diff --git a/GPy/core/variational.py b/GPy/core/variational.py deleted file mode 100644 index 74287dcf..00000000 --- a/GPy/core/variational.py +++ /dev/null @@ -1,19 +0,0 @@ -''' -Created on 6 Nov 2013 - -@author: maxz -''' -from parameterized import Parameterized -from parameter import Param - -class Normal(Parameterized): - ''' - Normal distribution for variational approximations. - - holds the means and variances for a factorizing multivariate normal distribution - ''' - def __init__(self, name, means, variances): - Parameterized.__init__(self, name=name) - self.means = Param("mean", means) - self.variances = Param('variance', variances) - self.add_parameters(self.means, self.variances) \ No newline at end of file diff --git a/GPy/testing/likelihoods_tests.py b/GPy/testing/likelihoods_tests.py index 58c9a64b..d14c9a41 100644 --- a/GPy/testing/likelihoods_tests.py +++ b/GPy/testing/likelihoods_tests.py @@ -593,7 +593,6 @@ class LaplaceTests(unittest.TestCase): grad.checkgrad(verbose=1) self.assertTrue(grad.checkgrad()) - #@unittest.skip('Not working yet, needs to be checked') def test_laplace_log_likelihood(self): debug = False real_std = 0.1 diff --git a/doc/GPy.core.rst b/doc/GPy.core.rst index d7f18192..c4f1849d 100644 --- a/doc/GPy.core.rst +++ b/doc/GPy.core.rst @@ -1,107 +1,102 @@ -core Package -============ +GPy.core package +================ -:mod:`core` Package -------------------- +Submodules +---------- -.. automodule:: GPy.core - :members: - :undoc-members: - :show-inheritance: - -:mod:`domains` Module ---------------------- +GPy.core.domains module +----------------------- .. automodule:: GPy.core.domains :members: :undoc-members: :show-inheritance: -:mod:`fitc` Module ------------------- +GPy.core.fitc module +-------------------- .. automodule:: GPy.core.fitc :members: :undoc-members: :show-inheritance: -:mod:`gp` Module ----------------- +GPy.core.gp module +------------------ .. automodule:: GPy.core.gp :members: :undoc-members: :show-inheritance: -:mod:`gp_base` Module ---------------------- +GPy.core.gp_base module +----------------------- .. automodule:: GPy.core.gp_base :members: :undoc-members: :show-inheritance: -:mod:`mapping` Module ---------------------- +GPy.core.mapping module +----------------------- .. automodule:: GPy.core.mapping :members: :undoc-members: :show-inheritance: -:mod:`model` Module -------------------- +GPy.core.model module +--------------------- .. automodule:: GPy.core.model :members: :undoc-members: :show-inheritance: -:mod:`parameterized` Module ---------------------------- +GPy.core.parameterized module +----------------------------- .. automodule:: GPy.core.parameterized :members: :undoc-members: :show-inheritance: -:mod:`priors` Module --------------------- +GPy.core.priors module +---------------------- .. automodule:: GPy.core.priors :members: :undoc-members: :show-inheritance: -:mod:`sparse_gp` Module ------------------------ +GPy.core.sparse_gp module +------------------------- .. automodule:: GPy.core.sparse_gp :members: :undoc-members: :show-inheritance: -:mod:`svigp` Module -------------------- +GPy.core.svigp module +--------------------- .. automodule:: GPy.core.svigp :members: :undoc-members: :show-inheritance: -:mod:`transformations` Module ------------------------------ +GPy.core.transformations module +------------------------------- .. automodule:: GPy.core.transformations :members: :undoc-members: :show-inheritance: -:mod:`variational` Module -------------------------- -.. automodule:: GPy.core.variational +Module contents +--------------- + +.. automodule:: GPy.core :members: :undoc-members: :show-inheritance: - diff --git a/doc/GPy.examples.rst b/doc/GPy.examples.rst index 176ae396..bde015dd 100644 --- a/doc/GPy.examples.rst +++ b/doc/GPy.examples.rst @@ -1,59 +1,62 @@ -examples Package -================ +GPy.examples package +==================== -:mod:`examples` Package ------------------------ +Submodules +---------- -.. automodule:: GPy.examples - :members: - :undoc-members: - :show-inheritance: - -:mod:`classification` Module ----------------------------- +GPy.examples.classification module +---------------------------------- .. automodule:: GPy.examples.classification :members: :undoc-members: :show-inheritance: -:mod:`dimensionality_reduction` Module --------------------------------------- +GPy.examples.dimensionality_reduction module +-------------------------------------------- .. automodule:: GPy.examples.dimensionality_reduction :members: :undoc-members: :show-inheritance: -:mod:`laplace_approximations` Module ------------------------------------- +GPy.examples.non_gaussian module +-------------------------------- -.. automodule:: GPy.examples.laplace_approximations +.. automodule:: GPy.examples.non_gaussian :members: :undoc-members: :show-inheritance: -:mod:`regression` Module ------------------------- +GPy.examples.regression module +------------------------------ .. automodule:: GPy.examples.regression :members: :undoc-members: :show-inheritance: -:mod:`stochastic` Module ------------------------- +GPy.examples.stochastic module +------------------------------ .. automodule:: GPy.examples.stochastic :members: :undoc-members: :show-inheritance: -:mod:`tutorials` Module ------------------------ +GPy.examples.tutorials module +----------------------------- .. automodule:: GPy.examples.tutorials :members: :undoc-members: :show-inheritance: + +Module contents +--------------- + +.. automodule:: GPy.examples + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/GPy.inference.rst b/doc/GPy.inference.rst index 6a1bef4a..28f42994 100644 --- a/doc/GPy.inference.rst +++ b/doc/GPy.inference.rst @@ -1,51 +1,62 @@ -inference Package -================= +GPy.inference package +===================== -:mod:`conjugate_gradient_descent` Module ----------------------------------------- +Submodules +---------- + +GPy.inference.conjugate_gradient_descent module +----------------------------------------------- .. automodule:: GPy.inference.conjugate_gradient_descent :members: :undoc-members: :show-inheritance: -:mod:`gradient_descent_update_rules` Module -------------------------------------------- +GPy.inference.gradient_descent_update_rules module +-------------------------------------------------- .. automodule:: GPy.inference.gradient_descent_update_rules :members: :undoc-members: :show-inheritance: -:mod:`optimization` Module --------------------------- +GPy.inference.optimization module +--------------------------------- .. automodule:: GPy.inference.optimization :members: :undoc-members: :show-inheritance: -:mod:`samplers` Module ----------------------- +GPy.inference.samplers module +----------------------------- .. automodule:: GPy.inference.samplers :members: :undoc-members: :show-inheritance: -:mod:`scg` Module ------------------ +GPy.inference.scg module +------------------------ .. automodule:: GPy.inference.scg :members: :undoc-members: :show-inheritance: -:mod:`sgd` Module ------------------ +GPy.inference.sgd module +------------------------ .. automodule:: GPy.inference.sgd :members: :undoc-members: :show-inheritance: + +Module contents +--------------- + +.. automodule:: GPy.inference + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/GPy.kern.parts.rst b/doc/GPy.kern.parts.rst index 45d3e235..59c48d96 100644 --- a/doc/GPy.kern.parts.rst +++ b/doc/GPy.kern.parts.rst @@ -1,275 +1,278 @@ -parts Package -============= +GPy.kern.parts package +====================== -:mod:`parts` Package --------------------- +Submodules +---------- -.. automodule:: GPy.kern.parts - :members: - :undoc-members: - :show-inheritance: - -:mod:`Brownian` Module ----------------------- +GPy.kern.parts.Brownian module +------------------------------ .. automodule:: GPy.kern.parts.Brownian :members: :undoc-members: :show-inheritance: -:mod:`Matern32` Module ----------------------- +GPy.kern.parts.Matern32 module +------------------------------ .. automodule:: GPy.kern.parts.Matern32 :members: :undoc-members: :show-inheritance: -:mod:`Matern52` Module ----------------------- +GPy.kern.parts.Matern52 module +------------------------------ .. automodule:: GPy.kern.parts.Matern52 :members: :undoc-members: :show-inheritance: -:mod:`ODE_1` Module -------------------- +GPy.kern.parts.ODE_1 module +--------------------------- .. automodule:: GPy.kern.parts.ODE_1 :members: :undoc-members: :show-inheritance: -:mod:`ODE_UY` Module --------------------- +GPy.kern.parts.ODE_UY module +---------------------------- .. automodule:: GPy.kern.parts.ODE_UY :members: :undoc-members: :show-inheritance: -:mod:`bias` Module ------------------- +GPy.kern.parts.bias module +-------------------------- .. automodule:: GPy.kern.parts.bias :members: :undoc-members: :show-inheritance: -:mod:`coregionalize` Module ---------------------------- +GPy.kern.parts.coregionalize module +----------------------------------- .. automodule:: GPy.kern.parts.coregionalize :members: :undoc-members: :show-inheritance: -:mod:`eq_ode1` Module ---------------------- +GPy.kern.parts.eq_ode1 module +----------------------------- .. automodule:: GPy.kern.parts.eq_ode1 :members: :undoc-members: :show-inheritance: -:mod:`exponential` Module -------------------------- +GPy.kern.parts.exponential module +--------------------------------- .. automodule:: GPy.kern.parts.exponential :members: :undoc-members: :show-inheritance: -:mod:`finite_dimensional` Module --------------------------------- +GPy.kern.parts.finite_dimensional module +---------------------------------------- .. automodule:: GPy.kern.parts.finite_dimensional :members: :undoc-members: :show-inheritance: -:mod:`fixed` Module -------------------- +GPy.kern.parts.fixed module +--------------------------- .. automodule:: GPy.kern.parts.fixed :members: :undoc-members: :show-inheritance: -:mod:`gibbs` Module -------------------- +GPy.kern.parts.gibbs module +--------------------------- .. automodule:: GPy.kern.parts.gibbs :members: :undoc-members: :show-inheritance: -:mod:`hetero` Module --------------------- +GPy.kern.parts.hetero module +---------------------------- .. automodule:: GPy.kern.parts.hetero :members: :undoc-members: :show-inheritance: -:mod:`hierarchical` Module --------------------------- +GPy.kern.parts.hierarchical module +---------------------------------- .. automodule:: GPy.kern.parts.hierarchical :members: :undoc-members: :show-inheritance: -:mod:`independent_outputs` Module ---------------------------------- +GPy.kern.parts.independent_outputs module +----------------------------------------- .. automodule:: GPy.kern.parts.independent_outputs :members: :undoc-members: :show-inheritance: -:mod:`kernpart` Module ----------------------- +GPy.kern.parts.kernpart module +------------------------------ .. automodule:: GPy.kern.parts.kernpart :members: :undoc-members: :show-inheritance: -:mod:`linear` Module --------------------- +GPy.kern.parts.linear module +---------------------------- .. automodule:: GPy.kern.parts.linear :members: :undoc-members: :show-inheritance: -:mod:`mlp` Module ------------------ +GPy.kern.parts.mlp module +------------------------- .. automodule:: GPy.kern.parts.mlp :members: :undoc-members: :show-inheritance: -:mod:`periodic_Matern32` Module -------------------------------- +GPy.kern.parts.periodic_Matern32 module +--------------------------------------- .. automodule:: GPy.kern.parts.periodic_Matern32 :members: :undoc-members: :show-inheritance: -:mod:`periodic_Matern52` Module -------------------------------- +GPy.kern.parts.periodic_Matern52 module +--------------------------------------- .. automodule:: GPy.kern.parts.periodic_Matern52 :members: :undoc-members: :show-inheritance: -:mod:`periodic_exponential` Module ----------------------------------- +GPy.kern.parts.periodic_exponential module +------------------------------------------ .. automodule:: GPy.kern.parts.periodic_exponential :members: :undoc-members: :show-inheritance: -:mod:`poly` Module ------------------- +GPy.kern.parts.poly module +-------------------------- .. automodule:: GPy.kern.parts.poly :members: :undoc-members: :show-inheritance: -:mod:`prod` Module ------------------- +GPy.kern.parts.prod module +-------------------------- .. automodule:: GPy.kern.parts.prod :members: :undoc-members: :show-inheritance: -:mod:`prod_orthogonal` Module ------------------------------ +GPy.kern.parts.prod_orthogonal module +------------------------------------- .. automodule:: GPy.kern.parts.prod_orthogonal :members: :undoc-members: :show-inheritance: -:mod:`rational_quadratic` Module --------------------------------- +GPy.kern.parts.rational_quadratic module +---------------------------------------- .. automodule:: GPy.kern.parts.rational_quadratic :members: :undoc-members: :show-inheritance: -:mod:`rbf` Module ------------------ +GPy.kern.parts.rbf module +------------------------- .. automodule:: GPy.kern.parts.rbf :members: :undoc-members: :show-inheritance: -:mod:`rbf_inv` Module ---------------------- +GPy.kern.parts.rbf_inv module +----------------------------- .. automodule:: GPy.kern.parts.rbf_inv :members: :undoc-members: :show-inheritance: -:mod:`rbfcos` Module --------------------- +GPy.kern.parts.rbfcos module +---------------------------- .. automodule:: GPy.kern.parts.rbfcos :members: :undoc-members: :show-inheritance: -:mod:`spline` Module --------------------- +GPy.kern.parts.spline module +---------------------------- .. automodule:: GPy.kern.parts.spline :members: :undoc-members: :show-inheritance: -:mod:`symmetric` Module ------------------------ +GPy.kern.parts.symmetric module +------------------------------- .. automodule:: GPy.kern.parts.symmetric :members: :undoc-members: :show-inheritance: -:mod:`sympy_helpers` Module ---------------------------- +GPy.kern.parts.sympy_helpers module +----------------------------------- .. automodule:: GPy.kern.parts.sympy_helpers :members: :undoc-members: :show-inheritance: -:mod:`sympykern` Module ------------------------ +GPy.kern.parts.sympykern module +------------------------------- .. automodule:: GPy.kern.parts.sympykern :members: :undoc-members: :show-inheritance: -:mod:`white` Module -------------------- +GPy.kern.parts.white module +--------------------------- .. automodule:: GPy.kern.parts.white :members: :undoc-members: :show-inheritance: + +Module contents +--------------- + +.. automodule:: GPy.kern.parts + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/GPy.kern.rst b/doc/GPy.kern.rst index 35d9ec00..b4b9d9aa 100644 --- a/doc/GPy.kern.rst +++ b/doc/GPy.kern.rst @@ -1,29 +1,5 @@ -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: +GPy.kern package +================ Subpackages ----------- @@ -32,3 +8,30 @@ 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: diff --git a/doc/GPy.likelihoods.noise_models.rst b/doc/GPy.likelihoods.noise_models.rst index 19e5e9fe..6fec5aff 100644 --- a/doc/GPy.likelihoods.noise_models.rst +++ b/doc/GPy.likelihoods.noise_models.rst @@ -1,75 +1,78 @@ -noise_models Package -==================== +GPy.likelihoods.noise_models package +==================================== -:mod:`noise_models` Package ---------------------------- +Submodules +---------- -.. automodule:: GPy.likelihoods.noise_models - :members: - :undoc-members: - :show-inheritance: - -:mod:`bernoulli_noise` Module ------------------------------ +GPy.likelihoods.noise_models.bernoulli_noise module +--------------------------------------------------- .. automodule:: GPy.likelihoods.noise_models.bernoulli_noise :members: :undoc-members: :show-inheritance: -:mod:`exponential_noise` Module -------------------------------- +GPy.likelihoods.noise_models.exponential_noise module +----------------------------------------------------- .. automodule:: GPy.likelihoods.noise_models.exponential_noise :members: :undoc-members: :show-inheritance: -:mod:`gamma_noise` Module -------------------------- +GPy.likelihoods.noise_models.gamma_noise module +----------------------------------------------- .. automodule:: GPy.likelihoods.noise_models.gamma_noise :members: :undoc-members: :show-inheritance: -:mod:`gaussian_noise` Module ----------------------------- +GPy.likelihoods.noise_models.gaussian_noise module +-------------------------------------------------- .. automodule:: GPy.likelihoods.noise_models.gaussian_noise :members: :undoc-members: :show-inheritance: -:mod:`gp_transformations` Module --------------------------------- +GPy.likelihoods.noise_models.gp_transformations module +------------------------------------------------------ .. automodule:: GPy.likelihoods.noise_models.gp_transformations :members: :undoc-members: :show-inheritance: -:mod:`noise_distributions` Module ---------------------------------- +GPy.likelihoods.noise_models.noise_distributions module +------------------------------------------------------- .. automodule:: GPy.likelihoods.noise_models.noise_distributions :members: :undoc-members: :show-inheritance: -:mod:`poisson_noise` Module ---------------------------- +GPy.likelihoods.noise_models.poisson_noise module +------------------------------------------------- .. automodule:: GPy.likelihoods.noise_models.poisson_noise :members: :undoc-members: :show-inheritance: -:mod:`student_t_noise` Module ------------------------------ +GPy.likelihoods.noise_models.