Python3

example/example_leaf_areas.py

@@ -59,7 +59,7 @@
 
         # Save variables
         for plant in recorders:
-            for lf, recorder in recorders[plant].iteritems():
+            for lf, recorder in recorders[plant].items():
                 recorder.update_vids_with_labels(adel_ids = adel_ids(g))
                 recorder.record_only_leaf_data(g, date, degree_days = canopy_iter.value.degree_days[-1])
 

example/reconstruction_digit.py

@@ -57,6 +57,6 @@
 stand = AgronomicStand(sowing_density=500, plant_density=500, inter_row=0.15, noise=0.03)
 adel = AdelDress(dimT=dimT, leaves=leaves, stand=stand)
 g = adel.canopy(nplants=10, species = {'soissons':0.5, 'cap_horn':0.5}, relative_inclination = {'soissons':1.5, 'cap_horn':1})
-print [v for k, v in g.property('species').iteritems() if k in g.vertices(1)]
+print [v for k, v in g.property('species').items() if k in g.vertices(1)]
 print adel.plot_statistics(g)
 

example/test_adelR.py

@@ -122,4 +122,4 @@ def testdyn(nplants=1,start = 100,step = 50, nstep=30,dec=10,az=0):
 # import numpy as np
 # from alinea.popdrops.Rain import get_area_and_normal
 # a1,_=get_area_and_normal(g1.property('geometry'))
-# a1 = dict(((k,np.sum(v)) for k,v in a1.iteritems()))
+# a1 = dict(((k,np.sum(v)) for k,v in a1.items()))

metainfo.ini

@@ -1,7 +1,7 @@
 
 [metainfo]
-version = 1.6.0
-release = 1.6
+version = 1.7.0
+release = 1.7
 ; must be in [openalea, vplants, alinea]
 project = alinea 
 ; the filename of the egg

setup.cfg

@@ -30,8 +30,8 @@ build_requires = python >= 2.6
            python-devel >= 2.6
            python-setuptools >= 0.6
            python-OpenAlea.Deploy >= 0.9
-provides = %{name} = %{version}
-obsoletes = %{name} < %{version}
+provides = %%{name} = %%{version}
+obsoletes = %%{name} < %%{version}
 doc_files = AUTHORS.txt ChangeLog.txt README.txt LICENSE.txt
 python = /usr/bin/python
 packager = OpenAlea Consortium

setup.py

@@ -1,66 +1,54 @@
 #!/usr/bin/env python
 # -*- coding: iso-8859-15 -*-
 
-
-import os, sys
-from setuptools import setup, find_packages
-from openalea.deploy.metainfo import read_metainfo
+import os, sys 
+from setuptools import setup, find_namespace_packages
+#from openalea.deploy.metainfo import read_metainfo
 pj = os.path.join
 
+version = '2.0.0'
+name = 'alinea.adel'
+
+description= '3D plant simulation of graminae crops'
+long_description= 'The Adel package characterise 3D plant development for graminae crops.'
 
-# Reads the metainfo file
-metadata = read_metainfo('metainfo.ini', verbose=True)
-for key,value in metadata.iteritems():
-    exec("%s = '%s'" % (key, value))
+authors= 'Christian Fournier, Christophe Pradal'
+authors_email = 'christian fournier at inrae fr'
 
-
-# #retrieving packages
-# pkg_root_dir = '.'
-# pkgs = [ pkg for pkg in find_packages(pkg_root_dir) if namespace not in pkg]
-# top_pkgs = [pkg for pkg in pkgs if  len(pkg.split('.')) < 2]
-# packages = [ namespace + "." + pkg for pkg in pkgs]
-# package_dir = dict( [('',pkg_root_dir)] + [(namespace + "." + pkg, pkg_root_dir + "/" + pkg) for pkg in top_pkgs] )
-# wralea_entry_points = ['%s = %s'%(pkg,namespace + '.' + pkg) for pkg in top_pkgs]
+url = 'https://github.com/openalea-incubator/adel'
+license = 'Cecill-C'
 
 # Main setup
 setup(
     name=name,
     version=version,
     description=description,
     long_description=long_description,
-    authors=authors,
-    authors_email=authors_email,
+    author=authors,
+    author_email=authors_email,
     url=url,
     license=license,
-
-    namespace_packages = [namespace],
-    create_namespaces = True,
-
-    py_modules = [],
+    #py_modules = [],
     # pure python  packages
-    packages= find_packages('src'),
+    packages= find_namespace_packages(where='src', 
+                                      include=['alinea.*', 'alinea']),
     # python packages directory
     package_dir= {'': 'src'},
 
