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

for new bug fix

GPy/core/model.py

@@ -368,4 +368,13 @@ class Model(Parameterized):
             self.optimizer_array = x
             return ret
 
+    def __str__(self):
+        model_details = [['Name', self.name],
+                         ['Log-likelihood', '{}'.format(float(self.log_likelihood()))],
+                         ["Number of Parameters", '{}'.format(self.size)]]
+        from operator import itemgetter
+        max_len = reduce(lambda a, b: max(len(b[0]), a), model_details, 0)
+        to_print = [""] + ["{0:{l}} : {1}".format(name, detail, l=max_len) for name, detail in model_details] + ["Parameters:"]
+        to_print.append(super(Model, self).__str__())
+        return "\n".join(to_print)
 

GPy/core/parameterization/param.py

@@ -155,31 +155,6 @@ class Param(Parameterizable, ObsAr):
         return self._raveled_index()
 
     #===========================================================================
-    # Index recreation
-    #===========================================================================
-    def _expand_index(self, slice_index=None):
-        # this calculates the full indexing arrays from the slicing objects given by get_item for _real..._ attributes
-        # it basically translates slices to their respective index arrays and turns negative indices around
-        # it tells you in the second return argument if it has only seen arrays as indices
-        if slice_index is None:
-            slice_index = self._current_slice_
-        def f(a):
-            a, b = a
-            if isinstance(a, numpy.ndarray) and a.dtype == bool:
-                raise ValueError, "Boolean indexing not implemented, use Param[np.where(index)] to index by boolean arrays!"
-            if a not in (slice(None), Ellipsis):
-                if isinstance(a, slice):
-                    start, stop, step = a.indices(b)
-                    return numpy.r_[start:stop:step]
-                elif isinstance(a, (list, numpy.ndarray, tuple)):
-                    a = numpy.asarray(a, dtype=int)
-                    a[a < 0] = b + a[a < 0]
-                elif a < 0:
-                    a = b + a
-                return numpy.r_[a]
-            return numpy.r_[:b]
-        return itertools.imap(f, itertools.izip_longest(slice_index[:self._realndim_], self._realshape_, fillvalue=slice(self.size)))
-    #===========================================================================
     # Constrainable
     #===========================================================================
     def _ensure_fixes(self):
@@ -261,7 +236,7 @@ class Param(Parameterizable, ObsAr):
         try:
             indices = np.indices(self._realshape_, dtype=int)
             indices = indices[(slice(None),)+slice_index]
-            indices = np.rollaxis(indices, 0, indices.ndim).reshape(-1,2)
+            indices = np.rollaxis(indices, 0, indices.ndim).reshape(-1,self._realndim_)
             #print indices_
             #if not np.all(indices==indices__):
             #    import ipdb; ipdb.set_trace()

GPy/core/parameterization/parameter_core.py

@@ -58,21 +58,49 @@ class Observable(object):
 
     @property
     def updates(self):
-        p = getattr(self, '_highest_parent_', None)
+        raise DeprecationWarning("updates is now a function, see update(True|False|None)")
-        if p is not None:
-            self._updates = p._updates
-        return self._updates
 
     @updates.setter
     def updates(self, ups):
-        assert isinstance(ups, bool), "updates are either on (True) or off (False)"
+        raise DeprecationWarning("updates is now a function, see update(True|False|None)")
+    
+    def update_model(self, updates=None):
+        """
+        Get or set, whether automatic updates are performed. When updates are
+        off, the model might be in a non-working state. To make the model work
+        turn updates on again.
+
+        :param bool|None updates:
+
+            bool: whether to do updates
+            None: get the current update state
+        """
+        if updates is None:
+            p = getattr(self, '_highest_parent_', None)
+            if p is not None:
+                self._updates = p._updates
+            return self._updates
+        assert isinstance(updates, bool), "updates are either on (True) or off (False)"
         p = getattr(self, '_highest_parent_', None)
         if p is not None:
-            p._updates = ups
+            p._updates = updates
         else:
-            self._updates = ups
+            self._updates = updates
-        if ups:
+        self.trigger_update()
-            self._trigger_params_changed()
+                            
+    def toggle_update(self):
+        self.update_model(not self.update())
+
+    def trigger_update(self):
+        """
+        Update the model from the current state.
+        Make sure that updates are on, otherwise this
+        method will do nothing
+        """
+        if not self.update_model():
+            #print "Warning: updates are off, updating the model will do nothing"
+            return
+        self._trigger_params_changed()
                 