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: diff --git a/doc/GPy.likelihoods.rst b/doc/GPy.likelihoods.rst index 5dcabbd1..34d98739 100644 --- a/doc/GPy.likelihoods.rst +++ b/doc/GPy.likelihoods.rst @@ -1,69 +1,5 @@ -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: +GPy.likelihoods package +======================= Subpackages ----------- @@ -72,3 +8,70 @@ 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: diff --git a/doc/GPy.mappings.rst b/doc/GPy.mappings.rst index b7444808..c48cb06e 100644 --- a/doc/GPy.mappings.rst +++ b/doc/GPy.mappings.rst @@ -1,35 +1,38 @@ -mappings Package -================ +GPy.mappings package +==================== -:mod:`mappings` Package ------------------------ +Submodules +---------- -.. automodule:: GPy.mappings - :members: - :undoc-members: - :show-inheritance: - -:mod:`kernel` Module --------------------- +GPy.mappings.kernel module +-------------------------- .. automodule:: GPy.mappings.kernel :members: :undoc-members: :show-inheritance: -:mod:`linear` Module --------------------- +GPy.mappings.linear module +-------------------------- .. automodule:: GPy.mappings.linear :members: :undoc-members: :show-inheritance: -:mod:`mlp` Module ------------------ +GPy.mappings.mlp module +----------------------- .. automodule:: GPy.mappings.mlp :members: :undoc-members: :show-inheritance: + +Module contents +--------------- + +.. automodule:: GPy.mappings + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/GPy.models_modules.rst b/doc/GPy.models_modules.rst index 4169ec3a..c16941b1 100644 --- a/doc/GPy.models_modules.rst +++ b/doc/GPy.models_modules.rst @@ -1,131 +1,134 @@ -models_modules Package -====================== +GPy.models_modules package +========================== -:mod:`models_modules` Package ------------------------------ +Submodules +---------- -.. automodule:: GPy.models_modules - :members: - :undoc-members: - :show-inheritance: - -:mod:`bayesian_gplvm` Module ----------------------------- +GPy.models_modules.bayesian_gplvm module +---------------------------------------- .. automodule:: GPy.models_modules.bayesian_gplvm :members: :undoc-members: :show-inheritance: -:mod:`bcgplvm` Module ---------------------- +GPy.models_modules.bcgplvm module +--------------------------------- .. automodule:: GPy.models_modules.bcgplvm :members: :undoc-members: :show-inheritance: -:mod:`fitc_classification` Module ---------------------------------- +GPy.models_modules.fitc_classification module +--------------------------------------------- .. automodule:: GPy.models_modules.fitc_classification :members: :undoc-members: :show-inheritance: -:mod:`gp_classification` Module -------------------------------- +GPy.models_modules.gp_classification module +------------------------------------------- .. automodule:: GPy.models_modules.gp_classification :members: :undoc-members: :show-inheritance: -:mod:`gp_multioutput_regression` Module ---------------------------------------- +GPy.models_modules.gp_multioutput_regression module +--------------------------------------------------- .. automodule:: GPy.models_modules.gp_multioutput_regression :members: :undoc-members: :show-inheritance: -:mod:`gp_regression` Module ---------------------------- +GPy.models_modules.gp_regression module +--------------------------------------- .. automodule:: GPy.models_modules.gp_regression :members: :undoc-members: :show-inheritance: -:mod:`gplvm` Module -------------------- +GPy.models_modules.gplvm module +------------------------------- .. automodule:: GPy.models_modules.gplvm :members: :undoc-members: :show-inheritance: -:mod:`gradient_checker` Module ------------------------------- +GPy.models_modules.gradient_checker module +------------------------------------------ .. automodule:: GPy.models_modules.gradient_checker :members: :undoc-members: :show-inheritance: -:mod:`mrd` Module ------------------ +GPy.models_modules.mrd module +----------------------------- .. automodule:: GPy.models_modules.mrd :members: :undoc-members: :show-inheritance: -:mod:`sparse_gp_classification` Module --------------------------------------- +GPy.models_modules.sparse_gp_classification module +-------------------------------------------------- .. automodule:: GPy.models_modules.sparse_gp_classification :members: :undoc-members: :show-inheritance: -:mod:`sparse_gp_multioutput_regression` Module ----------------------------------------------- +GPy.models_modules.sparse_gp_multioutput_regression module +---------------------------------------------------------- .. automodule:: GPy.models_modules.sparse_gp_multioutput_regression :members: :undoc-members: :show-inheritance: -:mod:`sparse_gp_regression` Module ----------------------------------- +GPy.models_modules.sparse_gp_regression module +---------------------------------------------- .. automodule:: GPy.models_modules.sparse_gp_regression :members: :undoc-members: :show-inheritance: -:mod:`sparse_gplvm` Module --------------------------- +GPy.models_modules.sparse_gplvm module +-------------------------------------- .. automodule:: GPy.models_modules.sparse_gplvm :members: :undoc-members: :show-inheritance: -:mod:`svigp_regression` Module ------------------------------- +GPy.models_modules.svigp_regression module +------------------------------------------ .. automodule:: GPy.models_modules.svigp_regression :members: :undoc-members: :show-inheritance: -:mod:`warped_gp` Module ------------------------ +GPy.models_modules.warped_gp module +----------------------------------- .. automodule:: GPy.models_modules.warped_gp :members: :undoc-members: :show-inheritance: + +Module contents +--------------- + +.. automodule:: GPy.models_modules + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/GPy.rst b/doc/GPy.rst index 31ec3562..cd1afd29 100644 --- a/doc/GPy.rst +++ b/doc/GPy.rst @@ -1,22 +1,6 @@ -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 ----------- @@ -32,3 +16,22 @@ Subpackages GPy.testing GPy.util +Submodules +---------- + +GPy.models module +----------------- + +.. automodule:: GPy.models + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: GPy + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/GPy.testing.rst b/doc/GPy.testing.rst index 15b0cc79..98b001c0 100644 --- a/doc/GPy.testing.rst +++ b/doc/GPy.testing.rst @@ -1,131 +1,134 @@ -testing Package -=============== +GPy.testing package +=================== -:mod:`testing` Package ----------------------- +Submodules +---------- -.. automodule:: GPy.testing - :members: - :undoc-members: - :show-inheritance: - -:mod:`bcgplvm_tests` Module ---------------------------- +GPy.testing.bcgplvm_tests module +-------------------------------- .. automodule:: GPy.testing.bcgplvm_tests :members: :undoc-members: :show-inheritance: -:mod:`bgplvm_tests` Module --------------------------- +GPy.testing.bgplvm_tests module +------------------------------- .. automodule:: GPy.testing.bgplvm_tests :members: :undoc-members: :show-inheritance: -:mod:`cgd_tests` Module ------------------------ +GPy.testing.cgd_tests module +---------------------------- .. automodule:: GPy.testing.cgd_tests :members: :undoc-members: :show-inheritance: -:mod:`examples_tests` Module ----------------------------- +GPy.testing.examples_tests module +--------------------------------- .. automodule:: GPy.testing.examples_tests :members: :undoc-members: :show-inheritance: -:mod:`gp_transformation_tests` Module -------------------------------------- +GPy.testing.gp_transformation_tests module +------------------------------------------ .. automodule:: GPy.testing.gp_transformation_tests :members: :undoc-members: :show-inheritance: -:mod:`gplvm_tests` Module -------------------------- +GPy.testing.gplvm_tests module +------------------------------ .. automodule:: GPy.testing.gplvm_tests :members: :undoc-members: :show-inheritance: -:mod:`kernel_tests` Module --------------------------- +GPy.testing.kernel_tests module +------------------------------- .. automodule:: GPy.testing.kernel_tests :members: :undoc-members: :show-inheritance: -:mod:`likelihoods_tests` Module -------------------------------- +GPy.testing.likelihoods_tests module +------------------------------------ .. automodule:: GPy.testing.likelihoods_tests :members: :undoc-members: :show-inheritance: -:mod:`mapping_tests` Module ---------------------------- +GPy.testing.mapping_tests module +-------------------------------- .. automodule:: GPy.testing.mapping_tests :members: :undoc-members: :show-inheritance: -:mod:`mrd_tests` Module ------------------------ +GPy.testing.mrd_tests module +---------------------------- .. automodule:: GPy.testing.mrd_tests :members: :undoc-members: :show-inheritance: -:mod:`prior_tests` Module -------------------------- +GPy.testing.prior_tests module +------------------------------ .. automodule:: GPy.testing.prior_tests :members: :undoc-members: :show-inheritance: -:mod:`psi_stat_expectation_tests` Module ----------------------------------------- +GPy.testing.psi_stat_expectation_tests module +--------------------------------------------- .. automodule:: GPy.testing.psi_stat_expectation_tests :members: :undoc-members: :show-inheritance: -:mod:`psi_stat_gradient_tests` Module -------------------------------------- +GPy.testing.psi_stat_gradient_tests module +------------------------------------------ .. automodule:: GPy.testing.psi_stat_gradient_tests :members: :undoc-members: :show-inheritance: -:mod:`sparse_gplvm_tests` Module --------------------------------- +GPy.testing.sparse_gplvm_tests module +------------------------------------- .. automodule:: GPy.testing.sparse_gplvm_tests :members: :undoc-members: :show-inheritance: -:mod:`unit_tests` Module ------------------------- +GPy.testing.unit_tests module +----------------------------- .. automodule:: GPy.testing.unit_tests :members: :undoc-members: :show-inheritance: + +Module contents +--------------- + +.. automodule:: GPy.testing + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/GPy.util.latent_space_visualizations.controllers.rst b/doc/GPy.util.latent_space_visualizations.controllers.rst index e78ade7b..a88c1f5c 100644 --- a/doc/GPy.util.latent_space_visualizations.controllers.rst +++ b/doc/GPy.util.latent_space_visualizations.controllers.rst @@ -1,27 +1,30 @@ -controllers Package -=================== +GPy.util.latent_space_visualizations.controllers package +======================================================== -:mod:`controllers` Package --------------------------- +Submodules +---------- -.. automodule:: GPy.util.latent_space_visualizations.controllers - :members: - :undoc-members: - :show-inheritance: - -:mod:`axis_event_controller` Module ------------------------------------ +GPy.util.latent_space_visualizations.controllers.axis_event_controller module +----------------------------------------------------------------------------- .. automodule:: GPy.util.latent_space_visualizations.controllers.axis_event_controller :members: :undoc-members: :show-inheritance: -:mod:`imshow_controller` Module -------------------------------- +GPy.util.latent_space_visualizations.controllers.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: diff --git a/doc/GPy.util.latent_space_visualizations.rst b/doc/GPy.util.latent_space_visualizations.rst index 4b440f61..d8cbd843 100644 --- a/doc/GPy.util.latent_space_visualizations.rst +++ b/doc/GPy.util.latent_space_visualizations.rst @@ -1,13 +1,5 @@ -latent_space_visualizations Package -=================================== - -:mod:`latent_space_visualizations` Package ------------------------------------------- - -.. automodule:: GPy.util.latent_space_visualizations - :members: - :undoc-members: - :show-inheritance: +GPy.util.latent_space_visualizations package +============================================ Subpackages ----------- @@ -15,5 +7,11 @@ 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: diff --git a/doc/GPy.util.rst b/doc/GPy.util.rst index 2e20c006..1c35a7ba 100644 --- a/doc/GPy.util.rst +++ b/doc/GPy.util.rst @@ -1,181 +1,5 @@ -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: +GPy.util package +================ Subpackages ----------- @@ -184,3 +8,190 @@ Subpackages GPy.util.latent_space_visualizations +Submodules +---------- + +GPy.util.Tango module +--------------------- + +.. automodule:: GPy.util.Tango + :members: + :undoc-members: + :show-inheritance: + +GPy.util.block_matrices module +------------------------------ + +.. automodule:: GPy.util.block_matrices + :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.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.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: + +GPy.util.netpbmfile module +-------------------------- + +.. automodule:: GPy.util.netpbmfile + :members: + :undoc-members: + :show-inheritance: + +GPy.util.plot module +-------------------- + +.. automodule:: GPy.util.plot + :members: + :undoc-members: + :show-inheritance: + +GPy.util.plot_latent module +--------------------------- + +.. automodule:: GPy.util.plot_latent + :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.symbolic module +------------------------ + +.. automodule:: GPy.util.symbolic + :members: + :undoc-members: + :show-inheritance: + +GPy.util.univariate_Gaussian module +----------------------------------- + +.. automodule:: GPy.util.univariate_Gaussian + :members: + :undoc-members: + :show-inheritance: + +GPy.util.visualize module +------------------------- + +.. automodule:: GPy.util.visualize + :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: