diff --git a/GPy/core/parameterization/parameterized.py b/GPy/core/parameterization/parameterized.py index 112af0fa..5aa95695 100644 --- a/GPy/core/parameterization/parameterized.py +++ b/GPy/core/parameterization/parameterized.py @@ -74,7 +74,7 @@ class Parameterized(Parameterizable): # Metaclass for parameters changed after init. # This makes sure, that parameters changed will always be called after __init__ # **Never** call parameters_changed() yourself - #This is ignored in Python 3 -- you need to put the meta class in the function definition. + #This is ignored in Python 3 -- you need to put the meta class in the function definition. #__metaclass__ = ParametersChangedMeta #The six module is used to support both Python 2 and 3 simultaneously #=========================================================================== @@ -316,7 +316,7 @@ class Parameterized(Parameterizable): param[:] = val; return except AttributeError: pass - object.__setattr__(self, name, val); + return object.__setattr__(self, name, val); #=========================================================================== # Pickling diff --git a/GPy/kern/_src/kern.py b/GPy/kern/_src/kern.py index 531137ae..924694e9 100644 --- a/GPy/kern/_src/kern.py +++ b/GPy/kern/_src/kern.py @@ -70,6 +70,9 @@ class Kern(Parameterized): """ Compute the kernel function. + .. math:: + K_{ij} = k(X_i, X_j) + :param X: the first set of inputs to the kernel :param X2: (optional) the second set of arguments to the kernel. If X2 is None, this is passed throgh to the 'part' object, which @@ -77,24 +80,64 @@ class Kern(Parameterized): """ raise NotImplementedError def Kdiag(self, X): + """ + The diagonal of the kernel matrix K + + .. math:: + Kdiag_{i} = k(X_i, X_i) + """ raise NotImplementedError def psi0(self, Z, variational_posterior): + """ + .. math:: + \psi_0 = \sum_{i=0}^{n}E_{q(X)}[k(X_i, X_i)] + """ return self.psicomp.psicomputations(self, Z, variational_posterior)[0] def psi1(self, Z, variational_posterior): + """ + .. math:: + \psi_1^{n,m} = E_{q(X)}[k(X_n, Z_m)] + """ return self.psicomp.psicomputations(self, Z, variational_posterior)[1] def psi2(self, Z, variational_posterior): + """ + .. math:: + \psi_2^{m,m'} = \sum_{i=0}^{n}E_{q(X)}[ k(Z_m, X_i) k(X_i, Z_{m'})] + """ return self.psicomp.psicomputations(self, Z, variational_posterior, return_psi2_n=False)[2] def psi2n(self, Z, variational_posterior): + """ + .. math:: + \psi_2^{n,m,m'} = E_{q(X)}[ k(Z_m, X_n) k(X_n, Z_{m'})] + + Thus, we do not sum out n, compared to psi2 + """ return self.psicomp.psicomputations(self, Z, variational_posterior, return_psi2_n=True)[2] def gradients_X(self, dL_dK, X, X2): + """ + .. math:: + + \\frac{\partial L}{\partial X} = \\frac{\partial L}{\partial K}\\frac{\partial K}{\partial X} + """ raise NotImplementedError def gradients_X_X2(self, dL_dK, X, X2): return self.gradients_X(dL_dK, X, X2), self.gradients_X(dL_dK.T, X2, X) def gradients_XX(self, dL_dK, X, X2): + """ + .. math:: + + \\frac{\partial^2 L}{\partial X\partial X_2} = \\frac{\partial L}{\partial K}\\frac{\partial^2 K}{\partial X\partial X_2} + """ raise(NotImplementedError, "This is the second derivative of K wrt X and X2, and not implemented for this kernel") def gradients_XX_diag(self, dL_dKdiag, X): + """ + The diagonal of the second derivative w.r.t. X and X2 + """ raise(NotImplementedError, "This is the diagonal of the second derivative of K wrt X and X2, and not implemented for this kernel") def gradients_X_diag(self, dL_dKdiag, X): + """ + The diagonal of the derivative w.r.t. X + """ raise NotImplementedError def update_gradients_diag(self, dL_dKdiag, X): @@ -110,11 +153,17 @@ class Kern(Parameterized): Set the gradients of all parameters when doing inference with uncertain inputs, using expectations of the kernel. - The esential maths is + The essential maths is - dL_d{theta_i} = dL_dpsi0 * dpsi0_d{theta_i} + - dL_dpsi1 * dpsi1_d{theta_i} + - dL_dpsi2 * dpsi2_d{theta_i} + .. math:: + + \\frac{\partial L}{\partial \\theta_i} & = \\frac{\partial L}{\partial \psi_0}\\frac{\partial \psi_0}{\partial \\theta_i}\\ + & \quad + \\frac{\partial L}{\partial \psi_1}\\frac{\partial \psi_1}{\partial \\theta_i}\\ + & \quad + \\frac{\partial L}{\partial \psi_2}\\frac{\partial \psi_2}{\partial \\theta_i} + + Thus, we push the different derivatives through the gradients of the psi + statistics. Be sure to set the gradients for all kernel + parameters here. """ dtheta = self.psicomp.psiDerivativecomputations(self, dL_dpsi0, dL_dpsi1, dL_dpsi2, Z, variational_posterior)[0] self.gradient[:] = dtheta diff --git a/GPy/kern/_src/kernel_slice_operations.py b/GPy/kern/_src/kernel_slice_operations.py index f274eef3..719d6b56 100644 --- a/GPy/kern/_src/kernel_slice_operations.py +++ b/GPy/kern/_src/kernel_slice_operations.py @@ -1,7 +1,11 @@ ''' Created on 11 Mar 2014 -@author: maxz +@author: @mzwiessele + +This module provides a meta class for the kernels. The meta class is for +slicing the inputs (X, X2) for the kernels, before K (or any other method involving X) +gets calls. The `active_dims` of a kernel decide which dimensions the kernel works on. ''' from ...core.parameterization.parameterized import ParametersChangedMeta import numpy as np diff --git a/GPy/kern/_src/linear.py b/GPy/kern/_src/linear.py index 1a9793b1..0a582ac8 100644 --- a/GPy/kern/_src/linear.py +++ b/GPy/kern/_src/linear.py @@ -17,7 +17,7 @@ class Linear(Kern): .. math:: - k(x,y) = \sum_{i=1}^input_dim \sigma^2_i x_iy_i + k(x,y) = \sum_{i=1}^{\\text{input_dim}} \sigma^2_i x_iy_i :param input_dim: the number of input dimensions :type input_dim: int diff --git a/GPy/kern/_src/stationary.py b/GPy/kern/_src/stationary.py index ab1ec282..d5f26798 100644 --- a/GPy/kern/_src/stationary.py +++ b/GPy/kern/_src/stationary.py @@ -25,13 +25,16 @@ class Stationary(Kern): Stationary covariance fucntion depend only on r, where r is defined as - r = \sqrt{ \sum_{q=1}^Q (x_q - x'_q)^2 } + .. math:: + r(x, x') = \\sqrt{ \\sum_{q=1}^Q (x_q - x'_q)^2 } The covariance function k(x, x' can then be written k(r). In this implementation, r is scaled by the lengthscales parameter(s): - r = \sqrt{ \sum_{q=1}^Q \frac{(x_q - x'_q)^2}{\ell_q^2} }. + .. math:: + + r(x, x') = \\sqrt{ \\sum_{q=1}^Q \\frac{(x_q - x'_q)^2}{\ell_q^2} }. By default, there's only one lengthscale: seaprate lengthscales for each dimension can be enables by setting ARD=True. @@ -39,11 +42,12 @@ class Stationary(Kern): To implement a stationary covariance function using this class, one need only define the covariance function k(r), and it derivative. - ... - def K_of_r(self, r): - return foo - def dK_dr(self, r): - return bar + ``` + def K_of_r(self, r): + return foo + def dK_dr(self, r): + return bar + ``` The lengthscale(s) and variance parameters are added to the structure automatically. @@ -128,7 +132,8 @@ class Stationary(Kern): """ Efficiently compute the scaled distance, r. - r = \sqrt( \sum_{q=1}^Q (x_q - x'q)^2/l_q^2 ) + ..math:: + r = \sqrt( \sum_{q=1}^Q (x_q - x'q)^2/l_q^2 ) Note that if thre is only one lengthscale, l comes outside the sum. In this case we compute the unscaled distance first (in a separate @@ -321,7 +326,7 @@ class OU(Stationary): .. math:: - k(r) = \\sigma^2 \exp(- r) \\ \\ \\ \\ \\text{ where } r = \sqrt{\sum_{i=1}^input_dim \\frac{(x_i-y_i)^2}{\ell_i^2} } + k(r) = \\sigma^2 \exp(- r) \\ \\ \\ \\ \\text{ where } r = \sqrt{\sum_{i=1}^{\text{input_dim}} \\frac{(x_i-y_i)^2}{\ell_i^2} } """ @@ -341,7 +346,7 @@ class Matern32(Stationary): .. math:: - k(r) = \\sigma^2 (1 + \\sqrt{3} r) \exp(- \sqrt{3} r) \\ \\ \\ \\ \\text{ where } r = \sqrt{\sum_{i=1}^input_dim \\frac{(x_i-y_i)^2}{\ell_i^2} } + k(r) = \\sigma^2 (1 + \\sqrt{3} r) \exp(- \sqrt{3} r) \\ \\ \\ \\ \\text{ where } r = \sqrt{\sum_{i=1}^{\\text{input_dim}} \\frac{(x_i-y_i)^2}{\ell_i^2} } """ @@ -388,7 +393,7 @@ class Matern52(Stationary): .. math:: k(r) = \sigma^2 (1 + \sqrt{5} r + \\frac53 r^2) \exp(- \sqrt{5} r) - """ + """ def __init__(self, input_dim, variance=1., lengthscale=None, ARD=False, active_dims=None, name='Mat52'): super(Matern52, self).__init__(input_dim, variance, lengthscale, ARD, active_dims, name) diff --git a/GPy/kern/_src/trunclinear.py b/GPy/kern/_src/trunclinear.py index 8c48f134..af90c4a5 100644 --- a/GPy/kern/_src/trunclinear.py +++ b/GPy/kern/_src/trunclinear.py @@ -15,7 +15,7 @@ class TruncLinear(Kern): .. math:: - k(x,y) = \sum_{i=1}^input_dim \sigma^2_i \max(0, x_iy_i - \simga_q) + k(x,y) = \sum_{i=1}^input_dim \sigma^2_i \max(0, x_iy_i - \sigma_q) :param input_dim: the number of input dimensions :type input_dim: int @@ -54,7 +54,7 @@ class TruncLinear(Kern): self.delta = Param('delta', delta) self.add_parameter(self.variances) self.add_parameter(self.delta) - + @Cache_this(limit=2) def K(self, X, X2=None): XX = self.variances*self._product(X, X2) @@ -114,7 +114,7 @@ class TruncLinear_inf(Kern): .. math:: - k(x,y) = \sum_{i=1}^input_dim \sigma^2_i \max(0, x_iy_i - \simga_q) + k(x,y) = \sum_{i=1}^input_dim \sigma^2_i \max(0, x_iy_i - \sigma_q) :param input_dim: the number of input dimensions :type input_dim: int @@ -148,8 +148,8 @@ class TruncLinear_inf(Kern): self.variances = Param('variances', variances, Logexp()) self.add_parameter(self.variances) - - + + # @Cache_this(limit=2) def K(self, X, X2=None): tmp = self._product(X, X2) diff --git a/GPy/testing/gp_tests.py b/GPy/testing/gp_tests.py index 07aa31a3..63345c18 100644 --- a/GPy/testing/gp_tests.py +++ b/GPy/testing/gp_tests.py @@ -88,7 +88,7 @@ class Test(unittest.TestCase): k.randomize() p = Parabola(.3) p.randomize() - Y = p.f(X) + np.random.multivariate_normal(np.zeros(X.shape[0]), k.K(X))[:,None] + np.random.normal(0, .1, (X.shape[0], 1)) + Y = p.f(X) + np.random.multivariate_normal(np.zeros(X.shape[0]), k.K(X)+np.eye(X.shape[0])*1e-8)[:,None] + np.random.normal(0, .1, (X.shape[0], 1)) m = GPy.models.GPRegression(X, Y, mean_function=p) m.randomize() assert(m.checkgrad()) diff --git a/GPy/testing/model_tests.py b/GPy/testing/model_tests.py index 75165c0e..1cfe8b48 100644 --- a/GPy/testing/model_tests.py +++ b/GPy/testing/model_tests.py @@ -62,6 +62,7 @@ class MiscTests(unittest.TestCase): def check_jacobian(self): try: import autograd.numpy as np, autograd as ag, GPy, matplotlib.pyplot as plt + from GPy.models import GradientChecker, GPRegression except: raise self.skipTest("autograd not available to check gradients") def k(X, X2, alpha=1., lengthscale=None): @@ -87,6 +88,20 @@ class MiscTests(unittest.TestCase): np.testing.assert_allclose(ke.gradients_X([[1.]], X, X2), dk(X, X2)) np.testing.assert_allclose(ke.gradients_XX([[1.]], X, X2).sum(0), dkdk(X, X2)) + m = GPRegression(self.X, self.Y) + def f(x): + m.X[:] = x + return m.log_likelihood() + def df(x): + m.X[:] = x + return m.kern.gradients_X(m.grad_dict['dL_dK'], X) + def ddf(x): + m.X[:] = x + return m.kern.gradients_XX(m.grad_dict['dL_dK'], X).sum(0) + gc = GradientChecker(f, df, self.X) + gc2 = GradientChecker(df, ddf, self.X) + assert(gc.checkgrad()) + assert(gc2.checkgrad()) def test_sparse_raw_predict(self): k = GPy.kern.RBF(1) diff --git a/doc/conf.py b/doc/conf.py index 91a6c75b..f63f2a13 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -92,13 +92,17 @@ print "Importing extensions" extensions = ['sphinx.ext.autodoc', #'sphinx.ext.doctest' 'sphinx.ext.viewcode', - 'sphinx.ext.pngmath', + #'sphinx.ext.pngmath', + 'sphinx.ext.mathjax', 'ipython_directive', 'ipython_console_highlighting' #'matplotlib.sphinxext.plot_directive' ] plot_formats = [('png', 80), ('pdf', 50)] +#pngmath_latex_preamble=r'\usepackage[active]{preview}\usepackage{MnSymbol}' # + other custom stuff for inline math, such as non-default math fonts etc. +#pngmath_use_preview=True + print "finished importing" ############################################################################## @@ -218,7 +222,7 @@ exclude_patterns = ['_build'] #show_authors = False # The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' +pygments_style = 'default' # A list of ignored prefixes for module index sorting. #modindex_common_prefix = [] @@ -228,10 +232,10 @@ pygments_style = 'sphinx' # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. -html_theme = 'default' +html_theme = 'alabaster' # This is to revert to the default theme on readthedocs -html_style = '/default.css' +html_style = '/alabaster.css' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the @@ -317,7 +321,7 @@ latex_elements = { #'pointsize': '10pt', # Additional stuff for the LaTeX preamble. - 'preamble': '\\usepackage{MnSymbol}', + 'preamble': '\\usepackage{MnSymbol,amsmath}', } # Grouping the document tree into LaTeX files. List of tuples diff --git a/doc/index.rst b/doc/index.rst index fec4aef1..b8e572a2 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -25,7 +25,7 @@ The code can be found on our `Github project page +ImportError: No module named svigp +/home/maxz/Documents/gpy/doc/GPy.core.rst:65: WARNING: autodoc: failed to import module u'GPy.core.symbolic'; the following exception was raised: +Traceback (most recent call last): + File "/home/maxz/anaconda/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/ext/autodoc.py", line 385, in import_object + __import__(self.modname) + File "/home/maxz/Documents/gpy/GPy/core/symbolic.py", line 10, in from sympy.utilities.lambdify import lambdastr, _imp_namespace, _get_namespace ImportError: No module named lambdify -/home/alans/Work/GPy/GPy/core/parameterization/parameter_core.py:docstring of GPy.core.parameterization.parameter_core.Indexable.unset_priors:1: WARNING: Inline emphasis start-string without end-string. -/home/alans/Work/GPy/GPy/core/parameterization/parameter_core.py:docstring of GPy.core.parameterization.parameter_core.Nameable.hierarchy_name:4: WARNING: Field list ends without a blank line; unexpected unindent. -/home/alans/Work/GPy/GPy/core/parameterization/parameter_core.py:docstring of GPy.core.parameterization.parameter_core.Observable.notify_observers:5: SEVERE: Unexpected section title or transition. - -^^^^^^^^^^^^^^^^ -/home/alans/Work/GPy/GPy/core/parameterization/parameter_core.py:docstring of GPy.core.parameterization.parameter_core.Observable.notify_observers:6: WARNING: Definition list ends without a blank line; unexpected unindent. -/home/alans/Work/GPy/GPy/core/parameterization/parameter_core.py:docstring of GPy.core.parameterization.parameter_core.Parameterizable.traverse:1: WARNING: Inline emphasis start-string without end-string. -/home/alans/Work/GPy/GPy/core/parameterization/parameter_core.py:docstring of GPy.core.parameterization.parameter_core.Parameterizable.traverse:1: WARNING: Inline strong start-string without end-string. -/home/alans/Work/GPy/GPy/core/parameterization/parameterized.py:docstring of GPy.core.parameterization.parameterized.Parameterized:18: ERROR: Unexpected indentation. -/home/alans/Work/GPy/GPy/core/parameterization/parameterized.py:docstring of GPy.core.parameterization.parameterized.Parameterized:20: WARNING: Block quote ends without a blank line; unexpected unindent. -/home/alans/Work/GPy/GPy/core/parameterization/ties_and_remappings.py:docstring of GPy.core.parameterization.ties_and_remappings.Tie:18: SEVERE: Unexpected section title or transition. +/home/maxz/Documents/gpy/GPy/core/parameterization/parameter_core.py:docstring of GPy.core.parameterization.parameter_core.Indexable.unset_priors:1: WARNING: Inline emphasis start-string without end-string. +/home/maxz/Documents/gpy/GPy/core/parameterization/parameter_core.py:docstring of GPy.core.parameterization.parameter_core.Nameable.hierarchy_name:4: WARNING: Field list ends without a blank line; unexpected unindent. +/home/maxz/Documents/gpy/GPy/core/parameterization/parameter_core.py:docstring of GPy.core.parameterization.parameter_core.Parameterizable.traverse:1: WARNING: Inline emphasis start-string without end-string. +/home/maxz/Documents/gpy/GPy/core/parameterization/parameter_core.py:docstring of GPy.core.parameterization.parameter_core.Parameterizable.traverse:1: WARNING: Inline strong start-string without end-string. +/home/maxz/Documents/gpy/GPy/core/parameterization/parameterized.py:docstring of GPy.core.parameterization.parameterized.Parameterized:18: ERROR: Unexpected indentation. +/home/maxz/Documents/gpy/GPy/core/parameterization/parameterized.py:docstring of GPy.core.parameterization.parameterized.Parameterized:20: WARNING: Block quote ends without a blank line; unexpected unindent. +/home/maxz/Documents/gpy/GPy/core/parameterization/ties_and_remappings.py:docstring of GPy.core.parameterization.ties_and_remappings.Tie:18: SEVERE: Unexpected section title or transition. ================================ -/home/alans/Work/GPy/GPy/kern/_src/coregionalize.py:docstring of GPy.kern._src.coregionalize.Coregionalize:5: ERROR: Unexpected indentation. -/home/alans/Work/GPy/doc/GPy.kern._src.rst:73: WARNING: autodoc: failed to import module u'GPy.kern._src.hierarchical'; the following exception was raised: +/home/maxz/Documents/gpy/doc/GPy.examples.rst:50: WARNING: autodoc: failed to import module u'GPy.examples.stochastic'; the following exception was raised: Traceback (most recent call last): - File "/home/alans/anaconda/envs/GPy/lib/python2.7/site-packages/sphinx/ext/autodoc.py", line 335, in import_object + File "/home/maxz/anaconda/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/ext/autodoc.py", line 385, in import_object __import__(self.modname) - File "/home/alans/Work/GPy/GPy/kern/_src/hierarchical.py", line 4, in - from kernpart import Kernpart -ImportError: No module named kernpart -/home/alans/Work/GPy/GPy/kern/_src/independent_outputs.py:docstring of GPy.kern._src.independent_outputs.IndependentOutputs:9: WARNING: Field list ends without a blank line; unexpected unindent. -/home/alans/Work/GPy/GPy/kern/_src/stationary.py:docstring of GPy.kern._src.stationary.Stationary:12: WARNING: Block quote ends without a blank line; unexpected unindent. -/home/alans/Work/GPy/GPy/kern/_src/stationary.py:docstring of GPy.kern._src.stationary.Stationary:22: ERROR: Unexpected indentation. -/home/alans/Work/GPy/GPy/kern/_src/stationary.py:docstring of GPy.kern._src.stationary.Stationary:23: WARNING: Block quote ends without a blank line; unexpected unindent. -/home/alans/Work/GPy/doc/GPy.kern._src.rst:177: WARNING: autodoc: failed to import module u'GPy.kern._src.symbolic'; the following exception was raised: +ImportError: No module named stochastic +/home/maxz/Documents/gpy/doc/GPy.examples.rst:58: WARNING: autodoc: failed to import module u'GPy.examples.tutorials'; the following exception was raised: Traceback (most recent call last): - File "/home/alans/anaconda/envs/GPy/lib/python2.7/site-packages/sphinx/ext/autodoc.py", line 335, in import_object + File "/home/maxz/anaconda/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/ext/autodoc.py", line 385, in import_object __import__(self.modname) - File "/home/alans/Work/GPy/GPy/kern/_src/symbolic.py", line 5, in +ImportError: No module named tutorials +/home/maxz/Documents/gpy/doc/GPy.inference.latent_function_inference.rst:82: WARNING: autodoc: failed to import module u'GPy.inference.latent_function_inference.var_dtc_gpu'; the following exception was raised: +Traceback (most recent call last): + File "/home/maxz/anaconda/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/ext/autodoc.py", line 385, in import_object + __import__(self.modname) +ImportError: No module named var_dtc_gpu +/home/maxz/Documents/gpy/doc/GPy.inference.optimization.rst:42: WARNING: autodoc: failed to import module u'GPy.inference.optimization.sgd'; the following exception was raised: +Traceback (most recent call last): + File "/home/maxz/anaconda/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/ext/autodoc.py", line 385, in import_object + __import__(self.modname) +ImportError: No module named sgd +/home/maxz/Documents/gpy/GPy/kern/_src/coregionalize.py:docstring of GPy.kern._src.coregionalize.Coregionalize:5: ERROR: Unexpected indentation. +/home/maxz/Documents/gpy/doc/GPy.kern._src.rst:73: WARNING: autodoc: failed to import module u'GPy.kern._src.hierarchical'; the following exception was raised: +Traceback (most recent call last): + File "/home/maxz/anaconda/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/ext/autodoc.py", line 385, in import_object + __import__(self.modname) +ImportError: No module named hierarchical +/home/maxz/Documents/gpy/GPy/kern/_src/independent_outputs.py:docstring of GPy.kern._src.independent_outputs.IndependentOutputs:9: WARNING: Field list ends without a blank line; unexpected unindent. +/home/maxz/Documents/gpy/GPy/kern/_src/stationary.py:docstring of GPy.kern._src.stationary.Stationary:24: ERROR: Unexpected indentation. +/home/maxz/Documents/gpy/GPy/kern/_src/stationary.py:docstring of GPy.kern._src.stationary.Stationary:22: WARNING: Inline literal start-string without end-string. +/home/maxz/Documents/gpy/GPy/kern/_src/stationary.py:docstring of GPy.kern._src.stationary.Stationary:25: WARNING: Block quote ends without a blank line; unexpected unindent. +/home/maxz/Documents/gpy/GPy/kern/_src/stationary.py:docstring of GPy.kern._src.stationary.Stationary:27: WARNING: Definition list ends without a blank line; unexpected unindent. +/home/maxz/Documents/gpy/GPy/kern/_src/stationary.py:docstring of GPy.kern._src.stationary.Stationary:27: WARNING: Inline literal start-string without end-string. +/home/maxz/Documents/gpy/GPy/kern/_src/stationary.py:docstring of GPy.kern._src.stationary.Stationary:27: WARNING: Inline interpreted text or phrase reference start-string without end-string. +/home/maxz/Documents/gpy/doc/GPy.kern._src.rst:177: WARNING: autodoc: failed to import module u'GPy.kern._src.symbolic'; the following exception was raised: +Traceback (most recent call last): + File "/home/maxz/anaconda/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/ext/autodoc.py", line 385, in import_object + __import__(self.modname) + File "/home/maxz/Documents/gpy/GPy/kern/_src/symbolic.py", line 5, in from ...core.symbolic import Symbolic_core - File "/home/alans/Work/GPy/GPy/core/symbolic.py", line 10, in + File "/home/maxz/Documents/gpy/GPy/core/symbolic.py", line 10, in from sympy.utilities.lambdify import lambdastr, _imp_namespace, _get_namespace ImportError: No module named lambdify -/home/alans/Work/GPy/GPy/models/gp_kronecker_gaussian_regression.py:docstring of GPy.models.gp_kronecker_gaussian_regression.GPKroneckerGaussianRegression:13: ERROR: Unexpected indentation. -/home/alans/Work/GPy/GPy/models/gp_kronecker_gaussian_regression.py:docstring of GPy.models.gp_kronecker_gaussian_regression.GPKroneckerGaussianRegression:18: WARNING: Block quote ends without a blank line; unexpected unindent. -/home/alans/Work/GPy/GPy/models/gp_var_gauss.py:docstring of GPy.models.gp_var_gauss.GPVariationalGaussianApproximation:9: WARNING: Definition list ends without a blank line; unexpected unindent. -/home/alans/Work/GPy/GPy/models/mrd.py:docstring of GPy.models.mrd.MRD:32: WARNING: Field list ends without a blank line; unexpected unindent. -/home/alans/Work/GPy/GPy/models/mrd.py:docstring of GPy.models.mrd.MRD:32: WARNING: Inline interpreted text or phrase reference start-string without end-string. -/home/alans/Work/GPy/GPy/models/mrd.py:docstring of GPy.models.mrd.MRD:34: WARNING: Definition list ends without a blank line; unexpected unindent. -/home/alans/Work/GPy/GPy/models/sparse_gp_minibatch.py:docstring of GPy.models.sparse_gp_minibatch.SparseGPMiniBatch:2: WARNING: Block quote ends without a blank line; unexpected unindent. -/home/alans/Work/GPy/GPy/plotting/matplot_dep/netpbmfile.py:docstring of GPy.plotting.matplot_dep.netpbmfile.imread:6: SEVERE: Unexpected section title. +/home/maxz/Documents/gpy/GPy/models/gp_kronecker_gaussian_regression.py:docstring of GPy.models.gp_kronecker_gaussian_regression.GPKroneckerGaussianRegression:13: ERROR: Unexpected indentation. +/home/maxz/Documents/gpy/GPy/models/gp_kronecker_gaussian_regression.py:docstring of GPy.models.gp_kronecker_gaussian_regression.GPKroneckerGaussianRegression:18: WARNING: Block quote ends without a blank line; unexpected unindent. +/home/maxz/Documents/gpy/doc/GPy.models.rst:66: WARNING: autodoc: failed to import module u'GPy.models.gp_multioutput_regression'; the following exception was raised: +Traceback (most recent call last): + File "/home/maxz/anaconda/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/ext/autodoc.py", line 385, in import_object + __import__(self.modname) +ImportError: No module named gp_multioutput_regression +/home/maxz/Documents/gpy/GPy/models/gp_var_gauss.py:docstring