     def add_observer(self, observer, callble, priority=0):
         """
@@ -110,7 +138,7 @@ class Observable(object):
         :param min_priority: only notify observers with priority > min_priority
                              if min_priority is None, notify all observers in order
         """
-        if not self.updates:
+        if not self.update_model():
             return
         if which is None:
             which = self
@@ -831,7 +859,7 @@ class OptimizationHandlable(Indexable):
         """
         # first take care of all parameters (from N(0,1))
         x = rand_gen(size=self._size_transformed(), *args, **kwargs)
-        self.updates = False # Switch off the updates
+        self.update_model(False) # Switch off the updates
         self.optimizer_array = x  # makes sure all of the tied parameters get the same init (since there's only one prior object...)
         # now draw from prior where possible
         x = self.param_array.copy()
@@ -839,7 +867,7 @@ class OptimizationHandlable(Indexable):
         unfixlist = np.ones((self.size,),dtype=np.bool)
         unfixlist[self.constraints[__fixed__]] = False
         self.param_array[unfixlist] = x[unfixlist]
-        self.updates = True 
+        self.update_model(True) 
 
     #===========================================================================
     # For shared memory arrays. This does nothing in Param, but sets the memory

GPy/core/parameterization/parameterized.py

@@ -367,7 +367,6 @@ class Parameterized(Parameterizable):
     def _ties_str(self):
         return [','.join(x._ties_str) for x in self.flattened_parameters]
     def __str__(self, header=True):
-
         name = adjust_name_for_printing(self.name) + "."
         constrs = self._constraints_str;
         ts = self._ties_str
@@ -382,11 +381,9 @@ class Parameterized(Parameterizable):
         to_print = []
         for n, d, c, t, p in itertools.izip(names, desc, constrs, ts, prirs):
             to_print.append(format_spec.format(name=n, desc=d, const=c, t=t, pri=p))
-        # to_print = [format_spec.format(p=p, const=c, t=t) if isinstance(p, Param) else p.__str__(header=False) for p, c, t in itertools.izip(self.parameters, constrs, ts)]
         sep = '-' * (nl + sl + cl + + pl + tl + 8 * 2 + 3)
         if header:
             header = "  {{0:<{0}s}}  |  {{1:^{1}s}}  |  {{2:^{2}s}}  |  {{3:^{3}s}}  |  {{4:^{4}s}}".format(nl, sl, cl, pl, tl).format(name, "Value", "Constraint", "Prior", "Tied to")
-            # header += '\n' + sep
             to_print.insert(0, header)
         return '\n'.format(sep).join(to_print)
     pass

GPy/kern/_src/linear.py

@@ -103,7 +103,7 @@ class Linear(Kern):
     def gradients_X_diag(self, dL_dKdiag, X):
         return 2.*self.variances*dL_dKdiag[:,None]*X
 
-    def input_sensitivity(self):
+    def input_sensitivity(self, summarize=True):
         return np.ones(self.input_dim) * self.variances
 
     #---------------------------------------#

GPy/plotting/matplot_dep/kernel_plots.py

@@ -72,11 +72,11 @@ def plot_ARD(kernel, fignum=None, ax=None, title='', legend=False, filtering=Non
 
     x = np.arange(kernel.input_dim)
 
-    if order is None:
+    if filtering is None:
-        order = kernel.parameter_names(recursive=False)
+        filtering = kernel.parameter_names(recursive=False)
 
     for i in range(ard_params.shape[0]):
-        if kernel.parameters[i].name in order:
+        if kernel.parameters[i].name in filtering:
             c = Tango.nextMedium()
             bars.append(plot_bars(fig, ax, x, ard_params[i,:], c, kernel.parameters[i].name, bottom=bottom))
             last_bottom = ard_params[i,:]

