[holy] example was run in examples

AUTHORS.txt

@@ -1 +1 @@
-[Humans](https://github.com/SheffieldML/GPy/graphs/contributors)
+[GPy Authors](https://github.com/SheffieldML/GPy/graphs/contributors)

GPy/__version__.py

@@ -1 +1 @@
-__version__ = "0.8.8dev3"
+__version__ = "0.8.8dev5"

GPy/examples/coreg_example.py

@@ -1,89 +0,0 @@
-# Copyright (c) 2012-2014, GPy authors (see AUTHORS.txt).
-# Licensed under the BSD 3-clause license (see LICENSE.txt)
-
-import numpy as np
-try:
-    from matplotlib import pyplot as pb
-except:
-    pass
-import GPy
-pb.ion()
-pb.close('all')
-
-X1 = np.arange(3)[:,None]
-X2 = np.arange(4)[:,None]
-I1 = np.zeros_like(X1)
-I2 = np.ones_like(X2)
-
-_X = np.vstack([ X1, X2 ])
-_I = np.vstack([ I1, I2 ])
-
-X = np.hstack([ _X, _I ])
-
-Y1 = np.sin(X1/8.)
-Y2 = np.cos(X2/8.)
-
-Bias = GPy.kern.Bias(1,active_dims=[0])
-Coreg = GPy.kern.Coregionalize(1,2,active_dims=[1])
-K = Bias.prod(Coreg,name='X')
-
-#K.coregion.W = 0
-#print K.coregion.W
-#print Bias.K(_X,_X)
-#print K.K(X,X)
-#pb.matshow(K.K(X,X))
-
-Mlist = [GPy.kern.Matern32(1,lengthscale=20.,name="Mat")]
-kern = GPy.util.multioutput.LCM(input_dim=1,num_outputs=2,kernels_list=Mlist,name='H')
-kern.B.W = 0
-kern.B.kappa = 1.
-#kern.B.W.fix()
-#kern.B.kappa.fix()
-#m = GPy.models.GPCoregionalizedRegression(X_list=[X1,X2], Y_list=[Y1,Y2], kernel=kern)
-
-
-Z1 = np.array([1.5,2.5])[:,None]
-
-m = GPy.models.SparseGPCoregionalizedRegression(X_list=[X1], Y_list=[Y1], Z_list = [Z1], kernel=kern)
-#m.optimize()
-m.checkgrad(verbose=1)
-
-"""
-fig = pb.figure()
-ax0 = fig.add_subplot(211)
-ax1 = fig.add_subplot(212)
-slices = GPy.util.multioutput.get_slices([Y1,Y2])
-m.plot(fixed_inputs=[(1,0)],which_data_rows=slices[0],ax=ax0)
-#m.plot(fixed_inputs=[(1,1)],which_data_rows=slices[1],ax=ax1)
-"""
-
-
-
-"""
-
-X1 = 100 * np.random.rand(100)[:,None]
-X2 = 100 * np.random.rand(100)[:,None]
-#X1.sort()
-#X2.sort()
-
-Y1 = np.sin(X1/10.) + np.random.rand(100)[:,None]
-Y2 = np.cos(X2/10.) + np.random.rand(100)[:,None]
-
-
-
-
-Mlist = [GPy.kern.Matern32(1,lengthscale=20.,name="Mat")]
-kern = GPy.util.multioutput.LCM(input_dim=1,num_outputs=12,kernels_list=Mlist,name='H')
-
-
-m = GPy.models.GPCoregionalizedRegression(X_list=[X1,X2], Y_list=[Y1,Y2], kernel=kern)
-m.optimize()
-
-fig = pb.figure()
-ax0 = fig.add_subplot(211)
-ax1 = fig.add_subplot(212)
-slices = GPy.util.multioutput.get_slices([Y1,Y2])
-m.plot(fixed_inputs=[(1,0)],which_data_rows=slices[0],ax=ax0)
-m.plot(fixed_inputs=[(1,1)],which_data_rows=slices[1],ax=ax1)
-
-"""

doc/source/conf.py

@@ -37,22 +37,22 @@ extensions = [
 ]
 
 #----- Autodoc
-#import sys
-#try:
-#    from unittest.mock import MagicMock
-#except:
-#    from mock import Mock as MagicMock
+import sys
+try:
+    from unittest.mock import MagicMock
+except:
+    from mock import Mock as MagicMock
 
-#class Mock(MagicMock):
-#    @classmethod
-#    def __getattr__(cls, name):
-#            return Mock()
+class Mock(MagicMock):
+    @classmethod
+    def __getattr__(cls, name):
+            return Mock()
 
-#MOCK_MODULES = ['scipy.linalg.blas', 'blas', 'scipy.optimize', 'scipy.optimize.linesearch', 'scipy.linalg', 'scipy', 'scipy.special', 'scipy.integrate', 'scipy.io', 'scipy.stats', 'GPy.util.choleskies_cython',
-#                'sympy', 'sympy.utilities.iterables', 'sympy.utilities.lambdify', 'sympy.utilities', 'sympy.utilities.codegen', 'sympy.core.cache', 'sympy.core', 'sympy.parsing', 'sympy.parsing.sympy_parser',
-#                'nose', 'nose.tools']
+MOCK_MODULES = ['scipy.linalg.blas', 'blas', 'scipy.optimize', 'scipy.optimize.linesearch', 'scipy.linalg', 'scipy', 'scipy.special', 'scipy.integrate', 'scipy.io', 'scipy.stats', 'GPy.util.choleskies_cython',
+                'sympy', 'sympy.utilities.iterables', 'sympy.utilities.lambdify', 'sympy.utilities', 'sympy.utilities.codegen', 'sympy.core.cache', 'sympy.core', 'sympy.parsing', 'sympy.parsing.sympy_parser',
+                'nose', 'nose.tools']
 
-#sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
+sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
 
 import sphinx_rtd_theme
 
@@ -182,7 +182,7 @@ html_theme = 'sphinx_rtd_theme'
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+#html_static_path = ['_static']
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.8.8dev3
+current_version = 0.8.8
 tag = True
 commit = True
 

setup.py

@@ -49,8 +49,8 @@ def read_to_rst(fname):
     try:
         import pypandoc
         rstname = "{}.{}".format(os.path.splitext(fname)[0], 'rst')
-        pypandoc.convert(read(fname), 'rst', format='md', outputfile=rstname)
-        return read(rstname)
+        return pypandoc.convert(read(fname), 'rst', format='md')
+        #return read(rstname)
     except ImportError:
         return read(fname)