Merge branch 'naniny' into devel

GPy/models.py

@@ -4,20 +4,20 @@ Created on 14 Nov 2013
 @author: maxz
 '''
 
-from _models.bayesian_gplvm import BayesianGPLVM
+from models_modules.bayesian_gplvm import BayesianGPLVM
-from _models.gp_regression import GPRegression
+from models_modules.gp_regression import GPRegression
-from _models.gp_classification import GPClassification#; _gp_classification = gp_classification ; del gp_classification 
+from models_modules.gp_classification import GPClassification#; _gp_classification = gp_classification ; del gp_classification 
-from _models.sparse_gp_regression import SparseGPRegression#; _sparse_gp_regression = sparse_gp_regression ; del sparse_gp_regression 
+from models_modules.sparse_gp_regression import SparseGPRegression#; _sparse_gp_regression = sparse_gp_regression ; del sparse_gp_regression 
-from _models.svigp_regression import SVIGPRegression#; _svigp_regression = svigp_regression ; del svigp_regression 
+from models_modules.svigp_regression import SVIGPRegression#; _svigp_regression = svigp_regression ; del svigp_regression 
-from _models.sparse_gp_classification import SparseGPClassification#; _sparse_gp_classification = sparse_gp_classification ; del sparse_gp_classification 
+from models_modules.sparse_gp_classification import SparseGPClassification#; _sparse_gp_classification = sparse_gp_classification ; del sparse_gp_classification 
-from _models.fitc_classification import FITCClassification#; _fitc_classification = fitc_classification ; del fitc_classification 
+from models_modules.fitc_classification import FITCClassification#; _fitc_classification = fitc_classification ; del fitc_classification 
-from _models.gplvm import GPLVM#; _gplvm = gplvm ; del gplvm 
+from models_modules.gplvm import GPLVM#; _gplvm = gplvm ; del gplvm 
-from _models.bcgplvm import BCGPLVM#; _bcgplvm = bcgplvm; del bcgplvm
+from models_modules.bcgplvm import BCGPLVM#; _bcgplvm = bcgplvm; del bcgplvm
-from _models.sparse_gplvm import SparseGPLVM#; _sparse_gplvm = sparse_gplvm ; del sparse_gplvm 
+from models_modules.sparse_gplvm import SparseGPLVM#; _sparse_gplvm = sparse_gplvm ; del sparse_gplvm 
-from _models.warped_gp import WarpedGP#; _warped_gp = warped_gp ; del warped_gp 
+from models_modules.warped_gp import WarpedGP#; _warped_gp = warped_gp ; del warped_gp 
-from _models.bayesian_gplvm import BayesianGPLVM#; _bayesian_gplvm = bayesian_gplvm ; del bayesian_gplvm 
+from models_modules.bayesian_gplvm import BayesianGPLVM#; _bayesian_gplvm = bayesian_gplvm ; del bayesian_gplvm 
-from _models.mrd import MRD#; _mrd = mrd; del mrd 
+from models_modules.mrd import MRD#; _mrd = mrd; del mrd 
-from _models.gradient_checker import GradientChecker#; _gradient_checker = gradient_checker ; del gradient_checker 
+from models_modules.gradient_checker import GradientChecker#; _gradient_checker = gradient_checker ; del gradient_checker 
-from _models.gp_multioutput_regression import GPMultioutputRegression#; _gp_multioutput_regression = gp_multioutput_regression ; del gp_multioutput_regression 
+from models_modules.gp_multioutput_regression import GPMultioutputRegression#; _gp_multioutput_regression = gp_multioutput_regression ; del gp_multioutput_regression 
-from _models.sparse_gp_multioutput_regression import SparseGPMultioutputRegression#; _sparse_gp_multioutput_regression = sparse_gp_multioutput_regression ; del sparse_gp_multioutput_regression 
+from models_modules.sparse_gp_multioutput_regression import SparseGPMultioutputRegression#; _sparse_gp_multioutput_regression = sparse_gp_multioutput_regression ; del sparse_gp_multioutput_regression 
-from _models.gradient_checker import GradientChecker
+from models_modules.gradient_checker import GradientChecker

GPy/models_modules/bayesian_gplvm.py

@@ -12,6 +12,7 @@ from GPy.util import plot_latent, linalg
 from .gplvm import GPLVM
 from GPy.util.plot_latent import most_significant_input_dimensions
 from matplotlib import pyplot
+from GPy.core.model import Model
 
 class BayesianGPLVM(SparseGP, GPLVM):
     """
@@ -285,6 +286,57 @@ class BayesianGPLVM(SparseGP, GPLVM):
         self.init = state.pop()
         SparseGP.setstate(self, state)
 