-
+
+    # Namespace packages creation by deploy
     # Add package platform libraries if any
     include_package_data=True,
     package_data = {'' : ['*.RData', '*.R', '*.8', '*.h', '*.str','*.txt', '*.l', '*.map', '*.csv', '*.png'],},
-    share_dirs = {os.path.join(*('alinea', 'adel', 'data')): os.path.join(*('src', 'alinea','adel', 'data'))},
+    share_dirs = {pj(*('alinea', 'adel', 'data')): pj(*('src', 'alinea','adel', 'data')),
+                  pj(*('alinea', 'adel', 'echap_leaf_data')): pj(*('src', 'alinea','adel', 'echap_leaf_data'))},
 
     # Add package platform libraries if any
     zip_safe = False,
 
-
     # Scripts
     entry_points = { 'wralea': [ 'adel= alinea.adel',] },
 
     # Dependencies (other are listed in doc to avoid setputools/pip/conda possible conflicts in automatic installs)
     setup_requires = ['openalea.deploy'],
-    install_requires = [],
-    dependency_links = [],
-   )
-
-
-
-
+)

src/alinea/adel/AdelR.py

@@ -137,7 +137,7 @@ def dataframe(d):
     if d is None:
         return r('as.null()')
     else:
-        for k, v in d.iteritems():
+        for k, v in d.items():
             rval = numpy2ri(numpy.array(v))
             if not _is_iterable(v):
                 v = [v]
@@ -211,17 +211,7 @@ def setAdel(devT,RcodegeoLeaf,RcodegeoAxe,nplants = 1,seed = None, xydb = None,
         ssipars = robj.r['list'](**ssipars)
     p = RsetAdel(RdevT,geoLeaf,geoAxe,nplants,sample,rseed,rxydb,rsrdb,ssipars)
     return p
-
-def leaf_keys(lindex, lseed, db):
-    """ convert R-style lindex/lseed (also called LcType/Lindex in canopy table)
-        into (keys,index) of python xy/sr data bases 
-    """
-    if 1 > lindex or lindex > len(db) or lseed < 1:
-        raise KeyError('invalid index for leaf shape database')
-    keys = db.keys()
-    keys.sort()
-    return keys[lindex - 1], lseed -1
-
+
 
 def plantSample(setAdelPars):
     """return id of plants used by setAdel to setup the canopy """

src/alinea/adel/adel.py

@@ -28,19 +28,19 @@ def flat_list(nested_list):
 
 def balanced_sample(n, proba):
     """ return a list of n keys found in proba, repecting probalities of proba values"""
-    card = {k: int(v * n) for k, v in proba.iteritems()}
+    card = {k: int(v * n) for k, v in proba.items()}
     missing = int(n - sum(card.values()))
     while (missing > 0):
         # current frequencies
-        freq = {k: float(v) / n for k, v in card.iteritems()}
+        freq = {k: float(v) / n for k, v in card.items()}
         # diff with probabilities
         dp = {k: abs(freq[k] - proba[k]) for k in freq}
-        sorted_p = sorted(dp.iteritems(), key=operator.itemgetter(1), reverse=True)
+        sorted_p = sorted(dp.items(), key=operator.itemgetter(1), reverse=True)
         k = sorted_p[0][0]
         card[k] += 1
         missing -= 1
-    card = {k: v for k, v in card.iteritems() if v > 0}
-    items = flat_list([[key] * val for key, val in card.iteritems()])
+    card = {k: v for k, v in card.items() if v > 0}
+    items = flat_list([[key] * val for key, val in card.items()])
     numpy.random.shuffle(items)
     return items
 
@@ -310,8 +310,8 @@ def save(self, g, index=0, dir='./adel_saved', basename=None,
         fgeom = basename_geom + '.bgeom'
         fg = basename_adel + '.pckl'
         s.save(fgeom, 'BGEOM')
-        with open(fg, 'w') as output:
-            pickle.dump(g, output)
+        with open(fg, 'wb') as output:
+            pickle.dump(g, output, protocol=2)
         # restore geometry
         g.add_property('geometry')
         g.property('geometry').update(geom)
@@ -331,8 +331,8 @@ def load(index=0, dir='./adel_saved', basename=None, load_geom=True):
         if not os.path.exists(fgeom) or not os.path.exists(fg):
             raise IOError('adel cannot find saved files')
 
-        f = open(fg)
-        g = pickle.load(f)
+        f = open(fg, 'rb')
+        g = pickle.load(f, encoding='bytes')
         f.close()
 
