[doc] some changes to the doc, using mathjax some additions in math

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

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} +
+        .. math::
-                        dL_dpsi1 * dpsi1_d{theta_i} +
+
-                        dL_dpsi2 * dpsi2_d{theta_i}
+            \\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

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

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

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):
+    def K_of_r(self, r):
-          return foo
+        return foo
-      def dK_dr(self, r):
+    def dK_dr(self, r):
-          return bar
+        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)
 

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)

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())

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)

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

doc/index.rst

@@ -25,7 +25,7 @@ The code can be found on our `Github project page <https://github.com/SheffieldM
 Contents:
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 3
    
    GPy
 

doc/log.txt

@@ -1,176 +1,222 @@
-/home/alans/Work/GPy/GPy/__init__.py:docstring of GPy.load:1: WARNING: Inline interpreted text or phrase reference start-string without end-string.
+/home/maxz/Documents/gpy/GPy/__init__.py:docstring of GPy.load:1: WARNING: Inline interpreted text or phrase reference start-string without end-string.
-/home/alans/Work/GPy/GPy/core/gp.py:docstring of GPy.core.gp.GP.optimize:8: ERROR: Unknown interpreted text role "module".
+/home/maxz/Documents/gpy/GPy/core/gp.py:docstring of GPy.core.gp.GP.optimize:8: ERROR: Unknown interpreted text role "module".
-/home/alans/Work/GPy/GPy/core/gp.py:docstring of GPy.core.gp.GP.predictive_gradients:5: ERROR: Unexpected indentation.
+/home/maxz/Documents/gpy/GPy/core/gp.py:docstring of GPy.core.gp.GP.predict_wishard_embedding:6: WARNING: Field list ends without a blank line; unexpected unindent.
-/home/alans/Work/GPy/GPy/core/gp.py:docstring of GPy.core.gp.GP.predictive_gradients:8: WARNING: Block quote ends without a blank line; unexpected unindent.
+/home/maxz/Documents/gpy/GPy/core/gp.py:docstring of GPy.core.gp.GP.predictive_gradients:5: ERROR: Unexpected indentation.
-/home/alans/Work/GPy/GPy/core/model.py:docstring of GPy.core.model.Model.optimize_restarts:29: WARNING: Explicit markup ends without a blank line; unexpected unindent.
+/home/maxz/Documents/gpy/GPy/core/gp.py:docstring of GPy.core.gp.GP.predictive_gradients:10: WARNING: Block quote ends without a blank line; unexpected unindent.
-/home/alans/Work/GPy/doc/GPy.core.rst:65: WARNING: autodoc: failed to import module u'GPy.core.symbolic'; the following exception was raised:
+/home/maxz/Documents/gpy/GPy/core/model.py:docstring of GPy.core.model.Model.optimize_restarts:29: WARNING: Explicit markup ends without a blank line; unexpected unindent.
+/home/maxz/Documents/gpy/doc/GPy.core.rst:57: WARNING: autodoc: failed to import module u'GPy.core.svigp'; 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/core/symbolic.py", line 10, in <module>
+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 <module>
     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/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/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/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/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/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/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/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/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/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/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/alans/Work/GPy/GPy/kern/_src/coregionalize.py:docstring of GPy.kern._src.coregionalize.Coregionalize:5: ERROR: Unexpected indentation.
+/home/maxz/Documents/gpy/doc/GPy.examples.rst:50: WARNING: autodoc: failed to import module u'GPy.examples.stochastic'; the following exception was raised:
-/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:
 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 <module>
+ImportError: No module named stochastic
-    from kernpart import Kernpart
+/home/maxz/Documents/gpy/doc/GPy.examples.rst:58: WARNING: autodoc: failed to import module u'GPy.examples.tutorials'; the following exception was raised:
-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:
 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 <module>
+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 <module>
     from ...core.symbolic import Symbolic_core
-  File "/home/alans/Work/GPy/GPy/core/symbolic.py", line 10, in <module>
+  File "/home/maxz/Documents/gpy/GPy/core/symbolic.py", line 10, in <module>
     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/maxz/Documents/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/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/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/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:
-/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.
+Traceback (most recent call last):
-/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.
+  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
-/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.
+    __import__(self.modname)
-/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.
+ImportError: No module named gp_multioutput_regression
-/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_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/maxz/Documents/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/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/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/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/alans/Work/GPy/GPy/testing/likelihood_tests.py:docstring of GPy.testing.likelihood_tests.dparam_partial:9: ERROR: Unexpected indentation.
+/home/maxz/Documents/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.
+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/maxz/Documents/gpy/doc/GPy.util.rst:74: WARNING: autodoc: failed to import module u'GPy.util.erfcx'; the following exception was raised:
-/home/alans/Work/GPy/GPy/util/netpbmfile.py:docstring of GPy.util.netpbmfile.imread:6: SEVERE: Unexpected section title.
+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/maxz/Documents/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/maxz/Documents/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/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/maxz/Documents/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/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/alans/Work/GPy/doc/installation.rst:22: ERROR: Unexpected indentation.
+/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/alans/Work/GPy/doc/installation.rst:27: ERROR: Unexpected indentation.
+/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/alans/Work/GPy/doc/tuto_creating_new_kernels.rst:58: WARNING: Inline literal start-string without end-string.
+/home/maxz/Documents/gpy/doc/installation.rst:22: ERROR: Unexpected indentation.
-/home/alans/Work/GPy/doc/tuto_creating_new_models.rst:24: ERROR: Unknown target name: "parameterized".
+/home/maxz/Documents/gpy/doc/installation.rst:27: ERROR: Unexpected indentation.
-/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:83: WARNING: Title underline too short.
+/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/maxz/Documents/gpy/doc/installation.rst:: WARNING: document isn't included in any toctree
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+/home/maxz/Documents/gpy/doc/kernel_implementation.rst:: WARNING: document isn't included in any toctree
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+/home/maxz/Documents/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/maxz/Documents/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/maxz/Documents/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/maxz/Documents/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/maxz/Documents/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/maxz/Documents/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
+/home/maxz/Documents/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/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)
-/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