+class BayesianGPLVMWithMissingData(Model):
+    """
+    Bayesian Gaussian Process Latent Variable Model with missing data support.
+    NOTE: Missing data is assumed to be missing at random!
+    
+    This extension comes with a large memory and computing time deficiency.
+    Use only if fraction of missing data at random is higher than 60%.
+    Otherwise, try filtering data before using this extension.
+    
+    Y can hold missing data as given by `missing`, standard is :class:`~numpy.nan`.
+    
+    If likelihood is given for Y, this likelihood will be discarded, but the parameters
+    of the likelihood will be taken. Also every effort of creating the same likelihood
+    will be done.
+     
+    :param likelihood_or_Y: observed data (np.ndarray) or GPy.likelihood
+    :type likelihood_or_Y: :class:`~numpy.ndarray` | :class:`~GPy.likelihoods.likelihood.likelihood` instance
+    :param int input_dim: latent dimensionality
+    :param init: initialisation method for the latent space
+    :type init: 'PCA' | 'random'
+    """
+    def __init__(self, likelihood_or_Y, input_dim, X=None, X_variance=None, init='PCA', num_inducing=10,
+                 Z=None, kernel=None, missing=np.nan, **kwargs):
+        if type(likelihood_or_Y) is np.ndarray:
+            likelihood = Gaussian(likelihood_or_Y)
+        else:
+            likelihood = likelihood_or_Y
+
+        if X == None:
+            X = self.initialise_latent(init, input_dim, likelihood.Y)
+        self.init = init
+
+        if X_variance is None:
+            X_variance = np.clip((np.ones_like(X) * 0.5) + .01 * np.random.randn(*X.shape), 0.001, 1)
+
+        if Z is None:
+            Z = np.random.permutation(X.copy())[:num_inducing]
+        assert Z.shape[1] == X.shape[1]
+
+        if kernel is None:
+            kernel = kern.rbf(input_dim) # + kern.white(input_dim)
+
+        SparseGP.__init__(self, X, likelihood, kernel, Z=Z, X_variance=X_variance, **kwargs)
+        self.ensure_default_constraints()
+
+    def _get_param_names(self):
+        X_names = sum([['X_%i_%i' % (n, q) for q in range(self.input_dim)] for n in range(self.num_data)], [])
+        S_names = sum([['X_variance_%i_%i' % (n, q) for q in range(self.input_dim)] for n in range(self.num_data)], [])
+        return (X_names + S_names + SparseGP._get_param_names(self))
+
+    pass
 
 def latent_cost_and_grad(mu_S, kern, Z, dL_dpsi0, dL_dpsi1, dL_dpsi2):
     """

doc/GPy.core.rst

@@ -1,102 +1,107 @@
-GPy.core package
+core Package
-================
+============
 
-Submodules
+:mod:`core` Package
-----------
+-------------------
 
-GPy.core.domains module
+.. automodule:: GPy.core
------------------------
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`domains` Module
+---------------------
 
 .. automodule:: GPy.core.domains
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.core.fitc module
+:mod:`fitc` Module
---------------------
+------------------
 
 .. automodule:: GPy.core.fitc
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.core.gp module
+:mod:`gp` Module
-------------------
+----------------
 
 .. automodule:: GPy.core.gp
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.core.gp_base module
+:mod:`gp_base` Module
------------------------
+---------------------
 
 .. automodule:: GPy.core.gp_base
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.core.mapping module
+:mod:`mapping` Module
------------------------
+---------------------
 
 .. automodule:: GPy.core.mapping
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.core.model module
+:mod:`model` Module
----------------------
+-------------------
 
 .. automodule:: GPy.core.model
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.core.parameterized module
+:mod:`parameterized` Module
------------------------------
+---------------------------
 
 .. automodule:: GPy.core.parameterized
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.core.priors module
+:mod:`priors` Module
-----------------------
+--------------------
 
 .. automodule:: GPy.core.priors
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.core.sparse_gp module
+:mod:`sparse_gp` Module
--------------------------
+-----------------------
 
 .. automodule:: GPy.core.sparse_gp
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.core.svigp module
+:mod:`svigp` Module
----------------------
+-------------------
 
 .. automodule:: GPy.core.svigp
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.core.transformations module
+:mod:`transformations` Module
--------------------------------
+-----------------------------
 
 .. automodule:: GPy.core.transformations
     :members:
     :undoc-members:
     :show-inheritance:
 
+:mod:`variational` Module
+-------------------------
 
-Module contents
+.. automodule:: GPy.core.variational
----------------
-
-.. automodule:: GPy.core
     :members:
     :undoc-members:
     :show-inheritance:
+

doc/GPy.examples.rst

@@ -1,62 +1,59 @@
-GPy.examples package
+examples Package
-====================
+================
 
-Submodules
+:mod:`examples` Package
-----------
+-----------------------
 
-GPy.examples.classification module
+.. automodule:: GPy.examples
-----------------------------------
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`classification` Module
+----------------------------
 
