mirror of
https://github.com/SheffieldML/GPy.git
synced 2026-05-04 09:12:38 +02:00
added robust pickling, switches to old behaviour, if get/setstate not implemented
This commit is contained in:
Max Zwiessele
parent
05e8e75c58
commit
f5effb8cb6
27 changed files with 392 additions and 283 deletions
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@ -9,6 +9,38 @@ core Package
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:undoc-members:
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:show-inheritance:
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:mod:`domains` Module
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---------------------
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.. automodule:: GPy.core.domains
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:members:
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:undoc-members:
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||||
:show-inheritance:
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||||
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:mod:`fitc` Module
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------------------
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.. automodule:: GPy.core.fitc
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`gp` Module
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----------------
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.. automodule:: GPy.core.gp
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`gp_base` Module
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---------------------
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.. automodule:: GPy.core.gp_base
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`model` Module
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-------------------
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@ -17,10 +49,10 @@ core Package
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:undoc-members:
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:show-inheritance:
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:mod:`parameterised` Module
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:mod:`parameterized` Module
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---------------------------
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.. automodule:: GPy.core.parameterised
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.. automodule:: GPy.core.parameterized
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:members:
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:undoc-members:
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:show-inheritance:
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@ -33,3 +65,27 @@ core Package
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:undoc-members:
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||||
:show-inheritance:
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:mod:`sparse_gp` Module
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-----------------------
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.. automodule:: GPy.core.sparse_gp
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`svigp` Module
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-------------------
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.. automodule:: GPy.core.svigp
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`transformations` Module
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-----------------------------
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.. automodule:: GPy.core.transformations
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:members:
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:undoc-members:
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:show-inheritance:
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||||
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@ -25,14 +25,6 @@ examples Package
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:undoc-members:
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:show-inheritance:
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:mod:`non_gaussian` Module
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--------------------------
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.. automodule:: GPy.examples.non_gaussian
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`regression` Module
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------------------------
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@ -41,6 +33,14 @@ examples Package
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:undoc-members:
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:show-inheritance:
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:mod:`stochastic` Module
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------------------------
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.. automodule:: GPy.examples.stochastic
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`tutorials` Module
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-----------------------
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@ -1,10 +1,18 @@
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inference Package
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=================
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:mod:`SGD` Module
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-----------------
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:mod:`conjugate_gradient_descent` Module
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----------------------------------------
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.. automodule:: GPy.inference.SGD
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.. automodule:: GPy.inference.conjugate_gradient_descent
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`gradient_descent_update_rules` Module
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-------------------------------------------
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.. automodule:: GPy.inference.gradient_descent_update_rules
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:members:
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:undoc-members:
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:show-inheritance:
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@ -25,3 +33,19 @@ inference Package
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:undoc-members:
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:show-inheritance:
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:mod:`scg` Module
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-----------------
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.. automodule:: GPy.inference.scg
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`sgd` Module
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-----------------
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.. automodule:: GPy.inference.sgd
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:members:
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:undoc-members:
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:show-inheritance:
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161
doc/GPy.kern.rst
161
doc/GPy.kern.rst
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@ -9,38 +9,6 @@ kern Package
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:undoc-members:
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:show-inheritance:
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:mod:`Brownian` Module
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----------------------
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.. automodule:: GPy.kern.Brownian
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`Matern32` Module
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----------------------
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.. automodule:: GPy.kern.Matern32
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`Matern52` Module
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----------------------
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.. automodule:: GPy.kern.Matern52
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`bias` Module
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------------------
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.. automodule:: GPy.kern.bias
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`constructors` Module
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--------------------------
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@ -49,30 +17,6 @@ kern Package
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:undoc-members:
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:show-inheritance:
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:mod:`coregionalise` Module
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---------------------------
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.. automodule:: GPy.kern.coregionalise
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`exponential` Module
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-------------------------
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.. automodule:: GPy.kern.exponential
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`finite_dimensional` Module
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--------------------------------
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.. automodule:: GPy.kern.finite_dimensional
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`kern` Module
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------------------
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@ -81,107 +25,10 @@ kern Package
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:undoc-members:
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:show-inheritance:
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:mod:`kernpart` Module
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----------------------
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Subpackages
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-----------
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.. automodule:: GPy.kern.kernpart
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:members:
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:undoc-members:
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:show-inheritance:
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.. toctree::
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:mod:`linear` Module
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--------------------
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.. automodule:: GPy.kern.linear
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`periodic_Matern32` Module
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-------------------------------
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.. automodule:: GPy.kern.periodic_Matern32
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`periodic_Matern52` Module
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-------------------------------
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.. automodule:: GPy.kern.periodic_Matern52
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`periodic_exponential` Module
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----------------------------------
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.. automodule:: GPy.kern.periodic_exponential
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`prod` Module
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------------------
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.. automodule:: GPy.kern.prod
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`prod_orthogonal` Module
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-----------------------------
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.. automodule:: GPy.kern.prod_orthogonal
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`rational_quadratic` Module
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--------------------------------
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.. automodule:: GPy.kern.rational_quadratic
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`rbf` Module
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-----------------
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.. automodule:: GPy.kern.rbf
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`spline` Module
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--------------------
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.. automodule:: GPy.kern.spline
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`symmetric` Module
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-----------------------
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.. automodule:: GPy.kern.symmetric
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`sympykern` Module
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-----------------------
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.. automodule:: GPy.kern.sympykern
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`white` Module
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-------------------
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.. automodule:: GPy.kern.white
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:members:
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:undoc-members:
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:show-inheritance:
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GPy.kern.parts
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@ -9,7 +9,7 @@ likelihoods Package
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:undoc-members:
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:show-inheritance:
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:mod:`EP` Module
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:mod:`ep` Module
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----------------
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.. automodule:: GPy.likelihoods.ep
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@ -17,7 +17,7 @@ likelihoods Package
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:undoc-members:
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:show-inheritance:
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:mod:`Gaussian` Module
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:mod:`gaussian` Module
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----------------------
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.. automodule:: GPy.likelihoods.gaussian
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@ -41,3 +41,11 @@ likelihoods Package
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:undoc-members:
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:show-inheritance:
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:mod:`link_functions` Module
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----------------------------
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.. automodule:: GPy.likelihoods.link_functions
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:members:
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:undoc-members:
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:show-inheritance:
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@ -9,7 +9,7 @@ models Package
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:undoc-members:
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:show-inheritance:
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:mod:`Bayesian_GPLVM` Module
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:mod:`bayesian_gplvm` Module
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----------------------------
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.. automodule:: GPy.models.bayesian_gplvm
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:undoc-members:
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:show-inheritance:
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:mod:`gp` Module
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----------------
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:mod:`fitc_classification` Module
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---------------------------------
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.. automodule:: GPy.models.gp
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.. automodule:: GPy.models.fitc_classification
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`gplvm` Module
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-------------------
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:mod:`gp_classification` Module
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-------------------------------
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.. automodule:: GPy.models.gplvm
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.. automodule:: GPy.models.gp_classification
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:members:
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:undoc-members:
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:show-inheritance:
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@ -41,18 +41,26 @@ models Package
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:undoc-members:
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:show-inheritance:
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:mod:`sparse_gp` Module
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-----------------------
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:mod:`gplvm` Module
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-------------------
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.. automodule:: GPy.models.sparse_gp
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.. automodule:: GPy.models.gplvm
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`SparseGPLVM` Module
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--------------------------
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:mod:`mrd` Module
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-----------------
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.. automodule:: GPy.models.sparse_gplvm
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.. automodule:: GPy.models.mrd
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`sparse_gp_classification` Module
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--------------------------------------
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.. automodule:: GPy.models.sparse_gp_classification
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:members:
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:undoc-members:
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:show-inheritance:
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@ -65,13 +73,21 @@ models Package
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:undoc-members:
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:show-inheritance:
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.. :mod:`uncollapsed_sparse_GP` Module
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.. -----------------------------------
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:mod:`sparse_gplvm` Module
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--------------------------
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.. .. automodule:: GPy.models.uncollapsed_sparse_GP
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.. :members:
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.. :undoc-members:
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.. :show-inheritance:
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.. automodule:: GPy.models.sparse_gplvm
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`svigp_regression` Module
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------------------------------
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.. automodule:: GPy.models.svigp_regression
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`warped_gp` Module
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-----------------------
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testing Package
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===============
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:mod:`testing` Package
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----------------------
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.. automodule:: GPy.testing
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`bgplvm_tests` Module
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--------------------------
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@ -9,6 +17,22 @@ testing Package
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:undoc-members:
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:show-inheritance:
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:mod:`cgd_tests` Module
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-----------------------
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.. automodule:: GPy.testing.cgd_tests
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`checkgrad` Module
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-----------------------
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.. automodule:: GPy.testing.checkgrad
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`examples_tests` Module
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----------------------------
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@ -33,6 +57,14 @@ testing Package
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:undoc-members:
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:show-inheritance:
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:mod:`mrd_tests` Module
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-----------------------
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.. automodule:: GPy.testing.mrd_tests
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`prior_tests` Module
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-------------------------
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@ -41,6 +73,22 @@ testing Package
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:undoc-members:
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:show-inheritance:
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:mod:`psi_stat_expactation_tests` Module
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----------------------------------------
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.. automodule:: GPy.testing.psi_stat_expactation_tests
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:members:
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||||
:undoc-members:
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:show-inheritance:
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:mod:`psi_stat_gradient_tests` Module
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-------------------------------------
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.. automodule:: GPy.testing.psi_stat_gradient_tests
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:members:
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:undoc-members:
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:show-inheritance:
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||||
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:mod:`sparse_gplvm_tests` Module
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--------------------------------
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@ -17,6 +17,14 @@ util Package
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:undoc-members:
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||||
:show-inheritance:
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:mod:`classification` Module
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----------------------------
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.. automodule:: GPy.util.classification
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
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:mod:`datasets` Module
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----------------------
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@ -25,6 +33,14 @@ util Package
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:undoc-members:
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||||
:show-inheritance:
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||||
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||||
:mod:`decorators` Module
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------------------------
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.. automodule:: GPy.util.decorators
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
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:mod:`linalg` Module
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--------------------
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@ -41,6 +57,22 @@ util Package
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|||
:undoc-members:
|
||||
:show-inheritance:
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||||
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||||
:mod:`mocap` Module
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-------------------
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.. automodule:: GPy.util.mocap
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
|
||||
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:mod:`pca` Module
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-----------------
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||||
|
||||
.. automodule:: GPy.util.pca
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`plot` Module
|
||||
------------------
|
||||
|
||||
|
|
@ -49,6 +81,14 @@ util Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`plot_latent` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: GPy.util.plot_latent
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`squashers` Module
|
||||
-----------------------
|
||||
|
||||
|
|
@ -57,6 +97,22 @@ util Package
|
|||
: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
|
||||
-------------------------------
|
||||
|
||||
|
|
|
|||
|
|
@ -103,8 +103,10 @@ class Mock(object):
|
|||
#import mock
|
||||
|
||||
print "Mocking"
|
||||
MOCK_MODULES = ['pylab', 'sympy', 'sympy.utilities', 'sympy.utilities.codegen', 'sympy.core.cache', 'sympy.core', 'sympy.parsing', 'sympy.parsing.sympy_parser', 'matplotlib']
|
||||
#'matplotlib', 'matplotlib.color', 'matplotlib.pyplot', 'pylab' ]
|
||||
MOCK_MODULES = ['sympy',
|
||||
'sympy.utilities', 'sympy.utilities.codegen', 'sympy.core.cache',
|
||||
'sympy.core', 'sympy.parsing', 'sympy.parsing.sympy_parser',
|
||||
]
|
||||
for mod_name in MOCK_MODULES:
|
||||
sys.modules[mod_name] = Mock()
|
||||
|
||||
|
|
@ -288,7 +290,7 @@ latex_elements = {
|
|||
#'pointsize': '10pt',
|
||||
|
||||
# Additional stuff for the LaTeX preamble.
|
||||
#'preamble': '',
|
||||
'preamble': '\\usepackage{MnSymbol}',
|
||||
}
|
||||
|
||||
# Grouping the document tree into LaTeX files. List of tuples
|
||||
|
|
|
|||
|
|
@ -11,6 +11,7 @@ For a quick start, you can have a look at one of the tutorials:
|
|||
* `Interacting with models <tuto_interacting_with_models.html>`_
|
||||
* `A kernel overview <tuto_kernel_overview.html>`_
|
||||
* `Writing new kernels <tuto_creating_new_kernels.html>`_
|
||||
* `Writing new models <tuto_creating_new_models.html>`_
|
||||
|
||||
You may also be interested by some examples in the GPy/examples folder.
|
||||
|
||||
|
|
|
|||
|
|
@ -1,3 +1,5 @@
|
|||
.. _interacting_with_models:
|
||||
|
||||
*************************************
|
||||
Interacting with models
|
||||
*************************************
|
||||
|
|
@ -210,6 +212,6 @@ white_variance and noise_variance are tied together.::
|
|||
|
||||
Further Reading
|
||||
===============
|
||||
All of the mechansiams for dealing with parameters are baked right into GPy.core.model, from which all of the classes in GPy.models inherrit. To learn how to construct your own model, you might want to read ??link?? creating_new_models.
|
||||
All of the mechansiams for dealing with parameters are baked right into GPy.core.model, from which all of the classes in GPy.models inherrit. To learn how to construct your own model, you might want to read :ref:`creating_new_models`.
|
||||
|
||||
By deafult, GPy uses the tnc optimizer (from scipy.optimize.tnc). To use other optimisers, and to control the setting of those optimisers, as well as other funky features like automated restarts and diagnostics, you can read the optimization tutorial ??link??.
|
||||
By deafult, GPy uses the scg optimizer. To use other optimisers, and to control the setting of those optimisers, as well as other funky features like automated restarts and diagnostics, you can read the optimization tutorial ??link??.
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue