diff --git a/doc/GPy.core.parameterization.rst b/doc/GPy.core.parameterization.rst new file mode 100644 index 00000000..4877a06d --- /dev/null +++ b/doc/GPy.core.parameterization.rst @@ -0,0 +1,102 @@ +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_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.variational module +-------------------------------------------- + +.. automodule:: GPy.core.parameterization.variational + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: GPy.core.parameterization + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/GPy.core.rst b/doc/GPy.core.rst index c4f1849d..3c236612 100644 --- a/doc/GPy.core.rst +++ b/doc/GPy.core.rst @@ -1,25 +1,16 @@ GPy.core package ================ +Subpackages +----------- + +.. toctree:: + + GPy.core.parameterization + Submodules ---------- -GPy.core.domains module ------------------------ - -.. automodule:: GPy.core.domains - :members: - :undoc-members: - :show-inheritance: - -GPy.core.fitc module --------------------- - -.. automodule:: GPy.core.fitc - :members: - :undoc-members: - :show-inheritance: - GPy.core.gp module ------------------ @@ -28,14 +19,6 @@ GPy.core.gp module :undoc-members: :show-inheritance: -GPy.core.gp_base module ------------------------ - -.. automodule:: GPy.core.gp_base - :members: - :undoc-members: - :show-inheritance: - GPy.core.mapping module ----------------------- @@ -52,22 +35,6 @@ GPy.core.model module :undoc-members: :show-inheritance: -GPy.core.parameterized module ------------------------------ - -.. automodule:: GPy.core.parameterized - :members: - :undoc-members: - :show-inheritance: - -GPy.core.priors module ----------------------- - -.. automodule:: GPy.core.priors - :members: - :undoc-members: - :show-inheritance: - GPy.core.sparse_gp module ------------------------- @@ -76,6 +43,14 @@ GPy.core.sparse_gp module :undoc-members: :show-inheritance: +GPy.core.sparse_gp_mpi module +----------------------------- + +.. automodule:: GPy.core.sparse_gp_mpi + :members: + :undoc-members: + :show-inheritance: + GPy.core.svigp module --------------------- @@ -84,10 +59,10 @@ GPy.core.svigp module :undoc-members: :show-inheritance: -GPy.core.transformations module -------------------------------- +GPy.core.symbolic module +------------------------ -.. automodule:: GPy.core.transformations +.. automodule:: GPy.core.symbolic :members: :undoc-members: :show-inheritance: diff --git a/doc/GPy.examples.rst b/doc/GPy.examples.rst index 4fd3528f..7fc8a123 100644 --- a/doc/GPy.examples.rst +++ b/doc/GPy.examples.rst @@ -12,6 +12,14 @@ GPy.examples.classification module :undoc-members: :show-inheritance: +GPy.examples.coreg_example module +--------------------------------- + +.. automodule:: GPy.examples.coreg_example + :members: + :undoc-members: + :show-inheritance: + GPy.examples.dimensionality_reduction module -------------------------------------------- @@ -20,6 +28,14 @@ GPy.examples.dimensionality_reduction module :undoc-members: :show-inheritance: +GPy.examples.non_gaussian module +-------------------------------- + +.. automodule:: GPy.examples.non_gaussian + :members: + :undoc-members: + :show-inheritance: + GPy.examples.regression module ------------------------------ diff --git a/doc/GPy.inference.latent_function_inference.rst b/doc/GPy.inference.latent_function_inference.rst new file mode 100644 index 00000000..c47da33a --- /dev/null +++ b/doc/GPy.inference.latent_function_inference.rst @@ -0,0 +1,94 @@ +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.expectation_propagation_dtc module +-------------------------------------------------------------------------- + +.. automodule:: GPy.inference.latent_function_inference.expectation_propagation_dtc + :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.