Merge branch 'devel' of github.com:SheffieldML/GPy into devel

GPy/core/sparse_gp.py

@@ -292,7 +292,7 @@ class SparseGP(GPBase):
                 Kxx = self.kern.Kdiag(Xnew, which_parts=which_parts)
                 var = Kxx - np.sum(Kx * np.dot(Kmmi_LmiBLmi, Kx), 0)
         else:
-            # assert which_p.Tarts=='all', "swithching out parts of variational kernels is not implemented"
+            # assert which_parts=='all', "swithching out parts of variational kernels is not implemented"
             Kx = self.kern.psi1(self.Z, Xnew, X_variance_new) # , which_parts=which_parts) TODO: which_parts
             mu = np.dot(Kx, self.Cpsi1V)
             if full_cov:

GPy/kern/parts/__init__.py

@@ -5,7 +5,7 @@ import exponential
 import finite_dimensional
 import fixed
 import gibbs
-#import hetero #hetero.py is not commited: omitting for now. JH. 
+import hetero
 import hierarchical
 import independent_outputs
 import linear

GPy/models/bayesian_gplvm.py

@@ -8,7 +8,7 @@ from .. import kern
 import itertools
 from matplotlib.colors import colorConverter
 from GPy.inference.optimization import SCG
-from GPy.util import plot_latent
+from GPy.util import plot_latent, linalg
 from GPy.models.gplvm import GPLVM
 from GPy.util.plot_latent import most_significant_input_dimensions
 from matplotlib import pyplot
@@ -140,12 +140,20 @@ class BayesianGPLVM(SparseGP, GPLVM):
         dpsi0 = -0.5 * self.input_dim * self.likelihood.precision
         dpsi2 = self.dL_dpsi2[0][None, :, :] # TODO: this may change if we ignore het. likelihoods
         V = self.likelihood.precision * Y
+
+        #compute CPsi1V
+        if self.Cpsi1V is None:
+            psi1V = np.dot(self.psi1.T, self.likelihood.V)
+            tmp, _ = linalg.dtrtrs(self._Lm, np.asfortranarray(psi1V), lower=1, trans=0)
+            tmp, _ = linalg.dpotrs(self.LB, tmp, lower=1)
+            self.Cpsi1V, _ = linalg.dtrtrs(self._Lm, tmp, lower=1, trans=1)
+
         dpsi1 = np.dot(self.Cpsi1V, V.T)
 
         start = np.zeros(self.input_dim * 2)
 
         for n, dpsi1_n in enumerate(dpsi1.T[:, :, None]):
-            args = (self.kern, self.Z, dpsi0, dpsi1_n, dpsi2)
+            args = (self.kern, self.Z, dpsi0, dpsi1_n.T, dpsi2)
             xopt, fopt, neval, status = SCG(f=latent_cost, gradf=latent_grad, x=start, optargs=args, display=False)
 
             mu, log_S = xopt.reshape(2, 1, -1)

README.md

@@ -1,10 +1,57 @@
 GPy
 ===
 
-A Gaussian processes framework in python
+A Gaussian processes framework in Python.
 
 * [Online documentation](https://gpy.readthedocs.org/en/latest/)
 * [Unit tests (Travis-CI)](https://travis-ci.org/SheffieldML/GPy)
 
 
 Continuous integration status: ![CI status](https://travis-ci.org/SheffieldML/GPy.png)
+
+
+Compiling documentation:
+========================
+
+The documentation is stored in doc/ and is compiled with the Sphinx Python documentation generator, and is written in the reStructuredText format.
+
+The Sphinx documentation is available here: http://sphinx-doc.org/latest/contents.html
+
+
+Installing dependencies:
+------------------------
+
+To compile the documentation, first ensure that Sphinx is installed. On Debian-based systems, this can be achieved as follows:
+
+    sudo apt-get install python-pip
+    sudo pip install sphinx
+
+A LaTeX distribution is also required to compile the equations. Note that the extra packages are necessary to install the unicode packages. To compile the equations to PNG format for use in HTML pages, the package *dvipng* must be installed. IPython is also required. On Debian-based systems, this can be achieved as follows:
+
+    sudo apt-get install texlive texlive-latex-extra texlive-base texlive-recommended
+    sudo apt-get install dvipng
+    sudo apt-get install ipython
+
+
+Compiling documentation:
+------------------------
+
+The documentation can be compiled as follows:
+
+    cd doc
+    make html
+
+The HTML files are then stored in doc/_build/
+
+
+Running unit tests:
+===================
+
+Ensure nose is installed via pip:
+
+    pip install nose
+
+Run nosetests from the root directory of the repository:
+
+    nosetests -v
+

doc/GPy.core.rst

@@ -1,91 +1,102 @@
-core Package
+GPy.core package
-============
+================
 