of GPy.models.gp_var_gauss.GPVariationalGaussianApproximation:9: WARNING: Definition list ends without a blank line; unexpected unindent. +/home/maxz/Documents/gpy/GPy/models/mrd.py:docstring of GPy.models.mrd.MRD:32: WARNING: Field list ends without a blank line; unexpected unindent. +/home/maxz/Documents/gpy/GPy/models/mrd.py:docstring of GPy.models.mrd.MRD:32: WARNING: Inline interpreted text or phrase reference start-string without end-string. +/home/maxz/Documents/gpy/GPy/models/mrd.py:docstring of GPy.models.mrd.MRD:34: WARNING: Definition list ends without a blank line; unexpected unindent. +/home/maxz/Documents/gpy/doc/GPy.models.rst:138: WARNING: autodoc: failed to import module u'GPy.models.sparse_gp_multioutput_regression'; the following exception was raised: +Traceback (most recent call last): + File "/home/maxz/anaconda/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/ext/autodoc.py", line 385, in import_object + __import__(self.modname) +ImportError: No module named sparse_gp_multioutput_regression +/home/maxz/Documents/gpy/doc/GPy.models.rst:178: WARNING: autodoc: failed to import module u'GPy.models.svigp_regression'; the following exception was raised: +Traceback (most recent call last): + File "/home/maxz/anaconda/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/ext/autodoc.py", line 385, in import_object + __import__(self.modname) +ImportError: No module named svigp_regression +/home/maxz/Documents/gpy/GPy/plotting/matplot_dep/netpbmfile.py:docstring of GPy.plotting.matplot_dep.netpbmfile.imread:6: SEVERE: Unexpected section title. Examples -------- -/home/alans/Work/GPy/GPy/plotting/matplot_dep/netpbmfile.py:docstring of GPy.plotting.matplot_dep.netpbmfile.imsave:4: SEVERE: Unexpected section title. +/home/maxz/Documents/gpy/GPy/plotting/matplot_dep/netpbmfile.py:docstring of GPy.plotting.matplot_dep.netpbmfile.imsave:4: SEVERE: Unexpected section title. Examples -------- -/home/alans/Work/GPy/GPy/testing/likelihood_tests.py:docstring of GPy.testing.likelihood_tests.dparam_checkgrad:6: ERROR: Unexpected indentation. -/home/alans/Work/GPy/GPy/testing/likelihood_tests.py:docstring of GPy.testing.likelihood_tests.dparam_checkgrad:7: WARNING: Block quote ends without a blank line; unexpected unindent. -/home/alans/Work/GPy/GPy/testing/likelihood_tests.py:docstring of GPy.testing.likelihood_tests.dparam_partial:7: WARNING: Definition list ends without a blank line; unexpected unindent. -/home/alans/Work/GPy/GPy/testing/likelihood_tests.py:docstring of GPy.testing.likelihood_tests.dparam_partial:9: ERROR: Unexpected indentation. -/home/alans/Work/GPy/GPy/util/datasets.py:docstring of GPy.util.datasets.hapmap3:7: WARNING: Block quote ends without a blank line; unexpected unindent. -/home/alans/Work/GPy/doc/GPy.util.rst:2: SEVERE: Duplicate ID: "module-GPy.util.diag". -/home/alans/Work/GPy/GPy/util/netpbmfile.py:docstring of GPy.util.netpbmfile.imread:6: SEVERE: Unexpected section title. +/home/maxz/Documents/gpy/GPy/testing/likelihood_tests.py:docstring of GPy.testing.likelihood_tests.dparam_checkgrad:6: ERROR: Unexpected indentation. +/home/maxz/Documents/gpy/GPy/testing/likelihood_tests.py:docstring of GPy.testing.likelihood_tests.dparam_checkgrad:7: WARNING: Block quote ends without a blank line; unexpected unindent. +/home/maxz/Documents/gpy/GPy/testing/likelihood_tests.py:docstring of GPy.testing.likelihood_tests.dparam_partial:7: WARNING: Definition list ends without a blank line; unexpected unindent. +/home/maxz/Documents/gpy/GPy/testing/likelihood_tests.py:docstring of GPy.testing.likelihood_tests.dparam_partial:9: ERROR: Unexpected indentation. +docstring of GPy.util.datasets.hapmap3:7: WARNING: Block quote ends without a blank line; unexpected unindent. +/home/maxz/Documents/gpy/doc/GPy.util.rst:74: WARNING: autodoc: failed to import module u'GPy.util.erfcx'; the following exception was raised: +Traceback (most recent call last): + File "/home/maxz/anaconda/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/ext/autodoc.py", line 385, in import_object + __import__(self.modname) +ImportError: No module named erfcx +/home/maxz/Documents/gpy/doc/GPy.util.rst:146: WARNING: autodoc: failed to import module u'GPy.util.mpi'; the following exception was raised: +Traceback (most recent call last): + File "/home/maxz/anaconda/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/ext/autodoc.py", line 385, in import_object + __import__(self.modname) +ImportError: No module named mpi +/home/maxz/Documents/gpy/GPy/util/netpbmfile.py:docstring of GPy.util.netpbmfile.imread:6: SEVERE: Unexpected section title. Examples -------- -/home/alans/Work/GPy/GPy/util/netpbmfile.py:docstring of GPy.util.netpbmfile.imsave:4: SEVERE: Unexpected section title. +/home/maxz/Documents/gpy/GPy/util/netpbmfile.py:docstring of GPy.util.netpbmfile.imsave:4: SEVERE: Unexpected section title. Examples -------- -/home/alans/Work/GPy/doc/GPy.util.rst:2: SEVERE: Duplicate ID: "module-GPy.util.subarray_and_sorting". -/home/alans/Work/GPy/GPy/util/subarray_and_sorting.py:docstring of GPy.util.subarray_and_sorting.common_subarrays:8: ERROR: Unexpected indentation. -/home/alans/Work/GPy/GPy/util/subarray_and_sorting.py:docstring of GPy.util.subarray_and_sorting.common_subarrays:11: SEVERE: Unexpected section title. +/home/maxz/Documents/gpy/doc/GPy.util.rst:2: SEVERE: Duplicate ID: "module-GPy.util.subarray_and_sorting". +/home/maxz/Documents/gpy/GPy/util/subarray_and_sorting.py:docstring of GPy.util.subarray_and_sorting.common_subarrays:8: ERROR: Unexpected indentation. +/home/maxz/Documents/gpy/GPy/util/subarray_and_sorting.py:docstring of GPy.util.subarray_and_sorting.common_subarrays:11: SEVERE: Unexpected section title. Examples: ========= -/home/alans/Work/GPy/GPy/util/subarray_and_sorting.py:docstring of GPy.util.subarray_and_sorting.common_subarrays:19: ERROR: Unexpected indentation. -/home/alans/Work/GPy/GPy/util/subarray_and_sorting.py:docstring of GPy.util.subarray_and_sorting.common_subarrays:21: WARNING: Block quote ends without a blank line; unexpected unindent. -/home/alans/Work/GPy/doc/installation.rst:22: ERROR: Unexpected indentation. -/home/alans/Work/GPy/doc/installation.rst:27: ERROR: Unexpected indentation. -/home/alans/Work/GPy/doc/tuto_creating_new_kernels.rst:58: WARNING: Inline literal start-string without end-string. -/home/alans/Work/GPy/doc/tuto_creating_new_models.rst:24: ERROR: Unknown target name: "parameterized". -/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:83: WARNING: Title underline too short. +/home/maxz/Documents/gpy/GPy/util/subarray_and_sorting.py:docstring of GPy.util.subarray_and_sorting.common_subarrays:19: ERROR: Unexpected indentation. +/home/maxz/Documents/gpy/GPy/util/subarray_and_sorting.py:docstring of GPy.util.subarray_and_sorting.common_subarrays:21: WARNING: Block quote ends without a blank line; unexpected unindent. +/home/maxz/Documents/gpy/GPy/util/block_matrices.py:docstring of GPy.util.block_matrices.block_dot:3: ERROR: Undefined substitution referenced: "A11.B11|B12.B12". +/home/maxz/Documents/gpy/GPy/util/block_matrices.py:docstring of GPy.util.block_matrices.block_dot:3: ERROR: Undefined substitution referenced: "A21.B21|A22.B22". +/home/maxz/Documents/gpy/doc/installation.rst:22: ERROR: Unexpected indentation. +/home/maxz/Documents/gpy/doc/installation.rst:27: ERROR: Unexpected indentation. +/home/maxz/Documents/gpy/doc/tuto_creating_new_kernels.rst:58: WARNING: Inline literal start-string without end-string. +/home/maxz/Documents/gpy/doc/tuto_creating_new_models.rst:24: ERROR: Unknown target name: "parameterized". +/home/maxz/Documents/gpy/doc/tuto_interacting_with_models.rst:83: WARNING: Title underline too short. Interacting with Parameters: ======================= -/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:83: WARNING: Title underline too short. +/home/maxz/Documents/gpy/doc/tuto_interacting_with_models.rst:83: WARNING: Title underline too short. Interacting with Parameters: ======================= -/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:109: WARNING: Title underline too short. +/home/maxz/Documents/gpy/doc/tuto_interacting_with_models.rst:109: WARNING: Title underline too short. Regular expressions ---------------- -/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:164: WARNING: Title underline too short. +/home/maxz/Documents/gpy/doc/tuto_interacting_with_models.rst:164: WARNING: Title underline too short. Setting and fetching parameters `parameter_array` ------------------------------------------ -/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:164: WARNING: Title underline too short. +/home/maxz/Documents/gpy/doc/tuto_interacting_with_models.rst:164: WARNING: Title underline too short. Setting and fetching parameters `parameter_array` ------------------------------------------ -/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:220: WARNING: Title underline too short. +/home/maxz/Documents/gpy/doc/tuto_interacting_with_models.rst:220: WARNING: Title underline too short. Getting the model parameter's gradients ============================ -/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:220: WARNING: Title underline too short. +/home/maxz/Documents/gpy/doc/tuto_interacting_with_models.rst:220: WARNING: Title underline too short. Getting the model parameter's gradients ============================ -/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:236: WARNING: Title underline too short. +/home/maxz/Documents/gpy/doc/tuto_interacting_with_models.rst:236: WARNING: Title underline too short. Adjusting the model's constraints ================================ -/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:236: WARNING: Title underline too short. +/home/maxz/Documents/gpy/doc/tuto_interacting_with_models.rst:236: WARNING: Title underline too short. Adjusting the model's constraints ================================ -/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:287: WARNING: Title underline too short. +/home/maxz/Documents/gpy/doc/tuto_interacting_with_models.rst:287: WARNING: Title underline too short. Available Constraints ============== -/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:287: WARNING: Title underline too short. +/home/maxz/Documents/gpy/doc/tuto_interacting_with_models.rst:287: WARNING: Title underline too short. Available Constraints ============== -/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:299: WARNING: Title underline too short. +/home/maxz/Documents/gpy/doc/tuto_interacting_with_models.rst:299: WARNING: Title underline too short. Tying Parameters ============ -/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:299: WARNING: Title underline too short. +/home/maxz/Documents/gpy/doc/tuto_interacting_with_models.rst:299: WARNING: Title underline too short. Tying Parameters ============ -/home/alans/Work/GPy/doc/tuto_parameterized.rst:3: WARNING: Title overline too short. +/home/maxz/Documents/gpy/doc/tuto_parameterized.rst:3: WARNING: Title overline too short. ******************* Parameterization handling ******************* -/home/alans/Work/GPy/doc/tuto_parameterized.rst:10: WARNING: Title underline too short. +/home/maxz/Documents/gpy/doc/tuto_parameterized.rst:10: WARNING: Title underline too short. Parameter handles ============== -/home/alans/Work/GPy/doc/tuto_parameterized.rst:16: WARNING: Title underline too short. +/home/maxz/Documents/gpy/doc/tuto_parameterized.rst:16: WARNING: Title underline too short. :py:class:`~GPy.core.parameterization.parameterized.Parameterized` ========== -/home/alans/Work/GPy/doc/tuto_parameterized.rst:16: WARNING: Title underline too short. +/home/maxz/Documents/gpy/doc/tuto_parameterized.rst:16: WARNING: Title underline too short. :py:class:`~GPy.core.parameterization.parameterized.Parameterized` ========== -/home/alans/Work/GPy/doc/tuto_parameterized.rst:21: WARNING: Title underline too short. +/home/maxz/Documents/gpy/doc/tuto_parameterized.rst:21: WARNING: Title underline too short. :py:class:`~GPy.core.parameterization.param.Param` =========== -/home/alans/Work/GPy/doc/tuto_parameterized.rst:21: WARNING: Title underline too short. +/home/maxz/Documents/gpy/doc/tuto_parameterized.rst:21: WARNING: Title underline too short. :py:class:`~GPy.core.parameterization.param.Param` =========== -/home/alans/Work/GPy/doc/installation.rst:: WARNING: document isn't included in any toctree -/home/alans/Work/GPy/doc/kernel_implementation.rst:: WARNING: document isn't included in any toctree -/home/alans/Work/GPy/doc/modules.rst:: WARNING: document isn't included in any toctree -/home/alans/Work/GPy/doc/tuto_GP_regression.rst:: WARNING: document isn't included in any toctree -/home/alans/Work/GPy/doc/tuto_creating_new_kernels.rst:: WARNING: document isn't included in any toctree -/home/alans/Work/GPy/doc/tuto_creating_new_models.rst:: WARNING: document isn't included in any toctree -/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:: WARNING: document isn't included in any toctree -/home/alans/Work/GPy/doc/tuto_kernel_overview.rst:: WARNING: document isn't included in any toctree -/home/alans/Work/GPy/doc/tuto_parameterized.rst:: WARNING: document isn't included in any toctree -WARNING: dvipng command 'dvipng' cannot be run (needed for math display), check the pngmath_dvipng setting -/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:336: WARNING: undefined label: creating_new_kernels (if the link has no caption the label must precede a section header) -WARNING: html_static_path entry u'/home/alans/Work/GPy/doc/_static' does not exist +/home/maxz/Documents/gpy/doc/installation.rst:: WARNING: document isn't included in any toctree +/home/maxz/Documents/gpy/doc/kernel_implementation.rst:: WARNING: document isn't included in any toctree +/home/maxz/Documents/gpy/doc/modules.rst:: WARNING: document isn't included in any toctree +/home/maxz/Documents/gpy/doc/tuto_GP_regression.rst:: WARNING: document isn't included in any toctree +/home/maxz/Documents/gpy/doc/tuto_creating_new_kernels.rst:: WARNING: document isn't included in any toctree +/home/maxz/Documents/gpy/doc/tuto_creating_new_models.rst:: WARNING: document isn't included in any toctree +/home/maxz/Documents/gpy/doc/tuto_interacting_with_models.rst:: WARNING: document isn't included in any toctree +/home/maxz/Documents/gpy/doc/tuto_kernel_overview.rst:: WARNING: document isn't included in any toctree +/home/maxz/Documents/gpy/doc/tuto_parameterized.rst:: WARNING: document isn't included in any toctree +/home/maxz/Documents/gpy/doc/tuto_interacting_with_models.rst:336: WARNING: undefined label: creating_new_kernels (if the link has no caption the label must precede a section header)