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.var_dtc module +------------------------------------------------------ + +.. automodule:: GPy.inference.latent_function_inference.var_dtc + :members: + :undoc-members: + :show-inheritance: + +GPy.inference.latent_function_inference.var_dtc_gpu module +---------------------------------------------------------- + +.. automodule:: GPy.inference.latent_function_inference.var_dtc_gpu + :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: + + +Module contents +--------------- + +.. automodule:: GPy.inference.latent_function_inference + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/GPy.inference.optimization.rst b/doc/GPy.inference.optimization.rst new file mode 100644 index 00000000..83339202 --- /dev/null +++ b/doc/GPy.inference.optimization.rst @@ -0,0 +1,78 @@ +GPy.inference.optimization package +================================== + +Submodules +---------- + +GPy.inference.optimization.BayesOpt module +------------------------------------------ + +.. automodule:: GPy.inference.optimization.BayesOpt + :members: + :undoc-members: + :show-inheritance: + +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.hmc module +------------------------------------- + +.. automodule:: GPy.inference.optimization.hmc + :members: + :undoc-members: + :show-inheritance: + +GPy.inference.optimization.optimization module +---------------------------------------------- + +.. automodule:: GPy.inference.optimization.optimization + :members: + :undoc-members: + :show-inheritance: + +GPy.inference.optimization.samplers module +------------------------------------------ + +.. automodule:: GPy.inference.optimization.samplers + :members: + :undoc-members: + :show-inheritance: + +GPy.inference.optimization.scg module +------------------------------------- + +.. automodule:: GPy.inference.optimization.scg + :members: + :undoc-members: + :show-inheritance: + +GPy.inference.optimization.sgd module +------------------------------------- + +.. automodule:: GPy.inference.optimization.sgd + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: GPy.inference.optimization + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/GPy.inference.rst b/doc/GPy.inference.rst index 28f42994..2aa7839f 100644 --- a/doc/GPy.inference.rst +++ b/doc/GPy.inference.rst @@ -1,57 +1,13 @@ GPy.inference package ===================== -Submodules ----------- +Subpackages +----------- -GPy.inference.conjugate_gradient_descent module ------------------------------------------------ - -.. automodule:: GPy.inference.conjugate_gradient_descent - :members: - :undoc-members: - :show-inheritance: - -GPy.inference.gradient_descent_update_rules module --------------------------------------------------- - -.. automodule:: GPy.inference.gradient_descent_update_rules - :members: - :undoc-members: - :show-inheritance: - -GPy.inference.optimization module ---------------------------------- - -.. automodule:: GPy.inference.optimization - :members: - :undoc-members: - :show-inheritance: - -GPy.inference.samplers module ------------------------------ - -.. automodule:: GPy.inference.samplers - :members: - :undoc-members: - :show-inheritance: - -GPy.inference.scg module ------------------------- - -.. automodule:: GPy.inference.scg - :members: - :undoc-members: - :show-inheritance: - -GPy.inference.sgd module ------------------------- - -.. automodule:: GPy.inference.sgd - :members: - :undoc-members: - :show-inheritance: +.. toctree:: + GPy.inference.latent_function_inference + GPy.inference.optimization Module contents --------------- diff --git a/doc/GPy.kern.rst b/doc/GPy.kern.rst index b4b9d9aa..9ee59ed6 100644 --- a/doc/GPy.kern.rst +++ b/doc/GPy.kern.rst @@ -1,33 +1,6 @@ GPy.kern package ================ -Subpackages ------------ - -.. toctree:: - - 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 --------------- diff --git a/doc/GPy.likelihoods.rst b/doc/GPy.likelihoods.rst index c3da2650..70679454 100644 --- a/doc/GPy.likelihoods.rst +++ b/doc/GPy.likelihoods.rst @@ -1,28 +1,29 @@ GPy.likelihoods package ======================= -Subpackages ------------ - -.. toctree:: - - GPy.likelihoods.noise_models - Submodules ---------- -GPy.likelihoods.ep module -------------------------- +GPy.likelihoods.bernoulli module +-------------------------------- -.. automodule:: GPy.likelihoods.ep +.. automodule:: GPy.likelihoods.bernoulli :members: :undoc-members: :show-inheritance: -GPy.likelihoods.ep_mixed_noise module -------------------------------------- +GPy.likelihoods.exponential module +---------------------------------- -.. automodule:: GPy.likelihoods.ep_mixed_noise +.. automodule:: GPy.likelihoods.exponential + :members: + :undoc-members: + :show-inheritance: + +GPy.likelihoods.gamma module +---------------------------- + +.. automodule:: GPy.likelihoods.gamma :members: :undoc-members: :show-inheritance: @@ -35,14 +36,6 @@ GPy.likelihoods.gaussian module :undoc-members: :show-inheritance: -GPy.likelihoods.gaussian_mixed_noise module -------------------------------------------- - -.. automodule:: GPy.likelihoods.gaussian_mixed_noise - :members: - :undoc-members: - :show-inheritance: - GPy.likelihoods.likelihood module --------------------------------- @@ -51,10 +44,82 @@ GPy.likelihoods.likelihood module :undoc-members: :show-inheritance: -GPy.likelihoods.noise_model_constructors module ------------------------------------------------ +GPy.likelihoods.link_functions module +------------------------------------- -.. automodule:: GPy.likelihoods.noise_model_constructors +.. 