diff --git a/AUTHORS.txt b/AUTHORS.txt index a6c2f7bc..08ee8401 100644 --- a/AUTHORS.txt +++ b/AUTHORS.txt @@ -1 +1 @@ -[Humans](https://github.com/SheffieldML/GPy/graphs/contributors) \ No newline at end of file +[GPy Authors](https://github.com/SheffieldML/GPy/graphs/contributors) \ No newline at end of file diff --git a/GPy/__version__.py b/GPy/__version__.py index 8f002e6a..8cce3f28 100644 --- a/GPy/__version__.py +++ b/GPy/__version__.py @@ -1 +1 @@ -__version__ = "0.8.8dev3" +__version__ = "0.8.8dev5" diff --git a/GPy/examples/coreg_example.py b/GPy/examples/coreg_example.py deleted file mode 100644 index 3afeb9fb..00000000 --- a/GPy/examples/coreg_example.py +++ /dev/null @@ -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) - -""" diff --git a/doc/source/conf.py b/doc/source/conf.py index 68d0c2a8..e023b70c 100644 --- a/doc/source/conf.py +++ b/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 diff --git a/setup.cfg b/setup.cfg index 70651dc0..d7da653a 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.8.8dev3 +current_version = 0.8.8 tag = True commit = True diff --git a/setup.py b/setup.py index ed7e8296..1d4e7321 100644 --- a/setup.py +++ b/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)