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

GPy/core/parameterization/variational.py

@@ -94,6 +94,9 @@ class VariationalPosterior(Parameterized):
         if self.has_uncertain_inputs():
             assert self.variance.shape == self.mean.shape, "need one variance per sample and dimenion"
 
+    def set_gradients(self, grad):
+        self.mean.gradient, self.variance.gradient = grad
+
     def _raveled_index(self):
         index = np.empty(dtype=int, shape=0)
         size = 0
@@ -158,6 +161,9 @@ class SpikeAndSlabPosterior(VariationalPosterior):
         self.gamma = Param("binary_prob",binary_prob, Logistic(1e-10,1.-1e-10))
         self.link_parameter(self.gamma)
 
+    def set_gradients(self, grad):
+        self.mean.gradient, self.variance.gradient, self.gamma.gradient = grad
+
     def __getitem__(self, s):
         if isinstance(s, (int, slice, tuple, list, np.ndarray)):
             import copy

GPy/inference/latent_function_inference/inferenceX.py

@@ -0,0 +1,128 @@
+"""
+"""
+import numpy as np
+from ...core import Model
+from ...core.parameterization import variational
+
+def infer_newX(model, Y_new, optimize=True, init='L2'):
+    """
+    Infer the distribution of X for the new observed data *Y_new*.
+    
+    :param model: the GPy model used in inference
+    :type model: GPy.core.Model
+    :param Y_new: the new observed data for inference
+    :type Y_new: numpy.ndarray
+    :param optimize: whether to optimize the location of new X (True by default)
+    :type optimize: boolean
+    :return: a tuple containing the estimated posterior distribution of X and the model that optimize X 
+    :rtype: (GPy.core.parameterization.variational.VariationalPosterior, GPy.core.Model)
+    """
+    infr_m = InferenceX(model, Y_new, init=init)
+    
+    if optimize:
+        infr_m.optimize()
+        
+    return infr_m.X, infr_m
+
+class InferenceX(Model):
+    """
+    The class for inference of new X with given new Y. (do_test_latent)
+    
+    :param model: the GPy model used in inference
+    :type model: GPy.core.Model
+    :param Y: the new observed data for inference
+    :type Y: numpy.ndarray
+    """
+    def __init__(self, model, Y, name='inferenceX', init='L2'):
+        if np.isnan(Y).any():
+            assert Y.shape[0]==1, "The current implementation of inference X only support one data point at a time with missing data!"
+            self.missing_data = True
+            self.valid_dim = np.logical_not(np.isnan(Y[0]))
+        else:
+            self.missing_data = False
+        super(InferenceX, self).__init__(name)
+        self.likelihood = model.likelihood.copy()
+        self.kern = model.kern.copy()
+        if model.kern.useGPU:
+            from ...models import SSGPLVM
+            if isinstance(model, SSGPLVM):
+                self.kern.GPU_SSRBF(True)
+            else:
+                self.kern.GPU(True)
+        from copy import deepcopy
+        self.posterior = deepcopy(model.posterior)
+        self.variational_prior = model.variational_prior.copy()
+        self.Z = model.Z.copy()
+        self.Y = Y
+        self.X = self._init_X(model, Y, init=init)
+        self.compute_dL()
+        
+        self.link_parameter(self.X)
+    
+    def _init_X(self, model, Y_new, init='L2'):
+        # Initialize the new X by finding the nearest point in Y space.
+        
+        Y = model.Y
+        if self.missing_data:
+            Y = Y[:,self.valid_dim]
+            Y_new = Y_new[:,self.valid_dim]
+            dist = -2.*Y_new.dot(Y.T) + np.square(Y_new).sum(axis=1)[:,None]+ np.square(Y).sum(axis=1)[None,:]
+        else:
+            if init=='L2':
+                dist = -2.*Y_new.dot(Y.T) + np.square(Y_new).sum(axis=1)[:,None]+ np.square(Y).sum(axis=1)[None,:]
+            elif init=='NCC':
+                dist = Y_new.dot(Y.T)
+        idx = dist.argmin(axis=1)
+        
+        from ...models import SSGPLVM
+        from ...util.misc import param_to_array
+        if isinstance(model, SSGPLVM):
+            X = variational.SpikeAndSlabPosterior(param_to_array(model.X.mean[idx]), param_to_array(model.X.variance[idx]), param_to_array(model.X.gamma[idx]))
+            if model.group_spike:
+                X.gamma.fix()
+        else:
+            X = variational.NormalPosterior(param_to_array(model.X.mean[idx]), param_to_array(model.X.variance[idx]))
+        
+        return X
+        
+    def compute_dL(self):
+        # Common computation
+        beta = 1./np.fmax(self.likelihood.variance, 1e-6)
+        output_dim = self.Y.shape[-1]
+        wv = self.posterior.woodbury_vector
+        if self.missing_data:
+            wv = wv[:,self.valid_dim]
+            output_dim = self.valid_dim.sum()
+            self.dL_dpsi2 = beta*(output_dim*self.posterior.woodbury_inv - np.einsum('md,od->mo',wv, wv))/2.
+            self.dL_dpsi1 = beta*np.dot(self.Y[:,self.valid_dim], wv.T)
+            self.dL_dpsi0 = - beta/2.* np.ones(self.Y.shape[0])
+        else:
+            self.dL_dpsi2 = beta*(output_dim*self.posterior.woodbury_inv - np.einsum('md,od->mo',wv, wv))/2.
+            self.dL_dpsi1 = beta*np.dot(self.Y, wv.T)
+            self.dL_dpsi0 = -beta/2.* np.ones(self.Y.shape[0])            #self.dL_dpsi0[:] = 0
+                
+    def parameters_changed(self):
+        psi0 = self.kern.psi0(self.Z, self.X)
+        psi1 = self.kern.psi1(self.Z, self.X)
+        psi2 = self.kern.psi2(self.Z, self.X)
+
+        self._log_marginal_likelihood = (self.dL_dpsi2*psi2).sum()+(self.dL_dpsi1*psi1).sum()+(self.dL_dpsi0*psi0).sum()
+        X_grad = self.kern.gradients_qX_expectations(variational_posterior=self.X, Z=self.Z, dL_dpsi0=self.dL_dpsi0, dL_dpsi1=self.dL_dpsi1, dL_dpsi2=self.dL_dpsi2)
+        self.X.set_gradients(X_grad)
+        
+        from ...core.parameterization.variational import SpikeAndSlabPrior
+        if isinstance(self.variational_prior, SpikeAndSlabPrior):
+            # Update Log-likelihood
+            KL_div = self.variational_prior.KL_divergence(self.X, N=self.Y.shape[0])
+            # update for the KL divergence
+            self.variational_prior.update_gradients_KL(self.X, N=self.Y.shape[0])
+        else:
+            # Update Log-likelihood
+            KL_div = self.variational_prior.KL_divergence(self.X)
+            # update for the KL divergence
+            self.variational_prior.update_gradients_KL(self.X)
+        self._log_marginal_likelihood += -KL_div
+        
+    def log_likelihood(self):
+        return self._log_marginal_likelihood
+

