Merging changed files.

GPy/core/gp.py

@@ -176,7 +176,7 @@ class GP(GPBase):
 
         .. Note:: For multiple output models only
         """
-        assert hasattr(self,'multioutput')
+        assert hasattr(self,'multioutput'), 'This function is for multiple output models only.'
         index = np.ones_like(Xnew)*output
         Xnew = np.hstack((Xnew,index))
 
@@ -204,8 +204,7 @@ class GP(GPBase):
 
         .. Note:: For multiple output models only
         """
-        assert hasattr(self,'multioutput')
+        assert hasattr(self,'multioutput'), 'This function is for multiple output models only.'
-
         # creates an index column and appends it to _Xnew
         index = np.ones_like(_Xnew)*output
         _Xnew = np.hstack((_Xnew,index))

GPy/core/gp_base.py

@@ -89,7 +89,9 @@ class GPBase(Model):
             fig = pb.figure(num=fignum)
             ax = fig.add_subplot(111)
 
-        if self.X.shape[1] == 1 and not hasattr(self,'multioutput'):
+        if not hasattr(self,'multioutput'):
+
+            if self.X.shape[1] == 1:
                 Xnew, xmin, xmax = x_frame1D(self.X, plot_limits=plot_limits)
                 if samples == 0:
                     m, v = self._raw_predict(Xnew, which_parts=which_parts)
@@ -97,17 +99,23 @@ class GPBase(Model):
                     ax.plot(self.X[which_data], self.likelihood.Y[which_data], 'kx', mew=1.5)
                 else:
                     m, v = self._raw_predict(Xnew, which_parts=which_parts, full_cov=True)
+                    v = v.reshape(m.size,-1) if len(v.shape)==3 else v
                     Ysim = np.random.multivariate_normal(m.flatten(), v, samples)
                     gpplot(Xnew, m, m - 2 * np.sqrt(np.diag(v)[:, None]), m + 2 * np.sqrt(np.diag(v))[:, None, ], axes=ax)
                     for i in range(samples):
                         ax.plot(Xnew, Ysim[i, :], Tango.colorsHex['darkBlue'], linewidth=0.25)
+
                 ax.plot(self.X[which_data], self.likelihood.Y[which_data], 'kx', mew=1.5)
                 ax.set_xlim(xmin, xmax)
                 ymin, ymax = min(np.append(self.likelihood.Y, m - 2 * np.sqrt(np.diag(v)[:, None]))), max(np.append(self.likelihood.Y, m + 2 * np.sqrt(np.diag(v)[:, None])))
                 ymin, ymax = ymin - 0.1 * (ymax - ymin), ymax + 0.1 * (ymax - ymin)
                 ax.set_ylim(ymin, ymax)
 
-        elif self.X.shape[1] == 2 and not hasattr(self,'multioutput'):
+                if hasattr(self,'Z'):
+                    Zu = self.Z * self._Xscale + self._Xoffset
+                    ax.plot(Zu, np.zeros_like(Zu) + ax.get_ylim()[0], 'r|', mew=1.5, markersize=12)
+
+            elif self.X.shape[1] == 2:
                 resolution = resolution or 50
                 Xnew, xmin, xmax, xx, yy = x_frame2D(self.X, plot_limits, resolution)
                 m, v = self._raw_predict(Xnew, which_parts=which_parts)
@@ -117,9 +125,12 @@ class GPBase(Model):
                 ax.set_xlim(xmin[0], xmax[0])
                 ax.set_ylim(xmin[1], xmax[1])
 
+            else:
+                raise NotImplementedError, "Cannot define a frame with more than two input dimensions"
+        else:
+            assert self.num_outputs > output, 'The model has only %s outputs.' %self.num_outputs
 
-        elif self.X.shape[1] == 2 and hasattr(self,'multioutput'):
+            if self.X.shape[1] == 2:
-            output -= 1
                 assert self.num_outputs >= output, 'The model has only %s outputs.' %self.num_outputs
                 Xu = self.X[self.X[:,-1]==output ,0:1]
                 Xnew, xmin, xmax = x_frame1D(Xu, plot_limits=plot_limits)
@@ -130,6 +141,7 @@ class GPBase(Model):
                     ax.plot(Xu[which_data], self.likelihood.Y[self.likelihood.index==output][:,None], 'kx', mew=1.5)
                 else:
                     m, v = self._raw_predict_single_output(Xnew, output=output, which_parts=which_parts, full_cov=True)
+                    v = v.reshape(m.size,-1) if len(v.shape)==3 else v
                     Ysim = np.random.multivariate_normal(m.flatten(), v, samples)
                     gpplot(Xnew, m, m - 2 * np.sqrt(np.diag(v)[:, None]), m + 2 * np.sqrt(np.diag(v))[:, None, ], axes=ax)
                     for i in range(samples):
@@ -139,19 +151,19 @@ class GPBase(Model):
                 ymin, ymax = ymin - 0.1 * (ymax - ymin), ymax + 0.1 * (ymax - ymin)
                 ax.set_ylim(ymin, ymax)
 
+            elif self.X.shape[1] == 3:
+                raise NotImplementedError, "Plots not implemented for multioutput models with 2D inputs...yet"
+                assert self.num_outputs >= output, 'The model has only %s outputs.' %self.num_outputs
+
+            else:
+                raise NotImplementedError, "Cannot define a frame with more than two input dimensions"
+
         if hasattr(self,'Z'):
             Zu = self.Z[self.Z[:,-1]==output,:]
             Zu = self.Z * self._Xscale + self._Xoffset
             Zu = self.Z[self.Z[:,-1]==output ,0:1] #??
             ax.plot(Zu, np.zeros_like(Zu) + ax.get_ylim()[0], 'r|', mew=1.5, markersize=12)
 
