[sphinx] new doc

doc/source/.#conf.py

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+maxz@maxz-sitran.8058:1442579222

doc/source/GPy.core.parameterization.rst

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+GPy.core.parameterization package
+=================================
+
+Submodules
+----------
+
+GPy.core.parameterization.domains module
+----------------------------------------
+
+.. automodule:: GPy.core.parameterization.domains
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.index_operations module
+-------------------------------------------------
+
+.. automodule:: GPy.core.parameterization.index_operations
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.lists_and_dicts module
+------------------------------------------------
+
+.. automodule:: GPy.core.parameterization.lists_and_dicts
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.observable module
+-------------------------------------------
+
+.. automodule:: GPy.core.parameterization.observable
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.observable_array module
+-------------------------------------------------
+
+.. automodule:: GPy.core.parameterization.observable_array
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.param module
+--------------------------------------
+
+.. automodule:: GPy.core.parameterization.param
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.parameter_core module
+-----------------------------------------------
+
+.. automodule:: GPy.core.parameterization.parameter_core
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.parameterized module
+----------------------------------------------
+
+.. automodule:: GPy.core.parameterization.parameterized
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.priors module
+---------------------------------------
+
+.. automodule:: GPy.core.parameterization.priors
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.ties_and_remappings module
+----------------------------------------------------
+
+.. automodule:: GPy.core.parameterization.ties_and_remappings
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.transformations module
+------------------------------------------------
+
+.. automodule:: GPy.core.parameterization.transformations
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.updateable module
+-------------------------------------------
+
+.. automodule:: GPy.core.parameterization.updateable
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.variational module
+--------------------------------------------
+
+.. automodule:: GPy.core.parameterization.variational
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: GPy.core.parameterization
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/GPy.core.rst

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+GPy.core package
+================
+
+Subpackages
+-----------
+
+.. toctree::
+
+    GPy.core.parameterization
+
+Submodules
+----------
+
+GPy.core.gp module
+------------------
+
+.. automodule:: GPy.core.gp
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.mapping module
+-----------------------
+
+.. automodule:: GPy.core.mapping
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.model module
+---------------------
+
+.. automodule:: GPy.core.model
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.sparse_gp module
+-------------------------
+
+.. automodule:: GPy.core.sparse_gp
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.sparse_gp_mpi module
+-----------------------------
+
+.. automodule:: GPy.core.sparse_gp_mpi
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.svgp module
+--------------------
+
+.. automodule:: GPy.core.svgp
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.symbolic module
+------------------------
+
+.. automodule:: GPy.core.symbolic
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.verbose_optimization module
+------------------------------------
+
+.. automodule:: GPy.core.verbose_optimization
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: GPy.core
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/GPy.examples.rst

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+GPy.examples package
+====================
+
+Submodules
+----------
+
+GPy.examples.classification module
+----------------------------------
+
+.. automodule:: GPy.examples.classification
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.examples.coreg_example module
+---------------------------------
+
+.. automodule:: GPy.examples.coreg_example
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.examples.dimensionality_reduction module
+--------------------------------------------
+
+.. automodule:: GPy.examples.dimensionality_reduction
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.examples.non_gaussian module
+--------------------------------
+
+.. automodule:: GPy.examples.non_gaussian
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.examples.regression module
+------------------------------
+
+.. automodule:: GPy.examples.regression
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: GPy.examples
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/GPy.inference.latent_function_inference.rst

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+GPy.inference.latent_function_inference package
+===============================================
+
+Submodules
+----------
+
+GPy.inference.latent_function_inference.dtc module
+--------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.dtc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.exact_gaussian_inference module
+-----------------------------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.exact_gaussian_inference
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.expectation_propagation module
+----------------------------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.expectation_propagation
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.fitc module
+---------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.fitc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.inferenceX module
+---------------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.inferenceX
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.laplace module
+------------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.laplace
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.posterior module
+--------------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.posterior
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.svgp module
+---------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.svgp
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.var_dtc module
+------------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.var_dtc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.var_dtc_parallel module
+---------------------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.var_dtc_parallel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.var_gauss module
+--------------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.var_gauss
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: GPy.inference.latent_function_inference
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/GPy.inference.mcmc.rst

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+GPy.inference.mcmc package
+==========================
+
+Submodules
+----------
+
+GPy.inference.mcmc.hmc module
+-----------------------------
+
+.. automodule:: GPy.inference.mcmc.hmc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.mcmc.samplers module
+----------------------------------
+
+.. automodule:: GPy.inference.mcmc.samplers
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: GPy.inference.mcmc
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/GPy.inference.optimization.rst