GPy/inference/latent_function_inference/var_dtc.py

@@ -167,7 +167,7 @@ class VarDTC(LatentFunctionInference):
             woodbury_vector = Cpsi1Vf # == Cpsi1V
         else:
             print 'foobar'
-            stop
+            import ipdb; ipdb.set_trace()
             psi1V = np.dot(Y.T*beta, psi1).T
             tmp, _ = dtrtrs(Lm, psi1V, lower=1, trans=0)
             tmp, _ = dpotrs(LB, tmp, lower=1)

GPy/likelihoods/ordinal.py

@@ -1,47 +0,0 @@
-# Copyright (c) 2014 The GPy authors (see AUTHORS.txt)
-# Licensed under the BSD 3-clause license (see LICENSE.txt)
-
-
-import sympy as sym
-from GPy.util.symbolic import gammaln, normcdfln, normcdf, IndMatrix, create_matrix
-import numpy as np
-import link_functions
-from symbolic import Symbolic
-from scipy import stats
-
-class Ordinal(Symbolic):
-    """
-    Ordinal
-
-    .. math::
-        p(y_{i}|\pi(f_{i})) = \left(\frac{r}{r+f_i}\right)^r \frac{\Gamma(r+y_i)}{y!\Gamma(r)}\left(\frac{f_i}{r+f_i}\right)^{y_i}
-
-    .. Note::
-        Y takes non zero integer values..
-        link function should have a positive domain, e.g. log (default).
-
-    .. See also::
-        symbolic.py, for the parent class
-    """
-    def __init__(self, categories=3, gp_link=None):
-        if gp_link is None:
-            gp_link = link_functions.Identity()
-
-        dispersion = sym.Symbol('width', positive=True, real=True)
-        y_0 = sym.Symbol('y_0', nonnegative=True, integer=True)
-        f_0 = sym.Symbol('f_0', positive=True, real=True) 
-        log_pdf = create_matrix('log_pdf', 1, categories)
-        log_pdf[0] = normcdfln(-f_0)
-        if categories>2:
-            w = create_matrix('w', 1, categories)
-            log_pdf[categories-1] = normcdfln(w.sum() + f_0)
-            for i in range(1, categories-1):
-                log_pdf[i] = sym.log(normcdf(w[0, 0:i-1].sum() + f_0) - normcdf(w[0, 0:i].sum()-f_0) )
-        else:
-            log_pdf[1] = normcdfln(f_0)
-        log_pdf.index_var = y_0
-        super(Ordinal, self).__init__(log_pdf=log_pdf, gp_link=gp_link, name='Ordinal')
-
-        # TODO: Check this.
-        self.log_concave = True
-

