mirror of
https://github.com/SheffieldML/GPy.git
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[doc] some changes to the doc, using mathjax some additions in math
This commit is contained in:
Max Zwiessele
parent
bcc1e7c8d4
commit
6996912184
11 changed files with 244 additions and 121 deletions
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@ -74,7 +74,7 @@ class Parameterized(Parameterizable):
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# Metaclass for parameters changed after init.
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# This makes sure, that parameters changed will always be called after __init__
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# **Never** call parameters_changed() yourself
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#This is ignored in Python 3 -- you need to put the meta class in the function definition.
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#This is ignored in Python 3 -- you need to put the meta class in the function definition.
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#__metaclass__ = ParametersChangedMeta
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#The six module is used to support both Python 2 and 3 simultaneously
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#===========================================================================
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@ -316,7 +316,7 @@ class Parameterized(Parameterizable):
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param[:] = val; return
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except AttributeError:
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pass
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object.__setattr__(self, name, val);
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return object.__setattr__(self, name, val);
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#===========================================================================
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# Pickling
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@ -70,6 +70,9 @@ class Kern(Parameterized):
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"""
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Compute the kernel function.
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.. math::
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K_{ij} = k(X_i, X_j)
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:param X: the first set of inputs to the kernel
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:param X2: (optional) the second set of arguments to the kernel. If X2
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is None, this is passed throgh to the 'part' object, which
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@ -77,24 +80,64 @@ class Kern(Parameterized):
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"""
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raise NotImplementedError
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def Kdiag(self, X):
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"""
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The diagonal of the kernel matrix K
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.. math::
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Kdiag_{i} = k(X_i, X_i)
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"""
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raise NotImplementedError
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def psi0(self, Z, variational_posterior):
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"""
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.. math::
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\psi_0 = \sum_{i=0}^{n}E_{q(X)}[k(X_i, X_i)]
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"""
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return self.psicomp.psicomputations(self, Z, variational_posterior)[0]
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def psi1(self, Z, variational_posterior):
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"""
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.. math::
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\psi_1^{n,m} = E_{q(X)}[k(X_n, Z_m)]
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"""
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return self.psicomp.psicomputations(self, Z, variational_posterior)[1]
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def psi2(self, Z, variational_posterior):
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"""
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.. math::
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\psi_2^{m,m'} = \sum_{i=0}^{n}E_{q(X)}[ k(Z_m, X_i) k(X_i, Z_{m'})]
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"""
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return self.psicomp.psicomputations(self, Z, variational_posterior, return_psi2_n=False)[2]
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def psi2n(self, Z, variational_posterior):
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"""
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.. math::
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\psi_2^{n,m,m'} = E_{q(X)}[ k(Z_m, X_n) k(X_n, Z_{m'})]
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Thus, we do not sum out n, compared to psi2
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"""
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return self.psicomp.psicomputations(self, Z, variational_posterior, return_psi2_n=True)[2]
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def gradients_X(self, dL_dK, X, X2):
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"""
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.. math::
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\\frac{\partial L}{\partial X} = \\frac{\partial L}{\partial K}\\frac{\partial K}{\partial X}
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"""
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raise NotImplementedError
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def gradients_X_X2(self, dL_dK, X, X2):
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return self.gradients_X(dL_dK, X, X2), self.gradients_X(dL_dK.T, X2, X)
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def gradients_XX(self, dL_dK, X, X2):
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"""
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.. math::
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\\frac{\partial^2 L}{\partial X\partial X_2} = \\frac{\partial L}{\partial K}\\frac{\partial^2 K}{\partial X\partial X_2}
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"""
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raise(NotImplementedError, "This is the second derivative of K wrt X and X2, and not implemented for this kernel")
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def gradients_XX_diag(self, dL_dKdiag, X):
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"""
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The diagonal of the second derivative w.r.t. X and X2
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"""
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raise(NotImplementedError, "This is the diagonal of the second derivative of K wrt X and X2, and not implemented for this kernel")
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def gradients_X_diag(self, dL_dKdiag, X):
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"""
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The diagonal of the derivative w.r.t. X
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"""
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raise NotImplementedError
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def update_gradients_diag(self, dL_dKdiag, X):
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@ -110,11 +153,17 @@ class Kern(Parameterized):
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Set the gradients of all parameters when doing inference with
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uncertain inputs, using expectations of the kernel.
