diff --git a/AUTHORS.txt b/AUTHORS.txt index 08ee8401..5a2a154c 100644 --- a/AUTHORS.txt +++ b/AUTHORS.txt @@ -1 +1 @@ -[GPy Authors](https://github.com/SheffieldML/GPy/graphs/contributors) \ No newline at end of file +GPy Authors: https://github.com/SheffieldML/GPy/graphs/contributors \ No newline at end of file diff --git a/GPy/__version__.py b/GPy/__version__.py index 976498ab..68cdeee4 100644 --- a/GPy/__version__.py +++ b/GPy/__version__.py @@ -1 +1 @@ -__version__ = "1.0.3" +__version__ = "1.0.5" diff --git a/GPy/core/gp.py b/GPy/core/gp.py index 0701935b..1434573a 100644 --- a/GPy/core/gp.py +++ b/GPy/core/gp.py @@ -532,21 +532,23 @@ class GP(Model): def get_most_significant_input_dimensions(self, which_indices=None): return self.kern.get_most_significant_input_dimensions(which_indices) - def optimize(self, optimizer=None, start=None, **kwargs): + def optimize(self, optimizer=None, start=None, messages=False, max_iters=1000, ipython_notebook=True, clear_after_finish=False, **kwargs): """ Optimize the model using self.log_likelihood and self.log_likelihood_gradient, as well as self.priors. kwargs are passed to the optimizer. They can be: - :param max_f_eval: maximum number of function evaluations - :type max_f_eval: int + :param max_iters: maximum number of function evaluations + :type max_iters: int :messages: whether to display during optimisation :type messages: bool :param optimizer: which optimizer to use (defaults to self.preferred optimizer), a range of optimisers can be found in :module:`~GPy.inference.optimization`, they include 'scg', 'lbfgs', 'tnc'. :type optimizer: string + :param bool ipython_notebook: whether to use ipython notebook widgets or not. + :param bool clear_after_finish: if in ipython notebook, we can clear the widgets after optimization. """ self.inference_method.on_optimization_start() try: - super(GP, self).optimize(optimizer, start, **kwargs) + super(GP, self).optimize(optimizer, start, messages, max_iters, ipython_notebook, clear_after_finish, **kwargs) except KeyboardInterrupt: print("KeyboardInterrupt caught, calling on_optimization_end() to round things up") self.inference_method.on_optimization_end() diff --git a/GPy/kern/src/stationary.py b/GPy/kern/src/stationary.py index 30116519..5e137abb 100644 --- a/GPy/kern/src/stationary.py +++ b/GPy/kern/src/stationary.py @@ -315,10 +315,10 @@ class Exponential(Stationary): super(Exponential, self).__init__(input_dim, variance, lengthscale, ARD, active_dims, name) def K_of_r(self, r): - return self.variance * np.exp(-0.5 * r) + return self.variance * np.exp(-r) def dK_dr(self, r): - return -0.5*self.K_of_r(r) + return -self.K_of_r(r) # def sde(self): # """ diff --git a/GPy/models/state_space_main.py b/GPy/models/state_space_main.py index d65364e5..891c0326 100644 --- a/GPy/models/state_space_main.py +++ b/GPy/models/state_space_main.py @@ -3237,6 +3237,7 @@ class ContDescrStateSpace(DescreteStateSpace): AB = np.dot(AB, np.vstack((np.zeros((n,n)),np.eye(n)))) Q_noise_1 = linalg.solve(AB[n:,:].T,AB[:n,:].T) + Q_noise_2 = P_inf - A.dot(P_inf).dot(A.T) # The covariance matrix Q by matrix fraction decomposition <- if compute_derivatives: @@ -3276,8 +3277,9 @@ class ContDescrStateSpace(DescreteStateSpace): else: dA = None dQ = None - Q_noise = Q_noise_1 - + Q_noise = Q_noise_2 + # Innacuracies have been observed when Q_noise_1 was used. + #Q_noise = Q_noise_1 # Return @@ -3484,4 +3486,4 @@ def balance_ss_model(F,L,Qc,H,Pinf,P0,dF=None,dQc=None,dPinf=None,dP0=None): # (F,L,Qc,H,Pinf,P0,dF,dQc,dPinf,dP0) - return bF, bL, bQc, bH, bPinf, bP0, bdF, bdQc, bdPinf, bdP0, T \ No newline at end of file + return bF, bL, bQc, bH, bPinf, bP0, bdF, bdQc, bdPinf, bdP0, T diff --git a/GPy/testing/baseline/coverage_3d_plot.png b/GPy/testing/baseline/coverage_3d_plot.png index 62638b03..43f165e6 100644 Binary files a/GPy/testing/baseline/coverage_3d_plot.png and b/GPy/testing/baseline/coverage_3d_plot.png differ diff --git a/GPy/testing/gpy_kernels_state_space_tests.py b/GPy/testing/gpy_kernels_state_space_tests.py index 1d03233a..fb5fa228 100644 --- a/GPy/testing/gpy_kernels_state_space_tests.py +++ b/GPy/testing/gpy_kernels_state_space_tests.py @@ -17,326 +17,334 @@ from .state_space_main_tests import generate_x_points, generate_sine_data, \ class StateSpaceKernelsTests(np.testing.TestCase): def setUp(self): pass - + def run_for_model(self, X, Y, ss_kernel, kalman_filter_type = 'regular', - use_cython=False, check_gradients=True, - optimize=True, optimize_max_iters=1000,predict_X=None, - compare_with_GP=True, gp_kernel=None, + use_cython=False, check_gradients=True, + optimize=True, optimize_max_iters=250, predict_X=None, + compare_with_GP=True, gp_kernel=None, mean_compare_decimal=10, var_compare_decimal=7): - - m1 = SS_model.StateSpace(X,Y, ss_kernel, + + m1 = SS_model.StateSpace(X,Y, ss_kernel, kalman_filter_type=kalman_filter_type, use_cython=use_cython) - + + m1.likelihood[:] = Y.var()/100. + if check_gradients: self.assertTrue(m1.checkgrad()) - - if optimize: - m1.optimize(optimizer='lbfgsb',max_iters=optimize_max_iters) - + + if 1:#optimize: + m1.optimize(optimizer='lbfgsb', max_iters=1) + if compare_with_GP and (predict_X is None): predict_X = X - - if (predict_X is not None): - x_pred_reg_1 = m1.predict(predict_X) - x_quant_reg_1 = m1.predict_quantiles(predict_X) - + + self.assertTrue(compare_with_GP) if compare_with_GP: m2 = GPy.models.GPRegression(X,Y, gp_kernel) - m2.optimize(optimizer='lbfgsb', max_iters=optimize_max_iters) - #print(m2) - + + m2[:] = m1[:] + + if (predict_X is not None): + x_pred_reg_1 = m1.predict(predict_X) + x_quant_reg_1 = m1.predict_quantiles(predict_X) + x_pred_reg_2 = m2.predict(predict_X) x_quant_reg_2 = m2.predict_quantiles(predict_X) - - # Test values - #print np.max(np.abs(x_pred_reg_1[0]-x_pred_reg_2[0])) - np.testing.assert_almost_equal(np.max(np.abs(x_pred_reg_1[0]- \ - x_pred_reg_2[0])), 0, decimal=mean_compare_decimal) - - # Test variances - #print np.max(np.abs(x_pred_reg_1[1]-x_pred_reg_2[1])) - - np.testing.assert_almost_equal(np.max(np.abs(x_pred_reg_1[1]- \ - x_pred_reg_2[1])), 0, decimal=var_compare_decimal) - + + np.testing.assert_array_almost_equal(x_pred_reg_1[0], x_pred_reg_2[0], mean_compare_decimal) + np.testing.assert_array_almost_equal(x_pred_reg_1[1], x_pred_reg_2[1], var_compare_decimal) + np.testing.assert_array_almost_equal(x_quant_reg_1[0], x_quant_reg_2[0], mean_compare_decimal) + np.testing.assert_array_almost_equal(x_quant_reg_1[1], x_quant_reg_2[1], mean_compare_decimal) + np.testing.assert_array_almost_equal(m1.gradient, m2.gradient, var_compare_decimal) + np.testing.assert_almost_equal(m1.log_likelihood(), m2.log_likelihood(), var_compare_decimal) + + def test_Matern32_kernel(self,): np.random.seed(234) # seed the random number generator (X,Y) = generate_sine_data(x_points=None, sin_period=5.0, sin_ampl=10.0, noise_var=2.0, plot = False, points_num=50, x_interval = (0, 20), random=True) X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) - + ss_kernel = GPy.kern.sde_Matern32(1,active_dims=[0,]) gp_kernel = GPy.kern.Matern32(1,active_dims=[0,]) - + self.run_for_model(X, Y, ss_kernel, check_gradients=True, predict_X=X, compare_with_GP=True, - gp_kernel=gp_kernel, - mean_compare_decimal=10, var_compare_decimal=7) - + gp_kernel=gp_kernel, + mean_compare_decimal=5, var_compare_decimal=5) + def test_Matern52_kernel(self,): np.random.seed(234) # seed the random number generator (X,Y) = generate_sine_data(x_points=None, sin_period=5.0, sin_ampl=10.0, noise_var=2.0, plot = False, points_num=50, x_interval = (0, 20), random=True) X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) - + ss_kernel = GPy.kern.sde_Matern52(1,active_dims=[0,]) gp_kernel = GPy.kern.Matern52(1,active_dims=[0,]) - - self.run_for_model(X, Y, ss_kernel, check_gradients=True, - optimize = True, predict_X=X, - compare_with_GP=True, gp_kernel=gp_kernel, - mean_compare_decimal=8, var_compare_decimal=7) - + + self.run_for_model(X, Y, ss_kernel, check_gradients=True, + optimize = True, predict_X=X, + compare_with_GP=True, gp_kernel=gp_kernel, + mean_compare_decimal=5, var_compare_decimal=5) + def test_RBF_kernel(self,): np.random.seed(234) # seed the random number generator (X,Y) = generate_sine_data(x_points=None, sin_period=5.0, sin_ampl=10.0, noise_var=2.0, plot = False, points_num=50, x_interval = (0, 