From ac1a7c9cb165a54bf8537c23fae5e48ea7d59835 Mon Sep 17 00:00:00 2001
From: pradal <christophe.pradal@cirad.fr>
Date: Tue, 2 Dec 2025 14:53:32 +0100
Subject: [PATCH 1/2] Remove alinea namespace

---
 src/alinea/astk/__init__.py | 5 -----
 1 file changed, 5 deletions(-)
 delete mode 100644 src/alinea/astk/__init__.py

diff --git a/src/alinea/astk/__init__.py b/src/alinea/astk/__init__.py
deleted file mode 100644
index dc63d20..0000000
--- a/src/alinea/astk/__init__.py
+++ /dev/null
@@ -1,5 +0,0 @@
-from openalea.astk import *
-
-from warnings import warn
-
-warn("This is deprecated; Use openalea namespace instead alinea!", DeprecationWarning, stacklevel=2)

From 96b37da484b9cadcd9ef568f0757687eeeb15279 Mon Sep 17 00:00:00 2001
From: pradal <christophe.pradal@cirad.fr>
Date: Tue, 2 Dec 2025 15:08:10 +0100
Subject: [PATCH 2/2] Modernize the code and document it!

---
 src/openalea/astk/TimeControl.py       | 17 ++++++++---------
 src/openalea/astk/Weather.py           |  5 +++--
 src/openalea/astk/colormap.py          |  2 +-
 src/openalea/astk/icosphere.py         | 21 ++++++++++++---------
 src/openalea/astk/pgl_display.py       | 16 ++++++++++++++++
 src/openalea/astk/plantgl_utils.py     | 17 +++++++++++++++--
 src/openalea/astk/sky_luminance.py     |  7 ++++++-
 src/openalea/astk/sky_sources.py       |  2 +-
 src/openalea/astk_wralea/__wralea__.py |  6 +++---
 9 files changed, 65 insertions(+), 28 deletions(-)

diff --git a/src/openalea/astk/TimeControl.py b/src/openalea/astk/TimeControl.py
index 88273bc..750bc35 100644
--- a/src/openalea/astk/TimeControl.py
+++ b/src/openalea/astk/TimeControl.py
@@ -15,12 +15,11 @@
 Provides utilities for scheduling models in simulation
 """
 from __future__ import division
-import numpy
-#from six.moves import map
-#from six.moves import zip
 from functools import reduce
 
-class TimeControlSet(object):
+import numpy
+
+class TimeControlSet:
 
     def __init__(self, **kwd):
         """  Create a TimeControlSet , that is a simple class container for named object"""
@@ -36,7 +35,7 @@ def simple_delay_timing(delay = 1, steps =1):
     return (TimeControlSet(dt=delay) if not i % delay  else TimeControlSet(dt=0) for i in range(steps))
             
             
-class TimeControl(object):
+class TimeControl:
 
     def __init__(self, delay=None, steps=None, model=None, weather=None, start_date=None):
         """ create a generator-like timecontrol object """
@@ -63,7 +62,7 @@ def __next__(self):
         return next(self._timing)
                   
             
-class TimeControler(object):
+class TimeControler:
 
     def __init__(self, **kwd):
         """ create a controler for parallel run of time controls
@@ -96,7 +95,7 @@ def evaluation_sequence(delays):
     seq = [[True if i == 0 else False for i in range(int(d))] for d in delays]
     return reduce(lambda x,y: x + y, seq)
 
-class EvalValue(object):
+class EvalValue:
     
     def __init__(self, eval, value, dt):
         self.eval = eval
@@ -106,7 +105,7 @@ def __init__(self, eval, value, dt):
     def __nonzero__(self):
         return self.eval
 
-class IterWithDelays(object):
+class IterWithDelays:
 
     def __init__(self, values = [None], delays = [1]):
         self.delays = delays
@@ -220,7 +219,7 @@ def rain_filter_node(time_sequence, weather):
     filter = rain_filter(time_sequence, weather)
     return time_sequence, filter, weather.data
    
-class DegreeDayModel(object):
+class DegreeDayModel:
     """ Classical degreeday model equation
     """
     
diff --git a/src/openalea/astk/Weather.py b/src/openalea/astk/Weather.py
index e8eafa4..358a1bd 100644
--- a/src/openalea/astk/Weather.py
+++ b/src/openalea/astk/Weather.py
@@ -20,13 +20,14 @@
 
 from __future__ import division
 from __future__ import print_function
-import pandas
 import pytz
 from datetime import timedelta
 from pathlib import Path
 
+import pandas
+
 from .TimeControl import *
-from openalea.astk.sun_position import sun_position
+from .sun_position import sun_position
 from . import sky_sources as sunsky
 from .data_access import meteo00_01
 
diff --git a/src/openalea/astk/colormap.py b/src/openalea/astk/colormap.py
index ca8a692..6287361 100644
--- a/src/openalea/astk/colormap.py
+++ b/src/openalea/astk/colormap.py
@@ -19,7 +19,7 @@
 
 from math import isnan
 
-class ColorMap(object):
+class ColorMap:
     """A RGB color map, between 2 colors defined in HSV code
 
     :Examples:
diff --git a/src/openalea/astk/icosphere.py b/src/openalea/astk/icosphere.py
index 1dde8b4..ea28e52 100644
--- a/src/openalea/astk/icosphere.py
+++ b/src/openalea/astk/icosphere.py
@@ -161,17 +161,17 @@ def split_triangles(vertices, faces, tags=None):
     """ Iterate an icosphere by sub-dividing each triangle into 4.
 
     Args:
-        vertices (list of tuples): list of 3D coordinates of icosphere vertices
-        faces (list of tuple): list of vertex indices defining the faces
-        tags (list of int): list of integer identifying a face. if None (default)
-        no tags are returned
+        - vertices (list of tuples): list of 3D coordinates of icosphere vertices
+        - faces (list of tuple): list of vertex indices defining the faces
+        - tags (list of int): list of integer identifying a face. if None (default)
+            no tags are returned
     Returns:
-        a list of vertices and a list of faces and, if tags is not None, a list
-        of tags referencing the tag of the parent face
+        - a list of vertices and a list of faces and, if tags is not None, a list
+            of tags referencing the tag of the parent face
 
     This is a python implementation of the C code found here:
     http://blog.andreaskahler.com/2009/06/creating-icosphere-mesh-in-code.html
-"""
+    """
     # copy input
     new_faces = [f for f in faces]
     new_vertices = [v for v in vertices]
@@ -224,8 +224,11 @@ def split_triangles(vertices, faces, tags=None):
 
 
 def sorted_faces(center, face_indices, faces):
-    """ return face indices sorted to form a counter clockwise rotation
-     around its centroid"""
+    """ Sort faces.
+    
+    Return face indices sorted to form a counter clockwise rotation
+    around its centroid.
+    """
     indices = [i for i in face_indices]
     sorted_indices = [indices.pop(0)]
     while len(indices) > 0:
diff --git a/src/openalea/astk/pgl_display.py b/src/openalea/astk/pgl_display.py
index 7e184bc..a2b1e32 100644
--- a/src/openalea/astk/pgl_display.py
+++ b/src/openalea/astk/pgl_display.py
@@ -1,4 +1,20 @@
 
+# -*- python -*-
+#
+#       Copyright 2016-2025 Inria - CIRAD - INRAe
+#
+#       Distributed under the Cecill-C License.
+#       See accompanying file LICENSE.txt or copy at
+#           http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html
+#
+#       WebSite : https://github.com/openalea-incubator/astk
+#
+#       File author(s): Christian Fournier <christian.fournier@inrae.fr>
+#
+#      
+#
+# ==============================================================================
+
 import warnings
 from openalea.astk.colormap import jet_colors
 
diff --git a/src/openalea/astk/plantgl_utils.py b/src/openalea/astk/plantgl_utils.py
index bf1fbcb..c7b42a8 100644
--- a/src/openalea/astk/plantgl_utils.py
+++ b/src/openalea/astk/plantgl_utils.py
@@ -14,7 +14,7 @@
 
 from __future__ import division
 from openalea.plantgl import all as pgl
-#from six.moves import range
+
 
 def _is_iterable(x):
     try:
@@ -23,8 +23,21 @@ def _is_iterable(x):
         return False
     return True
 
-
 def get_area_and_normal(scene_geometry):
+    """ Calculate the area and normal of objects in a PlantGL scene
+    
+    Parameters
+    ----------  
+    scene_geometry: dict([id, geometry])
+        Dictionnary of geometries of objects in the scene.
+
+    Returns
+    ------- 
+    areas: dict([id, list of float])
+        Dictionnary of list of surface of triangles composing each object in the scene.
+    normals: dict([id, list of pgl.Vector3])
+        Dictionnary of list of normal vectors of triangles composing each object in the scene.
+    """
 
     def _surf(ind,pts):
         A,B,C = [pts[i] for i in ind]
diff --git a/src/openalea/astk/sky_luminance.py b/src/openalea/astk/sky_luminance.py
index deaa70f..119bc12 100644
--- a/src/openalea/astk/sky_luminance.py
+++ b/src/openalea/astk/sky_luminance.py
@@ -20,7 +20,12 @@
     f_clear_sky,
     all_weather_sky_brightness
 )
-from openalea.astk.sky_map import ksi_grid, scale_sky, sky_ni, sky_lum
+from openalea.astk.sky_map import (
+    ksi_grid, 
+    scale_sky, 
+    sky_ni, 
+    sky_lum
+)
 
 
 def cie_luminance_gradation(z, a=4, b=-0.7):
diff --git a/src/openalea/astk/sky_sources.py b/src/openalea/astk/sky_sources.py
index 9098b1f..30c00f3 100644
--- a/src/openalea/astk/sky_sources.py
+++ b/src/openalea/astk/sky_sources.py
@@ -17,7 +17,7 @@
 import numpy
 
 from .icosphere import turtle_mesh, spherical_face_centers
-from openalea.astk.sky_luminance import sky_luminance
+from .sky_luminance import sky_luminance
 from .sky_map import sky_grid, sky_map, sky_hi
 
 
diff --git a/src/openalea/astk_wralea/__wralea__.py b/src/openalea/astk_wralea/__wralea__.py
index f0ec204..59974f7 100644
--- a/src/openalea/astk_wralea/__wralea__.py
+++ b/src/openalea/astk_wralea/__wralea__.py
@@ -9,11 +9,11 @@
 __editable__ = True
 __description__ = ''
 __license__ = 'CeCILL-C'
-__url__ = 'http://openalea.gforge.inria.fr'
+__url__ = 'https://openalea-astk.rtfd.io'
 __alias__ = []
-__version__ = '1.0.0'
+__version__ = '3.0.0'
 __authors__ = ''
-__institutes__ = None
+__institutes__ = 'inria, CIRAD, INRAE'
 __icon__ = ''