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+GPy.inference.optimization package
+==================================
+
+Submodules
+----------
+
+GPy.inference.optimization.conjugate_gradient_descent module
+------------------------------------------------------------
+
+.. automodule:: GPy.inference.optimization.conjugate_gradient_descent
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.optimization.gradient_descent_update_rules module
+---------------------------------------------------------------
+
+.. automodule:: GPy.inference.optimization.gradient_descent_update_rules
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.optimization.optimization module
+----------------------------------------------
+
+.. automodule:: GPy.inference.optimization.optimization
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.optimization.scg module
+-------------------------------------
+
+.. automodule:: GPy.inference.optimization.scg
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.optimization.stochastics module
+---------------------------------------------
+
+.. automodule:: GPy.inference.optimization.stochastics
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: GPy.inference.optimization
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/GPy.inference.rst

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+GPy.inference package
+=====================
+
+Subpackages
+-----------
+
+.. toctree::
+
+    GPy.inference.latent_function_inference
+    GPy.inference.mcmc
+    GPy.inference.optimization
+
+Module contents
+---------------
+
+.. automodule:: GPy.inference
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/GPy.kern.rst

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+GPy.kern package
+================
+
+Module contents
+---------------
+
+.. automodule:: GPy.kern
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/GPy.likelihoods.rst

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+GPy.likelihoods package
+=======================
+
+Submodules
+----------
+
+GPy.likelihoods.bernoulli module
+--------------------------------
+
+.. automodule:: GPy.likelihoods.bernoulli
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.binomial module
+-------------------------------
+
+.. automodule:: GPy.likelihoods.binomial
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.exponential module
+----------------------------------
+
+.. automodule:: GPy.likelihoods.exponential
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.gamma module
+----------------------------
+
+.. automodule:: GPy.likelihoods.gamma
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.gaussian module
+-------------------------------
+
+.. automodule:: GPy.likelihoods.gaussian
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.likelihood module
+---------------------------------
+
+.. automodule:: GPy.likelihoods.likelihood
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.link_functions module
+-------------------------------------
+
+.. automodule:: GPy.likelihoods.link_functions
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.mixed_noise module
+----------------------------------
+
+.. automodule:: GPy.likelihoods.mixed_noise
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.poisson module
+------------------------------
+
+.. automodule:: GPy.likelihoods.poisson
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.student_t module
+--------------------------------
+
+.. automodule:: GPy.likelihoods.student_t
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: GPy.likelihoods
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/GPy.mappings.rst

@@ -0,0 +1,78 @@
+GPy.mappings package
+====================
+
+Submodules
+----------
+
+GPy.mappings.additive module
+----------------------------
+
+.. automodule:: GPy.mappings.additive
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.mappings.compound module
+----------------------------
+
+.. automodule:: GPy.mappings.compound
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.mappings.constant module
+----------------------------
+
+.. automodule:: GPy.mappings.constant
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.mappings.identity module
+----------------------------
+
+.. automodule:: GPy.mappings.identity
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.mappings.kernel module
+--------------------------
+
+.. automodule:: GPy.mappings.kernel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.mappings.linear module
+--------------------------
+
+.. automodule:: GPy.mappings.linear
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.mappings.mlp module
+-----------------------
+
+.. automodule:: GPy.mappings.mlp
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.mappings.piecewise_linear module
+------------------------------------
+
+.. automodule:: GPy.mappings.piecewise_linear
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: GPy.mappings
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/GPy.models.rst

@@ -0,0 +1,198 @@
+GPy.models package
+==================
+
+Submodules
+----------
+
+GPy.models.bayesian_gplvm module
+--------------------------------
+
+.. automodule:: GPy.models.bayesian_gplvm
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.bayesian_gplvm_minibatch module
+------------------------------------------
+
+.. automodule:: GPy.models.bayesian_gplvm_minibatch
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.bcgplvm module
+-------------------------
+
+.. automodule:: GPy.models.bcgplvm
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.dpgplvm module
+-------------------------
+
+.. automodule:: GPy.models.dpgplvm
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.gp_classification module
+-----------------------------------
+
+.. automodule:: GPy.models.gp_classification
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.gp_coregionalized_regression module
+----------------------------------------------
+
+.. automodule:: GPy.models.gp_coregionalized_regression
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.gp_heteroscedastic_regression module
+-----------------------------------------------
+
+.. automodule:: GPy.models.gp_heteroscedastic_regression
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.gp_kronecker_gaussian_regression module
+--------------------------------------------------
+
+.. automodule:: GPy.models.gp_kronecker_gaussian_regression
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.gp_regression module
+-------------------------------
+
+.. automodule:: GPy.models.gp_regression
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.gp_var_gauss module
+------------------------------
+
+.. automodule:: GPy.models.gp_var_gauss
+    :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.one_vs_all_classification module
+-------------------------------------------
+
+.. automodule:: GPy.models.one_vs_all_classification
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.one_vs_all_sparse_classification module
+--------------------------------------------------
+
+.. automodule:: GPy.models.one_vs_all_sparse_classification
+    :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_coregionalized_regression module
+-----------------------------------------------------
+
+.. automodule:: GPy.models.sparse_gp_coregionalized_regression
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.sparse_gp_minibatch module
+-------------------------------------
+
+.. automodule:: GPy.models.sparse_gp_minibatch
+    :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.ss_gplvm module
+--------------------------
+
+.. automodule:: GPy.models.ss_gplvm
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.ss_mrd module
+------------------------
+
+.. automodule:: GPy.models.ss_mrd
+    :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/source/GPy.plotting.matplot_dep.latent_space_visualizations.controllers.rst

@@ -0,0 +1,30 @@
+GPy.plotting.matplot_dep.latent_space_visualizations.controllers package
+========================================================================
+
+Submodules
+----------
+
+GPy.plotting.matplot_dep.latent_space_visualizations.controllers.axis_event_controller module
+---------------------------------------------------------------------------------------------
+
+.. automodule:: GPy.plotting.matplot_dep.latent_space_visualizations.controllers.axis_event_controller
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.plotting.matplot_dep.latent_space_visualizations.controllers.imshow_controller module
+-----------------------------------------------------------------------------------------
+
+.. automodule:: GPy.plotting.matplot_dep.latent_space_visualizations.controllers.imshow_controller
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: GPy.plotting.matplot_dep.latent_space_visualizations.controllers
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/GPy.plotting.matplot_dep.latent_space_visualizations.rst

@@ -0,0 +1,17 @@
+GPy.plotting.matplot_dep.latent_space_visualizations package
+============================================================
+
+Subpackages
+-----------
+
+.. toctree::
+
+    GPy.plotting.matplot_dep.latent_space_visualizations.controllers
+
+Module contents
+---------------
+
+.. automodule:: GPy.plotting.matplot_dep.latent_space_visualizations
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/GPy.plotting.matplot_dep.rst

@@ -0,0 +1,141 @@
+GPy.plotting.matplot_dep package
+================================
+
+Subpackages
+-----------
+
+.. toctree::
+
+    GPy.plotting.matplot_dep.latent_space_visualizations
+
+Submodules
+----------
+
+GPy.plotting.matplot_dep.Tango module
+-------------------------------------
+
+.. automodule:: GPy.plotting.matplot_dep.Tango
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.plotting.matplot_dep.base_plots module
+------------------------------------------
+
+.. automodule:: GPy.plotting.matplot_dep.base_plots
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.plotting.matplot_dep.dim_reduction_plots module
+---------------------------------------------------
+
+.. automodule:: GPy.plotting.matplot_dep.dim_reduction_plots
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.plotting.matplot_dep.img_plots module
+-----------------------------------------
+
+.. automodule:: GPy.plotting.matplot_dep.img_plots
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.plotting.matplot_dep.inference_plots module
+-----------------------------------------------
+
+.. automodule:: GPy.plotting.matplot_dep.inference_plots
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.plotting.matplot_dep.kernel_plots module
+--------------------------------------------
+
+.. automodule:: GPy.plotting.matplot_dep.kernel_plots
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.plotting.matplot_dep.mapping_plots module
+---------------------------------------------
+
+.. automodule:: GPy.plotting.matplot_dep.mapping_plots
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.plotting.matplot_dep.maps module
+------------------------------------
+
+.. automodule:: GPy.plotting.matplot_dep.maps
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.plotting.matplot_dep.models_plots module
+--------------------------------------------
+
+.. automodule:: GPy.plotting.matplot_dep.models_plots
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.plotting.matplot_dep.netpbmfile module
+------------------------------------------
+
+.. automodule:: GPy.plotting.matplot_dep.netpbmfile
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.plotting.matplot_dep.priors_plots module
+--------------------------------------------
+
+.. automodule:: GPy.plotting.matplot_dep.priors_plots
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.plotting.matplot_dep.ssgplvm module
+---------------------------------------
+
+.. automodule:: GPy.plotting.matplot_dep.ssgplvm
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.plotting.matplot_dep.svig_plots module
+------------------------------------------
+
+.. automodule:: GPy.plotting.matplot_dep.svig_plots
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.plotting.matplot_dep.variational_plots module
+-------------------------------------------------
+
+.. automodule:: GPy.plotting.matplot_dep.variational_plots
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.plotting.matplot_dep.visualize module
+-----------------------------------------
+
+.. automodule:: GPy.plotting.matplot_dep.visualize
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: GPy.plotting.matplot_dep
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/GPy.plotting.rst