20), random=True) X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) - - ss_kernel = GPy.kern.sde_RBF(1,active_dims=[0,]) - gp_kernel = GPy.kern.RBF(1,active_dims=[0,]) + + ss_kernel = GPy.kern.sde_RBF(1, 110., 1.5, active_dims=[0,]) + gp_kernel = GPy.kern.RBF(1, 110., 1.5, active_dims=[0,]) self.run_for_model(X, Y, ss_kernel, check_gradients=True, - predict_X=X, - gp_kernel=gp_kernel, - mean_compare_decimal=1, var_compare_decimal=1) - + predict_X=X, + gp_kernel=gp_kernel, + optimize_max_iters=1000, + mean_compare_decimal=2, var_compare_decimal=1) + def test_periodic_kernel(self,): np.random.seed(322) # seed the random number generator (X,Y) = generate_sine_data(x_points=None, sin_period=5.0, sin_ampl=10.0, noise_var=2.0, plot = False, points_num=50, x_interval = (0, 20), random=True) X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) - + ss_kernel = GPy.kern.sde_StdPeriodic(1,active_dims=[0,]) ss_kernel.lengthscale.constrain_bounded(0.27, 1000) ss_kernel.period.constrain_bounded(0.17, 100) - + gp_kernel = GPy.kern.StdPeriodic(1,active_dims=[0,]) gp_kernel.lengthscale.constrain_bounded(0.27, 1000) - gp_kernel.period.constrain_bounded(0.17, 100) - + gp_kernel.period.constrain_bounded(0.17, 100) + self.run_for_model(X, Y, ss_kernel, check_gradients=True, - predict_X=X, - gp_kernel=gp_kernel, - mean_compare_decimal=3, var_compare_decimal=3) - + predict_X=X, + gp_kernel=gp_kernel, + mean_compare_decimal=3, var_compare_decimal=3) + def test_quasi_periodic_kernel(self,): np.random.seed(329) # seed the random number generator (X,Y) = generate_sine_data(x_points=None, sin_period=5.0, sin_ampl=10.0, noise_var=2.0, plot = False, points_num=50, x_interval = (0, 20), random=True) X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) - + ss_kernel = GPy.kern.sde_Matern32(1)*GPy.kern.sde_StdPeriodic(1,active_dims=[0,]) ss_kernel.std_periodic.lengthscale.constrain_bounded(0.25, 1000) ss_kernel.std_periodic.period.constrain_bounded(0.15, 100) - + gp_kernel = GPy.kern.Matern32(1)*GPy.kern.StdPeriodic(1,active_dims=[0,]) gp_kernel.std_periodic.lengthscale.constrain_bounded(0.25, 1000) - gp_kernel.std_periodic.period.constrain_bounded(0.15, 100) - + gp_kernel.std_periodic.period.constrain_bounded(0.15, 100) + self.run_for_model(X, Y, ss_kernel, check_gradients=True, - predict_X=X, - gp_kernel=gp_kernel, - mean_compare_decimal=1, var_compare_decimal=2) + predict_X=X, + gp_kernel=gp_kernel, + mean_compare_decimal=1, var_compare_decimal=2) def test_linear_kernel(self,): - + np.random.seed(234) # seed the random number generator (X,Y) = generate_linear_data(x_points=None, tangent=2.0, add_term=20.0, noise_var=2.0, plot = False, points_num=50, x_interval = (0, 20), random=True) - + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) - + ss_kernel = GPy.kern.sde_Linear(1,X,active_dims=[0,]) + GPy.kern.sde_Bias(1, active_dims=[0,]) gp_kernel = GPy.kern.Linear(1, active_dims=[0,]) + GPy.kern.Bias(1, active_dims=[0,]) - - self.run_for_model(X, Y, ss_kernel, check_gradients= False, - predict_X=X, - gp_kernel=gp_kernel, + + self.run_for_model(X, Y, ss_kernel, check_gradients= False, + predict_X=X, + gp_kernel=gp_kernel, mean_compare_decimal=5, var_compare_decimal=5) def test_brownian_kernel(self,): np.random.seed(234) # seed the random number generator (X,Y) = generate_brownian_data(x_points=None, kernel_var=2.0, noise_var = 0.1, plot = False, points_num=50, x_interval = (0, 20), random=True) - + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) - + ss_kernel = GPy.kern.sde_Brownian() gp_kernel = GPy.kern.Brownian() - - self.run_for_model(X, Y, ss_kernel, check_gradients=True, - predict_X=X, - gp_kernel=gp_kernel, - mean_compare_decimal=10, var_compare_decimal=7) - + + self.run_for_model(X, Y, ss_kernel, check_gradients=True, + predict_X=X, + gp_kernel=gp_kernel, + mean_compare_decimal=4, var_compare_decimal=4) + def test_exponential_kernel(self,): - np.random.seed(234) # seed the random number generator + np.random.seed(12345) # seed the random number generator (X,Y) = generate_linear_data(x_points=None, tangent=1.0, add_term=20.0, noise_var=2.0, - plot = False, points_num=50, x_interval = (0, 20), random=True) - + plot = False, points_num=10, x_interval = (0, 20), random=True) + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) - - ss_kernel = GPy.kern.sde_Exponential(1, active_dims=[0,]) - gp_kernel = GPy.kern.Exponential(1, active_dims=[0,]) - - self.run_for_model(X, Y, ss_kernel, check_gradients=True, - predict_X=X, - gp_kernel=gp_kernel, - mean_compare_decimal=5, var_compare_decimal=6) + + ss_kernel = GPy.kern.sde_Exponential(1, Y.var(), X.ptp()/2., active_dims=[0,]) + gp_kernel = GPy.kern.Exponential(1, Y.var(), X.ptp()/2., active_dims=[0,]) + + Y -= Y.mean() + + self.run_for_model(X, Y, ss_kernel, check_gradients=True, + predict_X=X, + gp_kernel=gp_kernel, + optimize_max_iters=1000, + mean_compare_decimal=2, var_compare_decimal=2) def test_kernel_addition(self,): #np.random.seed(329) # seed the random number generator np.random.seed(333) (X,Y) = generate_sine_data(x_points=None, sin_period=5.0, sin_ampl=5.0, noise_var=2.0, plot = False, points_num=100, x_interval = (0, 40), random=True) - + (X1,Y1) = generate_linear_data(x_points=X, tangent=1.0, add_term=20.0, noise_var=0.0, plot = False, points_num=100, x_interval = (0, 40), random=True) - + # Sine data <- Y = Y + Y1 - + Y -= Y.mean() + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) - + def get_new_kernels(): - ss_kernel = GPy.kern.sde_Linear(1,X) + GPy.kern.sde_StdPeriodic(1,active_dims=[0,]) - ss_kernel.std_periodic.lengthscale.constrain_bounded(0.25, 1000) - ss_kernel.std_periodic.period.constrain_bounded(3, 8) - - gp_kernel = GPy.kern.Linear(1) + GPy.kern.StdPeriodic(1,active_dims=[0,]) - gp_kernel.std_periodic.lengthscale.constrain_bounded(0.25, 1000) - gp_kernel.std_periodic.period.constrain_bounded(3, 8) - + ss_kernel = GPy.kern.sde_Linear(1,X,variances=1) + GPy.kern.sde_StdPeriodic(1,period=5.0, variance=300, lengthscale=3., active_dims=[0,]) + #ss_kernel.std_periodic.lengthscale.constrain_bounded(0.25, 1000) + #ss_kernel.std_periodic.period.constrain_bounded(3, 8) + + gp_kernel = GPy.kern.Linear(1,variances=1) + GPy.kern.StdPeriodic(1,period=5.0, variance=300, lengthscale=3., active_dims=[0,]) + #gp_kernel.std_periodic.lengthscale.constrain_bounded(0.25, 1000) + #gp_kernel.std_periodic.period.constrain_bounded(3, 8) + return ss_kernel, gp_kernel - + # Cython is available only with svd. ss_kernel, gp_kernel = get_new_kernels() self.run_for_model(X, Y, ss_kernel, kalman_filter_type = 'svd', use_cython=True, optimize_max_iters=10, check_gradients=False, - predict_X=X, - gp_kernel=gp_kernel, + predict_X=X, + gp_kernel=gp_kernel, mean_compare_decimal=5, var_compare_decimal=5) - + ss_kernel, gp_kernel = get_new_kernels() self.run_for_model(X, Y, ss_kernel, kalman_filter_type = 'regular', use_cython=False, optimize_max_iters=10, check_gradients=True, - predict_X=X, - gp_kernel=gp_kernel, + predict_X=X, + gp_kernel=gp_kernel, mean_compare_decimal=5, var_compare_decimal=5) - + ss_kernel, gp_kernel = get_new_kernels() self.run_for_model(X, Y, ss_kernel, kalman_filter_type = 'svd', use_cython=False, optimize_max_iters=10, check_gradients=False, - predict_X=X, - gp_kernel=gp_kernel, + predict_X=X, + gp_kernel=gp_kernel, mean_compare_decimal=5, var_compare_decimal=5) - - + + def test_kernel_multiplication(self,): np.random.seed(329) # seed the random number generator (X,Y) = generate_sine_data(x_points=None, sin_period=5.0, sin_ampl=10.0, noise_var=2.0, plot = False, points_num=50, x_interval = (0, 20), random=True) - + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) - + def get_new_kernels(): ss_kernel = GPy.kern.sde_Matern32(1)*GPy.kern.sde_Matern52(1) gp_kernel = GPy.kern.Matern32(1)*GPy.kern.sde_Matern52(1) - + return ss_kernel, gp_kernel - + ss_kernel, gp_kernel = get_new_kernels() + + #import ipdb;ipdb.set_trace() self.run_for_model(X, Y, ss_kernel, kalman_filter_type = 'svd', use_cython=True, optimize_max_iters=10, check_gradients=True, - predict_X=X, - gp_kernel=gp_kernel, - mean_compare_decimal=-1, var_compare_decimal=-1) - + predict_X=X, + gp_kernel=gp_kernel, + mean_compare_decimal=2, var_compare_decimal=2) + ss_kernel, gp_kernel = get_new_kernels() self.run_for_model(X, Y, ss_kernel, kalman_filter_type = 