-        elif self.X.shape[1] == 3 and hasattr(self,'multioutput'):
-            raise NotImplementedError, "Plots not implemented for multioutput models with 2D inputs...yet"
-            output -= 1
-            assert self.num_outputs >= output, 'The model has only %s outputs.' %self.num_outputs
-
-        else:
-            raise NotImplementedError, "Cannot define a frame with more than two input dimensions"
 
     def plot(self, plot_limits=None, which_data='all', which_parts='all', resolution=None, levels=20, samples=0, fignum=None, ax=None, output=None, fixed_inputs=[], linecol=Tango.colorsHex['darkBlue'],fillcol=Tango.colorsHex['lightBlue']):
         """
@@ -203,7 +215,7 @@ class GPBase(Model):
             if plotdims == 1:
                 resolution = resolution or 200
 
-                Xu = self.X * self._Xscale + self._Xoffset # NOTE self.X are the normalized values now
+                Xu = self.X * self._Xscale + self._Xoffset #NOTE self.X are the normalized values now
 
                 fixed_dims = np.array([i for i,v in fixed_inputs])
                 freedim = np.setdiff1d(np.arange(self.input_dim),fixed_dims)

GPy/core/model.py

@@ -31,8 +31,8 @@ class Model(Parameterized):
     def getstate(self):
         """
         Get the current state of the class.
-        
         Inherited from Parameterized, so add those parameters to the state
+
         :return: list of states from the model.
 
         """
@@ -397,17 +397,20 @@ class Model(Parameterized):
             return np.nan
         return 0.5 * self._get_params().size * np.log(2 * np.pi) + self.log_likelihood() - hld
 
-    def __str__(self, names=None):
+    def __str__(self):
-        if names is None:
+        s = Parameterized.__str__(self).split('\n')
-            names = self._get_print_names()
+        #def __str__(self, names=None):
-        s = Parameterized.__str__(self, names=names).split('\n')
+        #    if names is None:
+        #        names = self._get_print_names()
+        #s = Parameterized.__str__(self, names=names).split('\n')
         # add priors to the string
         if self.priors is not None:
             strs = [str(p) if p is not None else '' for p in self.priors]
         else:
-            strs = [''] * len(self._get_param_names())
+            strs = [''] * len(self._get_params())
-        name_indices = self.grep_param_names("|".join(names))
+       #         strs = [''] * len(self._get_param_names())
-        strs = np.array(strs)[name_indices]
+       #     name_indices = self.grep_param_names("|".join(names))
+       #     strs = np.array(strs)[name_indices]
         width = np.array(max([len(p) for p in strs] + [5])) + 4
 
         log_like = self.log_likelihood()

GPy/core/parameterized.py

@@ -27,9 +27,9 @@ class Parameterized(object):
 
     def _get_param_names(self):
         raise NotImplementedError, "this needs to be implemented to use the Parameterized class"
-    def _get_print_names(self):
+    #def _get_print_names(self):
-        """ Override for which names to print out, when using print m """
+    #    """ Override for which names to print out, when using print m """
-        return self._get_param_names()
+    #    return self._get_param_names()
 
     def pickle(self, filename, protocol=None):
         if protocol is None:
@@ -63,8 +63,8 @@ class Parameterized(object):
         """
         Get the current state of the class,
         here just all the indices, rest can get recomputed
-        
         For inheriting from Parameterized:
+
         Allways append the state of the inherited object
         and call down to the inherited object in setstate!!
         """
@@ -336,26 +336,30 @@ class Parameterized(object):
         n = [nn for i, nn in enumerate(n) if not i in remove]
         return n
 
-    @property
+    #@property
-    def all(self):
+    #def all(self):
-        return self.__str__(self._get_param_names())
+    #    return self.__str__(self._get_param_names())
 
 
-    def __str__(self, names=None, nw=30):
+    #def __str__(self, names=None, nw=30):
+    def __str__(self, nw=30):
         """
         Return a string describing the parameter names and their ties and constraints
         """
-        if names is None:
+        names = self._get_param_names()
-            names = self._get_print_names()
+        #if names is None:
-        name_indices = self.grep_param_names("|".join(names))
+        #    names = self._get_print_names()
+        #name_indices = self.grep_param_names("|".join(names))
         N = len(names)
 
         if not N:
             return "This object has no free parameters."
         header = ['Name', 'Value', 'Constraints', 'Ties']
-        values = self._get_params()[name_indices] # map(str,self._get_params())
+        values = self._get_params() # map(str,self._get_params())
+        #values = self._get_params()[name_indices] # map(str,self._get_params())
         # sort out the constraints
-        constraints = [''] * len(self._get_param_names())
+        constraints = [''] * len(names)
+        #constraints = [''] * len(self._get_param_names())
         for i, t in zip(self.constrained_indices, self.constraints):
             for ii in i:
                 constraints[ii] = t.__str__()
@@ -368,6 +372,9 @@ class Parameterized(object):
             for j in tie:
                 ties[j] = '(' + str(i) + ')'
 
+        if values.size == 1:
+            values = ['%.4f' %float(values)]
+        else:
             values = ['%.4f' % float(v) for v in values]
         max_names = max([len(names[i]) for i in range(len(names))] + [len(header[0])])
         max_values = max([len(values[i]) for i in range(len(values))] + [len(header[1])])
@@ -383,3 +390,77 @@ class Parameterized(object):
 