GPy/testing/model_tests.py

@@ -19,9 +19,10 @@ class MiscTests(unittest.TestCase):
         k = GPy.kern.RBF(1)
         m = GPy.models.GPRegression(self.X, self.Y, kernel=k)
         m.randomize()
-        Kinv = np.linalg.pinv(k.K(self.X) + np.eye(self.N)*m.Gaussian_noise.variance)
+        m.likelihood.variance = .5
+        Kinv = np.linalg.pinv(k.K(self.X) + np.eye(self.N)*m.likelihood.variance)
         K_hat = k.K(self.X_new) - k.K(self.X_new, self.X).dot(Kinv).dot(k.K(self.X, self.X_new))
-        mu_hat = k.K(self.X_new, self.X).dot(Kinv).dot(self.Y)
+        mu_hat = k.K(self.X_new, self.X).dot(Kinv).dot(m.Y_normalized)
 
         mu, covar = m._raw_predict(self.X_new, full_cov=True)
         self.assertEquals(mu.shape, (self.N_new, self.D))
@@ -431,6 +432,8 @@ class GradientTests(np.testing.TestCase):
         k1 = GPy.kern.RBF(1)  # + GPy.kern.White(1)
         k2 = GPy.kern.RBF(1)  # + GPy.kern.White(1)
         Y = np.random.randn(N1, N2)
+        Y = Y-Y.mean(0)
+        Y = Y/Y.std(0)
         m = GPy.models.GPKroneckerGaussianRegression(X1, X2, Y, k1, k2)
 
         # build the model the dumb way

GPy/testing/parameterized_tests.py

@@ -152,6 +152,12 @@ class ParameterizedTest(unittest.TestCase):
         self.test1.kern.randomize()
         self.assertEqual(val, self.rbf.variance)
 
+    def test_updates(self):
+        self.test1.update_model(False)
+        val = float(self.rbf.variance)
+        self.test1.kern.randomize()
+        self.assertEqual(val, self.rbf.variance)
+
     def test_fixing_optimize(self):
         self.testmodel.kern.lengthscale.fix()
         val = float(self.testmodel.kern.lengthscale)

doc/GPy.core.parameterization.rst

@@ -0,0 +1,102 @@
+GPy.core.parameterization package
+=================================
+
+Submodules
+----------
+
+GPy.core.parameterization.domains module
+----------------------------------------
+
+.. automodule:: GPy.core.parameterization.domains
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.index_operations module
+-------------------------------------------------
+
+.. automodule:: GPy.core.parameterization.index_operations
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.lists_and_dicts module
+------------------------------------------------
+
+.. automodule:: GPy.core.parameterization.lists_and_dicts
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.observable_array module
+-------------------------------------------------
+
+.. automodule:: GPy.core.parameterization.observable_array
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.param module
+--------------------------------------
+
+.. automodule:: GPy.core.parameterization.param
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.parameter_core module
+-----------------------------------------------
+
+.. automodule:: GPy.core.parameterization.parameter_core
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.parameterized module
+----------------------------------------------
+
+.. automodule:: GPy.core.parameterization.parameterized
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.priors module
+---------------------------------------
+
+.. automodule:: GPy.core.parameterization.priors
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.ties_and_remappings module
+----------------------------------------------------
+
+.. automodule:: GPy.core.parameterization.ties_and_remappings
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.transformations module
+------------------------------------------------
+
+.. automodule:: GPy.core.parameterization.transformations
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.core.parameterization.variational module
+--------------------------------------------
+
+.. automodule:: GPy.core.parameterization.variational
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: GPy.core.parameterization
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/GPy.core.rst

@@ -1,25 +1,16 @@
 GPy.core package
 ================
 
+Subpackages
+-----------
+
+.. toctree::
+
+    GPy.core.parameterization
+
 Submodules
 ----------
 
-GPy.core.domains module
------------------------
-
-.. automodule:: GPy.core.domains
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.core.fitc module
---------------------
-
-.. automodule:: GPy.core.fitc
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 GPy.core.gp module
 ------------------
 
@@ -28,14 +19,6 @@ GPy.core.gp module
     :undoc-members:
     :show-inheritance:
 
-GPy.core.gp_base module
------------------------
-
-.. automodule:: GPy.core.gp_base
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 GPy.core.mapping module
 -----------------------
 
@@ -52,22 +35,6 @@ GPy.core.model module
     :undoc-members:
     :show-inheritance:
 
-GPy.core.parameterized module
------------------------------
-
-.. automodule:: GPy.core.parameterized
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.core.priors module
-----------------------
-
-.. automodule:: GPy.core.priors
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 GPy.core.sparse_gp module
 -------------------------
 
@@ -76,6 +43,14 @@ GPy.core.sparse_gp module
     :undoc-members:
     :show-inheritance:
 
+GPy.core.sparse_gp_mpi module
+-----------------------------
+
+.. automodule:: GPy.core.sparse_gp_mpi
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 GPy.core.svigp module
 ---------------------
 
@@ -84,10 +59,10 @@ GPy.core.svigp module
     :undoc-members:
     :show-inheritance:
 
-GPy.core.transformations module
+GPy.core.symbolic module
--------------------------------
+------------------------
 
-.. automodule:: GPy.core.transformations
+.. automodule:: GPy.core.symbolic
     :members:
     :undoc-members:
     :show-inheritance:

doc/GPy.examples.rst

@@ -12,6 +12,14 @@ GPy.examples.classification module
     :undoc-members:
     :show-inheritance:
 
+GPy.examples.coreg_example module
+---------------------------------
+
+.. automodule:: GPy.examples.coreg_example
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 GPy.examples.dimensionality_reduction module
 --------------------------------------------
 
@@ -20,6 +28,14 @@ GPy.examples.dimensionality_reduction module
     :undoc-members:
     :show-inheritance:
 
+GPy.examples.non_gaussian module
+--------------------------------
+
+.. automodule:: GPy.examples.non_gaussian
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 GPy.examples.regression module
 ------------------------------
 

doc/GPy.inference.latent_function_inference.rst

@@ -0,0 +1,94 @@
+GPy.inference.latent_function_inference package
+===============================================
+
+Submodules
+----------
+
+GPy.inference.latent_function_inference.dtc module
+--------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.dtc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.exact_gaussian_inference module
+-----------------------------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.exact_gaussian_inference
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.expectation_propagation module
+----------------------------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.expectation_propagation
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.expectation_propagation_dtc module
+--------------------------------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.expectation_propagation_dtc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.fitc module
+---------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.fitc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.laplace module
+------------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.laplace
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.posterior module
+--------------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.posterior
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.var_dtc module
+------------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.var_dtc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.var_dtc_gpu module
+----------------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.var_dtc_gpu
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.latent_function_inference.var_dtc_parallel module
+---------------------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.var_dtc_parallel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: GPy.inference.latent_function_inference
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/GPy.inference.optimization.rst

@@ -0,0 +1,78 @@
+GPy.inference.optimization package
+==================================
+
+Submodules
+----------
+
+GPy.inference.optimization.BayesOpt module
+------------------------------------------
+
+.. automodule:: GPy.inference.optimization.BayesOpt
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.optimization.conjugate_gradient_descent module
+------------------------------------------------------------
+
+.. automodule:: GPy.inference.optimization.conjugate_gradient_descent
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.optimization.gradient_descent_update_rules module
+---------------------------------------------------------------
+
+.. automodule:: GPy.inference.optimization.gradient_descent_update_rules
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.optimization.hmc module
+-------------------------------------
+
+.. automodule:: GPy.inference.optimization.hmc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.optimization.optimization module
+----------------------------------------------
+
+.. automodule:: GPy.inference.optimization.optimization
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.optimization.samplers module
+------------------------------------------
+
+.. automodule:: GPy.inference.optimization.samplers
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.optimization.scg module
+-------------------------------------
+
+.. automodule:: GPy.inference.optimization.scg
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.optimization.sgd module
+-------------------------------------
+
+.. automodule:: GPy.inference.optimization.sgd
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: GPy.inference.optimization
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/GPy.inference.rst