 .. automodule:: GPy.examples.classification
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.examples.dimensionality_reduction module
+:mod:`dimensionality_reduction` Module
---------------------------------------------
+--------------------------------------
 
 .. automodule:: GPy.examples.dimensionality_reduction
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.examples.laplace_approximations module
+:mod:`laplace_approximations` Module
-------------------------------------------
+------------------------------------
 
 .. automodule:: GPy.examples.laplace_approximations
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.examples.regression module
+:mod:`regression` Module
-------------------------------
+------------------------
 
 .. automodule:: GPy.examples.regression
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.examples.stochastic module
+:mod:`stochastic` Module
-------------------------------
+------------------------
 
 .. automodule:: GPy.examples.stochastic
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.examples.tutorials module
+:mod:`tutorials` Module
------------------------------
+-----------------------
 
 .. automodule:: GPy.examples.tutorials
     :members:
     :undoc-members:
     :show-inheritance:
 
-
-Module contents
----------------
-
-.. automodule:: GPy.examples
-    :members:
-    :undoc-members:
-    :show-inheritance:

doc/GPy.inference.rst

@@ -1,62 +1,51 @@
-GPy.inference package
+inference Package
-=====================
+=================
 
-Submodules
+:mod:`conjugate_gradient_descent` Module
-----------
+----------------------------------------
-
-GPy.inference.conjugate_gradient_descent module
------------------------------------------------
 
 .. automodule:: GPy.inference.conjugate_gradient_descent
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.inference.gradient_descent_update_rules module
+:mod:`gradient_descent_update_rules` Module
---------------------------------------------------
+-------------------------------------------
 
 .. automodule:: GPy.inference.gradient_descent_update_rules
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.inference.optimization module
+:mod:`optimization` Module
----------------------------------
+--------------------------
 
 .. automodule:: GPy.inference.optimization
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.inference.samplers module
+:mod:`samplers` Module
------------------------------
+----------------------
 
 .. automodule:: GPy.inference.samplers
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.inference.scg module
+:mod:`scg` Module
-------------------------
+-----------------
 
 .. automodule:: GPy.inference.scg
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.inference.sgd module
+:mod:`sgd` Module
-------------------------
+-----------------
 
 .. automodule:: GPy.inference.sgd
     :members:
     :undoc-members:
     :show-inheritance:
 
-
-Module contents
----------------
-
-.. automodule:: GPy.inference
-    :members:
-    :undoc-members:
-    :show-inheritance:

doc/GPy.kern.parts.rst

@@ -1,262 +1,275 @@
-GPy.kern.parts package
+parts Package
-======================
+=============
 
-Submodules
+:mod:`parts` Package
-----------
+--------------------
 
-GPy.kern.parts.Brownian module
+.. automodule:: GPy.kern.parts
-------------------------------
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`Brownian` Module
+----------------------
 
 .. automodule:: GPy.kern.parts.Brownian
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.Matern32 module
+:mod:`Matern32` Module
-------------------------------
+----------------------
 
 .. automodule:: GPy.kern.parts.Matern32
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.Matern52 module
+:mod:`Matern52` Module
-------------------------------
+----------------------
 
 .. automodule:: GPy.kern.parts.Matern52
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.ODE_1 module
+:mod:`ODE_1` Module
----------------------------
+-------------------
 
 .. automodule:: GPy.kern.parts.ODE_1
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.bias module
+:mod:`ODE_UY` Module
---------------------------
+--------------------
+
+.. automodule:: GPy.kern.parts.ODE_UY
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`bias` Module
+------------------
 
 .. automodule:: GPy.kern.parts.bias
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.coregionalize module
+:mod:`coregionalize` Module
------------------------------------
+---------------------------
 
 .. automodule:: GPy.kern.parts.coregionalize
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.eq_ode1 module
+:mod:`eq_ode1` Module
------------------------------
+---------------------
 
 .. automodule:: GPy.kern.parts.eq_ode1
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.exponential module
+:mod:`exponential` Module
----------------------------------
+-------------------------
 
 .. automodule:: GPy.kern.parts.exponential
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.finite_dimensional module
+:mod:`finite_dimensional` Module
-----------------------------------------
+--------------------------------
 
 .. automodule:: GPy.kern.parts.finite_dimensional
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.fixed module
+:mod:`fixed` Module
----------------------------
+-------------------
 
 .. automodule:: GPy.kern.parts.fixed
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.gibbs module
+:mod:`gibbs` Module
----------------------------
+-------------------
 
 .. automodule:: GPy.kern.parts.gibbs
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.hetero module
+:mod:`hetero` Module
-----------------------------
+--------------------
 
 .. automodule:: GPy.kern.parts.hetero
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.hierarchical module
+:mod:`hierarchical` Module
-----------------------------------
+--------------------------
 