 
         return ('\n'.join([header_string[0], separator] + param_string)) + '\n'
+
+    def grep_model(self,regexp):
+        regexp_indices = self.grep_param_names(regexp)
+        all_names = self._get_param_names()
+
+        names = [all_names[pj] for pj in regexp_indices]
+        N = len(names)
+
+        if not N:
+            return "Match not found."
+
+        header = ['Name', 'Value', 'Constraints', 'Ties']
+        all_values = self._get_params()
+        values = np.array([all_values[pj] for pj in regexp_indices])
+        constraints = [''] * len(names)
+
+        _constrained_indices,aux = self._pick_elements(regexp_indices,self.constrained_indices)
+        _constraints = [self.constraints[pj] for pj in aux]
+
+        for i, t in zip(_constrained_indices, _constraints):
+            for ii in i:
+                iii = regexp_indices.tolist().index(ii)
+                constraints[iii] = t.__str__()
+
+        _fixed_indices,aux = self._pick_elements(regexp_indices,self.fixed_indices)
+        for i in _fixed_indices:
+            for ii in i:
+                iii = regexp_indices.tolist().index(ii)
+                constraints[ii] = 'Fixed'
+
+        _tied_indices,aux = self._pick_elements(regexp_indices,self.tied_indices)
+        ties = [''] * len(names)
+        for i,ti in zip(_tied_indices,aux):
+            for ii in i:
+                iii = regexp_indices.tolist().index(ii)
+                ties[iii] = '(' + str(ti) + ')'
+
+        if values.size == 1:
+            values = ['%.4f' %float(values)]
+        else:
+            values = ['%.4f' % float(v) for v in values]
+
+        max_names = max([len(names[i]) for i in range(len(names))] + [len(header[0])])
+        max_values = max([len(values[i]) for i in range(len(values))] + [len(header[1])])
+        max_constraint = max([len(constraints[i]) for i in range(len(constraints))] + [len(header[2])])
+        max_ties = max([len(ties[i]) for i in range(len(ties))] + [len(header[3])])
+        cols = np.array([max_names, max_values, max_constraint, max_ties]) + 4
+
+        header_string = ["{h:^{col}}".format(h=header[i], col=cols[i]) for i in range(len(cols))]
+        header_string = map(lambda x: '|'.join(x), [header_string])
+        separator = '-' * len(header_string[0])
+        param_string = ["{n:^{c0}}|{v:^{c1}}|{c:^{c2}}|{t:^{c3}}".format(n=names[i], v=values[i], c=constraints[i], t=ties[i], c0=cols[0], c1=cols[1], c2=cols[2], c3=cols[3]) for i in range(len(values))]
+
+        print header_string[0]
+        print separator
+        for string in param_string:
+            print string
+
+    def _pick_elements(self,regexp_ind,array_list):
+        """Removes from array_list the elements different from regexp_ind"""
+        new_array_list = [] #New list with elements matching regexp_ind
+        array_indices = [] #Indices that matches the arrays in new_array_list and array_list
+
+        array_index = 0
+        for array in array_list:
+            _new = []
+            for ai in array:
+                if ai in regexp_ind:
+                    _new.append(ai)
+            if len(_new):
+                new_array_list.append(np.array(_new))
+                array_indices.append(array_index)
+            array_index += 1
+        return new_array_list, array_indices

GPy/core/sparse_gp.py

@@ -165,13 +165,17 @@ class SparseGP(GPBase):
                 raise NotImplementedError, "heteroscedatic derivates with uncertain inputs not implemented"
 
             else:
+
+                LBi = chol_inv(self.LB)
                 Lmi_psi1, nil = dtrtrs(self._Lm, np.asfortranarray(self.psi1.T), lower=1, trans=0)
                 _LBi_Lmi_psi1, _ = dtrtrs(self.LB, np.asfortranarray(Lmi_psi1), lower=1, trans=0)
-                _Bi_Lmi_psi1, _ = dtrtrs(self.LB.T, np.asfortranarray(_LBi_Lmi_psi1), lower=1, trans=0)
+
 
                 self.partial_for_likelihood = -0.5 * self.likelihood.precision + 0.5 * self.likelihood.V**2
                 self.partial_for_likelihood += 0.5 * self.output_dim * (self.psi0 - np.sum(Lmi_psi1**2,0))[:,None] * self.likelihood.precision**2
-                self.partial_for_likelihood += 0.5*np.sum(_Bi_Lmi_psi1*Lmi_psi1,0)[:,None]*self.likelihood.precision**2 #NOTE this term has numerical issues
+
+                self.partial_for_likelihood += 0.5*np.sum(mdot(LBi.T,LBi,Lmi_psi1)*Lmi_psi1,0)[:,None]*self.likelihood.precision**2
+
                 self.partial_for_likelihood += -np.dot(self._LBi_Lmi_psi1Vf.T,_LBi_Lmi_psi1).T * self.likelihood.Y * self.likelihood.precision**2
                 self.partial_for_likelihood += 0.5*np.dot(self._LBi_Lmi_psi1Vf.T,_LBi_Lmi_psi1).T**2 * self.likelihood.precision**2
 
@@ -208,8 +212,8 @@ class SparseGP(GPBase):
         return sum([['iip_%i_%i' % (i, j) for j in range(self.Z.shape[1])] for i in range(self.Z.shape[0])], [])\
             + self.kern._get_param_names_transformed() + self.likelihood._get_param_names()
 
-    def _get_print_names(self):
+    #def _get_print_names(self):
-        return self.kern._get_param_names_transformed() + self.likelihood._get_param_names()
+    #    return self.kern._get_param_names_transformed() + self.likelihood._get_param_names()
 
     def update_likelihood_approximation(self):
         """
@@ -288,7 +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:
@@ -344,7 +348,10 @@ class SparseGP(GPBase):
             which_data = slice(None)
 
         GPBase.plot(self, samples=0, plot_limits=plot_limits, which_data='all', which_parts='all', resolution=None, levels=20, ax=ax, output=output)
-        if self.X.shape[1] == 1 and not hasattr(self,'multioutput'):
+
+        if not hasattr(self,'multioutput'):
+
+            if self.X.shape[1] == 1:
                 if self.has_uncertain_inputs:
                     Xu = self.X * self._Xscale + self._Xoffset # NOTE self.X are the normalized values now
                     ax.errorbar(Xu[which_data, 0], self.likelihood.data[which_data, 0],
@@ -353,11 +360,14 @@ class SparseGP(GPBase):
                 Zu = self.Z * self._Xscale + self._Xoffset
                 ax.plot(Zu, np.zeros_like(Zu) + ax.get_ylim()[0], 'r|', mew=1.5, markersize=12)
 
-        elif self.X.shape[1] == 2 and not hasattr(self,'multioutput'):
+            elif self.X.shape[1] == 2:
                 Zu = self.Z * self._Xscale + self._Xoffset
                 ax.plot(Zu[:, 0], Zu[:, 1], 'wo')
 
-        elif self.X.shape[1] == 2 and hasattr(self,'multioutput'):
+        else:
+            pass
+            """
+            if self.X.shape[1] == 2 and hasattr(self,'multioutput'):
                 Xu = self.X[self.X[:,-1]==output,:]
                 if self.has_uncertain_inputs:
                     Xu = self.X * self._Xscale + self._Xoffset  # NOTE self.X are the normalized values now
@@ -376,6 +386,7 @@ class SparseGP(GPBase):
 
             else:
                 raise NotImplementedError, "Cannot define a frame with more than two input dimensions"
+            """
 
     def predict_single_output(self, Xnew, output=0, which_parts='all', full_cov=False):
         """

GPy/examples/classification.py

@@ -166,3 +166,35 @@ def FITC_crescent_data(num_inducing=10, seed=default_seed):
     print(m)
     m.plot()
     return m
+
+
+def toy_heaviside(seed=default_seed):
+    """
+    Simple 1D classification example using a heavy side gp transformation
+    :param seed : seed value for data generation (default is 4).
+    :type seed: int
+    """
+
+    data = GPy.util.datasets.toy_linear_1d_classification(seed=seed)
+    Y = data['Y'][:, 0:1]
+    Y[Y.flatten() == -1] = 0
+
+    # Model definition
+    noise_model = GPy.likelihoods.binomial(GPy.likelihoods.noise_models.gp_transformations.Heaviside())
+    likelihood = GPy.likelihoods.EP(Y,noise_model)
+    m = GPy.models.GPClassification(data['X'], likelihood=likelihood)
+
+    # Optimize
+    m.update_likelihood_approximation()
+    # Parameters optimization:
+    m.optimize()
+    #m.pseudo_EM()
+
+    # Plot
+    fig, axes = pb.subplots(2,1)
+    m.plot_f(ax=axes[0])
+    m.plot(ax=axes[1])
+    print(m)
+
+    return m
+

GPy/examples/regression.py

@@ -9,9 +9,9 @@ import pylab as pb
 import numpy as np
 import GPy
 
-def coregionalisation_toy2(max_iters=100):
+def coregionalization_toy2(max_iters=100):
     """
-    A simple demonstration of coregionalisation on two sinusoidal functions.
+    A simple demonstration of coregionalization on two sinusoidal functions.
     """
     X1 = np.random.rand(50, 1) * 8
     X2 = np.random.rand(30, 1) * 5
@@ -40,9 +40,9 @@ def coregionalisation_toy2(max_iters=100):
     pb.plot(X2[:, 0], Y2[:, 0], 'gx', mew=2)
     return m
 
-def coregionalisation_toy(max_iters=100):
+def coregionalization_toy(max_iters=100):
     """
-    A simple demonstration of coregionalisation on two sinusoidal functions.
+    A simple demonstration of coregionalization on two sinusoidal functions.
     """
     X1 = np.random.rand(50, 1) * 8
     X2 = np.random.rand(30, 1) * 5
@@ -63,9 +63,9 @@ def coregionalisation_toy(max_iters=100):
     axes[1].set_title('Output 1')
     return m
 
-def coregionalisation_sparse(max_iters=100):
+def coregionalization_sparse(max_iters=100):
     """
-    A simple demonstration of coregionalisation on two sinusoidal functions using sparse approximations.
+    A simple demonstration of coregionalization on two sinusoidal functions using sparse approximations.
     """
     X1 = np.random.rand(500, 1) * 8
     X2 = np.random.rand(300, 1) * 5
@@ -75,41 +75,18 @@ def coregionalisation_sparse(max_iters=100):
     Y2 = -np.sin(X2) + np.random.randn(*X2.shape) * 0.05
     Y = np.vstack((Y1, Y2))
 
-    num_inducing = 40
-    Z = np.hstack((np.random.rand(num_inducing, 1) * 8, np.random.randint(0, 2, num_inducing)[:, None]))
-    Z = np.hstack((np.random.rand(num_inducing, 1) * 8, np.random.randint(0, 2, num_inducing)[:, None]))
-
     k1 = GPy.kern.rbf(1)
 
     m = GPy.models.SparseGPMultioutputRegression(X_list=[X1,X2],Y_list=[Y1,Y2],kernel_list=[k1],num_inducing=20)
-    #k2 = GPy.kern.coregionalize(2, 2)
+    m.constrain_fixed('.*rbf_var',1.)
-    #k = k1**k2 #.prod(k2, tensor=True) # + GPy.kern.white(2,0.001)
+    m.optimize(messages=1)
-    #m = GPy.models.SparseGPRegression(X, Y, kernel=k, Z=Z)
+    #m.optimize_restarts(5, robust=True, messages=1, max_iters=max_iters, optimizer='bfgs')
-    m.constrain_fixed('.*rbf_var', 1.)
-
-    #m.constrain_fixed('iip')
-    #m.constrain_bounded('noise_variance', 1e-3, 1e-1)
-#     m.optimize_restarts(5, robust=True, messages=1, max_iters=max_iters, optimizer='bfgs')
-    m.optimize(max_iters=max_iters)
 