-:mod:`core` Package
+Submodules
--------------------
+----------
 
-.. automodule:: GPy.core
+GPy.core.domains module
-    :members:
+-----------------------
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`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:`model` Module
+GPy.core.mapping module
--------------------
+-----------------------
+
+.. automodule:: GPy.core.mapping
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.model module
+---------------------
 
 .. automodule:: GPy.core.model
     :members:
     :undoc-members:
     :show-inheritance:
 
-: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:
 
+
+Module contents
+---------------
+
+.. automodule:: GPy.core
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/GPy.examples.rst

@@ -1,51 +1,54 @@
-examples Package
+GPy.examples package
-================
+====================
 
-:mod:`examples` Package
+Submodules
------------------------
+----------
 
-.. automodule:: GPy.examples
+GPy.examples.classification module
-    :members:
+----------------------------------
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`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:`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:

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:

doc/GPy.kern.parts.rst

@@ -0,0 +1,246 @@
+GPy.kern.parts package
+======================
+
+Submodules
+----------
+
+GPy.kern.parts.Brownian module
+------------------------------
+
+.. automodule:: GPy.kern.parts.Brownian
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.Matern32 module
+------------------------------
+
+.. automodule:: GPy.kern.parts.Matern32
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.Matern52 module
+------------------------------
+
+.. automodule:: GPy.kern.parts.Matern52
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.bias module
+--------------------------
+
+.. automodule:: GPy.kern.parts.bias
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.coregionalize module
+-----------------------------------
+
+.. automodule:: GPy.kern.parts.coregionalize
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.exponential module
+---------------------------------
+
+.. automodule:: GPy.kern.parts.exponential
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.finite_dimensional module
+----------------------------------------
+
+.. automodule:: GPy.kern.parts.finite_dimensional
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.fixed module
+---------------------------
+
+.. automodule:: GPy.kern.parts.fixed
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.gibbs module
+---------------------------
+
+.. automodule:: GPy.kern.parts.gibbs
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.hetero module
+----------------------------
+
+.. automodule:: GPy.kern.parts.hetero
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.hierarchical module
+----------------------------------
+
+.. automodule:: GPy.kern.parts.hierarchical
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.independent_outputs module
+-----------------------------------------
+
+.. automodule:: GPy.kern.parts.independent_outputs
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.kernpart module
+------------------------------
+
+.. automodule:: GPy.kern.parts.kernpart
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.linear module
+----------------------------
+
+.. automodule:: GPy.kern.parts.linear
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.mlp module
+-------------------------
+
+.. automodule:: GPy.kern.parts.mlp
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.periodic_Matern32 module
+---------------------------------------
+
+.. automodule:: GPy.kern.parts.periodic_Matern32
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.periodic_Matern52 module
+---------------------------------------
+
+.. automodule:: GPy.kern.parts.periodic_Matern52
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.periodic_exponential module
+------------------------------------------
+
+.. automodule:: GPy.kern.parts.periodic_exponential
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.poly module
+--------------------------
+
+.. automodule:: GPy.kern.parts.poly
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.prod module
+--------------------------
+
+.. automodule:: GPy.kern.parts.prod
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.prod_orthogonal module
+-------------------------------------
+
+.. automodule:: GPy.kern.parts.prod_orthogonal
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.rational_quadratic module
+----------------------------------------
+
+.. automodule:: GPy.kern.parts.rational_quadratic
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.rbf module
+-------------------------
+
+.. automodule:: GPy.kern.parts.rbf
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.rbf_inv module
+-----------------------------
+
+.. automodule:: GPy.kern.parts.rbf_inv
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.rbfcos module
+----------------------------
+
+.. automodule:: GPy.kern.parts.rbfcos
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.spline module
+----------------------------
+
+.. automodule:: GPy.kern.parts.spline
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.symmetric module
+-------------------------------
+
+.. automodule:: GPy.kern.parts.symmetric
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.kern.parts.sympykern module
+-------------------------------
+
+.. automodule:: GPy.kern.parts.sympykern
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+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:

doc/GPy.kern.rst

@@ -1,29 +1,5 @@
-kern Package
+GPy.kern package
-============
+================
-
-:mod:`kern` Package
--------------------
-
-.. automodule:: GPy.kern
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`constructors` Module
---------------------------
-
-.. automodule:: GPy.kern.constructors
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`kern` Module
-------------------
-
-.. automodule:: GPy.kern.kern
-    :members:
-    :undoc-members:
-    :show-inheritance:
 
 Subpackages
 -----------
@@ -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:

doc/GPy.likelihoods.noise_models.rst

@@ -0,0 +1,70 @@
+GPy.likelihoods.noise_models package
+====================================
+
+Submodules
+----------
+
+GPy.likelihoods.noise_models.binomial_noise module
+--------------------------------------------------
+
+.. automodule:: GPy.likelihoods.noise_models.binomial_noise
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.noise_models.exponential_noise module
+-----------------------------------------------------
+
+.. automodule:: GPy.likelihoods.noise_models.exponential_noise
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.noise_models.gamma_noise module
+-----------------------------------------------
+
+.. automodule:: GPy.likelihoods.noise_models.gamma_noise
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.noise_models.gaussian_noise module
+--------------------------------------------------
+
+.. automodule:: GPy.likelihoods.noise_models.gaussian_noise
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.noise_models.gp_transformations module
+------------------------------------------------------
+
+.. automodule:: GPy.likelihoods.noise_models.gp_transformations
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.noise_models.noise_distributions module
+-------------------------------------------------------
+
+.. automodule:: GPy.likelihoods.noise_models.noise_distributions
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.noise_models.poisson_noise module
+-------------------------------------------------
+
+.. automodule:: GPy.likelihoods.noise_models.poisson_noise
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: GPy.likelihoods.noise_models
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/GPy.likelihoods.rst

@@ -1,51 +1,69 @@
-likelihoods Package
+GPy.likelihoods package
-===================
+=======================
 
-:mod:`likelihoods` Package
+Subpackages
---------------------------
+-----------
 
-.. automodule:: GPy.likelihoods
+.. toctree::
-    :members:
-    :undoc-members:
-    :show-inheritance:
 
-:mod:`ep` Module
+    GPy.likelihoods.noise_models
-----------------
+
+Submodules
+----------
+
+GPy.likelihoods.ep module
+-------------------------
 
 .. automodule:: GPy.likelihoods.ep
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`gaussian` Module
+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:
 
-:mod:`likelihood` Module
+GPy.likelihoods.gaussian_mixed_noise module
-------------------------
+-------------------------------------------
+
+.. automodule:: GPy.likelihoods.gaussian_mixed_noise
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.likelihood module
+---------------------------------
 
 .. automodule:: GPy.likelihoods.likelihood
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`likelihood_functions` Module
+GPy.likelihoods.noise_model_constructors module
-----------------------------------
+-----------------------------------------------
 
-.. automodule:: GPy.likelihoods.likelihood_functions
+.. automodule:: GPy.likelihoods.noise_model_constructors
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`link_functions` Module
-----------------------------
 
-.. automodule:: GPy.likelihoods.link_functions
+Module contents
+---------------
+
+.. automodule:: GPy.likelihoods
     :members:
     :undoc-members:
     :show-inheritance:
-

doc/GPy.mappings.rst

@@ -0,0 +1,38 @@
+GPy.mappings package
+====================
+
+Submodules
+----------
+
+GPy.mappings.kernel module
+--------------------------
+
+.. automodule:: GPy.mappings.kernel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.mappings.linear module
+--------------------------
+
+.. automodule:: GPy.mappings.linear
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.mappings.mlp module
+-----------------------
+
+.. automodule:: GPy.mappings.mlp
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: GPy.mappings
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/GPy.models.rst

@@ -1,99 +1,134 @@
-models Package
+GPy.models package
-==============
+==================
 
