = prop)
                 else:
-                    plot_order(gcopy, has_radius=False, r_base = alpha * 1.e-3, r_tip = alpha * 9.9e-4)
+                    s = plot_order(gcopy, has_radius=False, r_base = alpha * 1.e-3, r_tip = alpha * 9.9e-4)
 
                 ## for display in the notebook, comment to display in the 3D viewer
-                pgl.Viewer.widgetGeometry.setSize(800, 800) # set the picture size in px
-                fn = tempfile.mktemp(suffix='.png')
-                pgl.Viewer.saveSnapshot(fn)
-                pgl.Viewer.stop()
-                img = Image(fn)
-                os.unlink(fn)
-                display(img)
+                view(s)

example/Boursiac2022/simulation_fig-5_sup-fig-8.py

@@ -85,7 +85,7 @@ def hydro_calculation(g, axfold = 1., radfold = 1., axial_data = None, k_radial
     count = 0
     # sensibility analyse using multiplying factor on K and k
     for id in dseeds.index:
-        seed = dseeds.seed[id]
+        seed = int(dseeds.seed[id]) # otherwise this a numpy.int64 and the function random.seed does not like it
         primary_length = dseeds.primary_length[id]
         delta = dseeds.delta[id]
         nude_length = dseeds.nude_length[id]

example/Boursiac2022/simulation_fig-6-B-C.py

@@ -79,7 +79,7 @@ def hydro_calculation(g, axfold = 1., radfold = 1., axial_data = None, k_radial
     count = 0
     nb_steps = len(dseeds) * len(parameter.output['axfold'])
     for id in dseeds.index:
-        seed = dseeds.seed[id]
+        seed = int(dseeds.seed[id]) # otherwise this a numpy.int64 and the function random.seed does not like it
         primary_length = dseeds.primary_length[id]
         delta = dseeds.delta[id]
         nude_length = dseeds.nude_length[id]
@@ -124,7 +124,7 @@ def hydro_calculation(g, axfold = 1., radfold = 1., axial_data = None, k_radial
     axfold = 1.0
     nb_steps = len(dseeds) * len(parameter.output['radfold'])
     for id in dseeds.index:
-            seed = dseeds.seed[id]
+            seed = int(dseeds.seed[id]) # otherwise this a numpy.int64 and the function random.seed does not like it
             primary_length = dseeds.primary_length[id]
             delta = dseeds.delta[id]
             nude_length = dseeds.nude_length[id]