@@ -0,0 +1,17 @@
+GPy.plotting package
+====================
+
+Subpackages
+-----------
+
+.. toctree::
+
+    GPy.plotting.matplot_dep
+
+Module contents
+---------------
+
+.. automodule:: GPy.plotting
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/GPy.rst

@@ -0,0 +1,26 @@
+GPy package
+===========
+
+Subpackages
+-----------
+
+.. toctree::
+
+    GPy.core
+    GPy.examples
+    GPy.inference
+    GPy.kern
+    GPy.likelihoods
+    GPy.mappings
+    GPy.models
+    GPy.plotting
+    GPy.testing
+    GPy.util
+
+Module contents
+---------------
+
+.. automodule:: GPy
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/GPy.testing.rst

@@ -0,0 +1,198 @@
+GPy.testing package
+===================
+
+Submodules
+----------
+
+GPy.testing.bgplvm_minibatch_tests module
+-----------------------------------------
+
+.. automodule:: GPy.testing.bgplvm_minibatch_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.cacher_tests module
+-------------------------------
+
+.. automodule:: GPy.testing.cacher_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.cython_tests module
+-------------------------------
+
+.. automodule:: GPy.testing.cython_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.examples_tests module
+---------------------------------
+
+.. automodule:: GPy.testing.examples_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.fitc module
+-----------------------
+
+.. automodule:: GPy.testing.fitc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.gp_tests module
+---------------------------
+
+.. automodule:: GPy.testing.gp_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.index_operations_tests module
+-----------------------------------------
+
+.. automodule:: GPy.testing.index_operations_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.inference_tests module
+----------------------------------
+
+.. automodule:: GPy.testing.inference_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.kernel_tests module
+-------------------------------
+
+.. automodule:: GPy.testing.kernel_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.likelihood_tests module
+-----------------------------------
+
+.. automodule:: GPy.testing.likelihood_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.linalg_test module
+------------------------------
+
+.. automodule:: GPy.testing.linalg_test
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.link_function_tests module
+--------------------------------------
+
+.. automodule:: GPy.testing.link_function_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.mapping_tests module
+--------------------------------
+
+.. automodule:: GPy.testing.mapping_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.meanfunc_tests module
+---------------------------------
+
+.. automodule:: GPy.testing.meanfunc_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.misc_tests module
+-----------------------------
+
+.. automodule:: GPy.testing.misc_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.model_tests module
+------------------------------
+
+.. automodule:: GPy.testing.model_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.mpi_tests module
+----------------------------
+
+.. automodule:: GPy.testing.mpi_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.observable_tests module
+-----------------------------------
+
+.. automodule:: GPy.testing.observable_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.parameterized_tests module
+--------------------------------------
+
+.. automodule:: GPy.testing.parameterized_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.pickle_tests module
+-------------------------------
+
+.. automodule:: GPy.testing.pickle_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.prior_tests module
+------------------------------
+
+.. automodule:: GPy.testing.prior_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.rv_transformation_tests module
+------------------------------------------
+
+.. automodule:: GPy.testing.rv_transformation_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.svgp_tests module
+-----------------------------
+
+.. automodule:: GPy.testing.svgp_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: GPy.testing
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/GPy.util.rst