-:mod:`models` Package
+Submodules
----------------------
+----------
 
-.. automodule:: GPy.models
+GPy.models.bayesian_gplvm module
-    :members:
+--------------------------------
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`bayesian_gplvm` Module
-----------------------------
 
 .. automodule:: GPy.models.bayesian_gplvm
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`fitc_classification` Module
+GPy.models.bcgplvm module
----------------------------------
+-------------------------
+
+.. automodule:: GPy.models.bcgplvm
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.fitc_classification module
+-------------------------------------
 
 .. automodule:: GPy.models.fitc_classification
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`gp_classification` Module
+GPy.models.gp_classification module
--------------------------------
+-----------------------------------
 
 .. automodule:: GPy.models.gp_classification
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`gp_regression` Module
+GPy.models.gp_multioutput_regression module
----------------------------
+-------------------------------------------
+
+.. automodule:: GPy.models.gp_multioutput_regression
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.gp_regression module
+-------------------------------
 
 .. automodule:: GPy.models.gp_regression
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`gplvm` Module
+GPy.models.gplvm module
--------------------
+-----------------------
 
 .. automodule:: GPy.models.gplvm
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`mrd` Module
+GPy.models.gradient_checker module
------------------
+----------------------------------
+
+.. automodule:: GPy.models.gradient_checker
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.mrd module
+---------------------
 
 .. automodule:: GPy.models.mrd
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`sparse_gp_classification` Module
+GPy.models.sparse_gp_classification module
---------------------------------------
+------------------------------------------
 
 .. automodule:: GPy.models.sparse_gp_classification
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`sparse_gp_regression` Module
+GPy.models.sparse_gp_multioutput_regression module
-----------------------------------
+--------------------------------------------------
+
+.. automodule:: GPy.models.sparse_gp_multioutput_regression
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.sparse_gp_regression module
+--------------------------------------
 
 .. automodule:: GPy.models.sparse_gp_regression
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`sparse_gplvm` Module
+GPy.models.sparse_gplvm module
---------------------------
+------------------------------
 
 .. automodule:: GPy.models.sparse_gplvm
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`svigp_regression` Module
+GPy.models.svigp_regression module
-------------------------------
+----------------------------------
 
 .. automodule:: GPy.models.svigp_regression
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`warped_gp` Module
+GPy.models.warped_gp module
------------------------
+---------------------------
 
 .. automodule:: GPy.models.warped_gp
     :members:
     :undoc-members:
     :show-inheritance:
 
+
+Module contents
+---------------
+
+.. automodule:: GPy.models
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/GPy.rst

@@ -1,14 +1,6 @@
-GPy Package
+GPy package
 ===========
 
-:mod:`GPy` Package
-------------------
-
-.. automodule:: GPy.__init__
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 Subpackages
 -----------
 
@@ -19,7 +11,15 @@ Subpackages
     GPy.inference
     GPy.kern
     GPy.likelihoods
+    GPy.mappings
     GPy.models
     GPy.testing
     GPy.util
 
+Module contents
+---------------
+
+.. automodule:: GPy
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/GPy.testing.rst

@@ -1,107 +1,110 @@
-testing Package
+GPy.testing package
-===============
+===================
 
-:mod:`testing` Package
+Submodules
-----------------------
+----------
 
-.. automodule:: GPy.testing
+GPy.testing.bgplvm_tests module
-    :members:
+-------------------------------
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`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:`checkgrad` Module
+GPy.testing.examples_tests module
------------------------
+---------------------------------
-
-.. automodule:: GPy.testing.checkgrad
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`examples_tests` Module
-----------------------------
 
 .. automodule:: GPy.testing.examples_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:`mrd_tests` Module
+GPy.testing.mapping_tests module
------------------------
+--------------------------------
+
+.. automodule:: GPy.testing.mapping_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+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_expactation_tests` Module
+GPy.testing.psi_stat_expectation_tests module
-----------------------------------------
+---------------------------------------------
 
-.. automodule:: GPy.testing.psi_stat_expactation_tests
+.. 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:

doc/GPy.util.latent_space_visualizations.controllers.rst

@@ -0,0 +1,30 @@
+GPy.util.latent_space_visualizations.controllers package
+========================================================
+
+Submodules
+----------
+
+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:
+
+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:

doc/GPy.util.latent_space_visualizations.rst

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

doc/GPy.util.rst

@@ -1,123 +1,133 @@
-util Package
+GPy.util package
-============
+================
 