GPy/models/bayesian_gplvm.py

@@ -141,6 +141,22 @@ class BayesianGPLVM(SparseGP_MPI):
                 resolution, ax, marker, s,
                 fignum, plot_inducing, legend,
                 plot_limits, aspect, updates, predict_kwargs, imshow_kwargs)
+        
+    def infer_newX(self, Y_new, optimize=True, ):
+        """
+        Infer the distribution of X for the new observed data *Y_new*.
+        
+        :param model: the GPy model used in inference
+        :type model: GPy.core.Model
+        :param Y_new: the new observed data for inference
+        :type Y_new: numpy.ndarray
+        :param optimize: whether to optimize the location of new X (True by default)
+        :type optimize: boolean
+        :return: a tuple containing the estimated posterior distribution of X and the model that optimize X 
+        :rtype: (GPy.core.parameterization.variational.VariationalPosterior, GPy.core.Model)
+        """
+        from ..inference.latent_function_inference.inferenceX import infer_newX
+        return infer_newX(self, Y_new, optimize=optimize)
 
     def do_test_latents(self, Y):
         """

GPy/testing/inference_tests.py

@@ -0,0 +1,71 @@
+
+"""
+The test cases for various inference algorithms
+"""
+
+import unittest, itertools
+import numpy as np
+import GPy
+
+
+class InferenceXTestCase(unittest.TestCase):
+    
+    def genData(self):
+        D1,D2,N = 12,12,50
+        np.random.seed(1234)
+    
+        x = np.linspace(0, 4 * np.pi, N)[:, None]
+        s1 = np.vectorize(lambda x: np.sin(x))
+        s2 = np.vectorize(lambda x: np.cos(x)**2)
+        s3 = np.vectorize(lambda x:-np.exp(-np.cos(2 * x)))
+        sS = np.vectorize(lambda x: np.cos(x))
+    
+        s1 = s1(x)
+        s2 = s2(x)
+        s3 = s3(x)
+        sS = sS(x)
+    
+        s1 -= s1.mean(); s1 /= s1.std(0)
+        s2 -= s2.mean(); s2 /= s2.std(0)
+        s3 -= s3.mean(); s3 /= s3.std(0)
+        sS -= sS.mean(); sS /= sS.std(0)
+    
+        S1 = np.hstack([s1, sS])
+        S2 = np.hstack([s3, sS])
+    
+        P1 = np.random.randn(S1.shape[1], D1)
+        P2 = np.random.randn(S2.shape[1], D2)
+    
+        Y1 = S1.dot(P1)
+        Y2 = S2.dot(P2)
+    
+        Y1 += .01 * np.random.randn(*Y1.shape)
+        Y2 += .01 * np.random.randn(*Y2.shape)
+    
+        Y1 -= Y1.mean(0)
+        Y2 -= Y2.mean(0)
+        Y1 /= Y1.std(0)
+        Y2 /= Y2.std(0)
+
+        slist = [s1, s2, s3, sS]
+        slist_names = ["s1", "s2", "s3", "sS"]
+        Ylist = [Y1, Y2]
+        
+        return Ylist
+    
+    def test_inferenceX_BGPLVM(self):
+        Ys = self.genData()
+        m = GPy.models.BayesianGPLVM(Ys[0],5,kernel=GPy.kern.Linear(5,ARD=True))
+        
+        x,mi = m.infer_newX(m.Y, optimize=False)
+        self.assertTrue(mi.checkgrad())
+        
+        m.optimize(max_iters=10000)
+        x,mi = m.infer_newX(m.Y)
+
+        self.assertTrue(np.allclose(m.X.mean, mi.X.mean))
+        self.assertTrue(np.allclose(m.X.variance, mi.X.variance))
+        
+
+if __name__ == "__main__":
+    unittest.main()

GPy/util/parallel.py

@@ -4,11 +4,10 @@ The module of tools for parallelization (MPI)
 
 try:
     from mpi4py import MPI
+    def get_id_within_node(comm=MPI.COMM_WORLD):
+        rank = comm.rank
+        nodename =  MPI.Get_processor_name()
+        nodelist = comm.allgather(nodename)
+        return len([i for i in nodelist[:rank] if i==nodename])
 except:
     pass
-
-def get_id_within_node(comm=MPI.COMM_WORLD):
-    rank = comm.rank
-    nodename =  MPI.Get_processor_name()
-    nodelist = comm.allgather(nodename)
-    return len([i for i in nodelist[:rank] if i==nodename])

doc/GPy.inference.latent_function_inference.rst

@@ -44,6 +44,14 @@ GPy.inference.latent_function_inference.fitc module
     :undoc-members:
     :show-inheritance:
 
+GPy.inference.latent_function_inference.inferenceX module
+---------------------------------------------------------
+
+.. automodule:: GPy.inference.latent_function_inference.inferenceX
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 GPy.inference.latent_function_inference.laplace module
 ------------------------------------------------------
 

doc/GPy.inference.mcmc.rst

@@ -0,0 +1,30 @@
+GPy.inference.mcmc package
+==========================
+
+Submodules
+----------
+
+GPy.inference.mcmc.hmc module
+-----------------------------
+
+.. automodule:: GPy.inference.mcmc.hmc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+GPy.inference.mcmc.samplers module
+----------------------------------
+
+.. automodule:: GPy.inference.mcmc.samplers
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: GPy.inference.mcmc
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/GPy.kern.parts.rst

@@ -1,246 +0,0 @@
-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.likelihoods.noise_models.rst

@@ -1,70 +0,0 @@
-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.models.rst

@@ -12,6 +12,14 @@ GPy.models.bayesian_gplvm module
     :undoc-members:
     :show-inheritance:
 
+GPy.models.bayesian_gplvm_minibatch module
+------------------------------------------
+
+.. automodule:: GPy.models.bayesian_gplvm_minibatch
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 GPy.models.bcgplvm module
 -------------------------
 
@@ -116,6 +124,14 @@ GPy.models.sparse_gp_coregionalized_regression module
     :undoc-members:
     :show-inheritance:
 
+GPy.models.sparse_gp_minibatch module
+-------------------------------------
+
+.. automodule:: GPy.models.sparse_gp_minibatch
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 GPy.models.sparse_gp_multioutput_regression module
 --------------------------------------------------
 

doc/GPy.testing.rst

@@ -28,6 +28,14 @@ GPy.testing.index_operations_tests module
     :undoc-members:
     :show-inheritance:
 
+GPy.testing.inference_tests module
+----------------------------------
+
+.. automodule:: GPy.testing.inference_tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 GPy.testing.kernel_tests module
 -------------------------------
 

doc/GPy.util.latent_space_visualizations.controllers.rst

@@ -1,30 +0,0 @@
-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

@@ -1,17 +0,0 @@
-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/conf.py

@@ -11,6 +11,9 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
+autodoc_default_flags = ['members', 'show-inheritance', 'private-members', 'special-members']
+autodoc_member_order = "source"
+
 import sys
 import os
 
@@ -114,7 +117,7 @@ for mod_name in MOCK_MODULES:
 # ----------------------- READTHEDOCS ------------------
 on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
 
-on_rtd = True
+#on_rtd = True
 if on_rtd:
     sys.path.append(os.path.abspath('../GPy'))
 
@@ -126,7 +129,8 @@ if on_rtd:
     proc = subprocess.Popen("ls ../", stdout=subprocess.PIPE, shell=True)
     (out, err) = proc.communicate()
     print "program output:", out
-    proc = subprocess.Popen("sphinx-apidoc -f -o . ../GPy", stdout=subprocess.PIPE, shell=True)
+    #proc = subprocess.Popen("sphinx-apidoc -f -o . ../GPy", stdout=subprocess.PIPE, shell=True)
+    proc = subprocess.Popen("make html", stdout=subprocess.PIPE, shell=True)
     (out, err) = proc.communicate()
     print "program output:", out
     #proc = subprocess.Popen("whereis numpy", stdout=subprocess.PIPE, shell=True)
@@ -397,5 +401,3 @@ epub_copyright = u'2013, Author'
 
 # Allow duplicate toc entries.
 #epub_tocdup = True
-
-autodoc_member_order = "source"