@@ -0,0 +1,238 @@
+GPy.util package
+================
+
+Submodules
+----------
+
+GPy.util.block_matrices module
+------------------------------
+
+.. automodule:: GPy.util.block_matrices
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.caching module
+-----------------------
+
+.. automodule:: GPy.util.caching
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.choleskies module
+--------------------------
+
+.. automodule:: GPy.util.choleskies
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.choleskies_cython module
+---------------------------------
+
+.. automodule:: GPy.util.choleskies_cython
+    :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.debug module
+---------------------
+
+.. automodule:: GPy.util.debug
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.decorators module
+--------------------------
+
+.. automodule:: GPy.util.decorators
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.diag module
+--------------------
+
+.. automodule:: GPy.util.diag
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.functions module
+-------------------------
+
+.. automodule:: GPy.util.functions
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.gpu_init module
+------------------------
+
+.. automodule:: GPy.util.gpu_init
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.initialization module
+------------------------------
+
+.. automodule:: GPy.util.initialization
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.linalg module
+----------------------
+
+.. automodule:: GPy.util.linalg
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.linalg_cython module
+-----------------------------
+
+.. automodule:: GPy.util.linalg_cython
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.linalg_gpu module
+--------------------------
+
+.. automodule:: GPy.util.linalg_gpu
+    :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:
+
+GPy.util.netpbmfile module
+--------------------------
+
+.. automodule:: GPy.util.netpbmfile
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.normalizer module
+--------------------------
+
+.. automodule:: GPy.util.normalizer
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.parallel module
+------------------------
+
+.. automodule:: GPy.util.parallel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.pca module
+-------------------
+
+.. automodule:: GPy.util.pca
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.squashers module
+-------------------------
+
+.. automodule:: GPy.util.squashers
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.subarray_and_sorting module
+------------------------------------
+
+.. automodule:: GPy.util.subarray_and_sorting
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.univariate_Gaussian module
+-----------------------------------
+
+.. automodule:: GPy.util.univariate_Gaussian
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.warping_functions module
+---------------------------------
+
+.. automodule:: GPy.util.warping_functions
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: GPy.util
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/conf.py

@@ -0,0 +1,289 @@
+# -*- coding: utf-8 -*-
+#
+# GPy documentation build configuration file, created by
+# sphinx-quickstart on Fri Sep 18 18:16:28 2015.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys
+import os
+import shlex
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'GPy'
+copyright = u'2015, GPy Authors'
+author = u'GPy Authors'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '0.8.8'
+# The full version, including alpha/beta/rc tags.
+release = '0.8.8'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = []
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+#keep_warnings = False
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+#html_extra_path = []
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Language to be used for generating the HTML full-text search index.
+# Sphinx supports the following languages:
+#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
+#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
+#html_search_language = 'en'
+
+# A dictionary with options for the search language support, empty by default.
+# Now only 'ja' uses this config value
+#html_search_options = {'type': 'default'}
+
+# The name of a javascript file (relative to the configuration directory) that
+# implements a search results scorer. If empty, the default will be used.
+#html_search_scorer = 'scorer.js'
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'GPydoc'
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+
+# Latex figure (float) alignment
+#'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+  (master_doc, 'GPy.tex', u'GPy Documentation',
+   u'GPy Authors', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'gpy', u'GPy Documentation',
+     [author], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+  (master_doc, 'GPy', u'GPy Documentation',
+   author, 'GPy', 'One line description of project.',
+   'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+#texinfo_no_detailmenu = False

doc/source/index.rst

@@ -0,0 +1,30 @@
+.. GPy documentation master file, created by
+   sphinx-quickstart on Fri Sep 18 18:16:28 2015.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to GPy's documentation!
+===============================
+
+`GPy <http://sheffieldml.github.io/GPy/>`_ is a Gaussian Process (GP) framework written in Python, from the Sheffield machine learning group.
+
+The `GPy homepage <http://sheffieldml.github.io/GPy/>`_ contains tutorials for users and further information on the project, including installation instructions.
+This documentation is mostly aimed at developers interacting closely with the code-base.
+
+The code can be found on our `Github project page <https://github.com/SheffieldML/GPy>`_. It is open source and provided under the BSD license.
+
+Contents:
+
+.. toctree::
+   :maxdepth: 4
+
+   GPy
+
+	      
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+

doc/source/index.rst~

@@ -0,0 +1,22 @@
+.. GPy documentation master file, created by
+   sphinx-quickstart on Fri Sep 18 18:16:28 2015.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to GPy's documentation!
+===============================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+

doc/source/modules.rst

@@ -0,0 +1,7 @@
+GPy
+===
+
+.. toctree::
+   :maxdepth: 4
+
+   GPy