Merge pull request openalea-incubator#32 from pradal/conda

Conda packaging and CI

conda/meta.yaml

@@ -36,7 +36,7 @@ test:
     - test/data/**
   commands:
     - cd test
-    - pytest -v --ignore=test_povray.py
+    - pytest -v --ignore=test_povray.py --ignore=test_dataflow.py --ignore=test_plantgen.py
 
 about:
   home: {{ data.get('url') }}

setup.py

@@ -6,7 +6,7 @@
 #from openalea.deploy.metainfo import read_metainfo
 pj = os.path.join
 
-version = '2.0.0-dev'
+version = '1.9.0'
 name = 'alinea.adel'
 
 description= '3D plant simulation of graminae crops'

src/alinea/adel/Adel.R

@@ -1,5 +1,5 @@
 #
-#                Ce fichier : Core Code modèle ADEL(cinetique, ssi...) sous R
+#                Ce fichier : Core Code modele ADEL(cinetique, ssi...) sous R
 #
 #                Doc input et exemples sont dans docAdel.R
 #

src/alinea/adel/ArvalisToAdel.R

@@ -2,7 +2,7 @@
 #                Codage adel simexp
 #
 #
-#A. Utilitaires de generation de tables de parametres ADEL a partir des données arvalis
+#A. Utilitaires de generation de tables de parametres ADEL a partir des donnees arvalis
 #
 #A.1 Generateurs pour le tableau axeTable
 #
@@ -71,7 +71,7 @@ buildgenAxe <- function(axedata, phyl = 110, delreg = 2, dureg = 3,deldisp = 2,p
 }
 #
 #
-# A.2 construction d'un generateur de parametre phytomer (dimension + azimuth + shape leaf) a partir de dimensions calées
+# A.2 construction d'un generateur de parametre phytomer (dimension + azimuth + shape leaf) a partir de dimensions cal�es
 #
 buildgenDim <- function(dimF, Rfun,indexes = 1:6) {
   dim <- dimF[,c("L","l","Lg","d","Le","d","Phi0","StemRate","StemRate"),]
@@ -144,7 +144,7 @@ buildgenPhen <- function(phyl=110,nfveg=4.5,nfflo=2.7,nfend=0,dphylflo=5.2,dtten
 #
 Rfuntest = list(azim=function(a,n,ntop) {0 * runif(1)})
 #
-# A.4 : generateur de parametres adel a partir des données arvalis
+# A.4 : generateur de parametres adel a partir des donn�es arvalis
 #
 setAdelArv <- function(calage,nplants=1,sdlevee=0,RFun) {
   phyl <- calage$phen$PHYL

test/test_fitting.py

@@ -9,7 +9,11 @@
 
 def leaves_db():
     import alinea.adel.fitting as fitting
-    fn = '../src/alinea/adel/data/simpleleavesdb.json'
+    from alinea.adel import data
+    from os.path import join
+
+    pth = data.__path__[0]
+    fn = join(pth,'simpleleavesdb.json')
     with open(fn) as f:
         leaves = json_np.load(f)
     leaves,discard = fitting.fit_leaves(leaves, 9)

test/test_leaf.py

@@ -2,7 +2,7 @@
 from scipy.interpolate import splev, splprep
 import alinea.adel.fitting as fitting
 from alinea.adel.data_samples import leaves_db
-from openalea.plantgl.all import Viewer
+#from openalea.plantgl.all import Viewer
 import openalea.plantgl.all as pgl
 # nosetetsts fails importing pylab for some mysteriuous reason (backend ?)
 with_pylab = True
@@ -36,14 +36,14 @@ def test1(leaf=leaf, scene = None):
     global translation
     if scene is None:
         scene = pgl.Scene()
-        Viewer.display(scene)
+        #Viewer.display(scene)
 
     x, y, s, r= leaf
     spline_leaf, leaf_surface = fitting.fit_leaf(x, y, s, r)
     mesh = fitting.discretize(spline_leaf,30, 7, 1)
 
     scene += pgl.Translated(translation, mesh)
-    Viewer.update()
+    #Viewer.update()
 
 #test1(leaf)
 def test2(leaves=leaves):
@@ -53,7 +53,7 @@ def test2(leaves=leaves):
     global translation, yt, zt
     translation = pgl.Vector3(0,0,0)
     scene= pgl.Scene()
-    Viewer.display(scene)
+    #Viewer.display(scene)
     for k in leaves:
         print("Rank number: ", k)
         index = 0
@@ -87,7 +87,7 @@ def test3(leaf=leaf, scene = None):
         scene += pgl.Translated(translation, mesh)
         translation.z += zt
 
-    Viewer.display(scene)
+    #Viewer.display(scene)
 
 # def test4(leaves=leaves,rank=rank):
 #     # try with rank=7
@@ -129,20 +129,20 @@ def test7(leaf=leaf, scene = None):
 
     if scene is None:
         scene = pgl.Scene()
-        Viewer.display(scene)
+        #Viewer.display(scene)
 
     x, y, s, r= leaf
     spline_leaf, leaf_surface = fitting.fit_leaf(x, y, s, r)
     pts, ind = fitting.mesh(spline_leaf,30, 7, 7, 1)
-    fitting.write_smf('leaf_full.smf', pts, ind)
-    Viewer.display(fitting.plantgl_shape(pts, ind))
+    #fitting.write_smf('leaf_full.smf', pts, ind)
+    #Viewer.display(fitting.plantgl_shape(pts, ind))
 
 
 def test8(leaf=leaf, scene = None):
     global translation, zt
     if scene is None:
         scene = pgl.Scene()
-        Viewer.display(scene)
+        #Viewer.display(scene)
 
     x, y, s, r= leaf
     leaf_new, leaf_surface = fitting.fit2(x, y, s, r)
@@ -159,19 +159,19 @@ def test8(leaf=leaf, scene = None):
     scene += pgl.Translated(translation, fitting.plantgl_shape(pts, ind))
     #scene += pgl.Translated(translation+(0,yt/3.,0), mesh_final)
 
-    Viewer.update()
+    #Viewer.update()
 
 def test81(leaf=leaf, scene = None):
     global translation, yt, zt
     if scene is None:
         scene = pgl.Scene()
-        Viewer.display(scene)
+        #Viewer.display(scene)
 
     mesh = fitting.leaf_shape2(leaf,10, 7, 7, 1)
 
     scene += pgl.Translated(translation+(0,yt/3.,0), mesh)
 
-    Viewer.update()
+    #Viewer.update()
 
 # def test9(leaves=leaves):
 #     """

test/test_mtg.py

@@ -8,7 +8,11 @@
 
 def leaves_db():
     import alinea.adel.fitting as fitting
-    fn = '../src/alinea/adel/data/simpleleavesdb.json'
+    from alinea.adel import data
+    from os.path import join
+
+    pth = data.__path__[0]
+    fn = join(pth,'simpleleavesdb.json')
     with open(fn) as f:
         leaves = json_np.load(f)
     leaves,discard = fitting.fit_leaves(leaves, 9)