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The esential maths is
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The essential maths is
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dL_d{theta_i} = dL_dpsi0 * dpsi0_d{theta_i} +
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dL_dpsi1 * dpsi1_d{theta_i} +
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dL_dpsi2 * dpsi2_d{theta_i}
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.. math::
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\\frac{\partial L}{\partial \\theta_i} & = \\frac{\partial L}{\partial \psi_0}\\frac{\partial \psi_0}{\partial \\theta_i}\\
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& \quad + \\frac{\partial L}{\partial \psi_1}\\frac{\partial \psi_1}{\partial \\theta_i}\\
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& \quad + \\frac{\partial L}{\partial \psi_2}\\frac{\partial \psi_2}{\partial \\theta_i}
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Thus, we push the different derivatives through the gradients of the psi
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statistics. Be sure to set the gradients for all kernel
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parameters here.
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"""
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dtheta = self.psicomp.psiDerivativecomputations(self, dL_dpsi0, dL_dpsi1, dL_dpsi2, Z, variational_posterior)[0]
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self.gradient[:] = dtheta
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@ -1,7 +1,11 @@
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'''
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Created on 11 Mar 2014
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@author: maxz
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@author: @mzwiessele
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This module provides a meta class for the kernels. The meta class is for
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slicing the inputs (X, X2) for the kernels, before K (or any other method involving X)
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gets calls. The `active_dims` of a kernel decide which dimensions the kernel works on.
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'''
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from ...core.parameterization.parameterized import ParametersChangedMeta
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import numpy as np
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@ -17,7 +17,7 @@ class Linear(Kern):
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.. math::
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k(x,y) = \sum_{i=1}^input_dim \sigma^2_i x_iy_i
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k(x,y) = \sum_{i=1}^{\\text{input_dim}} \sigma^2_i x_iy_i
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:param input_dim: the number of input dimensions
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:type input_dim: int
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@ -25,13 +25,16 @@ class Stationary(Kern):
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Stationary covariance fucntion depend only on r, where r is defined as
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r = \sqrt{ \sum_{q=1}^Q (x_q - x'_q)^2 }
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.. math::
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r(x, x') = \\sqrt{ \\sum_{q=1}^Q (x_q - x'_q)^2 }
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The covariance function k(x, x' can then be written k(r).
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In this implementation, r is scaled by the lengthscales parameter(s):
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r = \sqrt{ \sum_{q=1}^Q \frac{(x_q - x'_q)^2}{\ell_q^2} }.
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.. math::
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r(x, x') = \\sqrt{ \\sum_{q=1}^Q \\frac{(x_q - x'_q)^2}{\ell_q^2} }.
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By default, there's only one lengthscale: seaprate lengthscales for each
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dimension can be enables by setting ARD=True.
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@ -39,11 +42,12 @@ class Stationary(Kern):
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To implement a stationary covariance function using this class, one need
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only define the covariance function k(r), and it derivative.
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...
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def K_of_r(self, r):
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return foo
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def dK_dr(self, r):
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return bar
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```
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def K_of_r(self, r):
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return foo
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def dK_dr(self, r):
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return bar
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```
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The lengthscale(s) and variance parameters are added to the structure automatically.
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@ -128,7 +132,8 @@ class Stationary(Kern):
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"""
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Efficiently compute the scaled distance, r.
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r = \sqrt( \sum_{q=1}^Q (x_q - x'q)^2/l_q^2 )
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..math::
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r = \sqrt( \sum_{q=1}^Q (x_q - x'q)^2/l_q^2 )
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Note that if thre is only one lengthscale, l comes outside the sum. In
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this case we compute the unscaled distance first (in a separate
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@ -321,7 +326,7 @@ class OU(Stationary):
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.. math::
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k(r) = \\sigma^2 \exp(- r) \\ \\ \\ \\ \\text{ where } r = \sqrt{\sum_{i=1}^input_dim \\frac{(x_i-y_i)^2}{\ell_i^2} }
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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} }
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"""
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@ -341,7 +346,7 @@ class Matern32(Stationary):
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.. math::
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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} }
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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} }
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"""
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@ -388,7 +393,7 @@ class Matern52(Stationary):
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.. math::
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k(r) = \sigma^2 (1 + \sqrt{5} r + \\frac53 r^2) \exp(- \sqrt{5} r)
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"""
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"""
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def __init__(self, input_dim, variance=1., lengthscale=None, ARD=False, active_dims=None, name='Mat52'):
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super(Matern52, self).__init__(input_dim, variance, lengthscale, ARD, active_dims, name)
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@ -15,7 +15,7 @@ class TruncLinear(Kern):
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.. math::
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k(x,y) = \sum_{i=1}^input_dim \sigma^2_i \max(0, x_iy_i - \simga_q)
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k(x,y) = \sum_{i=1}^input_dim \sigma^2_i \max(0, x_iy_i - \sigma_q)