         # backward compatibility
@@ -374,7 +374,7 @@ def get_midribs(self, g, resample=False):
             vid
             in midribs}
         hins = {k: v[0][2] + midribs[k][2] for k, v in
-                midribs_anchor.iteritems() if len(v) > 0}
+                midribs_anchor.items() if len(v) > 0}
 
         ntop = g.property('ntop')
         res = [pandas.DataFrame({'vid': vid,

src/alinea/adel/adel_dynamic.py

@@ -1,18 +1,17 @@
 """ Prototype adel model that uses mtg edition functions"""
 from openalea.mtg import MTG
-from alinea.adel.astk_interface import AdelWheat
+from alinea.adel.adel import Adel
 from alinea.adel.mtg_editions import find_metamers, add_plant, add_vegetative_metamer, new_mtg_factory, update_organ_elements
-from alinea.adel.AdelR import plantSample
 from alinea.adel.mtg_interpreter import mtg_interpreter, transform_geom
 
 
-class AdelWheatDyn(AdelWheat):
+class AdelDyn(Adel):
 
-    def build_stand(self):
+    def build_stand(self, axeTable):
 
         g = MTG()
-        plants = self.axeT()
-        sample = [int(p) for p in plantSample(self.pars)]
+        plants = axeTable
+        sample = self.plant_references
         for i, plant in plants.groupby('plant'):
             plant_properties = {'position': self.positions[i - 1],
                                 'azimuth': self.plant_azimuths[i - 1],
@@ -21,16 +20,16 @@ def build_stand(self):
             ms_properties = {'HS_final': float(ms['HS_final'][0]),
                              'nff': int(ms['nf'][0]),
                              'hasEar': bool(int(ms['hasEar'][0])),
-                             'azimuth': float(ms['azTb'][0])}
+                             'azimuth': 0}
             add_plant(g, i, plant_properties=plant_properties,
                       axis_properties=ms_properties)
         return g
 
-    def add_metamer(self, g, plant=1, axe='MS'):
+    def add_metamer(self, g, phytoT, plant=1, axe='MS'):
         vid_plant, vid_axe, metamers = find_metamers(g, plant, axe)
         nff = g.property('nff')[vid_axe]
         num_metamer = len(metamers)
-        df = self.phytoT(axe)
+        df = phytoT.loc[phytoT['axe'] == axe,:]
         m = df.loc[df['n'] == num_metamer, :].to_dict('list')
         metamer_properties = {'L_shape': m['Ll'][0]}
         ntop = nff - num_metamer + 1
@@ -65,7 +64,7 @@ def build_mtg(self, parameters, stand, **kwds):
                             face_up=self.face_up)
         return g
 
-    def update_geometry(self, g, SI_units=False, properties_to_convert={'lengths':[], 'areas':[]}):
+    def update_geometry(self, g, phyllochron={'MS':88.92, 'T1':91.6}, SI_units=False, properties_to_convert={'lengths':[], 'areas':[]}):
         """Update MTG geometry.
 
         :Parameters:
@@ -82,7 +81,7 @@ def update_geometry(self, g, SI_units=False, properties_to_convert={'lengths':[]
             self.convert_to_ADEL_units(g, properties_to_convert)
 
         # update elements
-        g = update_organ_elements(g, self.leaves, self.split, self.phyllochron())
+        g = update_organ_elements(g, self.leaves, self.split, phyllochron)
         g = mtg_interpreter(g, self.leaves, face_up=self.face_up,
                             classic=self.classic)
         pos = g.property('position')
@@ -105,11 +104,11 @@ def convert_to_ADEL_units(self, g, properties_to_convert):
             - `properties_to_convert` (:class:`dict` of :class:`pandas.DataFrame`) - A dictionnary with the list of length properties area properties to be converted.
         """
         for length_property in properties_to_convert['lengths']:
-            for vid, length in g.properties()[length_property].iteritems():
+            for vid, length in g.properties()[length_property].items():
                 g.properties()[length_property][vid] = length * 100 # Converts m to cm
 
         for area_property in properties_to_convert['areas']:
-            for vid, area in g.properties()[area_property].iteritems():
+            for vid, area in g.properties()[area_property].items():
                 g.properties()[area_property][vid] = area * 10000 # Converts m2 to cm2
 
     def convert_to_SI_units(self, g, properties_to_convert):
@@ -120,9 +119,9 @@ def convert_to_SI_units(self, g, properties_to_convert):
             - `properties_to_convert` (:class:`dict` of :class:`pandas.DataFrame`) - A dictionnary with the list of length properties area properties to be converted.
         """
         for length_property in properties_to_convert['lengths']:
-            for vid, length in g.properties()[length_property].iteritems():
+            for vid, length in g.properties()[length_property].items():
                 g.properties()[length_property][vid] = length / 100 # Converts cm to m
 
         for area_property in properties_to_convert['areas']:
-            for vid, area in g.properties()[area_property].iteritems():
+            for vid, area in g.properties()[area_property].items():
                 g.properties()[area_property][vid] = area / 10000 # Converts cm2 to m2