diff --git a/GPy/examples/regression.py b/GPy/examples/regression.py index a37e32c3..1ddb0a69 100644 --- a/GPy/examples/regression.py +++ b/GPy/examples/regression.py @@ -1,7 +1,6 @@ # Copyright (c) 2012, GPy authors (see AUTHORS.txt). # Licensed under the BSD 3-clause license (see LICENSE.txt) - """ Gaussian Processes regression examples """ @@ -9,88 +8,107 @@ import pylab as pb import numpy as np import GPy -def coregionalization_toy2(max_iters=100): +def olympic_marathon_men(optimize=True, plot=True): + """Run a standard Gaussian process regression on the Olympic marathon data.""" + data = GPy.util.datasets.olympic_marathon_men() + + # create simple GP Model + m = GPy.models.GPRegression(data['X'], data['Y']) + + # set the lengthscale to be something sensible (defaults to 1) + m['rbf_lengthscale'] = 10 + + if optimize: + m.optimize('bfgs', max_iters=200) + if plot: + m.plot(plot_limits=(1850, 2050)) + + return m + +def coregionalization_toy2(optimize=True, plot=True): """ A simple demonstration of coregionalization on two sinusoidal functions. """ + #build a design matrix with a column of integers indicating the output 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))) X = np.hstack((np.vstack((X1, X2)), index)) + + #build a suitable set of observed variables Y1 = np.sin(X1) + np.random.randn(*X1.shape) * 0.05 Y2 = np.sin(X2) + np.random.randn(*X2.shape) * 0.05 + 2. Y = np.vstack((Y1, Y2)) + #build the kernel k1 = GPy.kern.rbf(1) + GPy.kern.bias(1) k2 = GPy.kern.coregionalize(2,1) - k = k1**k2 #k = k1.prod(k2,tensor=True) + k = k1**k2 m = GPy.models.GPRegression(X, Y, kernel=k) m.constrain_fixed('.*rbf_var', 1.) - # m.constrain_positive('.*kappa') - m.optimize('sim', messages=1, max_iters=max_iters) - 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) + if optimize: + m.optimize('bfgs', max_iters=100) + + if plot: + m.plot(fixed_inputs=[(1,0)]) + m.plot(fixed_inputs=[(1,1)], ax=pb.gca()) + return m -def coregionalization_toy(max_iters=100): - """ - A simple demonstration of coregionalization on two sinusoidal functions. - """ - X1 = np.random.rand(50, 1) * 8 - X2 = np.random.rand(30, 1) * 5 - X = np.vstack((X1, X2)) - Y1 = np.sin(X1) + np.random.randn(*X1.shape) * 0.05 - Y2 = -np.sin(X2) + np.random.randn(*X2.shape) * 0.05 - Y = np.vstack((Y1, Y2)) +#FIXME: Needs recovering once likelihoods are consolidated +#def coregionalization_toy(optimize=True, plot=True): +# """ +# A simple demonstration of coregionalization on two sinusoidal functions. +# """ +# X1 = np.random.rand(50, 1) * 8 +# X2 = np.random.rand(30, 1) * 5 +# X = np.vstack((X1, X2)) +# Y1 = np.sin(X1) + np.random.randn(*X1.shape) * 0.05 +# Y2 = -np.sin(X2) + np.random.randn(*X2.shape) * 0.05 +# Y = np.vstack((Y1, Y2)) +# +# k1 = GPy.kern.rbf(1) +# m = GPy.models.GPMultioutputRegression(X_list=[X1,X2],Y_list=[Y1,Y2],kernel_list=[k1]) +# m.constrain_fixed('.*rbf_var', 1.) +# m.optimize(max_iters=100) +# +# fig, axes = pb.subplots(2,1) +# m.plot(fixed_inputs=[(1,0)],ax=axes[0]) +# m.plot(fixed_inputs=[(1,1)],ax=axes[1]) +# axes[0].set_title('Output 0') +# axes[1].set_title('Output 1') +# return m - k1 = GPy.kern.rbf(1) - m = GPy.models.GPMultioutputRegression(X_list=[X1,X2],Y_list=[Y1,Y2],kernel_list=[k1]) - m.constrain_fixed('.*rbf_var', 1.) - m.optimize(max_iters=max_iters) - - fig, axes = pb.subplots(2,1) - m.plot(fixed_inputs=[(1,0)],ax=axes[0]) - m.plot(fixed_inputs=[(1,1)],ax=axes[1]) - axes[0].set_title('Output 0') - axes[1].set_title('Output 1') - return m - -def coregionalization_sparse(max_iters=100): +def coregionalization_sparse(optimize=True, plot=True): """ 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 - index = np.vstack((np.zeros_like(X1), np.ones_like(X2))) - X = np.hstack((np.vstack((X1, X2)), index)) - Y1 = np.sin(X1) + np.random.randn(*X1.shape) * 0.05 - Y2 = -np.sin(X2) + np.random.randn(*X2.shape) * 0.05 - Y = np.vstack((Y1, Y2)) + #fetch the data from the non sparse examples + m = coregionalization_toy2(optimize=False, plot=False) + X, Y = m.X, m.likelihood.Y - k1 = GPy.kern.rbf(1) + #construct a model + m = GPy.models.SparseGPRegression(X,Y) + m.constrain_fixed('iip_\d+_1') # don't optimize the inducing input indexes - m = GPy.models.SparseGPMultioutputRegression(X_list=[X1,X2],Y_list=[Y1,Y2],kernel_list=[k1],num_inducing=5) - m.constrain_fixed('.*rbf_var',1.) - #m.optimize(messages=1) - m.optimize_restarts(5, robust=True, messages=1, max_iters=max_iters, optimizer='bfgs') + if optimize: + m.optimize('bfgs', max_iters=100, messages=1) + + if plot: + m.plot(fixed_inputs=[(1,0)]) + m.plot(fixed_inputs=[(1,1)], ax=pb.gca()) - fig, axes = pb.subplots(2,1) - m.plot_single_output(output=0,ax=axes[0],plot_limits=(-1,9)) - m.plot_single_output(output=1,ax=axes[1],plot_limits=(-1,9)) - axes[0].set_title('Output 0') - axes[1].set_title('Output 1') return m -def epomeo_gpx(max_iters=100): - """Perform Gaussian process regression on the latitude and longitude data from the Mount Epomeo runs. Requires gpxpy to be installed on your system to load in the data.""" + + +def epomeo_gpx(optimize=True, plot=True): + """ + Perform Gaussian process regression on the latitude and longitude data + from the Mount Epomeo runs. Requires gpxpy to be installed on your system + to load in the data. + """ data = GPy.util.datasets.epomeo_gpx() num_data_list = [] for Xpart in data['X']: @@ -119,14 +137,17 @@ def epomeo_gpx(max_iters=100): 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,messages=True) return m def multiple_optima(gene_number=937, resolution=80, model_restarts=10, seed=10000, max_iters=300): - """Show an example of a multimodal error surface for Gaussian process regression. Gene 939 has bimodal behaviour where the noisy mode is higher.""" + """ + Show an example of a multimodal error surface for Gaussian process + regression. Gene 939 has bimodal behaviour where the noisy mode is + higher. + """ # Contour over a range of length scales and signal/noise ratios. length_scales = np.linspace(0.1, 60., resolution) @@ -175,12 +196,15 @@ def multiple_optima(gene_number=937, resolution=80, model_restarts=10, seed=1000 return m # (models, lls) def _contour_data(data, length_scales, log_SNRs, kernel_call=GPy.kern.rbf): - """Evaluate the GP objective function for a given data set for a range of signal to noise ratios and a range of lengthscales. + """ + Evaluate the GP objective function for a given data set for a range of + signal to noise ratios and a range of lengthscales. :data_set: A data set from the utils.datasets director. :length_scales: a list of length scales to explore for the contour plot. :log_SNRs: a list of base 10 logarithm signal to noise ratios to explore for the contour plot. - :kernel: a kernel to use for the 'signal' portion of the data.""" + :kernel: a kernel to use for the 'signal' portion of the data. + """ lls = [] total_var = np.var(data['Y']) @@ -203,79 +227,58 @@ def _contour_data(data, length_scales, log_SNRs, kernel_call=GPy.kern.rbf): return np.array(lls) -def olympic_100m_men(max_iters=100, kernel=None): +def olympic_100m_men(optimize=True, plot=True): """Run a standard Gaussian process regression on the Rogers and Girolami olympics data.""" data = GPy.util.datasets.olympic_100m_men() # create simple GP Model - m = GPy.models.GPRegression(data['X'], data['Y'], kernel) + m = GPy.models.GPRegression(data['X'], data['Y']) # set the lengthscale to be something sensible (defaults to 1) - if kernel==None: - m['rbf_lengthscale'] = 10 + m['rbf_lengthscale'] = 10 - # optimize - m.optimize(max_iters=max_iters) + if optimize: + m.optimize('bfgs', max_iters=200) - # plot - m.plot(plot_limits=(1850, 2050)) - print(m) + if plot: + m.plot(plot_limits=(1850, 2050)) return m -def olympic_marathon_men(max_iters=100, kernel=None): - """Run a standard Gaussian process regression on the Olympic marathon data.""" - data = GPy.util.datasets.olympic_marathon_men() - - # create simple GP Model - m = GPy.models.GPRegression(data['X'], data['Y'], kernel) - - # set the lengthscale to be something sensible (defaults to 1) - if kernel==None: - m['rbf_lengthscale'] = 10 - - # optimize - m.optimize(max_iters=max_iters) - - # plot - m.plot(plot_limits=(1850, 2050)) - print(m) - return m - -def toy_rbf_1d(optimizer='tnc', max_nb_eval_optim=100): +def toy_rbf_1d(optimize=True, plot=True): """Run a simple demonstration of a standard Gaussian process fitting it to data sampled from an RBF covariance.""" data = GPy.util.datasets.toy_rbf_1d() # create simple GP Model m = GPy.models.GPRegression(data['X'], data['Y']) - # optimize - m.optimize(optimizer, max_f_eval=max_nb_eval_optim) - # plot - m.plot() - print(m) + if optimize: + m.optimize('bfgs') + if plot: + m.plot() + return m -def toy_rbf_1d_50(max_iters=100): +def toy_rbf_1d_50(optimize=True, plot=True): """Run a simple demonstration of a standard Gaussian process fitting it to data sampled from an RBF covariance.""" data = GPy.util.datasets.toy_rbf_1d_50() # create simple GP Model m = GPy.models.GPRegression(data['X'], data['Y']) - # optimize - m.optimize(max_iters=max_iters) + if optimize: + m.optimize('bfgs') + if plot: + m.plot() - # plot - m.plot() - print(m) return m -def toy_poisson_rbf_1d(optimizer='bfgs', max_nb_eval_optim=100): + +def toy_poisson_rbf_1d(optimize=True, plot=True): """Run a simple demonstration of a standard Gaussian process fitting it to data sampled from an RBF covariance.""" x_len = 400 X = np.linspace(0, 10, x_len)[:, None] f_true = np.random.multivariate_normal(np.zeros(x_len), GPy.kern.rbf(1).K(X)) - Y = np.array([np.random.poisson(np.exp(f)) for f in f_true])[:,None] + Y = np.array([np.random.poisson(np.exp(f)) for f in f_true]).reshape(x_len,1) noise_model = GPy.likelihoods.poisson() likelihood = GPy.likelihoods.EP(Y,noise_model) @@ -283,14 +286,14 @@ def toy_poisson_rbf_1d(optimizer='bfgs', max_nb_eval_optim=100): # create simple GP Model m = GPy.models.GPRegression(X, Y, likelihood=likelihood) - # optimize - m.optimize(optimizer, max_f_eval=max_nb_eval_optim) - # plot - m.plot() - print(m) + if optimize: + m.optimize('bfgs') + if plot: + m.plot() + return m -def toy_poisson_rbf_1d_laplace(optimizer='bfgs', max_nb_eval_optim=100): +def toy_poisson_rbf_1d_laplace(optimize=True, plot=True): """Run a simple demonstration of a standard Gaussian process fitting it to data sampled from an RBF covariance.""" x_len = 30 X = np.linspace(0, 10, x_len)[:, None] @@ -303,13 +306,13 @@ def toy_poisson_rbf_1d_laplace(optimizer='bfgs', max_nb_eval_optim=100): # create simple GP Model m = GPy.models.GPRegression(X, Y, likelihood=likelihood) - # optimize - m.optimize(optimizer, max_f_eval=max_nb_eval_optim) - # plot - m.plot() - # plot the real underlying rate function - pb.plot(X, np.exp(f_true), '--k', linewidth=2) - print(m) + if optimize: + m.optimize(optimizer, max_f_eval=max_nb_eval_optim) + if plot: + m.plot() + # plot the real underlying rate function + pb.plot(X, np.exp(f_true), '--k', linewidth=2) + return m @@ -459,7 +462,7 @@ def sparse_GP_regression_2D(num_samples=400, num_inducing=50, max_iters=100): print(m) return m -def uncertain_inputs_sparse_regression(max_iters=100): +def uncertain_inputs_sparse_regression(optimize=True, plot=True): """Run a 1D example of a sparse GP regression with uncertain inputs.""" fig, axes = pb.subplots(1, 2, figsize=(12, 5)) diff --git a/GPy/models.py b/GPy/models.py index a56fb305..3b2683ea 100644 --- a/GPy/models.py +++ b/GPy/models.py @@ -1,23 +1,31 @@ ''' -Created on 14 Nov 2013 +GPy Models +========== -@author: maxz +Implementations for common models used in GP regression and classification. +The different models can be viewed in :mod:`GPy.models_modules`, which holds +detailed explanations for the different models. + +:warning: This module is a convienince module for endusers to use. For developers +see :mod:`GPy.models_modules`, which holds the implementions for each model. ''' -from _models.bayesian_gplvm import BayesianGPLVM -from _models.gp_regression import GPRegression -from _models.gp_classification import GPClassification#; _gp_classification = gp_classification ; del gp_classification -from _models.sparse_gp_regression import SparseGPRegression#; _sparse_gp_regression = sparse_gp_regression ; del sparse_gp_regression -from _models.svigp_regression import SVIGPRegression#; _svigp_regression = svigp_regression ; del svigp_regression -from _models.sparse_gp_classification import SparseGPClassification#; _sparse_gp_classification = sparse_gp_classification ; del sparse_gp_classification -from _models.fitc_classification import FITCClassification#; _fitc_classification = fitc_classification ; del fitc_classification -from _models.gplvm import GPLVM#; _gplvm = gplvm ; del gplvm -from _models.bcgplvm import BCGPLVM#; _bcgplvm = bcgplvm; del bcgplvm -from _models.sparse_gplvm import SparseGPLVM#; _sparse_gplvm = sparse_gplvm ; del sparse_gplvm -from _models.warped_gp import WarpedGP#; _warped_gp = warped_gp ; del warped_gp -from _models.bayesian_gplvm import BayesianGPLVM#; _bayesian_gplvm = bayesian_gplvm ; del bayesian_gplvm -from _models.mrd import MRD#; _mrd = mrd; del mrd -from _models.gradient_checker import GradientChecker#; _gradient_checker = gradient_checker ; del gradient_checker -from _models.gp_multioutput_regression import GPMultioutputRegression#; _gp_multioutput_regression = gp_multioutput_regression ; del gp_multioutput_regression -from _models.sparse_gp_multioutput_regression import SparseGPMultioutputRegression#; _sparse_gp_multioutput_regression = sparse_gp_multioutput_regression ; del sparse_gp_multioutput_regression -from _models.gradient_checker import GradientChecker \ No newline at end of file +__updated__ = '2013-11-28' + +from models_modules.bayesian_gplvm import BayesianGPLVM +from models_modules.gp_regression import GPRegression +from models_modules.gp_classification import GPClassification#; _gp_classification = gp_classification ; del gp_classification +from models_modules.sparse_gp_regression import SparseGPRegression#; _sparse_gp_regression = sparse_gp_regression ; del sparse_gp_regression +from models_modules.svigp_regression import SVIGPRegression#; _svigp_regression = svigp_regression ; del svigp_regression +from models_modules.sparse_gp_classification import SparseGPClassification#; _sparse_gp_classification = sparse_gp_classification ; del sparse_gp_classification +from models_modules.fitc_classification import FITCClassification#; _fitc_classification = fitc_classification ; del fitc_classification +from models_modules.gplvm import GPLVM#; _gplvm = gplvm ; del gplvm +from models_modules.bcgplvm import BCGPLVM#; _bcgplvm = bcgplvm; del bcgplvm +from models_modules.sparse_gplvm import SparseGPLVM#; _sparse_gplvm = sparse_gplvm ; del sparse_gplvm +from models_modules.warped_gp import WarpedGP#; _warped_gp = warped_gp ; del warped_gp +from models_modules.bayesian_gplvm import BayesianGPLVM#; _bayesian_gplvm = bayesian_gplvm ; del bayesian_gplvm +from models_modules.mrd import MRD#; _mrd = mrd; del mrd +from models_modules.gradient_checker import GradientChecker#; _gradient_checker = gradient_checker ; del gradient_checker +from models_modules.gp_multioutput_regression import GPMultioutputRegression#; _gp_multioutput_regression = gp_multioutput_regression ; del gp_multioutput_regression +from models_modules.sparse_gp_multioutput_regression import SparseGPMultioutputRegression#; _sparse_gp_multioutput_regression = sparse_gp_multioutput_regression ; del sparse_gp_multioutput_regression +from models_modules.gradient_checker import GradientChecker \ No newline at end of file diff --git a/GPy/_models/__init__.py b/GPy/models_modules/__init__.py similarity index 100% rename from GPy/_models/__init__.py rename to GPy/models_modules/__init__.py diff --git a/GPy/_models/bayesian_gplvm.py b/GPy/models_modules/bayesian_gplvm.py similarity index 85% rename from GPy/_models/bayesian_gplvm.py rename to GPy/models_modules/bayesian_gplvm.py index 2b299ad8..90e54111 100644 --- a/GPy/_models/bayesian_gplvm.py +++ b/GPy/models_modules/bayesian_gplvm.py @@ -12,6 +12,7 @@ from GPy.util import plot_latent, linalg from .gplvm import GPLVM from GPy.util.plot_latent import most_significant_input_dimensions from matplotlib import pyplot +from GPy.core.model import Model class BayesianGPLVM(SparseGP, GPLVM): """ @@ -285,6 +286,57 @@ class BayesianGPLVM(SparseGP, GPLVM): self.init = state.pop() SparseGP.setstate(self, state) +class BayesianGPLVMWithMissingData(Model): + """ + Bayesian Gaussian Process Latent Variable Model with missing data support. + NOTE: Missing data is assumed to be missing at random! + + This extension comes with a large memory and computing time deficiency. + Use only if fraction of missing data at random is higher than 60%. + Otherwise, try filtering data before using this extension. + + Y can hold missing data as given by `missing`, standard is :class:`~numpy.nan`. + + If likelihood is given for Y, this likelihood will be discarded, but the parameters + of the likelihood will be taken. Also every effort of creating the same likelihood + will be done. + + :param likelihood_or_Y: observed data (np.ndarray) or GPy.likelihood + :type likelihood_or_Y: :class:`~numpy.ndarray` | :class:`~GPy.likelihoods.likelihood.likelihood` instance + :param int input_dim: latent dimensionality + :param init: initialisation method for the latent space + :type init: 'PCA' | 'random' + """ + def __init__(self, likelihood_or_Y, input_dim, X=None, X_variance=None, init='PCA', num_inducing=10, + Z=None, kernel=None, missing=np.nan, **kwargs): + if type(likelihood_or_Y) is np.ndarray: + likelihood = Gaussian(likelihood_or_Y) + else: + likelihood = likelihood_or_Y + + if X == None: + X = self.initialise_latent(init, input_dim, likelihood.Y) + self.init = init + + if X_variance is None: + X_variance = np.clip((np.ones_like(X) * 0.5) + .01 * np.random.randn(*X.shape), 0.001, 1) + + if Z is None: + Z = np.random.permutation(X.copy())[:num_inducing] + assert Z.shape[1] == X.shape[1] + + if kernel is None: + kernel = kern.rbf(input_dim) # + kern.white(input_dim) + + SparseGP.__init__(self, X, likelihood, kernel, Z=Z, X_variance=X_variance, **kwargs) + self.ensure_default_constraints() + + 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)], []) + return (X_names + S_names + SparseGP._get_param_names(self)) + + pass def latent_cost_and_grad(mu_S, kern, Z, dL_dpsi0, dL_dpsi1, dL_dpsi2): """ diff --git a/GPy/_models/bcgplvm.py b/GPy/models_modules/bcgplvm.py similarity index 100% rename from GPy/_models/bcgplvm.py rename to GPy/models_modules/bcgplvm.py diff --git a/GPy/_models/fitc_classification.py b/GPy/models_modules/fitc_classification.py similarity index 100% rename from GPy/_models/fitc_classification.py rename to GPy/models_modules/fitc_classification.py diff --git a/GPy/_models/gp_classification.py b/GPy/models_modules/gp_classification.py similarity index 100% rename from GPy/_models/gp_classification.py rename to GPy/models_modules/gp_classification.py diff --git a/GPy/_models/gp_multioutput_regression.py b/GPy/models_modules/gp_multioutput_regression.py similarity index 100% rename from GPy/_models/gp_multioutput_regression.py rename to GPy/models_modules/gp_multioutput_regression.py diff --git a/GPy/_models/gp_regression.py b/GPy/models_modules/gp_regression.py similarity index 100% rename from GPy/_models/gp_regression.py rename to GPy/models_modules/gp_regression.py diff --git a/GPy/_models/gplvm.py b/GPy/models_modules/gplvm.py similarity index 100% rename from GPy/_models/gplvm.py rename to GPy/models_modules/gplvm.py diff --git a/GPy/_models/gradient_checker.py b/GPy/models_modules/gradient_checker.py similarity index 100% rename from GPy/_models/gradient_checker.py rename to GPy/models_modules/gradient_checker.py diff --git a/GPy/_models/mrd.py b/GPy/models_modules/mrd.py similarity index 100% rename from GPy/_models/mrd.py rename to GPy/models_modules/mrd.py diff --git a/GPy/_models/sparse_gp_classification.py b/GPy/models_modules/sparse_gp_classification.py similarity index 100% rename from GPy/_models/sparse_gp_classification.py rename to GPy/models_modules/sparse_gp_classification.py diff --git a/GPy/_models/sparse_gp_multioutput_regression.py b/GPy/models_modules/sparse_gp_multioutput_regression.py similarity index 100% rename from GPy/_models/sparse_gp_multioutput_regression.py rename to GPy/models_modules/sparse_gp_multioutput_regression.py diff --git a/GPy/_models/sparse_gp_regression.py b/GPy/models_modules/sparse_gp_regression.py similarity index 100% rename from GPy/_models/sparse_gp_regression.py rename to GPy/models_modules/sparse_gp_regression.py diff --git a/GPy/_models/sparse_gplvm.py b/GPy/models_modules/sparse_gplvm.py similarity index 100% rename from GPy/_models/sparse_gplvm.py rename to GPy/models_modules/sparse_gplvm.py diff --git a/GPy/_models/svigp_regression.py b/GPy/models_modules/svigp_regression.py similarity index 100% rename from GPy/_models/svigp_regression.py rename to GPy/models_modules/svigp_regression.py diff --git a/GPy/_models/warped_gp.py b/GPy/models_modules/warped_gp.py similarity index 100% rename from GPy/_models/warped_gp.py rename to GPy/models_modules/warped_gp.py diff --git a/doc/GPy.core.rst b/doc/GPy.core.rst index c4f1849d..d7f18192 100644 --- a/doc/GPy.core.rst +++ b/doc/GPy.core.rst @@ -1,102 +1,107 @@ -GPy.core package -================ +core Package +============ -Submodules ----------- +:mod:`core` Package +------------------- -GPy.core.domains module ------------------------ +.. automodule:: GPy.core + :members: + :undoc-members: + :show-inheritance: + +:mod:`domains` Module +--------------------- .. automodule:: GPy.core.domains :members: :undoc-members: :show-inheritance: -GPy.core.fitc module --------------------- +:mod:`fitc` Module +------------------ .. automodule:: GPy.core.fitc :members: :undoc-members: :show-inheritance: -GPy.core.gp module ------------------- +:mod:`gp` Module +---------------- .. automodule:: GPy.core.gp :members: :undoc-members: :show-inheritance: -GPy.core.gp_base module ------------------------ +:mod:`gp_base` Module +--------------------- .. automodule:: GPy.core.gp_base :members: :undoc-members: :show-inheritance: -GPy.core.mapping module ------------------------ +:mod:`mapping` Module +--------------------- .. automodule:: GPy.core.mapping :members: :undoc-members: :show-inheritance: -GPy.core.model module ---------------------- +:mod:`model` Module +------------------- .. automodule:: GPy.core.model :members: :undoc-members: :show-inheritance: -GPy.core.parameterized module ------------------------------ +:mod:`parameterized` Module +--------------------------- .. automodule:: GPy.core.parameterized :members: :undoc-members: :show-inheritance: -GPy.core.priors module ----------------------- +:mod:`priors` Module +-------------------- .. automodule:: GPy.core.priors :members: :undoc-members: :show-inheritance: -GPy.core.sparse_gp module -------------------------- +:mod:`sparse_gp` Module +----------------------- .. automodule:: GPy.core.sparse_gp :members: :undoc-members: :show-inheritance: -GPy.core.svigp module ---------------------- +:mod:`svigp` Module +------------------- .. automodule:: GPy.core.svigp :members: :undoc-members: :show-inheritance: -GPy.core.transformations module -------------------------------- +:mod:`transformations` Module +----------------------------- .. automodule:: GPy.core.transformations :members: :undoc-members: :show-inheritance: +:mod:`variational` Module +------------------------- -Module contents ---------------- - -.. automodule:: GPy.core +.. automodule:: GPy.core.variational :members: :undoc-members: :show-inheritance: + diff --git a/doc/GPy.examples.rst b/doc/GPy.examples.rst index 288ff631..176ae396 100644 --- a/doc/GPy.examples.rst +++ b/doc/GPy.examples.rst @@ -1,62 +1,59 @@ -GPy.examples package -==================== +examples Package +================ -Submodules ----------- +:mod:`examples` Package +----------------------- -GPy.examples.classification module ----------------------------------- +.. automodule:: GPy.examples + :members: + :undoc-members: + :show-inheritance: + +:mod:`classification` Module +---------------------------- .. automodule:: GPy.examples.classification :members: :undoc-members: :show-inheritance: -GPy.examples.dimensionality_reduction module --------------------------------------------- +:mod:`dimensionality_reduction` Module +-------------------------------------- .. automodule:: GPy.examples.dimensionality_reduction :members: :undoc-members: :show-inheritance: -GPy.examples.laplace_approximations module ------------------------------------------- +:mod:`laplace_approximations` Module +------------------------------------ .. automodule:: GPy.examples.laplace_approximations :members: :undoc-members: :show-inheritance: -GPy.examples.regression module ------------------------------- +:mod:`regression` Module +------------------------ .. automodule:: GPy.examples.regression :members: :undoc-members: :show-inheritance: -GPy.examples.stochastic module ------------------------------- +:mod:`stochastic` Module +------------------------ .. automodule:: GPy.examples.stochastic :members: :undoc-members: :show-inheritance: -GPy.examples.tutorials module ------------------------------ +:mod:`tutorials` Module +----------------------- .. automodule:: GPy.examples.tutorials :members: :undoc-members: :show-inheritance: - -Module contents ---------------- - -.. automodule:: GPy.examples - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/GPy.inference.rst b/doc/GPy.inference.rst index 28f42994..6a1bef4a 100644 --- a/doc/GPy.inference.rst +++ b/doc/GPy.inference.rst @@ -1,62 +1,51 @@ -GPy.inference package -===================== +inference Package +================= -Submodules ----------- - -GPy.inference.conjugate_gradient_descent module ------------------------------------------------ +:mod:`conjugate_gradient_descent` Module +---------------------------------------- .. automodule:: GPy.inference.conjugate_gradient_descent :members: :undoc-members: :show-inheritance: -GPy.inference.gradient_descent_update_rules module --------------------------------------------------- +:mod:`gradient_descent_update_rules` Module +------------------------------------------- .. automodule:: GPy.inference.gradient_descent_update_rules :members: :undoc-members: :show-inheritance: -GPy.inference.optimization module ---------------------------------- +:mod:`optimization` Module +-------------------------- .. automodule:: GPy.inference.optimization :members: :undoc-members: :show-inheritance: -GPy.inference.samplers module ------------------------------ +:mod:`samplers` Module +---------------------- .. automodule:: GPy.inference.samplers :members: :undoc-members: :show-inheritance: -GPy.inference.scg module ------------------------- +:mod:`scg` Module +----------------- .. automodule:: GPy.inference.scg :members: :undoc-members: :show-inheritance: -GPy.inference.sgd module ------------------------- +:mod:`sgd` Module +----------------- .. automodule:: GPy.inference.sgd :members: :undoc-members: :show-inheritance: - -Module contents ---------------- - -.. automodule:: GPy.inference - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/GPy.kern.parts.rst b/doc/GPy.kern.parts.rst index 650fe5cb..45d3e235 100644 --- a/doc/GPy.kern.parts.rst +++ b/doc/GPy.kern.parts.rst @@ -1,262 +1,275 @@ -GPy.kern.parts package -====================== +parts Package +============= -Submodules ----------- +:mod:`parts` Package +-------------------- -GPy.kern.parts.Brownian module ------------------------------- +.. automodule:: GPy.kern.parts + :members: + :undoc-members: + :show-inheritance: + +:mod:`Brownian` Module +---------------------- .. automodule:: GPy.kern.parts.Brownian :members: :undoc-members: :show-inheritance: -GPy.kern.parts.Matern32 module ------------------------------- +:mod:`Matern32` Module +---------------------- .. automodule:: GPy.kern.parts.Matern32 :members: :undoc-members: :show-inheritance: -GPy.kern.parts.Matern52 module ------------------------------- +:mod:`Matern52` Module +---------------------- .. automodule:: GPy.kern.parts.Matern52 :members: :undoc-members: :show-inheritance: -GPy.kern.parts.ODE_1 module ---------------------------- +:mod:`ODE_1` Module +------------------- .. automodule:: GPy.kern.parts.ODE_1 :members: :undoc-members: :show-inheritance: -GPy.kern.parts.bias module --------------------------- +:mod:`ODE_UY` Module +-------------------- + +.. automodule:: GPy.kern.parts.ODE_UY + :members: + :undoc-members: + :show-inheritance: + +:mod:`bias` Module +------------------ .. automodule:: GPy.kern.parts.bias :members: :undoc-members: :show-inheritance: -GPy.kern.parts.coregionalize module ------------------------------------ +:mod:`coregionalize` Module +--------------------------- .. automodule:: GPy.kern.parts.coregionalize :members: :undoc-members: :show-inheritance: -GPy.kern.parts.eq_ode1 module ------------------------------ +:mod:`eq_ode1` Module +--------------------- .. automodule:: GPy.kern.parts.eq_ode1 :members: :undoc-members: :show-inheritance: -GPy.kern.parts.exponential module ---------------------------------- +:mod:`exponential` Module +------------------------- .. automodule:: GPy.kern.parts.exponential :members: :undoc-members: :show-inheritance: -GPy.kern.parts.finite_dimensional module ----------------------------------------- +:mod:`finite_dimensional` Module +-------------------------------- .. automodule:: GPy.kern.parts.finite_dimensional :members: :undoc-members: :show-inheritance: -GPy.kern.parts.fixed module ---------------------------- +:mod:`fixed` Module +------------------- .. automodule:: GPy.kern.parts.fixed :members: :undoc-members: :show-inheritance: -GPy.kern.parts.gibbs module ---------------------------- +:mod:`gibbs` Module +------------------- .. automodule:: GPy.kern.parts.gibbs :members: :undoc-members: :show-inheritance: -GPy.kern.parts.hetero module ----------------------------- +:mod:`hetero` Module +-------------------- .. automodule:: GPy.kern.parts.hetero :members: :undoc-members: :show-inheritance: -GPy.kern.parts.hierarchical module ----------------------------------- +:mod:`hierarchical` Module +-------------------------- .. automodule:: GPy.kern.parts.hierarchical :members: :undoc-members: :show-inheritance: -GPy.kern.parts.independent_outputs module ------------------------------------------ +:mod:`independent_outputs` Module +--------------------------------- .. automodule:: GPy.kern.parts.independent_outputs :members: :undoc-members: :show-inheritance: -GPy.kern.parts.kernpart module ------------------------------- +:mod:`kernpart` Module +---------------------- .. automodule:: GPy.kern.parts.kernpart :members: :undoc-members: :show-inheritance: -GPy.kern.parts.linear module ----------------------------- +:mod:`linear` Module +-------------------- .. automodule:: GPy.kern.parts.linear :members: :undoc-members: :show-inheritance: -GPy.kern.parts.mlp module -------------------------- +:mod:`mlp` Module +----------------- .. automodule:: GPy.kern.parts.mlp :members: :undoc-members: :show-inheritance: -GPy.kern.parts.periodic_Matern32 module ---------------------------------------- +:mod:`periodic_Matern32` Module +------------------------------- .. automodule:: GPy.kern.parts.periodic_Matern32 :members: :undoc-members: :show-inheritance: -GPy.kern.parts.periodic_Matern52 module ---------------------------------------- +:mod:`periodic_Matern52` Module +------------------------------- .. automodule:: GPy.kern.parts.periodic_Matern52 :members: :undoc-members: :show-inheritance: -GPy.kern.parts.periodic_exponential module ------------------------------------------- +:mod:`periodic_exponential` Module +---------------------------------- .. automodule:: GPy.kern.parts.periodic_exponential :members: :undoc-members: :show-inheritance: -GPy.kern.parts.poly module --------------------------- +:mod:`poly` Module +------------------ .. automodule:: GPy.kern.parts.poly :members: :undoc-members: :show-inheritance: -GPy.kern.parts.prod module --------------------------- +:mod:`prod` Module +------------------ .. automodule:: GPy.kern.parts.prod :members: :undoc-members: :show-inheritance: -GPy.kern.parts.prod_orthogonal module -------------------------------------- +:mod:`prod_orthogonal` Module +----------------------------- .. automodule:: GPy.kern.parts.prod_orthogonal :members: :undoc-members: :show-inheritance: -GPy.kern.parts.rational_quadratic module ----------------------------------------- +:mod:`rational_quadratic` Module +-------------------------------- .. automodule:: GPy.kern.parts.rational_quadratic :members: :undoc-members: :show-inheritance: -GPy.kern.parts.rbf module -------------------------- +:mod:`rbf` Module +----------------- .. automodule:: GPy.kern.parts.rbf :members: :undoc-members: :show-inheritance: -GPy.kern.parts.rbf_inv module ------------------------------ +:mod:`rbf_inv` Module +--------------------- .. automodule:: GPy.kern.parts.rbf_inv :members: :undoc-members: :show-inheritance: -GPy.kern.parts.rbfcos module ----------------------------- +:mod:`rbfcos` Module +-------------------- .. automodule:: GPy.kern.parts.rbfcos :members: :undoc-members: :show-inheritance: -GPy.kern.parts.spline module ----------------------------- +:mod:`spline` Module +-------------------- .. automodule:: GPy.kern.parts.spline :members: :undoc-members: :show-inheritance: -GPy.kern.parts.symmetric module -------------------------------- +:mod:`symmetric` Module +----------------------- .. automodule:: GPy.kern.parts.symmetric :members: :undoc-members: :show-inheritance: -GPy.kern.parts.sympykern module -------------------------------- +:mod:`sympy_helpers` Module +--------------------------- + +.. automodule:: GPy.kern.parts.sympy_helpers + :members: + :undoc-members: + :show-inheritance: + +:mod:`sympykern` Module +----------------------- .. automodule:: GPy.kern.parts.sympykern :members: :undoc-members: :show-inheritance: -GPy.kern.parts.white module ---------------------------- +:mod:`white` Module +------------------- .. automodule:: GPy.kern.parts.white :members: :undoc-members: :show-inheritance: - -Module contents ---------------- - -.. automodule:: GPy.kern.parts - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/GPy.kern.rst b/doc/GPy.kern.rst index b4b9d9aa..35d9ec00 100644 --- a/doc/GPy.kern.rst +++ b/doc/GPy.kern.rst @@ -1,5 +1,29 @@ -GPy.kern package -================ +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 ----------- @@ -8,30 +32,3 @@ 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: diff --git a/doc/GPy.likelihoods.noise_models.rst b/doc/GPy.likelihoods.noise_models.rst index 6fec5aff..19e5e9fe 100644 --- a/doc/GPy.likelihoods.noise_models.rst +++ b/doc/GPy.likelihoods.noise_models.rst @@ -1,78 +1,75 @@ -GPy.likelihoods.noise_models package -==================================== +noise_models Package +==================== -Submodules ----------- +:mod:`noise_models` Package +--------------------------- -GPy.likelihoods.noise_models.bernoulli_noise module ---------------------------------------------------- +.. automodule:: GPy.likelihoods.noise_models + :members: + :undoc-members: + :show-inheritance: + +:mod:`bernoulli_noise` Module +----------------------------- .. automodule:: GPy.likelihoods.noise_models.bernoulli_noise :members: :undoc-members: :show-inheritance: -GPy.likelihoods.noise_models.exponential_noise module ------------------------------------------------------ +:mod:`exponential_noise` Module +------------------------------- .. automodule:: GPy.likelihoods.noise_models.exponential_noise :members: :undoc-members: :show-inheritance: -GPy.likelihoods.noise_models.gamma_noise module ------------------------------------------------ +:mod:`gamma_noise` Module +------------------------- .. automodule:: GPy.likelihoods.noise_models.gamma_noise :members: :undoc-members: :show-inheritance: -GPy.likelihoods.noise_models.gaussian_noise module --------------------------------------------------- +:mod:`gaussian_noise` Module +---------------------------- .. automodule:: GPy.likelihoods.noise_models.gaussian_noise :members: :undoc-members: :show-inheritance: -GPy.likelihoods.noise_models.gp_transformations module ------------------------------------------------------- +:mod:`gp_transformations` Module +-------------------------------- .. automodule:: GPy.likelihoods.noise_models.gp_transformations :members: :undoc-members: :show-inheritance: -GPy.likelihoods.noise_models.noise_distributions module -------------------------------------------------------- +:mod:`noise_distributions` Module +--------------------------------- .. automodule:: GPy.likelihoods.noise_models.noise_distributions :members: :undoc-members: :show-inheritance: -GPy.likelihoods.noise_models.poisson_noise module -------------------------------------------------- +:mod:`poisson_noise` Module +--------------------------- .. automodule:: GPy.likelihoods.noise_models.poisson_noise :members: :undoc-members: :show-inheritance: -GPy.likelihoods.noise_models.student_t_noise module ---------------------------------------------------- +:mod:`student_t_noise` Module +----------------------------- .. automodule:: GPy.likelihoods.noise_models.student_t_noise :members: :undoc-members: :show-inheritance: - -Module contents ---------------- - -.. automodule:: GPy.likelihoods.noise_models - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/GPy.likelihoods.rst b/doc/GPy.likelihoods.rst index 34d98739..5dcabbd1 100644 --- a/doc/GPy.likelihoods.rst +++ b/doc/GPy.likelihoods.rst @@ -1,5 +1,69 @@ -GPy.likelihoods package -======================= +likelihoods Package +=================== + +:mod:`likelihoods` Package +-------------------------- + +.. automodule:: GPy.likelihoods + :members: + :undoc-members: + :show-inheritance: + +:mod:`ep` Module +---------------- + +.. automodule:: GPy.likelihoods.ep + :members: + :undoc-members: + :show-inheritance: + +:mod:`ep_mixed_noise` Module +---------------------------- + +.. automodule:: GPy.likelihoods.ep_mixed_noise + :members: + :undoc-members: + :show-inheritance: + +:mod:`gaussian` Module +---------------------- + +.. automodule:: GPy.likelihoods.gaussian + :members: + :undoc-members: + :show-inheritance: + +:mod:`gaussian_mixed_noise` Module +---------------------------------- + +.. automodule:: GPy.likelihoods.gaussian_mixed_noise + :members: + :undoc-members: + :show-inheritance: + +:mod:`laplace` Module +--------------------- + +.. automodule:: GPy.likelihoods.laplace + :members: + :undoc-members: + :show-inheritance: + +:mod:`likelihood` Module +------------------------ + +.. automodule:: GPy.likelihoods.likelihood + :members: + :undoc-members: + :show-inheritance: + +:mod:`noise_model_constructors` Module +-------------------------------------- + +.. automodule:: GPy.likelihoods.noise_model_constructors + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- @@ -8,70 +72,3 @@ Subpackages GPy.likelihoods.noise_models -Submodules ----------- - -GPy.likelihoods.ep module -------------------------- - -.. automodule:: GPy.likelihoods.ep - :members: - :undoc-members: - :show-inheritance: - -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: - -GPy.likelihoods.gaussian_mixed_noise module -------------------------------------------- - -.. automodule:: GPy.likelihoods.gaussian_mixed_noise - :members: - :undoc-members: - :show-inheritance: - -GPy.likelihoods.laplace module ------------------------------- - -.. automodule:: GPy.likelihoods.laplace - :members: - :undoc-members: - :show-inheritance: - -GPy.likelihoods.likelihood module ---------------------------------- - -.. automodule:: GPy.likelihoods.likelihood - :members: - :undoc-members: - :show-inheritance: - -GPy.likelihoods.noise_model_constructors module ------------------------------------------------ - -.. automodule:: GPy.likelihoods.noise_model_constructors - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: GPy.likelihoods - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/GPy.mappings.rst b/doc/GPy.mappings.rst index c48cb06e..b7444808 100644 --- a/doc/GPy.mappings.rst +++ b/doc/GPy.mappings.rst @@ -1,38 +1,35 @@ -GPy.mappings package -==================== +mappings Package +================ -Submodules ----------- +:mod:`mappings` Package +----------------------- -GPy.mappings.kernel module --------------------------- +.. automodule:: GPy.mappings + :members: + :undoc-members: + :show-inheritance: + +:mod:`kernel` Module +-------------------- .. automodule:: GPy.mappings.kernel :members: :undoc-members: :show-inheritance: -GPy.mappings.linear module --------------------------- +:mod:`linear` Module +-------------------- .. automodule:: GPy.mappings.linear :members: :undoc-members: :show-inheritance: -GPy.mappings.mlp module ------------------------ +:mod:`mlp` Module +----------------- .. automodule:: GPy.mappings.mlp :members: :undoc-members: :show-inheritance: - -Module contents ---------------- - -.. automodule:: GPy.mappings - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/GPy.models.rst b/doc/GPy.models.rst deleted file mode 100644 index 4440513e..00000000 --- a/doc/GPy.models.rst +++ /dev/null @@ -1,134 +0,0 @@ -GPy.models package -================== - -Submodules ----------- - -GPy.models.bayesian_gplvm module --------------------------------- - -.. automodule:: GPy.models.bayesian_gplvm - :members: - :undoc-members: - :show-inheritance: - -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: - -GPy.models.gp_classification module ------------------------------------ - -.. automodule:: GPy.models.gp_classification - :members: - :undoc-members: - :show-inheritance: - -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: - -GPy.models.gplvm module ------------------------ - -.. automodule:: GPy.models.gplvm - :members: - :undoc-members: - :show-inheritance: - -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: - -GPy.models.sparse_gp_classification module ------------------------------------------- - -.. automodule:: GPy.models.sparse_gp_classification - :members: - :undoc-members: - :show-inheritance: - -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: - -GPy.models.sparse_gplvm module ------------------------------- - -.. automodule:: GPy.models.sparse_gplvm - :members: - :undoc-members: - :show-inheritance: - -GPy.models.svigp_regression module ----------------------------------- - -.. automodule:: GPy.models.svigp_regression - :members: - :undoc-members: - :show-inheritance: - -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: diff --git a/doc/GPy.models_modules.rst b/doc/GPy.models_modules.rst new file mode 100644 index 00000000..4169ec3a --- /dev/null +++ b/doc/GPy.models_modules.rst @@ -0,0 +1,131 @@ +models_modules Package +====================== + +:mod:`models_modules` Package +----------------------------- + +.. automodule:: GPy.models_modules + :members: + :undoc-members: + :show-inheritance: + +:mod:`bayesian_gplvm` Module +---------------------------- + +.. automodule:: GPy.models_modules.bayesian_gplvm + :members: + :undoc-members: + :show-inheritance: + +:mod:`bcgplvm` Module +--------------------- + +.. automodule:: GPy.models_modules.bcgplvm + :members: + :undoc-members: + :show-inheritance: + +:mod:`fitc_classification` Module +--------------------------------- + +.. automodule:: GPy.models_modules.fitc_classification + :members: + :undoc-members: + :show-inheritance: + +:mod:`gp_classification` Module +------------------------------- + +.. automodule:: GPy.models_modules.gp_classification + :members: + :undoc-members: + :show-inheritance: + +:mod:`gp_multioutput_regression` Module +--------------------------------------- + +.. automodule:: GPy.models_modules.gp_multioutput_regression + :members: + :undoc-members: + :show-inheritance: + +:mod:`gp_regression` Module +--------------------------- + +.. automodule:: GPy.models_modules.gp_regression + :members: + :undoc-members: + :show-inheritance: + +:mod:`gplvm` Module +------------------- + +.. automodule:: GPy.models_modules.gplvm + :members: + :undoc-members: + :show-inheritance: + +:mod:`gradient_checker` Module +------------------------------ + +.. automodule:: GPy.models_modules.gradient_checker + :members: + :undoc-members: + :show-inheritance: + +:mod:`mrd` Module +----------------- + +.. automodule:: GPy.models_modules.mrd + :members: + :undoc-members: + :show-inheritance: + +:mod:`sparse_gp_classification` Module +-------------------------------------- + +.. automodule:: GPy.models_modules.sparse_gp_classification + :members: + :undoc-members: + :show-inheritance: + +:mod:`sparse_gp_multioutput_regression` Module +---------------------------------------------- + +.. automodule:: GPy.models_modules.sparse_gp_multioutput_regression + :members: + :undoc-members: + :show-inheritance: + +:mod:`sparse_gp_regression` Module +---------------------------------- + +.. automodule:: GPy.models_modules.sparse_gp_regression + :members: + :undoc-members: + :show-inheritance: + +:mod:`sparse_gplvm` Module +-------------------------- + +.. automodule:: GPy.models_modules.sparse_gplvm + :members: + :undoc-members: + :show-inheritance: + +:mod:`svigp_regression` Module +------------------------------ + +.. automodule:: GPy.models_modules.svigp_regression + :members: + :undoc-members: + :show-inheritance: + +:mod:`warped_gp` Module +----------------------- + +.. automodule:: GPy.models_modules.warped_gp + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/GPy.rst b/doc/GPy.rst index 60092e91..31ec3562 100644 --- a/doc/GPy.rst +++ b/doc/GPy.rst @@ -1,6 +1,22 @@ -GPy package +GPy Package =========== +:mod:`GPy` Package +------------------ + +.. automodule:: GPy.__init__ + :members: + :undoc-members: + :show-inheritance: + +:mod:`models` Module +-------------------- + +.. automodule:: GPy.models + :members: + :undoc-members: + :show-inheritance: + Subpackages ----------- @@ -12,14 +28,7 @@ Subpackages GPy.kern GPy.likelihoods GPy.mappings - GPy.models + GPy.models_modules GPy.testing GPy.util -Module contents ---------------- - -.. automodule:: GPy - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/GPy.testing.rst b/doc/GPy.testing.rst index 98b001c0..15b0cc79 100644 --- a/doc/GPy.testing.rst +++ b/doc/GPy.testing.rst @@ -1,134 +1,131 @@ -GPy.testing package -=================== +testing Package +=============== -Submodules ----------- +:mod:`testing` Package +---------------------- -GPy.testing.bcgplvm_tests module --------------------------------- +.. automodule:: GPy.testing + :members: + :undoc-members: + :show-inheritance: + +:mod:`bcgplvm_tests` Module +--------------------------- .. automodule:: GPy.testing.bcgplvm_tests :members: :undoc-members: :show-inheritance: -GPy.testing.bgplvm_tests module -------------------------------- +:mod:`bgplvm_tests` Module +-------------------------- .. automodule:: GPy.testing.bgplvm_tests :members: :undoc-members: :show-inheritance: -GPy.testing.cgd_tests module ----------------------------- +:mod:`cgd_tests` Module +----------------------- .. automodule:: GPy.testing.cgd_tests :members: :undoc-members: :show-inheritance: -GPy.testing.examples_tests module ---------------------------------- +:mod:`examples_tests` Module +---------------------------- .. automodule:: GPy.testing.examples_tests :members: :undoc-members: :show-inheritance: -GPy.testing.gp_transformation_tests module ------------------------------------------- +:mod:`gp_transformation_tests` Module +------------------------------------- .. automodule:: GPy.testing.gp_transformation_tests :members: :undoc-members: :show-inheritance: -GPy.testing.gplvm_tests module ------------------------------- +:mod:`gplvm_tests` Module +------------------------- .. automodule:: GPy.testing.gplvm_tests :members: :undoc-members: :show-inheritance: -GPy.testing.kernel_tests module -------------------------------- +:mod:`kernel_tests` Module +-------------------------- .. automodule:: GPy.testing.kernel_tests :members: :undoc-members: :show-inheritance: -GPy.testing.likelihoods_tests module ------------------------------------- +:mod:`likelihoods_tests` Module +------------------------------- .. automodule:: GPy.testing.likelihoods_tests :members: :undoc-members: :show-inheritance: -GPy.testing.mapping_tests module --------------------------------- +:mod:`mapping_tests` Module +--------------------------- .. automodule:: GPy.testing.mapping_tests :members: :undoc-members: :show-inheritance: -GPy.testing.mrd_tests module ----------------------------- +:mod:`mrd_tests` Module +----------------------- .. automodule:: GPy.testing.mrd_tests :members: :undoc-members: :show-inheritance: -GPy.testing.prior_tests module ------------------------------- +:mod:`prior_tests` Module +------------------------- .. automodule:: GPy.testing.prior_tests :members: :undoc-members: :show-inheritance: -GPy.testing.psi_stat_expectation_tests module ---------------------------------------------- +:mod:`psi_stat_expectation_tests` Module +---------------------------------------- .. automodule:: GPy.testing.psi_stat_expectation_tests :members: :undoc-members: :show-inheritance: -GPy.testing.psi_stat_gradient_tests module ------------------------------------------- +:mod:`psi_stat_gradient_tests` Module +------------------------------------- .. automodule:: GPy.testing.psi_stat_gradient_tests :members: :undoc-members: :show-inheritance: -GPy.testing.sparse_gplvm_tests module -------------------------------------- +:mod:`sparse_gplvm_tests` Module +-------------------------------- .. automodule:: GPy.testing.sparse_gplvm_tests :members: :undoc-members: :show-inheritance: -GPy.testing.unit_tests module ------------------------------ +:mod:`unit_tests` Module +------------------------ .. automodule:: GPy.testing.unit_tests :members: :undoc-members: :show-inheritance: - -Module contents ---------------- - -.. automodule:: GPy.testing - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/GPy.util.latent_space_visualizations.controllers.rst b/doc/GPy.util.latent_space_visualizations.controllers.rst index a88c1f5c..e78ade7b 100644 --- a/doc/GPy.util.latent_space_visualizations.controllers.rst +++ b/doc/GPy.util.latent_space_visualizations.controllers.rst @@ -1,30 +1,27 @@ -GPy.util.latent_space_visualizations.controllers package -======================================================== +controllers Package +=================== -Submodules ----------- +:mod:`controllers` Package +-------------------------- -GPy.util.latent_space_visualizations.controllers.axis_event_controller module ------------------------------------------------------------------------------ +.. automodule:: GPy.util.latent_space_visualizations.controllers + :members: + :undoc-members: + :show-inheritance: + +:mod:`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 -------------------------------------------------------------------------- +:mod:`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: diff --git a/doc/GPy.util.latent_space_visualizations.rst b/doc/GPy.util.latent_space_visualizations.rst index d8cbd843..4b440f61 100644 --- a/doc/GPy.util.latent_space_visualizations.rst +++ b/doc/GPy.util.latent_space_visualizations.rst @@ -1,5 +1,13 @@ -GPy.util.latent_space_visualizations package -============================================ +latent_space_visualizations Package +=================================== + +:mod:`latent_space_visualizations` Package +------------------------------------------ + +.. automodule:: GPy.util.latent_space_visualizations + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- @@ -7,11 +15,5 @@ Subpackages .. toctree:: GPy.util.latent_space_visualizations.controllers + GPy.util.latent_space_visualizations.views -Module contents ---------------- - -.. automodule:: GPy.util.latent_space_visualizations - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/GPy.util.rst b/doc/GPy.util.rst index f2aaed7f..2e20c006 100644 --- a/doc/GPy.util.rst +++ b/doc/GPy.util.rst @@ -1,5 +1,181 @@ -GPy.util package -================ +util Package +============ + +:mod:`util` Package +------------------- + +.. automodule:: GPy.util + :members: + :undoc-members: + :show-inheritance: + +:mod:`Tango` Module +------------------- + +.. automodule:: GPy.util.Tango + :members: + :undoc-members: + :show-inheritance: + +:mod:`block_matrices` Module +---------------------------- + +.. automodule:: GPy.util.block_matrices + :members: + :undoc-members: + :show-inheritance: + +:mod:`classification` Module +---------------------------- + +.. automodule:: GPy.util.classification + :members: + :undoc-members: + :show-inheritance: + +:mod:`config` Module +-------------------- + +.. automodule:: GPy.util.config + :members: + :undoc-members: + :show-inheritance: + +:mod:`datasets` Module +---------------------- + +.. automodule:: GPy.util.datasets + :members: + :undoc-members: + :show-inheritance: + +:mod:`decorators` Module +------------------------ + +.. automodule:: GPy.util.decorators + :members: + :undoc-members: + :show-inheritance: + +:mod:`erfcx` Module +------------------- + +.. automodule:: GPy.util.erfcx + :members: + :undoc-members: + :show-inheritance: + +:mod:`linalg` Module +-------------------- + +.. automodule:: GPy.util.linalg + :members: + :undoc-members: + :show-inheritance: + +:mod:`ln_diff_erfs` Module +-------------------------- + +.. automodule:: GPy.util.ln_diff_erfs + :members: + :undoc-members: + :show-inheritance: + +:mod:`misc` Module +------------------ + +.. automodule:: GPy.util.misc + :members: + :undoc-members: + :show-inheritance: + +:mod:`mocap` Module +------------------- + +.. automodule:: GPy.util.mocap + :members: + :undoc-members: + :show-inheritance: + +:mod:`multioutput` Module +------------------------- + +.. automodule:: GPy.util.multioutput + :members: + :undoc-members: + :show-inheritance: + +:mod:`netpbmfile` Module +------------------------ + +.. automodule:: GPy.util.netpbmfile + :members: + :undoc-members: + :show-inheritance: + +:mod:`pca` Module +----------------- + +.. automodule:: GPy.util.pca + :members: + :undoc-members: + :show-inheritance: + +:mod:`plot` Module +------------------ + +.. automodule:: GPy.util.plot + :members: + :undoc-members: + :show-inheritance: + +:mod:`plot_latent` Module +------------------------- + +.. automodule:: GPy.util.plot_latent + :members: + :undoc-members: + :show-inheritance: + +:mod:`squashers` Module +----------------------- + +.. automodule:: GPy.util.squashers + :members: + :undoc-members: + :show-inheritance: + +:mod:`symbolic` Module +---------------------- + +.. automodule:: GPy.util.symbolic + :members: + :undoc-members: + :show-inheritance: + +:mod:`univariate_Gaussian` Module +--------------------------------- + +.. automodule:: GPy.util.univariate_Gaussian + :members: + :undoc-members: + :show-inheritance: + +:mod:`visualize` Module +----------------------- + +.. automodule:: GPy.util.visualize + :members: + :undoc-members: + :show-inheritance: + +:mod:`warping_functions` Module +------------------------------- + +.. automodule:: GPy.util.warping_functions + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- @@ -8,166 +184,3 @@ Subpackages GPy.util.latent_space_visualizations -Submodules ----------- - -GPy.util.Tango module ---------------------- - -.. automodule:: GPy.util.Tango - :members: - :undoc-members: - :show-inheritance: - -GPy.util.classification module ------------------------------- - -.. automodule:: GPy.util.classification - :members: - :undoc-members: - :show-inheritance: - -GPy.util.config module ----------------------- - -.. automodule:: GPy.util.config - :members: - :undoc-members: - :show-inheritance: - -GPy.util.datasets module ------------------------- - -.. automodule:: GPy.util.datasets - :members: - :undoc-members: - :show-inheritance: - -GPy.util.decorators module --------------------------- - -.. automodule:: GPy.util.decorators - :members: - :undoc-members: - :show-inheritance: - -GPy.util.erfcx module ---------------------- - -.. automodule:: GPy.util.erfcx - :members: - :undoc-members: - :show-inheritance: - -GPy.util.linalg module ----------------------- - -.. automodule:: GPy.util.linalg - :members: - :undoc-members: - :show-inheritance: - -GPy.util.ln_diff_erfs module ----------------------------- - -.. automodule:: GPy.util.ln_diff_erfs - :members: - :undoc-members: - :show-inheritance: - -GPy.util.misc module --------------------- - -.. automodule:: GPy.util.misc - :members: - :undoc-members: - :show-inheritance: - -GPy.util.mocap module ---------------------- - -.. automodule:: GPy.util.mocap - :members: - :undoc-members: - :show-inheritance: - -GPy.util.multioutput module ---------------------------- - -.. automodule:: GPy.util.multioutput - :members: - :undoc-members: - :show-inheritance: - -GPy.util.netpbmfile module --------------------------- - -.. automodule:: GPy.util.netpbmfile - :members: - :undoc-members: - :show-inheritance: - -GPy.util.plot module --------------------- - -.. automodule:: GPy.util.plot - :members: - :undoc-members: - :show-inheritance: - -GPy.util.plot_latent module ---------------------------- - -.. automodule:: GPy.util.plot_latent - :members: - :undoc-members: - :show-inheritance: - -GPy.util.squashers module -------------------------- - -.. automodule:: GPy.util.squashers - :members: - :undoc-members: - :show-inheritance: - -GPy.util.symbolic module ------------------------- - -.. automodule:: GPy.util.symbolic - :members: - :undoc-members: - :show-inheritance: - -GPy.util.univariate_Gaussian module ------------------------------------ - -.. automodule:: GPy.util.univariate_Gaussian - :members: - :undoc-members: - :show-inheritance: - -GPy.util.visualize module -------------------------- - -.. automodule:: GPy.util.visualize - :members: - :undoc-members: - :show-inheritance: - -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: diff --git a/doc/index.rst b/doc/index.rst index 29b4cf43..f6207963 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -15,6 +15,9 @@ For a quick start, you can have a look at one of the tutorials: You may also be interested by some examples in the GPy/examples folder. +The detailed Developers Documentation is listed below +===================================================== + Contents: .. toctree:: diff --git a/setup.py b/setup.py index 88ee6257..3b493022 100644 --- a/setup.py +++ b/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', 'GPy.util.latent_space_visualizations', 'GPy.util.latent_space_visualizations.controllers', 'GPy.likelihoods.noise_models', 'GPy.kern.parts', 'GPy.mappings'], + packages = ['GPy', 'GPy.core', 'GPy.kern', 'GPy.util', 'GPy.models_modules', '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', 'gpy_config.cfg']}, py_modules = ['GPy.__init__'],