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:param input_dim: the number of input dimensions
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:type input_dim: int
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@ -54,7 +54,7 @@ class TruncLinear(Kern):
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self.delta = Param('delta', delta)
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self.add_parameter(self.variances)
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self.add_parameter(self.delta)
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@Cache_this(limit=2)
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def K(self, X, X2=None):
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XX = self.variances*self._product(X, X2)
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@ -114,7 +114,7 @@ class TruncLinear_inf(Kern):
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.. math::
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k(x,y) = \sum_{i=1}^input_dim \sigma^2_i \max(0, x_iy_i - \simga_q)
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k(x,y) = \sum_{i=1}^input_dim \sigma^2_i \max(0, x_iy_i - \sigma_q)
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:param input_dim: the number of input dimensions
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:type input_dim: int
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@ -148,8 +148,8 @@ class TruncLinear_inf(Kern):
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self.variances = Param('variances', variances, Logexp())
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self.add_parameter(self.variances)
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# @Cache_this(limit=2)
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def K(self, X, X2=None):
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tmp = self._product(X, X2)
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@ -88,7 +88,7 @@ class Test(unittest.TestCase):
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k.randomize()
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p = Parabola(.3)
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p.randomize()
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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))
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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))
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m = GPy.models.GPRegression(X, Y, mean_function=p)
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m.randomize()
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assert(m.checkgrad())
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@ -62,6 +62,7 @@ class MiscTests(unittest.TestCase):
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def check_jacobian(self):
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try:
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import autograd.numpy as np, autograd as ag, GPy, matplotlib.pyplot as plt
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from GPy.models import GradientChecker, GPRegression
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except:
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raise self.skipTest("autograd not available to check gradients")
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def k(X, X2, alpha=1., lengthscale=None):
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@ -87,6 +88,20 @@ class MiscTests(unittest.TestCase):
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np.testing.assert_allclose(ke.gradients_X([[1.]], X, X2), dk(X, X2))
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np.testing.assert_allclose(ke.gradients_XX([[1.]], X, X2).sum(0), dkdk(X, X2))
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m = GPRegression(self.X, self.Y)
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def f(x):
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m.X[:] = x
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return m.log_likelihood()
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def df(x):
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m.X[:] = x
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return m.kern.gradients_X(m.grad_dict['dL_dK'], X)
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def ddf(x):
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m.X[:] = x
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return m.kern.gradients_XX(m.grad_dict['dL_dK'], X).sum(0)
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gc = GradientChecker(f, df, self.X)
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gc2 = GradientChecker(df, ddf, self.X)
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assert(gc.checkgrad())
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assert(gc2.checkgrad())
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def test_sparse_raw_predict(self):
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k = GPy.kern.RBF(1)
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14
doc/conf.py
14
doc/conf.py
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@ -92,13 +92,17 @@ print "Importing extensions"
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extensions = ['sphinx.ext.autodoc',
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#'sphinx.ext.doctest'
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'sphinx.ext.viewcode',
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'sphinx.ext.pngmath',
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#'sphinx.ext.pngmath',
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'sphinx.ext.mathjax',
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'ipython_directive',
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'ipython_console_highlighting'
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#'matplotlib.sphinxext.plot_directive'
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]
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plot_formats = [('png', 80), ('pdf', 50)]
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#pngmath_latex_preamble=r'\usepackage[active]{preview}\usepackage{MnSymbol}' # + other custom stuff for inline math, such as non-default math fonts etc.
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#pngmath_use_preview=True
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print "finished importing"
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##############################################################################
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@ -218,7 +222,7 @@ exclude_patterns = ['_build']
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#show_authors = False
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# The name of the Pygments (syntax highlighting) style to use.
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pygments_style = 'sphinx'
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pygments_style = 'default'
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# A list of ignored prefixes for module index sorting.
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#modindex_common_prefix = []
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@ -228,10 +232,10 @@ pygments_style = 'sphinx'
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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html_theme = 'default'
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html_theme = 'alabaster'
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# This is to revert to the default theme on readthedocs
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html_style = '/default.css'
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html_style = '/alabaster.css'
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# Theme options are theme-specific and customize the look and feel of a theme
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# further. For a list of options available for each theme, see the
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@ -317,7 +321,7 @@ latex_elements = {
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#'pointsize': '10pt',
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# Additional stuff for the LaTeX preamble.