@@ -1,57 +1,13 @@
 GPy.inference package
 =====================
 
-Submodules
+Subpackages
-----------
+-----------
 
-GPy.inference.conjugate_gradient_descent module
+.. toctree::
------------------------------------------------
-
-.. automodule:: GPy.inference.conjugate_gradient_descent
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.inference.gradient_descent_update_rules module
---------------------------------------------------
-
-.. automodule:: GPy.inference.gradient_descent_update_rules
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.inference.optimization module
----------------------------------
-
-.. automodule:: GPy.inference.optimization
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.inference.samplers module
------------------------------
-
-.. automodule:: GPy.inference.samplers
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.inference.scg module
-------------------------
-
-.. automodule:: GPy.inference.scg
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.inference.sgd module
-------------------------
-
-.. automodule:: GPy.inference.sgd
-    :members:
-    :undoc-members:
-    :show-inheritance:
 
+    GPy.inference.latent_function_inference
+    GPy.inference.optimization
 
 Module contents
 ---------------

doc/GPy.kern.rst

@@ -1,33 +1,6 @@
 GPy.kern package
 ================
 
-Subpackages
------------
-
-.. toctree::
-
-    GPy.kern.parts
-
-Submodules
-----------
-
-GPy.kern.constructors module
-----------------------------
-
-.. automodule:: GPy.kern.constructors
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.kern.kern module
---------------------
-
-.. automodule:: GPy.kern.kern
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
 Module contents
 ---------------
 

doc/GPy.likelihoods.rst

@@ -1,28 +1,29 @@
 GPy.likelihoods package
 =======================
 
-Subpackages
------------
-
-.. toctree::
-
-    GPy.likelihoods.noise_models
-
 Submodules
 ----------
 
-GPy.likelihoods.ep module
+GPy.likelihoods.bernoulli module
--------------------------
+--------------------------------
 
-.. automodule:: GPy.likelihoods.ep
+.. automodule:: GPy.likelihoods.bernoulli
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.likelihoods.ep_mixed_noise module
+GPy.likelihoods.exponential module
--------------------------------------
+----------------------------------
 
-.. automodule:: GPy.likelihoods.ep_mixed_noise
+.. automodule:: GPy.likelihoods.exponential
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.gamma module
+----------------------------
+
+.. automodule:: GPy.likelihoods.gamma
     :members:
     :undoc-members:
     :show-inheritance:
@@ -35,14 +36,6 @@ GPy.likelihoods.gaussian module
     :undoc-members:
     :show-inheritance:
 
-GPy.likelihoods.gaussian_mixed_noise module
--------------------------------------------
-
-.. automodule:: GPy.likelihoods.gaussian_mixed_noise
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 GPy.likelihoods.likelihood module
 ---------------------------------
 
@@ -51,10 +44,82 @@ GPy.likelihoods.likelihood module
     :undoc-members:
     :show-inheritance:
 
-GPy.likelihoods.noise_model_constructors module
+GPy.likelihoods.link_functions module
------------------------------------------------
+-------------------------------------
 
-.. automodule:: GPy.likelihoods.noise_model_constructors
+.. automodule:: GPy.likelihoods.link_functions
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.mixed_noise module
+----------------------------------
+
+.. automodule:: GPy.likelihoods.mixed_noise
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.negative_binomial module
+----------------------------------------
+
+.. automodule:: GPy.likelihoods.negative_binomial
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.ordinal module
+------------------------------
+
+.. automodule:: GPy.likelihoods.ordinal
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.poisson module
+------------------------------
+
+.. automodule:: GPy.likelihoods.poisson
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.skew_exponential module
+---------------------------------------
+
+.. automodule:: GPy.likelihoods.skew_exponential
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.skew_normal module
+----------------------------------
+
+.. automodule:: GPy.likelihoods.skew_normal
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.sstudent_t module
+---------------------------------
+
+.. automodule:: GPy.likelihoods.sstudent_t
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.student_t module
+--------------------------------
+
+.. automodule:: GPy.likelihoods.student_t
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.likelihoods.symbolic module
+-------------------------------
+
+.. automodule:: GPy.likelihoods.symbolic
     :members:
     :undoc-members:
     :show-inheritance:

doc/GPy.mappings.rst

@@ -4,6 +4,14 @@ GPy.mappings package
 Submodules
 ----------
 
+GPy.mappings.additive module
+----------------------------
+
+.. automodule:: GPy.mappings.additive
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 GPy.mappings.kernel module
 --------------------------
 
@@ -28,6 +36,14 @@ GPy.mappings.mlp module
     :undoc-members:
     :show-inheritance:
 
+GPy.mappings.symbolic module
+----------------------------
+
+.. automodule:: GPy.mappings.symbolic
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 
 Module contents
 ---------------

doc/GPy.models.rst

@@ -20,14 +20,6 @@ GPy.models.bcgplvm module
     :undoc-members:
     :show-inheritance:
 
-GPy.models.fitc_classification module
--------------------------------------
-
-.. automodule:: GPy.models.fitc_classification
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 GPy.models.gp_classification module
 -----------------------------------
 
@@ -36,6 +28,30 @@ GPy.models.gp_classification module
     :undoc-members:
     :show-inheritance:
 
+GPy.models.gp_coregionalized_regression module
+----------------------------------------------
+
+.. automodule:: GPy.models.gp_coregionalized_regression
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.gp_heteroscedastic_regression module
+-----------------------------------------------
+
+.. automodule:: GPy.models.gp_heteroscedastic_regression
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.gp_kronecker_gaussian_regression module
+--------------------------------------------------
+
+.. automodule:: GPy.models.gp_kronecker_gaussian_regression
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 GPy.models.gp_multioutput_regression module
 -------------------------------------------
 
@@ -52,6 +68,14 @@ GPy.models.gp_regression module
     :undoc-members:
     :show-inheritance:
 
+GPy.models.gp_var_gauss module
+------------------------------
+
+.. automodule:: GPy.models.gp_var_gauss
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 GPy.models.gplvm module
 -----------------------
 
@@ -84,6 +108,14 @@ GPy.models.sparse_gp_classification module
     :undoc-members:
     :show-inheritance:
 
+GPy.models.sparse_gp_coregionalized_regression module
+-----------------------------------------------------
+
+.. automodule:: GPy.models.sparse_gp_coregionalized_regression
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 GPy.models.sparse_gp_multioutput_regression module
 --------------------------------------------------
 
@@ -108,6 +140,22 @@ GPy.models.sparse_gplvm module
     :undoc-members:
     :show-inheritance:
 
+GPy.models.ss_gplvm module
+--------------------------
+
+.. automodule:: GPy.models.ss_gplvm
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.models.ss_mrd module
+------------------------
+
+.. automodule:: GPy.models.ss_mrd
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 GPy.models.svigp_regression module
 ----------------------------------
 

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

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

doc/GPy.plotting.matplot_dep.latent_space_visualizations.rst

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

doc/GPy.plotting.matplot_dep.rst

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

doc/GPy.plotting.rst

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

doc/GPy.rst

@@ -13,6 +13,7 @@ Subpackages
     GPy.likelihoods
     GPy.mappings
     GPy.models
+    GPy.plotting
     GPy.testing
     GPy.util
 

doc/GPy.testing.rst

@@ -4,22 +4,6 @@ GPy.testing package
 Submodules
 ----------
 
-GPy.testing.bgplvm_tests module
--------------------------------
-
-.. automodule:: GPy.testing.bgplvm_tests
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.testing.cgd_tests module
-----------------------------
-
-.. automodule:: GPy.testing.cgd_tests
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 GPy.testing.examples_tests module
 ---------------------------------
 
@@ -28,10 +12,18 @@ GPy.testing.examples_tests module
     :undoc-members:
     :show-inheritance:
 
-GPy.testing.gplvm_tests module
+GPy.testing.fitc module
-------------------------------
+-----------------------
 
-.. automodule:: GPy.testing.gplvm_tests
+.. automodule:: GPy.testing.fitc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.index_operations_tests module
+-----------------------------------------
+
+.. automodule:: GPy.testing.index_operations_tests
     :members:
     :undoc-members:
     :show-inheritance:
@@ -44,18 +36,42 @@ GPy.testing.kernel_tests module
     :undoc-members:
     :show-inheritance:
 