 .. automodule:: GPy.kern.parts.hierarchical
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.independent_outputs module
+:mod:`independent_outputs` Module
------------------------------------------
+---------------------------------
 
 .. automodule:: GPy.kern.parts.independent_outputs
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.kernpart module
+:mod:`kernpart` Module
-------------------------------
+----------------------
 
 .. automodule:: GPy.kern.parts.kernpart
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.linear module
+:mod:`linear` Module
-----------------------------
+--------------------
 
 .. automodule:: GPy.kern.parts.linear
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.mlp module
+:mod:`mlp` Module
--------------------------
+-----------------
 
 .. automodule:: GPy.kern.parts.mlp
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.periodic_Matern32 module
+:mod:`periodic_Matern32` Module
----------------------------------------
+-------------------------------
 
 .. automodule:: GPy.kern.parts.periodic_Matern32
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.periodic_Matern52 module
+:mod:`periodic_Matern52` Module
----------------------------------------
+-------------------------------
 
 .. automodule:: GPy.kern.parts.periodic_Matern52
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.periodic_exponential module
+:mod:`periodic_exponential` Module
-------------------------------------------
+----------------------------------
 
 .. automodule:: GPy.kern.parts.periodic_exponential
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.poly module
+:mod:`poly` Module
---------------------------
+------------------
 
 .. automodule:: GPy.kern.parts.poly
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.prod module
+:mod:`prod` Module
---------------------------
+------------------
 
 .. automodule:: GPy.kern.parts.prod
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.prod_orthogonal module
+:mod:`prod_orthogonal` Module
--------------------------------------
+-----------------------------
 
 .. automodule:: GPy.kern.parts.prod_orthogonal
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.rational_quadratic module
+:mod:`rational_quadratic` Module
-----------------------------------------
+--------------------------------
 
 .. automodule:: GPy.kern.parts.rational_quadratic
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.rbf module
+:mod:`rbf` Module
--------------------------
+-----------------
 
 .. automodule:: GPy.kern.parts.rbf
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.rbf_inv module
+:mod:`rbf_inv` Module
------------------------------
+---------------------
 
 .. automodule:: GPy.kern.parts.rbf_inv
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.rbfcos module
+:mod:`rbfcos` Module
-----------------------------
+--------------------
 
 .. automodule:: GPy.kern.parts.rbfcos
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.spline module
+:mod:`spline` Module
-----------------------------
+--------------------
 
 .. automodule:: GPy.kern.parts.spline
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.symmetric module
+:mod:`symmetric` Module
--------------------------------
+-----------------------
 
 .. automodule:: GPy.kern.parts.symmetric
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.sympykern module
+:mod:`sympy_helpers` Module
--------------------------------
+---------------------------
+
+.. automodule:: GPy.kern.parts.sympy_helpers
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`sympykern` Module
+-----------------------
 
 .. automodule:: GPy.kern.parts.sympykern
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.kern.parts.white module
+:mod:`white` Module
----------------------------
+-------------------
 
 .. automodule:: GPy.kern.parts.white
     :members:
     :undoc-members:
     :show-inheritance:
 
-
-Module contents
----------------
-
-.. automodule:: GPy.kern.parts
-    :members:
-    :undoc-members:
-    :show-inheritance:

doc/GPy.kern.rst

@@ -1,5 +1,29 @@
-GPy.kern package
+kern Package
-================
+============
+
+:mod:`kern` Package
+-------------------
+
+.. automodule:: GPy.kern
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`constructors` Module
+--------------------------
+
+.. automodule:: GPy.kern.constructors
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`kern` Module
+------------------
+
+.. automodule:: GPy.kern.kern
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
 Subpackages
 -----------
@@ -8,30 +32,3 @@ Subpackages
 
     GPy.kern.parts
 
-Submodules
-----------
-
-GPy.kern.constructors module
-----------------------------
-
-.. automodule:: GPy.kern.constructors
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.kern.kern module
---------------------
-
-.. automodule:: GPy.kern.kern
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: GPy.kern
-    :members:
-    :undoc-members:
-    :show-inheritance:

doc/GPy.likelihoods.noise_models.rst

@@ -1,78 +1,75 @@
-GPy.likelihoods.noise_models package
+noise_models Package
-====================================
+====================
 
-Submodules
+:mod:`noise_models` Package
-----------
+---------------------------
 
-GPy.likelihoods.noise_models.bernoulli_noise module
+.. automodule:: GPy.likelihoods.noise_models
----------------------------------------------------
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`bernoulli_noise` Module
+-----------------------------
 
 .. automodule:: GPy.likelihoods.noise_models.bernoulli_noise
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.likelihoods.noise_models.exponential_noise module
+:mod:`exponential_noise` Module
------------------------------------------------------
+-------------------------------
 