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.negative_binomial module +---------------------------------------- + +.. automodule:: GPy.likelihoods.negative_binomial + :members: + :undoc-members: + :show-inheritance: + +GPy.likelihoods.ordinal module +------------------------------ + +.. automodule:: GPy.likelihoods.ordinal + :members: + :undoc-members: + :show-inheritance: + +GPy.likelihoods.poisson module +------------------------------ + +.. automodule:: GPy.likelihoods.poisson + :members: + :undoc-members: + :show-inheritance: + +GPy.likelihoods.skew_exponential module +--------------------------------------- + +.. automodule:: GPy.likelihoods.skew_exponential + :members: + :undoc-members: + :show-inheritance: + +GPy.likelihoods.skew_normal module +---------------------------------- + +.. automodule:: GPy.likelihoods.skew_normal + :members: + :undoc-members: + :show-inheritance: + +GPy.likelihoods.sstudent_t module +--------------------------------- + +.. automodule:: GPy.likelihoods.sstudent_t + :members: + :undoc-members: + :show-inheritance: + +GPy.likelihoods.student_t module +-------------------------------- + +.. automodule:: GPy.likelihoods.student_t + :members: + :undoc-members: + :show-inheritance: + +GPy.likelihoods.symbolic module +------------------------------- + +.. automodule:: GPy.likelihoods.symbolic :members: :undoc-members: :show-inheritance: diff --git a/doc/GPy.mappings.rst b/doc/GPy.mappings.rst index c48cb06e..e5d89872 100644 --- a/doc/GPy.mappings.rst +++ b/doc/GPy.mappings.rst @@ -4,6 +4,14 @@ GPy.mappings package Submodules ---------- +GPy.mappings.additive module +---------------------------- + +.. automodule:: GPy.mappings.additive + :members: + :undoc-members: + :show-inheritance: + GPy.mappings.kernel module -------------------------- @@ -28,6 +36,14 @@ GPy.mappings.mlp module :undoc-members: :show-inheritance: +GPy.mappings.symbolic module +---------------------------- + +.. automodule:: GPy.mappings.symbolic + :members: + :undoc-members: + :show-inheritance: + Module contents --------------- diff --git a/doc/GPy.models.rst b/doc/GPy.models.rst index 4440513e..5ee7e3a9 100644 --- a/doc/GPy.models.rst +++ b/doc/GPy.models.rst @@ -20,14 +20,6 @@ GPy.models.bcgplvm module :undoc-members: :show-inheritance: -GPy.models.fitc_classification module -------------------------------------- - -.. automodule:: GPy.models.fitc_classification - :members: - :undoc-members: - :show-inheritance: - GPy.models.gp_classification module ----------------------------------- @@ -36,6 +28,30 @@ GPy.models.gp_classification module :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_multioutput_regression module ------------------------------------------- @@ -52,6 +68,14 @@ GPy.models.gp_regression module :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 ----------------------- @@ -84,6 +108,14 @@ GPy.models.sparse_gp_classification module :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_multioutput_regression module -------------------------------------------------- @@ -108,6 +140,22 @@ GPy.models.sparse_gplvm module :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.svigp_regression module ---------------------------------- diff --git a/doc/GPy.plotting.matplot_dep.latent_space_visualizations.controllers.rst b/doc/GPy.plotting.matplot_dep.latent_space_visualizations.controllers.rst new file mode 100644 index 00000000..71826ed6 --- /dev/null +++ b/doc/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: diff --git a/doc/GPy.plotting.matplot_dep.latent_space_visualizations.rst b/doc/GPy.plotting.matplot_dep.latent_space_visualizations.rst new file mode 100644 index 00000000..6e5cf4bd --- /dev/null +++ b/doc/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: diff --git a/doc/GPy.plotting.matplot_dep.rst b/doc/GPy.plotting.matplot_dep.rst new file mode 100644 index 00000000..77780708 --- /dev/null +++ b/doc/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: diff --git a/doc/GPy.plotting.rst b/doc/GPy.plotting.rst new file mode 100644 index 00000000..af035515 --- /dev/null +++ b/doc/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: diff --git a/doc/GPy.rst b/doc/GPy.rst index 60092e91..9be6dbec 100644 --- a/doc/GPy.rst +++ b/doc/GPy.rst @@ -13,6 +13,7 @@ Subpackages GPy.likelihoods GPy.mappings GPy.models + GPy.plotting GPy.testing GPy.util diff --git a/doc/GPy.testing.rst b/doc/GPy.testing.rst index bd5258b7..2d1132d7 100644 --- a/doc/GPy.testing.rst +++ b/doc/GPy.testing.rst @@ -4,22 +4,6 @@ GPy.testing package Submodules ---------- -GPy.testing.bgplvm_tests module -------------------------------- - -.. automodule:: GPy.testing.bgplvm_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.cgd_tests module ----------------------------- - -.. automodule:: GPy.testing.cgd_tests - :members: - :undoc-members: - :show-inheritance: - GPy.testing.examples_tests module --------------------------------- @@ -28,10 +12,18 @@ GPy.testing.examples_tests module :undoc-members: :show-inheritance: -GPy.testing.gplvm_tests module ------------------------------- +GPy.testing.fitc module +----------------------- -.. automodule:: GPy.testing.gplvm_tests +.. automodule:: GPy.testing.fitc + :members: + :undoc-members: + :show-inheritance: + +GPy.testing.index_operations_tests module +----------------------------------------- + +.. automodule:: GPy.testing.index_operations_tests :members: :undoc-members: :show-inheritance: @@ -44,18 +36,42 @@ GPy.testing.kernel_tests module :undoc-members: :show-inheritance: -GPy.testing.mapping_tests module --------------------------------- +GPy.testing.likelihood_tests module +----------------------------------- -.. automodule:: GPy.testing.mapping_tests +.. automodule:: GPy.testing.likelihood_tests :members: :undoc-members: :show-inheritance: -GPy.testing.mrd_tests module ----------------------------- +GPy.testing.model_tests module +------------------------------ -.. automodule:: GPy.testing.mrd_tests +.. automodule:: GPy.testing.model_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: @@ -68,38 +84,6 @@ GPy.testing.prior_tests module :undoc-members: :show-inheritance: -GPy.testing.psi_stat_expectation_tests module ---------------------------------------------- - -.. automodule:: GPy.testing.psi_stat_expectation_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.psi_stat_gradient_tests module ------------------------------------------- - -.. automodule:: GPy.testing.psi_stat_gradient_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.sparse_gplvm_tests module -------------------------------------- - -.. automodule:: GPy.testing.sparse_gplvm_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.unit_tests module ------------------------------ - -.. automodule:: GPy.testing.unit_tests - :members: - :undoc-members: - :show-inheritance: - Module contents --------------- diff --git a/doc/GPy.util.rst b/doc/GPy.util.rst index c86280a7..14c7643b 100644 --- a/doc/GPy.util.rst +++ b/doc/GPy.util.rst @@ -1,20 +1,21 @@ GPy.util package ================ -Subpackages ------------ - -.. toctree:: - - GPy.util.latent_space_visualizations - Submodules ---------- -GPy.util.Tango module ---------------------- +GPy.util.block_matrices module +------------------------------ -.. automodule:: GPy.util.Tango +.. automodule:: GPy.util.block_matrices + :members: + :undoc-members: + :show-inheritance: + +GPy.util.caching module +----------------------- + +.. automodule:: GPy.util.caching :members: :undoc-members: :show-inheritance: @@ -27,6 +28,14 @@ GPy.util.classification module :undoc-members: :show-inheritance: +GPy.util.config module +---------------------- + +.. automodule:: GPy.util.config + :members: + :undoc-members: + :show-inheritance: + GPy.util.datasets module ------------------------ @@ -35,6 +44,14 @@ GPy.util.datasets module :undoc-members: :show-inheritance: +GPy.util.debug module +--------------------- + +.. automodule:: GPy.util.debug + :members: + :undoc-members: + :show-inheritance: + GPy.util.decorators module -------------------------- @@ -43,6 +60,46 @@ GPy.util.decorators