Merging master into new_python_api

stat_tool/src/openalea/stat_tool/mixture.py

@@ -84,7 +84,7 @@ def Mixture(*args):
         # Extract weights ands distributions
         weights = []
         dists = []
-        for i in range(nb_param / 2):
+        for i in range(nb_param // 2):
             weights.append(args[i * 2])
             error.CheckType([args[i * 2 + 1]], [types], arg_id=[i * 2 + 1])
             error.CheckType([args[i * 2]], [float], arg_id=[i * 2])

stat_tool/test/test_cluster.py

@@ -11,11 +11,14 @@
 from openalea.stat_tool.vectors import Vectors, VectorDistance
 from openalea.stat_tool.comparison import Compare
 from openalea.stat_tool.data_transform import SelectVariable
-from openalea.stat_tool.cluster import Transcode, Clustering, \
-    ToDistanceMatrix, Cluster
+from openalea.stat_tool.cluster import (Transcode, Clustering, 
+    ToDistanceMatrix, Cluster)
 
-from tools import runTestClass
-from openalea.stat_tool import get_shared_data
+from tools import runTestClass, robust_path
+import openalea.stat_tool as st
+#from openalea.stat_tool import get_shared_data, get_shared_data_path
+
+get_shared_data = robust_path
 
 
 class Test:

stat_tool/test/test_cluster_and_distance_matrix.py

@@ -20,7 +20,8 @@
 from openalea.stat_tool import ExtractHistogram
 from openalea.stat_tool import Display
 
-from openalea.stat_tool import get_shared_data
+#from openalea.stat_tool import get_shared_data
+from tools import robust_path as get_shared_data
 
 def test():
     vec10 = Vectors(get_shared_data('chene_sessile.vec'))

stat_tool/test/test_comparison.py

@@ -17,9 +17,10 @@
 from openalea.stat_tool.data_transform import SelectVariable
 from openalea.stat_tool.comparison import Compare, ComparisonTest
 
-from tools import runTestClass
+from tools import runTestClass, robust_path as get_shared_data
+
+#from openalea.stat_tool import get_shared_data
 
-from openalea.stat_tool import get_shared_data
 class TestHisto():
     """a simple unittest class"""
 

stat_tool/test/test_compound_functional.py

@@ -5,14 +5,15 @@
 """
 __version__ = "$Id$"
 
+import os
 
 from openalea.stat_tool import Compound, Histogram, Distribution
 
-from openalea.stat_tool import Simulate, ExtractHistogram, ToHistogram
-from openalea.stat_tool import Estimate, ExtractData, ExtractDistribution
-from openalea.stat_tool import Plot, Shift
-from openalea.stat_tool import shared_data_path
-import os
+from openalea.stat_tool import (
+    Simulate, ExtractHistogram, ToHistogram,
+    Estimate, ExtractData, ExtractDistribution,
+    Plot, Shift
+)
 
 # read data file
 def test():

stat_tool/test/test_convolution.py

@@ -94,7 +94,7 @@ def test_extract_data(self):
         eprime = Estimate(s, "CONVOLUTION", Binomial(0, 10, 0.5))
 
         # todo: find robust assert ?
-        print eprime.get_mean
+        print(eprime.get_mean)
 
     def test_truncate(self):
         s = self.data

stat_tool/test/test_data_transform.py

@@ -8,20 +8,22 @@
 
 from openalea.stat_tool.vectors import Vectors
 from openalea.stat_tool.histogram import Histogram
-from openalea.stat_tool.distribution import Distribution, Uniform, Binomial, \
+from openalea.stat_tool.distribution import (
+    Distribution, Uniform, Binomial, 
     NegativeBinomial
+    )
 from openalea.stat_tool.mixture import Mixture
 from openalea.stat_tool.convolution import Convolution
 from openalea.stat_tool.simulate import Simulate
 from openalea.stat_tool.compound import Compound
 from openalea.stat_tool.output import Plot
-from openalea.stat_tool.data_transform import Shift, Merge, Fit, ValueSelect, \
-    SelectVariable, SelectIndividual, MergeVariable, ExtractDistribution, \
+from openalea.stat_tool.data_transform import (
+    Shift, Merge, Fit, ValueSelect, 
+    SelectVariable, SelectIndividual, MergeVariable, ExtractDistribution, 
     ExtractHistogram, ExtractData, SelectStep
+    )
 
-from tools import runTestClass
-
-from openalea.stat_tool import get_shared_data
+from tools import runTestClass, robust_path as get_shared_data
 
 class data():
     """Create some common data sets for the classes

stat_tool/test/test_distance_matrix.py

@@ -13,8 +13,7 @@
 from openalea.stat_tool.cluster import Clustering, ToDistanceMatrix
 
 from tools import interface
-from tools import runTestClass
-from openalea.stat_tool import get_shared_data
+from tools import runTestClass, robust_path as get_shared_data
 
 class Test(interface):
 

stat_tool/test/test_distribution.py

@@ -3,16 +3,13 @@
 __version__ = "$Id$"
 
 
-from openalea.stat_tool import _stat_tool
 from openalea.stat_tool.distribution import Distribution, Uniform, Binomial
 from openalea.stat_tool.distribution import NegativeBinomial, Poisson
 from openalea.stat_tool.distribution import Multinomial
 from openalea.stat_tool.distribution import ToHistogram, ToDistribution
 from openalea.stat_tool.histogram import Histogram
 from openalea.stat_tool import Estimate
 
-
-
 from openalea.stat_tool._stat_tool import _DiscreteParametricModel
 
 from tools import interface

stat_tool/test/test_distribution_functional.py

@@ -37,7 +37,7 @@
 
 
 from openalea.stat_tool.plot import DISABLE_PLOT
-
+DISABLE_PLOT = False
 
 from openalea.stat_tool.data_transform import ExtractDistribution
 from openalea.stat_tool.histogram import Histogram
@@ -49,7 +49,7 @@
 from openalea.stat_tool.simulate import Simulate
 from openalea.stat_tool.cluster import Cluster
 
-from openalea.stat_tool import get_shared_data
+from tools import robust_path as get_shared_data
 
 plot.DISABLE_PLOT = DISABLE_PLOT
 
@@ -92,7 +92,7 @@ def test():
     Plot(mixt2)
     Plot(ExtractDistribution(mixt2, "Mixture"))
 
-    print type(ExtractDistribution(mixt2, "Component", 1))
+    print(type(ExtractDistribution(mixt2, "Component", 1)))
 
 
     Plot(ExtractDistribution(mixt2, "Component", 1),

stat_tool/test/test_error.py

@@ -162,4 +162,4 @@ def test_class_error():
     fe._error()
     fe = FormatError(error="test")
     fe._error()
-    print fe
+    print(fe)

stat_tool/test/test_estimate.py

@@ -18,11 +18,9 @@
 
 from openalea.stat_tool.estimate import Estimate, likelihood_penalty_type
 
-from tools import runTestClass
+from tools import runTestClass, robust_path as get_shared_data
 
 
-from openalea.stat_tool import get_shared_data
-
 class Test():
 
     def __init__(self):

stat_tool/test/test_histogram.py

@@ -7,9 +7,8 @@
 from openalea.stat_tool.distribution import Distribution
 
 from tools import interface
-from tools import runTestClass
+from tools import runTestClass, robust_path as get_shared_data
 
-from openalea.stat_tool import get_shared_data
 
 class Test(interface):
     """a simple unittest class
@@ -122,7 +121,7 @@ def test_extract_vec():
     vs = stat_tool.Vectors("data/cvectors.vec")
     h = vs.extract(4)
     assert h
-    print h
+    print(h)
 
 
 if __name__ == "__main__":

stat_tool/test/test_matrix.py

@@ -6,8 +6,7 @@
 from openalea.stat_tool.comparison import Compare
 
 from tools import interface
-from tools import runTestClass
-from openalea.stat_tool import get_shared_data
+from tools import runTestClass, robust_path as get_shared_data
 
 class Test(interface):
     """a simple unittest class for distance matrix"""

stat_tool/test/test_mixture.py

@@ -9,9 +9,7 @@
 from openalea.stat_tool.estimate import Estimate
 
 from tools import interface
-from tools import runTestClass
-
-from openalea.stat_tool import get_shared_data
+from tools import runTestClass, robust_path as get_shared_data
 
 class Test(interface):
     """a simple unittest class"""

stat_tool/test/test_multivariate_mixture_functional.py

@@ -23,7 +23,7 @@ def test1():
     d23 = Poisson(0, 0.2)
 
     m = _MultivariateMixture([0.1, 0.2, 0.7], [[d11, d21], [d12, d22], [d13, d23]])
-    print m
+    print(m)
 
     #m2 = _MultivariateMixture("mixture_mv1.mixt")
     #print m2
@@ -34,22 +34,22 @@ def test1():
     #m = _MultivariateMixture("mixture_mv_nonparam.mixt")
    # print m
 
-    print "Simulation de melanges multivaries : "
+    print("Simulation de melanges multivaries : ")
     v = m.simulate(5000)
-    print v
+    print(v)
 
     Plot(m, variable=1, Title="Simulated mixture")
 
-    print "Estimation de melanges multivaries ", \
+    print("Estimation de melanges multivaries ")
     #    "d'apres un modele initial : "
     m_estim_model = v.mixture_estimation(m, 100,  [True, True])
 
     extracted_mixture = m_estim_model.extract_mixture(1)
     extracted_mixture.old_plot(variable=1, Title="Marginal distribution")
     Plot(m_estim_model, variable = 1, Title="Estimated mixture")
 
-    print "Estimation de melanges multivaries ", \
-        "d'apres un nombre de composantes : "
+    print("Estimation de melanges multivaries ", 
+        "d'apres un nombre de composantes : ")
 
     m_estim_nbcomp = v.mixture_estimation(2, 100, [True, True])
 

stat_tool/test/test_output.py

@@ -11,9 +11,8 @@
 from openalea.stat_tool.output import Plot, Display
 from openalea.stat_tool.plot import DISABLE_PLOT
 
-from tools import runTestClass
+from tools import runTestClass, robust_path as get_shared_data
 
-from openalea.stat_tool import get_shared_data
 
 class Test:
     """a simple unittest class"""

stat_tool/test/test_plot.py

@@ -4,6 +4,7 @@
 from openalea.stat_tool import _stat_tool
 from openalea.stat_tool.plot import get_plotter, gnuplot 
 from openalea.stat_tool.plot import DISABLE_PLOT
+DISABLE_PLOT = True
 
 from tools import runTestClass
 

stat_tool/test/test_vectors.py

@@ -9,9 +9,8 @@
 from openalea.stat_tool.enums import variance_type
 
 from tools import interface
-from tools import runTestClass
+from tools import runTestClass, robust_path as get_shared_data
 
-from openalea.stat_tool import get_shared_data
 
 class Test(interface):
     """a simple unittest class

stat_tool/test/test_vectors_functional.py

@@ -18,12 +18,18 @@
 """
 __version__ = "$Id$"
 
-from openalea.stat_tool.vectors import Vectors, \
-    VarianceAnalysis, ContingencyTable
+from openalea.stat_tool.vectors import (
+    Vectors, 
+    VarianceAnalysis, 
+    ContingencyTable
+)
 from openalea.stat_tool.data_transform import ValueSelect
 from openalea.stat_tool.regression import Regression
-from openalea.stat_tool.data_transform import ExtractHistogram, \
-     SelectVariable, ExtractDistribution
+from openalea.stat_tool.data_transform import (
+    ExtractHistogram, 
+    SelectVariable, 
+    ExtractDistribution
+)
 from openalea.stat_tool.comparison import Compare
 from openalea.stat_tool.estimate import Estimate
 from openalea.stat_tool.output import Display, Plot
@@ -72,22 +78,22 @@ def test():
     Plot(ExtractHistogram(vec11, 5), ExtractHistogram(vec12, 5),
         ExtractHistogram(vec13, 5))
 
-    mixt20 = Estimate(ExtractHistogram(vec10, 2), \
-                      "MIXTURE", "NB", "NB", "NB", "NB", \
+    mixt20 = Estimate(ExtractHistogram(vec10, 2), 
+                      "MIXTURE", "NB", "NB", "NB", "NB", 
                       NbComponent="Estimated")
     Display(mixt20)
 
     Plot(mixt20)
     Plot(ExtractDistribution(mixt20, "Mixture"))
 
-    _mixt21 = Estimate(ExtractHistogram(vec10, 5), \
-                       "MIXTURE", "NB", "NB", "NB", "NB", \
+    _mixt21 = Estimate(ExtractHistogram(vec10, 5), 
+                       "MIXTURE", "NB", "NB", "NB", "NB", 
                        NbComponent="Estimated")
 
     vec9596 = ValueSelect(vec10, 1, 1995, 1996)
 
-    Plot(ExtractHistogram(ValueSelect(vec9596, 4, 1), 6), \
-         ExtractHistogram(ValueSelect(vec9596, 4, 2), 6), \
+    Plot(ExtractHistogram(ValueSelect(vec9596, 4, 1), 6), 
+         ExtractHistogram(ValueSelect(vec9596, 4, 2), 6), 
          ExtractHistogram(ValueSelect(vec9596, 4, 3, 4), 6))
 
     # linear regression

stat_tool/test/tools.py

@@ -5,12 +5,17 @@
 """
 __version__ = "$Id$"
 
+import os
+
 
 from openalea.stat_tool import Simulate
 from openalea.stat_tool.plot import DISABLE_PLOT
-import os
 from openalea.stat_tool.output import Display, Save
+DISABLE_PLOT=True
 
+from pathlib import Path
+from openalea.stat_tool import get_shared_data, get_shared_data_path
+import openalea.stat_tool as st
 
 def runTestClass(myclass):
     functions = [x for x in dir(myclass) if x.startswith('test')]
@@ -205,3 +210,15 @@ def test_extract(self):
     def test_extract_data(self):
         raise NotImplementedError()
 
+
+def robust_path(filename):
+    p = get_shared_data_path(st)
+    if p is not None:
+        # module in develop mode?
+        return get_shared_data(filename)
+
+    p = Path(st.__path__[0])
+    if 'src' in str(p):
+        root_pkg = p/'../../..'
+        data = get_shared_data_path(root_pkg)
+        return os.path.join(data,filename)