 .. automodule:: GPy.likelihoods.noise_models.exponential_noise
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.likelihoods.noise_models.gamma_noise module
+:mod:`gamma_noise` Module
------------------------------------------------
+-------------------------
 
 .. automodule:: GPy.likelihoods.noise_models.gamma_noise
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.likelihoods.noise_models.gaussian_noise module
+:mod:`gaussian_noise` Module
---------------------------------------------------
+----------------------------
 
 .. automodule:: GPy.likelihoods.noise_models.gaussian_noise
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.likelihoods.noise_models.gp_transformations module
+:mod:`gp_transformations` Module
-------------------------------------------------------
+--------------------------------
 
 .. automodule:: GPy.likelihoods.noise_models.gp_transformations
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.likelihoods.noise_models.noise_distributions module
+:mod:`noise_distributions` Module
--------------------------------------------------------
+---------------------------------
 
 .. automodule:: GPy.likelihoods.noise_models.noise_distributions
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.likelihoods.noise_models.poisson_noise module
+:mod:`poisson_noise` Module
--------------------------------------------------
+---------------------------
 
 .. automodule:: GPy.likelihoods.noise_models.poisson_noise
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.likelihoods.noise_models.student_t_noise module
+:mod:`student_t_noise` Module
----------------------------------------------------
+-----------------------------
 
 .. automodule:: GPy.likelihoods.noise_models.student_t_noise
     :members:
     :undoc-members:
     :show-inheritance:
 
-
-Module contents
----------------
-
-.. automodule:: GPy.likelihoods.noise_models
-    :members:
-    :undoc-members:
-    :show-inheritance:

doc/GPy.likelihoods.rst

@@ -1,5 +1,69 @@
-GPy.likelihoods package
+likelihoods Package
-=======================
+===================
+
+:mod:`likelihoods` Package
+--------------------------
+
+.. automodule:: GPy.likelihoods
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`ep` Module
+----------------
+
+.. automodule:: GPy.likelihoods.ep
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`ep_mixed_noise` Module
+----------------------------
+
+.. automodule:: GPy.likelihoods.ep_mixed_noise
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`gaussian` Module
+----------------------
+
+.. automodule:: GPy.likelihoods.gaussian
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`gaussian_mixed_noise` Module
+----------------------------------
+
+.. automodule:: GPy.likelihoods.gaussian_mixed_noise
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`laplace` Module
+---------------------
+
+.. automodule:: GPy.likelihoods.laplace
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`likelihood` Module
+------------------------
+
+.. automodule:: GPy.likelihoods.likelihood
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`noise_model_constructors` Module
+--------------------------------------
+
+.. automodule:: GPy.likelihoods.noise_model_constructors
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
 Subpackages
 -----------
@@ -8,70 +72,3 @@ Subpackages
 
     GPy.likelihoods.noise_models
 
-Submodules
-----------
-
-GPy.likelihoods.ep module
--------------------------
-
-.. automodule:: GPy.likelihoods.ep
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.likelihoods.ep_mixed_noise module
--------------------------------------
-
-.. automodule:: GPy.likelihoods.ep_mixed_noise
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.likelihoods.gaussian module
--------------------------------
-
-.. automodule:: GPy.likelihoods.gaussian
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.likelihoods.gaussian_mixed_noise module
--------------------------------------------
-
-.. automodule:: GPy.likelihoods.gaussian_mixed_noise
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.likelihoods.laplace module
-------------------------------
-
-.. automodule:: GPy.likelihoods.laplace
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.likelihoods.likelihood module
----------------------------------
-
-.. automodule:: GPy.likelihoods.likelihood
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.likelihoods.noise_model_constructors module
------------------------------------------------
-
-.. automodule:: GPy.likelihoods.noise_model_constructors
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: GPy.likelihoods
-    :members:
-    :undoc-members:
-    :show-inheritance:

doc/GPy.mappings.rst

@@ -1,38 +1,35 @@
-GPy.mappings package
+mappings Package
-====================
+================
 
-Submodules
+:mod:`mappings` Package
-----------
+-----------------------
 
-GPy.mappings.kernel module
+.. automodule:: GPy.mappings
---------------------------
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`kernel` Module
+--------------------
 
 .. automodule:: GPy.mappings.kernel
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.mappings.linear module
+:mod:`linear` Module
---------------------------
+--------------------
 
 .. automodule:: GPy.mappings.linear
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.mappings.mlp module
+:mod:`mlp` Module
------------------------
+-----------------
 
 .. automodule:: GPy.mappings.mlp
     :members:
     :undoc-members:
     :show-inheritance:
 