module :undoc-members: :show-inheritance: +GPy.util.diag module +-------------------- + +.. automodule:: GPy.util.diag + :members: + :undoc-members: + :show-inheritance: + +GPy.util.erfcx module +--------------------- + +.. automodule:: GPy.util.erfcx + :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 ---------------------- @@ -51,6 +108,22 @@ GPy.util.linalg module :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 -------------------- @@ -67,6 +140,14 @@ GPy.util.mocap module :undoc-members: :show-inheritance: +GPy.util.mpi module +------------------- + +.. automodule:: GPy.util.mpi + :members: + :undoc-members: + :show-inheritance: + GPy.util.multioutput module --------------------------- @@ -75,18 +156,34 @@ GPy.util.multioutput module :undoc-members: :show-inheritance: -GPy.util.plot module --------------------- +GPy.util.netpbmfile module +-------------------------- -.. automodule:: GPy.util.plot +.. automodule:: GPy.util.netpbmfile :members: :undoc-members: :show-inheritance: -GPy.util.plot_latent module ---------------------------- +GPy.util.normalizer module +-------------------------- -.. automodule:: GPy.util.plot_latent +.. 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: @@ -99,18 +196,26 @@ GPy.util.squashers module :undoc-members: :show-inheritance: -GPy.util.univariate_Gaussian module ------------------------------------ +GPy.util.subarray_and_sorting module +------------------------------------ -.. automodule:: GPy.util.univariate_Gaussian +.. automodule:: GPy.util.subarray_and_sorting :members: :undoc-members: :show-inheritance: -GPy.util.visualize module -------------------------- +GPy.util.symbolic module +------------------------ -.. automodule:: GPy.util.visualize +.. automodule:: GPy.util.symbolic + :members: + :undoc-members: + :show-inheritance: + +GPy.util.univariate_Gaussian module +----------------------------------- + +.. automodule:: GPy.util.univariate_Gaussian :members: :undoc-members: :show-inheritance: diff --git a/doc/tuto_creating_new_models.rst b/doc/tuto_creating_new_models.rst index 5c51cdad..c5196c33 100644 --- a/doc/tuto_creating_new_models.rst +++ b/doc/tuto_creating_new_models.rst @@ -39,8 +39,9 @@ Obligatory methods :py:meth:`~GPy.core.model.Model.parameters_changed` : Updates the internal state of the model and sets the gradient of each parameter handle in the hierarchy with respect to the - log_likelihod. Thus here we need to put the negative derivative of - the rosenbrock function: + log_likelihod. Thus here we need to set the negative derivative of + the rosenbrock function for the parameters. In this case it is the + gradient for self.X: self.X.gradient = -scipy.optimize.rosen_der(self.X) diff --git a/doc/tuto_interacting_with_models.rst b/doc/tuto_interacting_with_models.rst index 5bd0511e..27980665 100644 --- a/doc/tuto_interacting_with_models.rst +++ b/doc/tuto_interacting_with_models.rst @@ -40,24 +40,21 @@ is shown. For each parameter, the table contains the name of the parameter, the current value, and in case there are defined: constraints, ties and prior distrbutions associated. :: - Log-likelihood: 6.309e+02 + Name : sparse gp + Log-likelihood : -405.646051581 + Number of Parameters : 8 + Parameters: + sparse_gp. | Value | Constraint | Prior | Tied to + inducing inputs | (5, 1) | | | + rbf.variance | 1.0 | +ve | | + rbf.lengthscale | 1.0 | +ve | | + Gaussian_noise.variance | 1.0 | +ve | | + - Name | Value | Constraints | Ties | Prior - ------------------------------------------------------------------ - iip_0_0 | -1.4671 | | | - iip_1_0 | 2.6378 | | | - iip_2_0 | -0.0396 | | | - iip_3_0 | -2.6372 | | | - iip_4_0 | 1.4704 | | | - rbf_variance | 1.5672 | (+ve) | | - rbf_lengthscale | 2.5625 | (+ve) | | - white_variance | 0.0000 | (+ve) | | - noise_variance | 0.0022 | (+ve) | | - -In this case the kernel parameters (``rbf_variance``, -``rbf_lengthscale`` and ``white_variance``) as well as -the noise parameter (``noise_variance``), are constrained -to be positive, while the inducing inputs have not +In this case the kernel parameters (``rbf.variance``, +``rbf.lengthscale``) as well as +the likelihood noise parameter (``Gaussian_noise.variance``), are constrained +to be positive, while the inducing inputs have no constraints associated. Also there are no ties or prior defined. Setting and fetching parameters by name