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'preamble': '\\usepackage{MnSymbol}',
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'preamble': '\\usepackage{MnSymbol,amsmath}',
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}
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# Grouping the document tree into LaTeX files. List of tuples
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@ -25,7 +25,7 @@ The code can be found on our `Github project page <https://github.com/SheffieldM
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Contents:
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.. toctree::
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:maxdepth: 2
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:maxdepth: 3
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GPy
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226
doc/log.txt
226
doc/log.txt
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@ -1,176 +1,222 @@
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/home/alans/Work/GPy/GPy/__init__.py:docstring of GPy.load:1: WARNING: Inline interpreted text or phrase reference start-string without end-string.
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/home/alans/Work/GPy/GPy/core/gp.py:docstring of GPy.core.gp.GP.optimize:8: ERROR: Unknown interpreted text role "module".
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/home/alans/Work/GPy/GPy/core/gp.py:docstring of GPy.core.gp.GP.predictive_gradients:5: ERROR: Unexpected indentation.
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/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.
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/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.
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/home/alans/Work/GPy/doc/GPy.core.rst:65: WARNING: autodoc: failed to import module u'GPy.core.symbolic'; the following exception was raised:
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/home/maxz/Documents/gpy/GPy/__init__.py:docstring of GPy.load:1: WARNING: Inline interpreted text or phrase reference start-string without end-string.
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/home/maxz/Documents/gpy/GPy/core/gp.py:docstring of GPy.core.gp.GP.optimize:8: ERROR: Unknown interpreted text role "module".
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/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.
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/home/maxz/Documents/gpy/GPy/core/gp.py:docstring of GPy.core.gp.GP.predictive_gradients:5: ERROR: Unexpected indentation.
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/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.
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/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.
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/home/maxz/Documents/gpy/doc/GPy.core.rst:57: WARNING: autodoc: failed to import module u'GPy.core.svigp'; the following exception was raised:
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Traceback (most recent call last):
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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/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 <module>
|
||||
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 <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/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".
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/home/maxz/Documents/gpy/doc/installation.rst:22: ERROR: Unexpected indentation.
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/home/maxz/Documents/gpy/doc/installation.rst:27: ERROR: Unexpected indentation.
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/home/maxz/Documents/gpy/doc/tuto_creating_new_kernels.rst:58: WARNING: Inline literal start-string without end-string.
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/home/maxz/Documents/gpy/doc/tuto_creating_new_models.rst:24: ERROR: Unknown target name: "parameterized".
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Interacting with Parameters:
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=======================
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Interacting with Parameters:
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=======================
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Regular expressions
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----------------
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Setting and fetching parameters `parameter_array`
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------------------------------------------
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Setting and fetching parameters `parameter_array`
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------------------------------------------
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Getting the model parameter's gradients
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============================
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Getting the model parameter's gradients
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============================
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/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:236: WARNING: Title underline too short.
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Adjusting the model's constraints
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================================
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/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:236: WARNING: Title underline too short.
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Adjusting the model's constraints
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================================
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Available Constraints
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==============
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Available Constraints
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==============
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/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:299: WARNING: Title underline too short.
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Tying Parameters
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============
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/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:299: WARNING: Title underline too short.
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Tying Parameters
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============
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/home/alans/Work/GPy/doc/tuto_parameterized.rst:3: WARNING: Title overline too short.
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/home/maxz/Documents/gpy/doc/tuto_parameterized.rst:3: WARNING: Title overline too short.
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*******************
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Parameterization handling
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*******************
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/home/alans/Work/GPy/doc/tuto_parameterized.rst:10: WARNING: Title underline too short.
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/home/maxz/Documents/gpy/doc/tuto_parameterized.rst:10: WARNING: Title underline too short.
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Parameter handles
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==============
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/home/alans/Work/GPy/doc/tuto_parameterized.rst:16: WARNING: Title underline too short.
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/home/maxz/Documents/gpy/doc/tuto_parameterized.rst:16: WARNING: Title underline too short.
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:py:class:`~GPy.core.parameterization.parameterized.Parameterized`
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==========
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:py:class:`~GPy.core.parameterization.parameterized.Parameterized`
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==========
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:py:class:`~GPy.core.parameterization.param.Param`
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===========
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:py:class:`~GPy.core.parameterization.param.Param`
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===========
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WARNING: dvipng command 'dvipng' cannot be run (needed for math display), check the pngmath_dvipng setting
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/home/maxz/Documents/gpy/doc/tuto_parameterized.rst:: WARNING: document isn't included in any toctree
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