-:mod:`util` Package
+Subpackages
--------------------
+-----------
 
-.. automodule:: GPy.util
+.. toctree::
-    :members:
-    :undoc-members:
-    :show-inheritance:
 
-:mod:`Tango` Module
+    GPy.util.latent_space_visualizations
--------------------
+
+Submodules
+----------
+
+GPy.util.Tango module
+---------------------
 
 .. automodule:: GPy.util.Tango
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`classification` Module
+GPy.util.classification module
-----------------------------
+------------------------------
 
 .. automodule:: GPy.util.classification
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`datasets` Module
+GPy.util.datasets module
-----------------------
+------------------------
 
 .. automodule:: GPy.util.datasets
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`decorators` Module
+GPy.util.decorators module
-------------------------
+--------------------------
 
 .. automodule:: GPy.util.decorators
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`linalg` Module
+GPy.util.linalg module
---------------------
+----------------------
 
 .. automodule:: GPy.util.linalg
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`misc` Module
+GPy.util.misc module
-------------------
+--------------------
 
 .. automodule:: GPy.util.misc
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`mocap` Module
+GPy.util.mocap module
--------------------
+---------------------
 
 .. automodule:: GPy.util.mocap
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`pca` Module
+GPy.util.multioutput module
------------------
+---------------------------
 
-.. automodule:: GPy.util.pca
+.. automodule:: GPy.util.multioutput
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`plot` Module
+GPy.util.plot module
-------------------
+--------------------
 
 .. automodule:: GPy.util.plot
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`plot_latent` Module
+GPy.util.plot_latent module
--------------------------
+---------------------------
 
 .. automodule:: GPy.util.plot_latent
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`squashers` Module
+GPy.util.squashers module
------------------------
+-------------------------
 
 .. automodule:: GPy.util.squashers
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`univariate_Gaussian` Module
+GPy.util.univariate_Gaussian module
----------------------------------
+-----------------------------------
 
 .. automodule:: GPy.util.univariate_Gaussian
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`visualize` Module
+GPy.util.visualize module
------------------------
+-------------------------
 
 .. automodule:: GPy.util.visualize
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`warping_functions` Module
+GPy.util.warping_functions module
--------------------------------
+---------------------------------
 
 .. automodule:: GPy.util.warping_functions
     :members:
     :undoc-members:
     :show-inheritance:
 
+
+Module contents
+---------------
+
+.. automodule:: GPy.util
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/conf.py

@@ -83,6 +83,7 @@ print "finished importing"
 #############################################################################
 
 class Mock(object):
+    __all__ = []
     def __init__(self, *args, **kwargs):
         pass
 
@@ -105,8 +106,7 @@ class Mock(object):
 print "Mocking"
 MOCK_MODULES = ['sympy',
     'sympy.utilities', 'sympy.utilities.codegen', 'sympy.core.cache',
-    'sympy.core', 'sympy.parsing', 'sympy.parsing.sympy_parser',
+    'sympy.core', 'sympy.parsing', 'sympy.parsing.sympy_parser'
-    'matplotlib.pyplot'
     ]
 for mod_name in MOCK_MODULES:
     sys.modules[mod_name] = Mock()

setup.py

@@ -18,7 +18,7 @@ setup(name = 'GPy',
       license = "BSD 3-clause",
       keywords = "machine-learning gaussian-processes kernels",
       url = "http://sheffieldml.github.com/GPy/",
-      packages = ['GPy', 'GPy.core', 'GPy.kern', 'GPy.util', 'GPy.models', 'GPy.inference', 'GPy.examples', 'GPy.likelihoods', 'GPy.testing'],
+      packages = ['GPy', 'GPy.core', 'GPy.kern', 'GPy.util', 'GPy.models', 'GPy.inference', 'GPy.examples', 'GPy.likelihoods', 'GPy.testing', 'GPy.util.latent_space_visualizations', 'GPy.util.latent_space_visualizations.controllers', 'GPy.likelihoods.noise_models', 'GPy.kern.parts', 'GPy.mappings'],
       package_dir={'GPy': 'GPy'},
       package_data = {'GPy': ['GPy/examples']},
       py_modules = ['GPy.__init__'],