-
-Module contents
----------------
-
-.. automodule:: GPy.mappings
-    :members:
-    :undoc-members:
-    :show-inheritance:

doc/GPy.models.rst

@@ -1,134 +0,0 @@
-GPy.models package
-==================
-
-Submodules
-----------
-
-GPy.models.bayesian_gplvm module
---------------------------------
-
-.. automodule:: GPy.models.bayesian_gplvm
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.models.bcgplvm module
--------------------------
-
-.. automodule:: GPy.models.bcgplvm
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.models.fitc_classification module
--------------------------------------
-
-.. automodule:: GPy.models.fitc_classification
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.models.gp_classification module
------------------------------------
-
-.. automodule:: GPy.models.gp_classification
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.models.gp_multioutput_regression module
--------------------------------------------
-
-.. automodule:: GPy.models.gp_multioutput_regression
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.models.gp_regression module
--------------------------------
-
-.. automodule:: GPy.models.gp_regression
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.models.gplvm module
------------------------
-
-.. automodule:: GPy.models.gplvm
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.models.gradient_checker module
-----------------------------------
-
-.. automodule:: GPy.models.gradient_checker
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.models.mrd module
----------------------
-
-.. automodule:: GPy.models.mrd
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.models.sparse_gp_classification module
-------------------------------------------
-
-.. automodule:: GPy.models.sparse_gp_classification
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.models.sparse_gp_multioutput_regression module
---------------------------------------------------
-
-.. automodule:: GPy.models.sparse_gp_multioutput_regression
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.models.sparse_gp_regression module
---------------------------------------
-
-.. automodule:: GPy.models.sparse_gp_regression
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.models.sparse_gplvm module
-------------------------------
-
-.. automodule:: GPy.models.sparse_gplvm
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.models.svigp_regression module
-----------------------------------
-
-.. automodule:: GPy.models.svigp_regression
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.models.warped_gp module
----------------------------
-
-.. automodule:: GPy.models.warped_gp
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: GPy.models
-    :members:
-    :undoc-members:
-    :show-inheritance:

doc/GPy.models_modules.rst

@@ -0,0 +1,131 @@
+models_modules Package
+======================
+
+:mod:`models_modules` Package
+-----------------------------
+
+.. automodule:: GPy.models_modules
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`bayesian_gplvm` Module
+----------------------------
+
+.. automodule:: GPy.models_modules.bayesian_gplvm
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`bcgplvm` Module
+---------------------
+
+.. automodule:: GPy.models_modules.bcgplvm
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`fitc_classification` Module
+---------------------------------
+
+.. automodule:: GPy.models_modules.fitc_classification
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`gp_classification` Module
+-------------------------------
+
+.. automodule:: GPy.models_modules.gp_classification
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`gp_multioutput_regression` Module
+---------------------------------------
+
+.. automodule:: GPy.models_modules.gp_multioutput_regression
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`gp_regression` Module
+---------------------------
+
+.. automodule:: GPy.models_modules.gp_regression
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`gplvm` Module
+-------------------
+
+.. automodule:: GPy.models_modules.gplvm
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`gradient_checker` Module
+------------------------------
+
+.. automodule:: GPy.models_modules.gradient_checker
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`mrd` Module
+-----------------
+
+.. automodule:: GPy.models_modules.mrd
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`sparse_gp_classification` Module
+--------------------------------------
+
+.. automodule:: GPy.models_modules.sparse_gp_classification
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`sparse_gp_multioutput_regression` Module
+----------------------------------------------
+
+.. automodule:: GPy.models_modules.sparse_gp_multioutput_regression
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`sparse_gp_regression` Module
+----------------------------------
+
+.. automodule:: GPy.models_modules.sparse_gp_regression
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`sparse_gplvm` Module
+--------------------------
+
+.. automodule:: GPy.models_modules.sparse_gplvm
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`svigp_regression` Module
+------------------------------
+
+.. automodule:: GPy.models_modules.svigp_regression
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`warped_gp` Module
+-----------------------
+
+.. automodule:: GPy.models_modules.warped_gp
+    :members:
+    :undoc-members:
+    :show-inheritance:
+

doc/GPy.rst

@@ -1,6 +1,22 @@
-GPy package
+GPy Package
 ===========
 
+:mod:`GPy` Package
+------------------
+
+.. automodule:: GPy.__init__
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`models` Module
+--------------------
+
+.. automodule:: GPy.models
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 Subpackages
 -----------
 
@@ -12,14 +28,7 @@ Subpackages
     GPy.kern
     GPy.likelihoods
     GPy.mappings
-    GPy.models
+    GPy.models_modules
     GPy.testing
     GPy.util
 
-Module contents
----------------
-
-.. automodule:: GPy
-    :members:
-    :undoc-members:
-    :show-inheritance:

doc/GPy.testing.rst

@@ -1,134 +1,131 @@
-GPy.testing package
+testing Package
-===================
+===============
 
-Submodules
+:mod:`testing` Package
-----------
+----------------------
 
-GPy.testing.bcgplvm_tests module
+.. automodule:: GPy.testing
---------------------------------
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`bcgplvm_tests` Module
+---------------------------
 
 .. automodule:: GPy.testing.bcgplvm_tests
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.testing.bgplvm_tests module
+:mod:`bgplvm_tests` Module
--------------------------------
+--------------------------
 
 .. automodule:: GPy.testing.bgplvm_tests
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.testing.cgd_tests module
+:mod:`cgd_tests` Module
-----------------------------
+-----------------------
 
 .. automodule:: GPy.testing.cgd_tests
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.testing.examples_tests module
+:mod:`examples_tests` Module
----------------------------------
+----------------------------
 
 .. automodule:: GPy.testing.examples_tests
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.testing.gp_transformation_tests module
+:mod:`gp_transformation_tests` Module
-------------------------------------------
+-------------------------------------
 
 .. automodule:: GPy.testing.gp_transformation_tests
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.testing.gplvm_tests module
+:mod:`gplvm_tests` Module
-------------------------------
+-------------------------
 
 .. automodule:: GPy.testing.gplvm_tests
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.testing.kernel_tests module
+:mod:`kernel_tests` Module
--------------------------------
+--------------------------
 
 .. automodule:: GPy.testing.kernel_tests
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.testing.likelihoods_tests module
+:mod:`likelihoods_tests` Module
-------------------------------------
+-------------------------------
 
 .. automodule:: GPy.testing.likelihoods_tests
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.testing.mapping_tests module
+:mod:`mapping_tests` Module
---------------------------------
+---------------------------
 
 .. automodule:: GPy.testing.mapping_tests
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.testing.mrd_tests module
+:mod:`mrd_tests` Module
-----------------------------
+-----------------------
 
 .. automodule:: GPy.testing.mrd_tests
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.testing.prior_tests module
+:mod:`prior_tests` Module
-------------------------------
+-------------------------
 
 .. automodule:: GPy.testing.prior_tests
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.testing.psi_stat_expectation_tests module
+:mod:`psi_stat_expectation_tests` Module
----------------------------------------------
+----------------------------------------
 
 .. automodule:: GPy.testing.psi_stat_expectation_tests
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.testing.psi_stat_gradient_tests module
+:mod:`psi_stat_gradient_tests` Module
-------------------------------------------
+-------------------------------------
 
 .. automodule:: GPy.testing.psi_stat_gradient_tests
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.testing.sparse_gplvm_tests module
+:mod:`sparse_gplvm_tests` Module
--------------------------------------
+--------------------------------
 
 .. automodule:: GPy.testing.sparse_gplvm_tests
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.testing.unit_tests module
+:mod:`unit_tests` Module
------------------------------
+------------------------
 
 .. automodule:: GPy.testing.unit_tests
     :members:
     :undoc-members:
     :show-inheritance:
 
-
-Module contents
----------------
-
-.. automodule:: GPy.testing
-    :members:
-    :undoc-members:
-    :show-inheritance:

doc/GPy.util.latent_space_visualizations.controllers.rst

@@ -1,30 +1,27 @@
-GPy.util.latent_space_visualizations.controllers package
+controllers Package
-========================================================
+===================
 
-Submodules
+:mod:`controllers` Package
-----------
+--------------------------
 
-GPy.util.latent_space_visualizations.controllers.axis_event_controller module
+.. automodule:: GPy.util.latent_space_visualizations.controllers
------------------------------------------------------------------------------
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`axis_event_controller` Module
+-----------------------------------
 
 .. automodule:: GPy.util.latent_space_visualizations.controllers.axis_event_controller
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.util.latent_space_visualizations.controllers.imshow_controller module
+:mod:`imshow_controller` Module
--------------------------------------------------------------------------
+-------------------------------
 
 .. automodule:: GPy.util.latent_space_visualizations.controllers.imshow_controller
     :members:
     :undoc-members:
     :show-inheritance:
 
-
-Module contents
----------------
-
-.. automodule:: GPy.util.latent_space_visualizations.controllers
-    :members:
-    :undoc-members:
-    :show-inheritance:

doc/GPy.util.latent_space_visualizations.rst

@@ -1,5 +1,13 @@
-GPy.util.latent_space_visualizations package
+latent_space_visualizations Package
-============================================
+===================================
+
+:mod:`latent_space_visualizations` Package
+------------------------------------------
+
+.. automodule:: GPy.util.latent_space_visualizations
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
 Subpackages
 -----------
@@ -7,11 +15,5 @@ Subpackages
 .. toctree::
 
     GPy.util.latent_space_visualizations.controllers
+    GPy.util.latent_space_visualizations.views
 
-Module contents
----------------
-
-.. automodule:: GPy.util.latent_space_visualizations
-    :members:
-    :undoc-members:
-    :show-inheritance:

doc/GPy.util.rst

@@ -1,5 +1,181 @@
-GPy.util package
+util Package
-================
+============
+
+:mod:`util` Package
+-------------------
+
+.. automodule:: GPy.util
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`Tango` Module
+-------------------
+
+.. automodule:: GPy.util.Tango
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`block_matrices` Module
+----------------------------
+
+.. automodule:: GPy.util.block_matrices
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`classification` Module
+----------------------------
+
+.. automodule:: GPy.util.classification
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`config` Module
+--------------------
+
+.. automodule:: GPy.util.config
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`datasets` Module
+----------------------
+
+.. automodule:: GPy.util.datasets
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`decorators` Module
+------------------------
+
+.. automodule:: GPy.util.decorators
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`erfcx` Module
+-------------------
+
+.. automodule:: GPy.util.erfcx
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`linalg` Module
+--------------------
+
+.. automodule:: GPy.util.linalg
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`ln_diff_erfs` Module
+--------------------------
+
+.. automodule:: GPy.util.ln_diff_erfs
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`misc` Module
+------------------
+
+.. automodule:: GPy.util.misc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`mocap` Module
+-------------------
+
+.. automodule:: GPy.util.mocap
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`multioutput` Module
+-------------------------
+
+.. automodule:: GPy.util.multioutput
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`netpbmfile` Module
+------------------------
+
+.. automodule:: GPy.util.netpbmfile
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`pca` Module
+-----------------
+
+.. automodule:: GPy.util.pca
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`plot` Module
+------------------
+
+.. automodule:: GPy.util.plot
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`plot_latent` Module
+-------------------------
+
+.. automodule:: GPy.util.plot_latent
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`squashers` Module
+-----------------------
+
+.. automodule:: GPy.util.squashers
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`symbolic` Module
+----------------------
+
+.. automodule:: GPy.util.symbolic
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`univariate_Gaussian` Module
+---------------------------------
+
+.. automodule:: GPy.util.univariate_Gaussian
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`visualize` Module
+-----------------------
+
+.. automodule:: GPy.util.visualize
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`warping_functions` Module
+-------------------------------
+
+.. automodule:: GPy.util.warping_functions
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
 Subpackages
 -----------
@@ -8,166 +184,3 @@ Subpackages
 
     GPy.util.latent_space_visualizations
 
-Submodules
-----------
-
-GPy.util.Tango module
----------------------
-
-.. automodule:: GPy.util.Tango
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.util.classification module
-------------------------------
-
-.. automodule:: GPy.util.classification
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.util.config module
-----------------------
-
-.. automodule:: GPy.util.config
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.util.datasets module
-------------------------
-
-.. automodule:: GPy.util.datasets
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.util.decorators module
---------------------------
-
-.. automodule:: GPy.util.decorators
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.util.erfcx module
----------------------
-
-.. automodule:: GPy.util.erfcx
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.util.linalg module
-----------------------
-
-.. automodule:: GPy.util.linalg
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.util.ln_diff_erfs module
-----------------------------
-
-.. automodule:: GPy.util.ln_diff_erfs
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.util.misc module
---------------------
-
-.. automodule:: GPy.util.misc
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.util.mocap module
----------------------
-
-.. automodule:: GPy.util.mocap
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.util.multioutput module
----------------------------
-
-.. automodule:: GPy.util.multioutput
-    :members:
-    :undoc-members:
-    :show-inheritance:
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-GPy.util.netpbmfile module
---------------------------
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-.. automodule:: GPy.util.netpbmfile
-    :members:
-    :undoc-members:
-    :show-inheritance:
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-GPy.util.plot module
---------------------
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-.. automodule:: GPy.util.plot
-    :members:
-    :undoc-members:
-    :show-inheritance:
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-GPy.util.plot_latent module
----------------------------
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-.. automodule:: GPy.util.plot_latent
-    :members:
-    :undoc-members:
-    :show-inheritance:
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-GPy.util.squashers module
--------------------------
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-.. automodule:: GPy.util.squashers
-    :members:
-    :undoc-members:
-    :show-inheritance:
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-GPy.util.symbolic module
-------------------------
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-.. automodule:: GPy.util.symbolic
-    :members:
-    :undoc-members:
-    :show-inheritance:
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-GPy.util.univariate_Gaussian module
------------------------------------
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-.. automodule:: GPy.util.univariate_Gaussian
-    :members:
-    :undoc-members:
-    :show-inheritance:
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-GPy.util.visualize module
--------------------------
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-.. automodule:: GPy.util.visualize
-    :members:
-    :undoc-members:
-    :show-inheritance:
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-GPy.util.warping_functions module
----------------------------------
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-.. automodule:: GPy.util.warping_functions
-    :members:
-    :undoc-members:
-    :show-inheritance:
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-
-Module contents
----------------
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-.. automodule:: GPy.util
-    :members:
-    :undoc-members:
-    :show-inheritance: