From dff84dc4d4db05df1d407b919ed125c55bb3ab01 Mon Sep 17 00:00:00 2001
From: baugetfa <fabrice.bauget@cirad.fr>
Date: Mon, 8 Dec 2025 14:23:11 +0100
Subject: [PATCH 1/2] updated conda channel and only one environment.yml

---
 .readthedocs.yml      | 4 ++--
 conda/environment.yml | 8 +++++++-
 doc/usage.rst         | 4 ++--
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index cce3e91..0842047 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -1,12 +1,12 @@
 version: 2
 
 build:
-  os: "ubuntu-lts-latest"
+  os: "ubuntu-24.04"
   tools:
     python: "miniconda3-3.12-24.9"
 
 conda:
-  environment: doc/environment.yml
+  environment: conda/environment.yml
 
 sphinx:
   # Path to your Sphinx configuration file.
diff --git a/conda/environment.yml b/conda/environment.yml
index d951756..44fb66e 100644
--- a/conda/environment.yml
+++ b/conda/environment.yml
@@ -1,4 +1,4 @@
-name: hydroroot_dev
+name: hydroshoot
 channels:
   - openalea3/label/dev
   - openalea3/label/rc
@@ -9,6 +9,12 @@ dependencies:
   - openalea.plantgl
   - openalea.caribu
   - openalea.astk
+  - numpy
+  - scipy
+  - sympy
+  - pandas
+  - jsonschema
+  - pvlib-python
   - pip
   - pip:
       - -e .."[test,doc]"
diff --git a/doc/usage.rst b/doc/usage.rst
index eb19b2f..955df9b 100644
--- a/doc/usage.rst
+++ b/doc/usage.rst
@@ -106,7 +106,7 @@ Let's build the mock-up using the digitalization data provided in "grapevine_pot
     from openalea.hydroshoot import architecture, display, model
 
     # Path for plant digitalization data.
-    g = architecture.vine_mtg('grapevine_pot.csv')
+    grapevine_mtg = architecture.vine_mtg('grapevine_pot.csv')
 
     for v in traversal.iter_mtg2(grapevine_mtg, grapevine_mtg.root):
         architecture.vine_phyto_modular(grapevine_mtg, v)
@@ -118,7 +118,7 @@ Display now the scene using **display** module, you should be having something l
 
 .. code-block:: python
 
-    scene = display.visu(g, def_elmnt_color_dict=True, scene=Scene(),
+    scene = display.visu(grapevine_mtg, def_elmnt_color_dict=True, scene=Scene(),
                          view_result=True)
 
 

From f019da7055b6db7e479f4fc5160c31f9df7cddeb Mon Sep 17 00:00:00 2001
From: baugetfa <fabrice.bauget@cirad.fr>
Date: Mon, 8 Dec 2025 15:20:28 +0100
Subject: [PATCH 2/2] corrected code lines to get example working

---
 doc/usage.rst | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/doc/usage.rst b/doc/usage.rst
index 955df9b..15bc80c 100644
--- a/doc/usage.rst
+++ b/doc/usage.rst
@@ -104,6 +104,7 @@ Let's build the mock-up using the digitalization data provided in "grapevine_pot
     from openalea.mtg import traversal
     from openalea.plantgl.all import Scene
     from openalea.hydroshoot import architecture, display, model
+    from pathlib import Path
 
     # Path for plant digitalization data.
     grapevine_mtg = architecture.vine_mtg('grapevine_pot.csv')
@@ -134,9 +135,12 @@ potential to a fixed value of -0.5 :math:`MPa`. Ensure first that the model will
 start and end dates of the simulation in the "params.json" file ("sdate": "2012-08-01 11:00:00",
 "edate": "2012-08-01 11:00:00").
 
+Create a folder named 'output' and run the model.
+
 .. code-block:: python
 
-    model.run(g, str(getcwd()) + '/', scene, psi_soil=-0.2, gdd_since_budbreak=100.)
+    model.run(grapevine_mtg, Path(str(getcwd()) + '/'), Path(str(getcwd()) + '/meteo.input'),
+                Scene = scene, psi_soil=-0.2, gdd_since_budbreak=100.)
 
 You should now have created the '/output/' folder where output files ("time_series.ouput", "mtg20120801110000.pckl")
 are stored. "time_series.ouput" file should contain close values to those below: