diff --git a/stat_tool/src/openalea/stat_tool/mixture.py b/stat_tool/src/openalea/stat_tool/mixture.py index 8b2ed58c..dd4e5c29 100644 --- a/stat_tool/src/openalea/stat_tool/mixture.py +++ b/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]) diff --git a/stat_tool/test/test_cluster.py b/stat_tool/test/test_cluster.py index 4ace74b0..f8bda166 100644 --- a/stat_tool/test/test_cluster.py +++ b/stat_tool/test/test_cluster.py @@ -9,11 +9,14 @@ 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: diff --git a/stat_tool/test/test_cluster_and_distance_matrix.py b/stat_tool/test/test_cluster_and_distance_matrix.py index 8c73c382..f2a3bbb2 100644 --- a/stat_tool/test/test_cluster_and_distance_matrix.py +++ b/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')) diff --git a/stat_tool/test/test_comparison.py b/stat_tool/test/test_comparison.py index 40f414b1..84788f04 100644 --- a/stat_tool/test/test_comparison.py +++ b/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""" diff --git a/stat_tool/test/test_compound_functional.py b/stat_tool/test/test_compound_functional.py index d85dcd24..a14ff1d7 100644 --- a/stat_tool/test/test_compound_functional.py +++ b/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(): diff --git a/stat_tool/test/test_convolution.py b/stat_tool/test/test_convolution.py index 455be015..352b146f 100644 --- a/stat_tool/test/test_convolution.py +++ b/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 diff --git a/stat_tool/test/test_data_transform.py b/stat_tool/test/test_data_transform.py index 1029219b..87e953ed 100644 --- a/stat_tool/test/test_data_transform.py +++ b/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 diff --git a/stat_tool/test/test_distance_matrix.py b/stat_tool/test/test_distance_matrix.py index eb73331b..f7eb4e01 100644 --- a/stat_tool/test/test_distance_matrix.py +++ b/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): diff --git a/stat_tool/test/test_distribution.py b/stat_tool/test/test_distribution.py index 7f4f347b..9dfb7018 100644 --- a/stat_tool/test/test_distribution.py +++ b/stat_tool/test/test_distribution.py @@ -3,7 +3,6 @@ __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 @@ -11,8 +10,6 @@ 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 diff --git a/stat_tool/test/test_distribution_functional.py b/stat_tool/test/test_distribution_functional.py index 8b3a2d91..029448c5 100644 --- a/stat_tool/test/test_distribution_functional.py +++ b/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), diff --git a/stat_tool/test/test_error.py b/stat_tool/test/test_error.py index e4c23830..210c9150 100644 --- a/stat_tool/test/test_error.py +++ b/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) diff --git a/stat_tool/test/test_estimate.py b/stat_tool/test/test_estimate.py index 97f828ce..3689a190 100644 --- a/stat_tool/test/test_estimate.py +++ b/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): diff --git a/stat_tool/test/test_histogram.py b/stat_tool/test/test_histogram.py index 90bb1cfc..99b487ae 100644 --- a/stat_tool/test/test_histogram.py +++ b/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__": diff --git a/stat_tool/test/test_matrix.py b/stat_tool/test/test_matrix.py index ece4a79e..ed0a68cd 100644 --- a/stat_tool/test/test_matrix.py +++ b/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""" diff --git a/stat_tool/test/test_mixture.py b/stat_tool/test/test_mixture.py index e04749d5..82a14f9e 100644 --- a/stat_tool/test/test_mixture.py +++ b/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""" diff --git a/stat_tool/test/test_multivariate_mixture_functional.py b/stat_tool/test/test_multivariate_mixture_functional.py index fd43167e..85e32870 100644 --- a/stat_tool/test/test_multivariate_mixture_functional.py +++ b/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 @@ -34,13 +34,13 @@ 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]) @@ -48,8 +48,8 @@ def test1(): 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]) diff --git a/stat_tool/test/test_output.py b/stat_tool/test/test_output.py index 9d57a2ea..49afe50f 100644 --- a/stat_tool/test/test_output.py +++ b/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""" diff --git a/stat_tool/test/test_plot.py b/stat_tool/test/test_plot.py index 9f244381..39a869a6 100644 --- a/stat_tool/test/test_plot.py +++ b/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 diff --git a/stat_tool/test/test_vectors.py b/stat_tool/test/test_vectors.py index 820543b6..8acc47f2 100644 --- a/stat_tool/test/test_vectors.py +++ b/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 diff --git a/stat_tool/test/test_vectors_functional.py b/stat_tool/test/test_vectors_functional.py index 88e64bf8..a7e160af 100644 --- a/stat_tool/test/test_vectors_functional.py +++ b/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 diff --git a/stat_tool/test/tools.py b/stat_tool/test/tools.py index b7769569..3d50dfee 100644 --- a/stat_tool/test/tools.py +++ b/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)