-GPy.testing.mapping_tests module
+GPy.testing.likelihood_tests module
---------------------------------
+-----------------------------------
 
-.. automodule:: GPy.testing.mapping_tests
+.. automodule:: GPy.testing.likelihood_tests
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.testing.mrd_tests module
+GPy.testing.model_tests module
-----------------------------
+------------------------------
 
-.. automodule:: GPy.testing.mrd_tests
+.. automodule:: GPy.testing.model_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.observable_tests module
+-----------------------------------
+
+.. automodule:: GPy.testing.observable_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.parameterized_tests module
+--------------------------------------
+
+.. automodule:: GPy.testing.parameterized_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.testing.pickle_tests module
+-------------------------------
+
+.. automodule:: GPy.testing.pickle_tests
     :members:
     :undoc-members:
     :show-inheritance:
@@ -68,38 +84,6 @@ GPy.testing.prior_tests module
     :undoc-members:
     :show-inheritance:
 
-GPy.testing.psi_stat_expectation_tests module
----------------------------------------------
-
-.. automodule:: GPy.testing.psi_stat_expectation_tests
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.testing.psi_stat_gradient_tests module
-------------------------------------------
-
-.. automodule:: GPy.testing.psi_stat_gradient_tests
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.testing.sparse_gplvm_tests module
--------------------------------------
-
-.. automodule:: GPy.testing.sparse_gplvm_tests
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-GPy.testing.unit_tests module
------------------------------
-
-.. automodule:: GPy.testing.unit_tests
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 
 Module contents
 ---------------

doc/GPy.util.rst

@@ -1,20 +1,21 @@
 GPy.util package
 ================
 
-Subpackages
------------
-
-.. toctree::
-
-    GPy.util.latent_space_visualizations
-
 Submodules
 ----------
 
-GPy.util.Tango module
+GPy.util.block_matrices module
----------------------
+------------------------------
 
-.. automodule:: GPy.util.Tango
+.. automodule:: GPy.util.block_matrices
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.caching module
+-----------------------
+
+.. automodule:: GPy.util.caching
     :members:
     :undoc-members:
     :show-inheritance:
@@ -27,6 +28,14 @@ GPy.util.classification module
     :undoc-members:
     :show-inheritance:
 
+GPy.util.config module
+----------------------
+
+.. automodule:: GPy.util.config
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 GPy.util.datasets module
 ------------------------
 
@@ -35,6 +44,14 @@ GPy.util.datasets module
     :undoc-members:
     :show-inheritance:
 
+GPy.util.debug module
+---------------------
+
+.. automodule:: GPy.util.debug
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 GPy.util.decorators module
 --------------------------
 
@@ -43,6 +60,46 @@ GPy.util.decorators module
     :undoc-members:
     :show-inheritance:
 
+GPy.util.diag module
+--------------------
+
+.. automodule:: GPy.util.diag
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.erfcx module
+---------------------
+
+.. automodule:: GPy.util.erfcx
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.functions module
+-------------------------
+
+.. automodule:: GPy.util.functions
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.gpu_init module
+------------------------
+
+.. automodule:: GPy.util.gpu_init
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.initialization module
+------------------------------
+
+.. automodule:: GPy.util.initialization
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 GPy.util.linalg module
 ----------------------
 
@@ -51,6 +108,22 @@ GPy.util.linalg module
     :undoc-members:
     :show-inheritance:
 
+GPy.util.linalg_gpu module
+--------------------------
+
+.. automodule:: GPy.util.linalg_gpu
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.ln_diff_erfs module
+----------------------------
+
+.. automodule:: GPy.util.ln_diff_erfs
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 GPy.util.misc module
 --------------------
 
@@ -67,6 +140,14 @@ GPy.util.mocap module
     :undoc-members:
     :show-inheritance:
 
+GPy.util.mpi module
+-------------------
+
+.. automodule:: GPy.util.mpi
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 GPy.util.multioutput module
 ---------------------------
 
@@ -75,18 +156,34 @@ GPy.util.multioutput module
     :undoc-members:
     :show-inheritance:
 
-GPy.util.plot module
+GPy.util.netpbmfile module
---------------------
+--------------------------
 
-.. automodule:: GPy.util.plot
+.. automodule:: GPy.util.netpbmfile
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.util.plot_latent module
+GPy.util.normalizer module
----------------------------
+--------------------------
 
-.. automodule:: GPy.util.plot_latent
+.. automodule:: GPy.util.normalizer
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.parallel module
+------------------------
+
+.. automodule:: GPy.util.parallel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.pca module
+-------------------
+
+.. automodule:: GPy.util.pca
     :members:
     :undoc-members:
     :show-inheritance:
@@ -99,18 +196,26 @@ GPy.util.squashers module
     :undoc-members:
     :show-inheritance:
 
-GPy.util.univariate_Gaussian module
+GPy.util.subarray_and_sorting module
------------------------------------
+------------------------------------
 
-.. automodule:: GPy.util.univariate_Gaussian
+.. automodule:: GPy.util.subarray_and_sorting
     :members:
     :undoc-members:
     :show-inheritance:
 
-GPy.util.visualize module
+GPy.util.symbolic module
--------------------------
+------------------------
 
-.. automodule:: GPy.util.visualize
+.. automodule:: GPy.util.symbolic
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.util.univariate_Gaussian module
+-----------------------------------
+
+.. automodule:: GPy.util.univariate_Gaussian
     :members:
     :undoc-members:
     :show-inheritance:

doc/tuto_creating_new_models.rst

@@ -39,8 +39,9 @@ Obligatory methods
 :py:meth:`~GPy.core.model.Model.parameters_changed` :
     Updates the internal state of the model and sets the gradient of
     each parameter handle in the hierarchy with respect to the
-    log_likelihod. Thus here we need to put the negative derivative of
+    log_likelihod. Thus here we need to set the negative derivative of
-    the rosenbrock function:
+    the rosenbrock function for the parameters. In this case it is the
+    gradient for self.X:
 
  		self.X.gradient = -scipy.optimize.rosen_der(self.X)
 

doc/tuto_interacting_with_models.rst

@@ -40,24 +40,21 @@ is shown. For each parameter, the table contains the name
 of the parameter, the current value, and in case there are 
 defined: constraints, ties and prior distrbutions associated. ::
 
-	Log-likelihood: 6.309e+02
+  Name                 : sparse gp
+  Log-likelihood       : -405.646051581
+  Number of Parameters : 8
+  Parameters:
+    sparse_gp.               |  Value   |  Constraint  |  Prior  |  Tied to
+    inducing inputs          |  (5, 1)  |              |         |         
+    rbf.variance             |     1.0  |     +ve      |         |         
+    rbf.lengthscale          |     1.0  |     +ve      |         |         
+    Gaussian_noise.variance  |     1.0  |     +ve      |         |         
   
-	     Name        |   Value   |  Constraints  |  Ties  |  Prior  
-	------------------------------------------------------------------
-	    iip_0_0      |  -1.4671  |               |        |         
-	    iip_1_0      |  2.6378   |               |        |         
-	    iip_2_0      |  -0.0396  |               |        |         
-	    iip_3_0      |  -2.6372  |               |        |         
-	    iip_4_0      |  1.4704   |               |        |         
-	 rbf_variance    |  1.5672   |     (+ve)     |        |         
-	rbf_lengthscale  |  2.5625   |     (+ve)     |        |         
-	white_variance   |  0.0000   |     (+ve)     |        |         
-	noise_variance   |  0.0022   |     (+ve)     |        |         
 
-In this case the kernel parameters (``rbf_variance``, 
+In this case the kernel parameters (``rbf.variance``, 
-``rbf_lengthscale`` and ``white_variance``) as well as 
+``rbf.lengthscale``) as well as 
-the noise parameter (``noise_variance``), are constrained 
+the likelihood noise parameter (``Gaussian_noise.variance``), are constrained 
-to be positive, while the inducing inputs have not 
+to be positive, while the inducing inputs have no
 constraints associated. Also there are no ties or prior defined.
 
 Setting and fetching parameters by name