     fig, axes = pb.subplots(2,1)
     m.plot(output=0,ax=axes[0])
     m.plot(output=1,ax=axes[1])
     axes[0].set_title('Output 0')
     axes[1].set_title('Output 1')
-    # plotting:
-    #pb.figure()
-    #Xtest1 = np.hstack((np.linspace(0, 9, 100)[:, None], np.zeros((100, 1))))
-    #Xtest2 = np.hstack((np.linspace(0, 9, 100)[:, None], np.ones((100, 1))))
-    #mean, var, low, up = m.predict(Xtest1)
-    #GPy.util.plot.gpplot(Xtest1[:, 0], mean, low, up)
-    #mean, var, low, up = m.predict(Xtest2)
-    #GPy.util.plot.gpplot(Xtest2[:, 0], mean, low, up)
-    #pb.plot(X1[:, 0], Y1[:, 0], 'rx', mew=2)
-    #pb.plot(X2[:, 0], Y2[:, 0], 'gx', mew=2)
-    #y = pb.ylim()[0]
-    #pb.plot(Z[:, 0][Z[:, 1] == 0], np.zeros(np.sum(Z[:, 1] == 0)) + y, 'r|', mew=2)
-    #pb.plot(Z[:, 0][Z[:, 1] == 1], np.zeros(np.sum(Z[:, 1] == 1)) + y, 'g|', mew=2)
     return m
 
 def epomeo_gpx(max_iters=100):

GPy/kern/constructors.py

@@ -373,7 +373,7 @@ def symmetric(k):
     k_.parts = [symmetric.Symmetric(p) for p in k.parts]
     return k_
 
-def coregionalize(output_dim,W_columns=1, W=None, kappa=None):
+def coregionalize(output_dim,rank=1, W=None, kappa=None):
     """
     Coregionlization matrix B, of the form:
     .. math::
@@ -387,16 +387,16 @@ def coregionalize(output_dim,W_columns=1, W=None, kappa=None):
 
     :param output_dim: the number of outputs to corregionalize
     :type output_dim: int
-    :param W_columns: number of columns of the W matrix (this parameter is ignored if parameter W is not None)
+    :param rank: number of columns of the W matrix (this parameter is ignored if parameter W is not None)
-    :type W_colunns: int
+    :type rank: int
-    :param W: a low rank matrix that determines the correlations between the different outputs, together with kappa it forms the coregionalisation matrix B
+    :param W: a low rank matrix that determines the correlations between the different outputs, together with kappa it forms the coregionalization matrix B
-    :type W: numpy array of dimensionality (num_outpus, W_columns)
+    :type W: numpy array of dimensionality (num_outpus, rank)
     :param kappa: a vector which allows the outputs to behave independently
     :type kappa: numpy array of dimensionality  (output_dim,)
     :rtype: kernel object
 
     """
-    p = parts.coregionalize.Coregionalize(output_dim,W_columns,W,kappa)
+    p = parts.coregionalize.Coregionalize(output_dim,rank,W,kappa)
     return kern(1,[p])
 
 
@@ -456,7 +456,7 @@ def hierarchical(k):
     _parts = [parts.hierarchical.Hierarchical(k.parts)]
     return kern(k.input_dim+len(k.parts),_parts)
 
-def build_lcm(input_dim, output_dim, kernel_list = [], W_columns=1,W=None,kappa=None):
+def build_lcm(input_dim, output_dim, kernel_list = [], rank=1,W=None,kappa=None):
     """
     Builds a kernel of a linear coregionalization model
 
@@ -464,8 +464,8 @@ def build_lcm(input_dim, output_dim, kernel_list = [], W_columns=1,W=None,kappa=
     :output_dim: Number of outputs
     :kernel_list: List of coregionalized kernels, each element in the list will be multiplied by a different corregionalization matrix
     :type kernel_list: list of GPy kernels
-    :param W_columns: number tuples of the corregionalization parameters 'coregion_W'
+    :param rank: number tuples of the corregionalization parameters 'coregion_W'
-    :type W_columns: integer
+    :type rank: integer
 
     ..Note the kernels dimensionality is overwritten to fit input_dim
     """
@@ -475,11 +475,11 @@ def build_lcm(input_dim, output_dim, kernel_list = [], W_columns=1,W=None,kappa=
             k.input_dim = input_dim
             warnings.warn("kernel's input dimension overwritten to fit input_dim parameter.")
 
-    k_coreg = coregionalize(output_dim,W_columns,W,kappa)
+    k_coreg = coregionalize(output_dim,rank,W,kappa)
     kernel = kernel_list[0]**k_coreg.copy()
 
     for k in kernel_list[1:]:
-        k_coreg = coregionalize(output_dim,W_columns,W,kappa)
+        k_coreg = coregionalize(output_dim,rank,W,kappa)
         kernel += k**k_coreg.copy()
 
     return kernel

GPy/kern/parts/__init__.py

@@ -6,7 +6,7 @@ import eq_ode1
 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/kern/parts/coregionalize.py

@@ -24,8 +24,8 @@ class Coregionalize(Kernpart):
 
     :param output_dim: number of outputs to coregionalize
     :type output_dim: int
-    :param W_columns: number of columns of the W matrix (this parameter is ignored if parameter W is not None)
+    :param rank: number of columns of the W matrix (this parameter is ignored if parameter W is not None)
-    :type W_colunns: int
+    :type rank: int
     :param W: a low rank matrix that determines the correlations between the different outputs, together with kappa it forms the coregionalization matrix B
     :type W: numpy array of dimensionality (num_outpus, W_columns)
     :param kappa: a vector which allows the outputs to behave independently
@@ -38,6 +38,8 @@ class Coregionalize(Kernpart):
         self.name = 'coregion'
         self.output_dim = output_dim
         self.rank = rank
+        if self.rank>output_dim-1:
+            print("Warning: Unusual choice of rank, it should normally be less than the output_dim.")
         if W is None:
             self.W = 0.5*np.random.randn(self.output_dim,self.rank)/np.sqrt(self.rank)
         else:
@@ -158,4 +160,5 @@ class Coregionalize(Kernpart):
         target += np.hstack([dW.flatten(),dkappa])
 
     def dK_dX(self,dL_dK,X,X2,target):
+        #NOTE In this case, pass is equivalent to returning zero.
         pass

GPy/kern/parts/poly.py

@@ -20,8 +20,8 @@ class POLY(Kernpart):
 
     The kernel is not recommended as it is badly behaved when the
     \sigma^2_w*x'*y + \sigma^2_b has a magnitude greater than one. For completeness
-    there is an automatic relevance determination version of this
+    there will be an automatic relevance determination version of this
-    kernel provided.
+    kernel provided (NOT YET IMPLEMENTED!).
 
     :param input_dim: the number of input dimensions
     :type input_dim: int 

GPy/kern/parts/prod.py

@@ -2,6 +2,7 @@
 # Licensed under the BSD 3-clause license (see LICENSE.txt)
 
 from kernpart import Kernpart
+from coregionalize import Coregionalize
 import numpy as np
 import hashlib
 
@@ -18,7 +19,7 @@ class Prod(Kernpart):
     """
     def __init__(self,k1,k2,tensor=False):
         self.num_params = k1.num_params + k2.num_params
-        self.name = '['+k1.name + '(x)' + k2.name +']'
+        self.name = '['+k1.name + '**' + k2.name +']'
         self.k1 = k1
         self.k2 = k2
         if tensor:
@@ -90,6 +91,16 @@ class Prod(Kernpart):
     def dK_dX(self,dL_dK,X,X2,target):
         """derivative of the covariance matrix with respect to X."""
         self._K_computations(X,X2)
+        if X2 is None:
+            if not isinstance(self.k1,Coregionalize) and not isinstance(self.k2,Coregionalize):
+                self.k1.dK_dX(dL_dK*self._K2, X[:,self.slice1], None, target[:,self.slice1])
+                self.k2.dK_dX(dL_dK*self._K1, X[:,self.slice2], None, target[:,self.slice2])
+            else:#if isinstance(self.k1,Coregionalize) or isinstance(self.k2,Coregionalize):
+                #NOTE The indices column in the inputs makes the ki.dK_dX fail when passing None instead of X[:,self.slicei]
+                X2 = X
+                self.k1.dK_dX(2.*dL_dK*self._K2, X[:,self.slice1], X2[:,self.slice1], target[:,self.slice1])
+                self.k2.dK_dX(2.*dL_dK*self._K1, X[:,self.slice2], X2[:,self.slice2], target[:,self.slice2])
+        else:
             self.k1.dK_dX(dL_dK*self._K2, X[:,self.slice1], X2[:,self.slice1], target[:,self.slice1])
             self.k2.dK_dX(dL_dK*self._K1, X[:,self.slice2], X2[:,self.slice2], target[:,self.slice2])
 

GPy/kern/parts/rational_quadratic.py

@@ -57,7 +57,7 @@ class RationalQuadratic(Kernpart):
         dist2 = np.square((X-X2.T)/self.lengthscale)
 
         dvar = (1 + dist2/2.)**(-self.power)
-        dl = self.power * self.variance * dist2 * self.lengthscale**(-3) * (1 + dist2/2./self.power)**(-self.power-1)
+        dl = self.power * self.variance * dist2 / self.lengthscale * (1 + dist2/2.)**(-self.power-1)
         dp = - self.variance * np.log(1 + dist2/2.) * (1 + dist2/2.)**(-self.power)
 
         target[0] += np.sum(dvar*dL_dK)

GPy/likelihoods/ep.py

@@ -37,6 +37,8 @@ class EP(likelihood):
         self.VVT_factor = self.V
         self.trYYT = 0.
 
+        super(EP, self).__init__()
+
     def restart(self):
         self.tau_tilde = np.zeros(self.N)
         self.v_tilde = np.zeros(self.N)

GPy/likelihoods/gaussian.py

@@ -34,6 +34,8 @@ class Gaussian(likelihood):
         self._variance = np.asarray(variance) + 1.
         self._set_params(np.asarray(variance))
 
+        super(Gaussian, self).__init__()
+
     def set_data(self, data):
         self.data = data
         self.N, D = data.shape

GPy/likelihoods/gaussian_mixed_noise.py

@@ -45,6 +45,8 @@ class Gaussian_Mixed_Noise(likelihood):
         self.set_data(data_list)
         self._set_params(np.asarray(noise_params))
 
+        super(Gaussian_Mixed_Noise, self).__init__()
+
     def set_data(self, data_list):
         self.data = np.vstack(data_list)
         self.N, D = self.data.shape

GPy/likelihoods/likelihood.py

@@ -1,7 +1,8 @@
 import numpy as np
 import copy
+from ..core.parameterized import Parameterized
 
-class likelihood:
+class likelihood(Parameterized):
     """
     The atom for a likelihood class
 
@@ -18,8 +19,8 @@ class likelihood:
     self.YYT : (optional) = np.dot(self.Y, self.Y.T) enables computational savings for D>N
     self.V : self.precision * self.Y
     """
-    def __init__(self,data):
+    def __init__(self):
-        raise ValueError, "this class is not to be instantiated"
+        Parameterized.__init__(self)
 
     def _get_params(self):
         raise NotImplementedError
@@ -38,7 +39,3 @@ class likelihood:
 
     def predictive_values(self, mu, var):
         raise NotImplementedError
-
-    def copy(self):
-        """ Returns a (deep) copy of the current likelihood """
-        return copy.deepcopy(self)

GPy/likelihoods/noise_model_constructors.py

@@ -19,7 +19,7 @@ def binomial(gp_link=None):
         analytical_mean = True
         analytical_variance = False
 
-    elif isinstance(gp_link,noise_models.gp_transformations.Step):
+    elif isinstance(gp_link,noise_models.gp_transformations.Heaviside):
         analytical_mean = True
         analytical_variance = True
 
@@ -42,7 +42,7 @@ def exponential(gp_link=None):
     analytical_variance = False
     return noise_models.exponential_noise.Exponential(gp_link,analytical_mean,analytical_variance)
 
-def gaussian(gp_link=None,variance=1.):
+def gaussian_ep(gp_link=None,variance=1.):
     """
     Construct a gaussian likelihood
 

GPy/likelihoods/noise_models/binomial_noise.py

@@ -49,15 +49,30 @@ class Binomial(NoiseDistribution):
             mu_hat = v_i/tau_i + data_i*phi/(Z_hat*np.sqrt(tau_i**2 + tau_i))
             sigma2_hat = 1./tau_i - (phi/((tau_i**2+tau_i)*Z_hat))*(z+phi/Z_hat)
 
-        elif isinstance(self.gp_link,gp_transformations.Step):
+        elif isinstance(self.gp_link,gp_transformations.Heaviside):
-            Z_hat = None
+            a = data_i*v_i/np.sqrt(tau_i)
-            mu_hat = None
+            Z_hat = std_norm_cdf(a)
-            sigma2_hat = None
+            N = std_norm_pdf(a)
+            mu_hat = v_i/tau_i + data_i*N/Z_hat/np.sqrt(tau_i)
+            sigma2_hat = (1. - a*N/Z_hat - np.square(N/Z_hat))/tau_i
+            if np.any(np.isnan([Z_hat, mu_hat, sigma2_hat])):
+                stop
 
         return Z_hat, mu_hat, sigma2_hat
 
     def _predictive_mean_analytical(self,mu,sigma):
+        if isinstance(self.gp_link,gp_transformations.Probit):
             return stats.norm.cdf(mu/np.sqrt(1+sigma**2))
+        elif isinstance(self.gp_link,gp_transformations.Heaviside):
+            return stats.norm.cdf(mu/sigma)
+        else:
+            raise NotImplementedError
+
+    def _predictive_variance_analytical(self,mu,sigma, pred_mean):
+        if isinstance(self.gp_link,gp_transformations.Heaviside):
+            return 0.
+        else:
+            raise NotImplementedError
 
     def _mass(self,gp,obs):
         #NOTE obs must be in {0,1}

GPy/likelihoods/noise_models/gp_transformations.py

@@ -108,7 +108,7 @@ class Reciprocal(GPTransformation):
     def d2transf_df2(self,f):
         return 2./f**3
 
-class Step(GPTransformation):
+class Heaviside(GPTransformation):
     """
     $$
     g(f) = I_{x \in A}
@@ -116,10 +116,10 @@ class Step(GPTransformation):
     """
     def transf(self,f):
         #transformation goes here
-        return np.where(f>0, 1, -1)
+        return np.where(f>0, 1, 0)
 
     def dtransf_df(self,f):
-        pass
+        raise NotImplementedError, "This function is not differentiable!"
 
     def d2transf_df2(self,f):
-        pass
+        raise NotImplementedError, "This function is not differentiable!"

GPy/likelihoods/noise_models/noise_distributions.py

@@ -107,7 +107,7 @@ class NoiseDistribution(object):
         :param mu: cavity distribution mean
         :param sigma: cavity distribution standard deviation
         """
-        return sp.optimize.fmin_ncg(self._nlog_product_scaled,x0=mu,fprime=self._dnlog_product_dgp,fhess=self._d2nlog_product_dgp2,args=(obs,mu,sigma))
+        return sp.optimize.fmin_ncg(self._nlog_product_scaled,x0=mu,fprime=self._dnlog_product_dgp,fhess=self._d2nlog_product_dgp2,args=(obs,mu,sigma),disp=False)
 
     def _moments_match_analytical(self,obs,tau,v):
         """
@@ -244,7 +244,7 @@ class NoiseDistribution(object):
         :param mu: cavity distribution mean
         :param sigma: cavity distribution standard deviation
         """
-        maximum = sp.optimize.fmin_ncg(self._nlog_conditional_mean_scaled,x0=self._mean(mu),fprime=self._dnlog_conditional_mean_dgp,fhess=self._d2nlog_conditional_mean_dgp2,args=(mu,sigma))
+        maximum = sp.optimize.fmin_ncg(self._nlog_conditional_mean_scaled,x0=self._mean(mu),fprime=self._dnlog_conditional_mean_dgp,fhess=self._d2nlog_conditional_mean_dgp2,args=(mu,sigma),disp=False)
         mean = np.exp(-self._nlog_conditional_mean_scaled(maximum,mu,sigma))/(np.sqrt(self._d2nlog_conditional_mean_dgp2(maximum,mu,sigma))*sigma)
         """
 
@@ -267,7 +267,7 @@ class NoiseDistribution(object):
         :param mu: cavity distribution mean
         :param sigma: cavity distribution standard deviation
         """
-        maximum = sp.optimize.fmin_ncg(self._nlog_exp_conditional_mean_sq_scaled,x0=self._mean(mu),fprime=self._dnlog_exp_conditional_mean_sq_dgp,fhess=self._d2nlog_exp_conditional_mean_sq_dgp2,args=(mu,sigma))
+        maximum = sp.optimize.fmin_ncg(self._nlog_exp_conditional_mean_sq_scaled,x0=self._mean(mu),fprime=self._dnlog_exp_conditional_mean_sq_dgp,fhess=self._d2nlog_exp_conditional_mean_sq_dgp2,args=(mu,sigma),disp=False)
         mean_squared = np.exp(-self._nlog_exp_conditional_mean_sq_scaled(maximum,mu,sigma))/(np.sqrt(self._d2nlog_exp_conditional_mean_sq_dgp2(maximum,mu,sigma))*sigma)
         return mean_squared
 
@@ -280,7 +280,7 @@ class NoiseDistribution(object):
         :predictive_mean: output's predictive mean, if None _predictive_mean function will be called.
         """
         # E( V(Y_star|f_star) )
-        maximum = sp.optimize.fmin_ncg(self._nlog_exp_conditional_variance_scaled,x0=self._variance(mu),fprime=self._dnlog_exp_conditional_variance_dgp,fhess=self._d2nlog_exp_conditional_variance_dgp2,args=(mu,sigma))
+        maximum = sp.optimize.fmin_ncg(self._nlog_exp_conditional_variance_scaled,x0=self._variance(mu),fprime=self._dnlog_exp_conditional_variance_dgp,fhess=self._d2nlog_exp_conditional_variance_dgp2,args=(mu,sigma),disp=False)
         exp_var = np.exp(-self._nlog_exp_conditional_variance_scaled(maximum,mu,sigma))/(np.sqrt(self._d2nlog_exp_conditional_variance_dgp2(maximum,mu,sigma))*sigma)
 
         """
@@ -357,7 +357,7 @@ class NoiseDistribution(object):
         :param mu: latent variable's predictive mean
         :param sigma: latent variable's predictive standard deviation
         """
-        return sp.optimize.fmin_ncg(self._nlog_joint_predictive_scaled,x0=(mu,self.gp_link.transf(mu)),fprime=self._gradient_nlog_joint_predictive,fhess=self._hessian_nlog_joint_predictive,args=(mu,sigma))
+        return sp.optimize.fmin_ncg(self._nlog_joint_predictive_scaled,x0=(mu,self.gp_link.transf(mu)),fprime=self._gradient_nlog_joint_predictive,fhess=self._hessian_nlog_joint_predictive,args=(mu,sigma),disp=False)
 
     def predictive_values(self,mu,var):
         """

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
@@ -66,8 +66,8 @@ class BayesianGPLVM(SparseGP, GPLVM):
         S_names = sum([['X_variance_%i_%i' % (n, q) for q in range(self.input_dim)] for n in range(self.num_data)], [])
         return (X_names + S_names + SparseGP._get_param_names(self))
 
-    def _get_print_names(self):
+    #def _get_print_names(self):
-        return SparseGP._get_print_names(self)
+    #    return SparseGP._get_print_names(self)
 
     def _get_params(self):
         """
@@ -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)

GPy/models/gp_classification.py

@@ -14,7 +14,7 @@ class GPClassification(GP):
     This is a thin wrapper around the models.GP class, with a set of sensible defaults
 
     :param X: input observations
-    :param Y: observed values
+    :param Y: observed values, can be None if likelihood is not None
     :param likelihood: a GPy likelihood, defaults to Binomial with probit link_function
     :param kernel: a GPy kernel, defaults to rbf
     :param normalize_X:  whether to normalize the input data before computing (predictions will be in original scales)

GPy/models/gp_multioutput_regression.py

@@ -6,7 +6,6 @@ import numpy as np
 from ..core import GP
 from .. import likelihoods
 from .. import kern
-#from ..util import multioutput
 
 class GPMultioutputRegression(GP):
     """

GPy/models/mrd.py

@@ -163,28 +163,31 @@ class MRD(Model):
         self._init_X(initx, self.likelihood_list)
         self._init_Z(initz, self.X)
 
-    def _get_latent_param_names(self):
+    #def _get_latent_param_names(self):
+    def _get_param_names(self):
         n1 = self.gref._get_param_names()
         n1var = n1[:self.NQ * 2 + self.MQ]
-        return n1var
+    #    return n1var
-
+    #
-
+    #def _get_kernel_names(self):
-    def _get_kernel_names(self):
         map_names = lambda ns, name: map(lambda x: "{1}_{0}".format(*x),
                                          itertools.izip(ns,
                                                         itertools.repeat(name)))
-        kernel_names = (map_names(SparseGP._get_param_names(g)[self.MQ:], n) for g, n in zip(self.bgplvms, self.names))
+        return list(itertools.chain(n1var, *(map_names(\
-        return kernel_names
+                SparseGP._get_param_names(g)[self.MQ:], n) \
+                for g, n in zip(self.bgplvms, self.names))))
+    #    kernel_names = (map_names(SparseGP._get_param_names(g)[self.MQ:], n) for g, n in zip(self.bgplvms, self.names))
+    #    return kernel_names
 
-    def _get_param_names(self):
+    #def _get_param_names(self):
         # X_names = sum([['X_%i_%i' % (n, q) for q in range(self.input_dim)] for n in range(self.num_data)], [])
         # S_names = sum([['X_variance_%i_%i' % (n, q) for q in range(self.input_dim)] for n in range(self.num_data)], [])
-        n1var = self._get_latent_param_names()
+    #    n1var = self._get_latent_param_names()
-        kernel_names = self._get_kernel_names()
+    #    kernel_names = self._get_kernel_names()
-        return list(itertools.chain(n1var, *kernel_names))
+    #    return list(itertools.chain(n1var, *kernel_names))
 
-    def _get_print_names(self):
+    #def _get_print_names(self):
-        return list(itertools.chain(*self._get_kernel_names()))
+    #    return list(itertools.chain(*self._get_kernel_names()))
 
     def _get_params(self):
         """

GPy/testing/kernel_tests.py

@@ -79,7 +79,7 @@ class KernelTests(unittest.TestCase):
         kern = GPy.kern.poly(5, degree=4)
         self.assertTrue(GPy.kern.kern_test(kern, verbose=verbose))
 
-    def test_coregionalisation(self):
+    def test_coregionalization(self):
         X1 = np.random.rand(50,1)*8
         X2 = np.random.rand(30,1)*5
         index = np.vstack((np.zeros_like(X1),np.ones_like(X2)))

GPy/util/__init__.py

@@ -14,4 +14,3 @@ import visualize
 import decorators
 import classification
 import latent_space_visualizations
-#import multioutput

GPy/util/linalg.py

@@ -51,7 +51,7 @@ def dpotri(A, lower=0):
 
     :param A: Matrix A
     :param lower: is matrix lower (true) or upper (false)
-    :returns:
+    :returns: A inverse
     """
     return lapack.dpotri(A, lower=lower)
 

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__'],