'regular', use_cython=False, optimize_max_iters=10, check_gradients=True, - predict_X=X, - gp_kernel=gp_kernel, - mean_compare_decimal=-1, var_compare_decimal=-1) - + predict_X=X, + gp_kernel=gp_kernel, + mean_compare_decimal=2, var_compare_decimal=2) + ss_kernel, gp_kernel = get_new_kernels() self.run_for_model(X, Y, ss_kernel, kalman_filter_type = 'svd', use_cython=False, optimize_max_iters=10, check_gradients=True, - predict_X=X, - gp_kernel=gp_kernel, - mean_compare_decimal=-1, var_compare_decimal=0) + predict_X=X, + gp_kernel=gp_kernel, + mean_compare_decimal=2, var_compare_decimal=2) def test_forecast(self,): """ Test time-series forecasting. """ - + # Generate data -> np.random.seed(339) # seed the random number generator #import pdb; pdb.set_trace() (X,Y) = generate_sine_data(x_points=None, sin_period=5.0, sin_ampl=5.0, noise_var=2.0, plot = False, points_num=100, x_interval = (0, 40), random=True) - + (X1,Y1) = generate_linear_data(x_points=X, tangent=1.0, add_term=20.0, noise_var=0.0, plot = False, points_num=100, x_interval = (0, 40), random=True) - + Y = Y + Y1 X_train = X[X <= 20] - Y_train = Y[X <= 20] + Y_train = Y[X <= 20] X_test = X[X > 20] Y_test = Y[X > 20] - - X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) - X_train.shape = (X_train.shape[0],1); Y_train.shape = (Y_train.shape[0],1) - X_test.shape = (X_test.shape[0],1); Y_test.shape = (Y_test.shape[0],1) + + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) + X_train.shape = (X_train.shape[0],1); Y_train.shape = (Y_train.shape[0],1) + X_test.shape = (X_test.shape[0],1); Y_test.shape = (Y_test.shape[0],1) # Generate data <- - + #import pdb; pdb.set_trace() - + def get_new_kernels(): periodic_kernel = GPy.kern.StdPeriodic(1,active_dims=[0,]) gp_kernel = GPy.kern.Linear(1, active_dims=[0,]) + GPy.kern.Bias(1, active_dims=[0,]) + periodic_kernel gp_kernel.std_periodic.lengthscale.constrain_bounded(0.25, 1000) gp_kernel.std_periodic.period.constrain_bounded(0.15, 100) - + periodic_kernel = GPy.kern.sde_StdPeriodic(1,active_dims=[0,]) ss_kernel = GPy.kern.sde_Linear(1,X,active_dims=[0,]) + \ GPy.kern.sde_Bias(1, active_dims=[0,]) + periodic_kernel - + ss_kernel.std_periodic.lengthscale.constrain_bounded(0.25, 1000) ss_kernel.std_periodic.period.constrain_bounded(0.15, 100) - + return ss_kernel, gp_kernel - + ss_kernel, gp_kernel = get_new_kernels() self.run_for_model(X_train, Y_train, ss_kernel, kalman_filter_type = 'regular', use_cython=False, optimize_max_iters=30, check_gradients=True, - predict_X=X_test, - gp_kernel=gp_kernel, - mean_compare_decimal=0, var_compare_decimal=-1) - + predict_X=X_test, + gp_kernel=gp_kernel, + mean_compare_decimal=2, var_compare_decimal=2) + + ss_kernel, gp_kernel = get_new_kernels() self.run_for_model(X_train, Y_train, ss_kernel, kalman_filter_type = 'svd', use_cython=False, optimize_max_iters=30, check_gradients=False, - predict_X=X_test, - gp_kernel=gp_kernel, - mean_compare_decimal=-1, var_compare_decimal=-1) - + predict_X=X_test, + gp_kernel=gp_kernel, + mean_compare_decimal=2, var_compare_decimal=2) + ss_kernel, gp_kernel = get_new_kernels() self.run_for_model(X_train, Y_train, ss_kernel, kalman_filter_type = 'svd', use_cython=True, optimize_max_iters=30, check_gradients=False, - predict_X=X_test, - gp_kernel=gp_kernel, - mean_compare_decimal=-1, var_compare_decimal=-1) - + predict_X=X_test, + gp_kernel=gp_kernel, + mean_compare_decimal=2, var_compare_decimal=2) + if __name__ == "__main__": print("Running state-space inference tests...") unittest.main() - + #tt = StateSpaceKernelsTests('test_periodic_kernel') #import pdb; pdb.set_trace() #tt.test_Matern32_kernel() @@ -350,4 +358,4 @@ if __name__ == "__main__": #tt.test_kernel_addition() #tt.test_kernel_multiplication() #tt.test_forecast() - + diff --git a/GPy/testing/kernel_tests.py b/GPy/testing/kernel_tests.py index eafde0ec..6b620406 100644 --- a/GPy/testing/kernel_tests.py +++ b/GPy/testing/kernel_tests.py @@ -395,14 +395,12 @@ class KernelTestsNonContinuous(unittest.TestCase): self.X2[:(N0*2), -1] = 0 self.X2[(N0*2):, -1] = 1 - #@unittest.expectedFailure def test_IndependentOutputs(self): k = [GPy.kern.RBF(1, active_dims=[1], name='rbf1'), GPy.kern.RBF(self.D, active_dims=range(self.D), name='rbf012'), GPy.kern.RBF(2, active_dims=[0,2], name='rbf02')] kern = GPy.kern.IndependentOutputs(k, -1, name='ind_split') np.testing.assert_array_equal(kern.active_dims, [-1,0,1,2]) np.testing.assert_array_equal(kern._all_dims_active, [0,1,2,-1]) - #@skip('Gradients for independend outputs with different X do not work correctly') def testIndependendGradients(self): k = GPy.kern.RBF(self.D, active_dims=range(self.D)) kern = GPy.kern.IndependentOutputs(k, -1, 'ind_single') @@ -411,14 +409,12 @@ class KernelTestsNonContinuous(unittest.TestCase): kern = GPy.kern.IndependentOutputs(k, -1, name='ind_split') self.assertTrue(check_kernel_gradient_functions(kern, X=self.X, X2=self.X2, verbose=verbose, fixed_X_dims=-1)) - #@unittest.expectedFailure def test_Hierarchical(self): k = [GPy.kern.RBF(2, active_dims=[0,2], name='rbf1'), GPy.kern.RBF(2, active_dims=[0,2], name='rbf2')] kern = GPy.kern.IndependentOutputs(k, -1, name='ind_split') np.testing.assert_array_equal(kern.active_dims, [-1,0,2]) np.testing.assert_array_equal(kern._all_dims_active, [0,1,2,-1]) - #@skip('Gradients for independend outputs with different X do not work correctly') def test_Hierarchical_gradients(self): k = [GPy.kern.RBF(2, active_dims=[0,2], name='rbf1'), GPy.kern.RBF(2, active_dims=[0,2], name='rbf2')] kern = GPy.kern.IndependentOutputs(k, -1, name='ind_split') diff --git a/README.md b/README.md index c81ef5da..21b19c6b 100644 --- a/README.md +++ b/README.md @@ -5,11 +5,11 @@ The Gaussian processes framework in Python. * GPy [homepage](http://sheffieldml.github.io/GPy/) * Tutorial [notebooks](http://nbviewer.ipython.org/github/SheffieldML/notebook/blob/master/GPy/index.ipynb) * User [mailing-list](https://lists.shef.ac.uk/sympa/subscribe/gpy-users) -* Developer [documentation](http://gpy.readthedocs.org/en/devel/) +* Developer [documentation](http://pythonhosted.org/GPy/) * Travis-CI [unit-tests](https://travis-ci.org/SheffieldML/GPy) * [![licence](https://img.shields.io/badge/licence-BSD-blue.svg)](http://opensource.org/licenses/BSD-3-Clause) -[![develstat](https://travis-ci.org/SheffieldML/GPy.svg?branch=devel)](https://travis-ci.org/SheffieldML/GPy) [![covdevel](http://codecov.io/github/SheffieldML/GPy/coverage.svg?branch=devel)](http://codecov.io/github/SheffieldML/GPy?branch=devel) [![docdevel](https://readthedocs.org/projects/gpy/badge/?version=devel)](http://gpy.readthedocs.org/en/devel/) [![Research software impact](http://depsy.org/api/package/pypi/GPy/badge.svg)](http://depsy.org/package/python/GPy) +[![develstat](https://travis-ci.org/SheffieldML/GPy.svg?branch=devel)](https://travis-ci.org/SheffieldML/GPy) [![covdevel](http://codecov.io/github/SheffieldML/GPy/coverage.svg?branch=devel)](http://codecov.io/github/SheffieldML/GPy?branch=devel) [![Research software impact](http://depsy.org/api/package/pypi/GPy/badge.svg)](http://depsy.org/package/python/GPy) ## Updated Structure diff --git a/README.rst b/README.rst index 9436b462..ffd47a40 100644 --- a/README.rst +++ b/README.rst @@ -1,12 +1,16 @@ -# GPy +=== +GPy +=== The Gaussian processes framework in Python. +------------------------------------------- -* GPy [homepage](http://sheffieldml.github.io/GPy/) -* Tutorial [notebooks](http://nbviewer.ipython.org/github/SheffieldML/notebook/blob/master/GPy/index.ipynb) -* User [mailing-list](https://lists.shef.ac.uk/sympa/subscribe/gpy-users) -* Developer [documentation](http://gpy.readthedocs.org/en/devel/) -* Travis-CI [unit-tests](https://travis-ci.org/SheffieldML/GPy) -* [![licence](https://img.shields.io/badge/licence-BSD-blue.svg)](http://opensource.org/licenses/BSD-3-Clause) +- `GPy homepage `_ +- `Tutorial notebooks `_ +- `User mailing-list `_ +- `Developer documentation `_ +- `Travis-CI unit-tests `_ +- .. image:: https://img.shields.io/badge/licence-BSD-blue.svg + :target: https://opensource.org/licenses/BSD-3-Clause -For full description please refer to the [github page](http://sheffieldml.github.io/GPy/) +For full description and installation instructions please refer to the github page. diff --git a/doc/source/GPy.core.parameterization.rst b/doc/source/GPy.core.parameterization.rst deleted file mode 100644 index 788e3af8..00000000 --- a/doc/source/GPy.core.parameterization.rst +++ /dev/null @@ -1,118 +0,0 @@ -GPy.core.parameterization package -================================= - -Submodules ----------- - -GPy.core.parameterization.domains module ----------------------------------------- - -.. automodule:: GPy.core.parameterization.domains - :members: - :undoc-members: - :show-inheritance: - -GPy.core.parameterization.index_operations module -------------------------------------------------- - -.. automodule:: GPy.core.parameterization.index_operations - :members: - :undoc-members: - :show-inheritance: - -GPy.core.parameterization.lists_and_dicts module ------------------------------------------------- - -.. automodule:: GPy.core.parameterization.lists_and_dicts - :members: - :undoc-members: - :show-inheritance: - -GPy.core.parameterization.observable module -------------------------------------------- - -.. automodule:: GPy.core.parameterization.observable - :members: - :undoc-members: - :show-inheritance: - -GPy.core.parameterization.observable_array module -------------------------------------------------- - -.. automodule:: GPy.core.parameterization.observable_array - :members: - :undoc-members: - :show-inheritance: - -GPy.core.parameterization.param module --------------------------------------- - -.. automodule:: GPy.core.parameterization.param - :members: - :undoc-members: - :show-inheritance: - -GPy.core.parameterization.parameter_core module ------------------------------------------------ - -.. automodule:: GPy.core.parameterization.parameter_core - :members: - :undoc-members: - :show-inheritance: - -GPy.core.parameterization.parameterized module ----------------------------------------------- - -.. automodule:: GPy.core.parameterization.parameterized - :members: - :undoc-members: - :show-inheritance: - -GPy.core.parameterization.priors module ---------------------------------------- - -.. automodule:: GPy.core.parameterization.priors - :members: - :undoc-members: - :show-inheritance: - -GPy.core.parameterization.ties_and_remappings module ----------------------------------------------------- - -.. automodule:: GPy.core.parameterization.ties_and_remappings - :members: - :undoc-members: - :show-inheritance: - -GPy.core.parameterization.transformations module ------------------------------------------------- - -.. automodule:: GPy.core.parameterization.transformations - :members: - :undoc-members: - :show-inheritance: - -GPy.core.parameterization.updateable module -------------------------------------------- - -.. automodule:: GPy.core.parameterization.updateable - :members: - :undoc-members: - :show-inheritance: - -GPy.core.parameterization.variational module --------------------------------------------- - -.. automodule:: GPy.core.parameterization.variational - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: GPy.core.parameterization - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/GPy.core.rst b/doc/source/GPy.core.rst deleted file mode 100644 index 66878101..00000000 --- a/doc/source/GPy.core.rst +++ /dev/null @@ -1,85 +0,0 @@ -GPy.core package -================ - -Subpackages ------------ - -.. toctree:: - - GPy.core.parameterization - -Submodules ----------- - -GPy.core.gp module ------------------- - -.. automodule:: GPy.core.gp - :members: - :undoc-members: - :show-inheritance: - -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: - -GPy.core.sparse_gp module -------------------------- - -.. automodule:: GPy.core.sparse_gp - :members: - :undoc-members: - :show-inheritance: - -GPy.core.sparse_gp_mpi module ------------------------------ - -.. automodule:: GPy.core.sparse_gp_mpi - :members: - :undoc-members: - :show-inheritance: - -GPy.core.svgp module --------------------- - -.. automodule:: GPy.core.svgp - :members: - :undoc-members: - :show-inheritance: - -GPy.core.symbolic module ------------------------- - -.. automodule:: GPy.core.symbolic - :members: - :undoc-members: - :show-inheritance: - -GPy.core.verbose_optimization module ------------------------------------- - -.. automodule:: GPy.core.verbose_optimization - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: GPy.core - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/GPy.examples.rst b/doc/source/GPy.examples.rst deleted file mode 100644 index a2919eab..00000000 --- a/doc/source/GPy.examples.rst +++ /dev/null @@ -1,54 +0,0 @@ -GPy.examples package -==================== - -Submodules ----------- - -GPy.examples.classification module ----------------------------------- - -.. automodule:: GPy.examples.classification - :members: - :undoc-members: - :show-inheritance: - -GPy.examples.coreg_example module ---------------------------------- - -.. automodule:: GPy.examples.coreg_example - :members: - :undoc-members: - :show-inheritance: - -GPy.examples.dimensionality_reduction module --------------------------------------------- - -.. automodule:: GPy.examples.dimensionality_reduction - :members: - :undoc-members: - :show-inheritance: - -GPy.examples.non_gaussian module --------------------------------- - -.. automodule:: GPy.examples.non_gaussian - :members: - :undoc-members: - :show-inheritance: - -GPy.examples.regression module ------------------------------- - -.. automodule:: GPy.examples.regression - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: GPy.examples - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/GPy.inference.latent_function_inference.rst b/doc/source/GPy.inference.latent_function_inference.rst deleted file mode 100644 index c374e73b..00000000 --- a/doc/source/GPy.inference.latent_function_inference.rst +++ /dev/null @@ -1,102 +0,0 @@ -GPy.inference.latent_function_inference package -=============================================== - -Submodules ----------- - -GPy.inference.latent_function_inference.dtc module --------------------------------------------------- - -.. automodule:: GPy.inference.latent_function_inference.dtc - :members: - :undoc-members: - :show-inheritance: - -GPy.inference.latent_function_inference.exact_gaussian_inference module ------------------------------------------------------------------------ - -.. automodule:: GPy.inference.latent_function_inference.exact_gaussian_inference - :members: - :undoc-members: - :show-inheritance: - -GPy.inference.latent_function_inference.expectation_propagation module ----------------------------------------------------------------------- - -.. automodule:: GPy.inference.latent_function_inference.expectation_propagation - :members: - :undoc-members: - :show-inheritance: - -GPy.inference.latent_function_inference.fitc module ---------------------------------------------------- - -.. automodule:: GPy.inference.latent_function_inference.fitc - :members: - :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 ------------------------------------------------------- - -.. automodule:: GPy.inference.latent_function_inference.laplace - :members: - :undoc-members: - :show-inheritance: - -GPy.inference.latent_function_inference.posterior module --------------------------------------------------------- - -.. automodule:: GPy.inference.latent_function_inference.posterior - :members: - :undoc-members: - :show-inheritance: - -GPy.inference.latent_function_inference.svgp module ---------------------------------------------------- - -.. automodule:: GPy.inference.latent_function_inference.svgp - :members: - :undoc-members: - :show-inheritance: - -GPy.inference.latent_function_inference.var_dtc module ------------------------------------------------------- - -.. automodule:: GPy.inference.latent_function_inference.var_dtc - :members: - :undoc-members: - :show-inheritance: - -GPy.inference.latent_function_inference.var_dtc_parallel module ---------------------------------------------------------------- - -.. automodule:: GPy.inference.latent_function_inference.var_dtc_parallel - :members: - :undoc-members: - :show-inheritance: - -GPy.inference.latent_function_inference.var_gauss module --------------------------------------------------------- - -.. automodule:: GPy.inference.latent_function_inference.var_gauss - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: GPy.inference.latent_function_inference - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/GPy.inference.mcmc.rst b/doc/source/GPy.inference.mcmc.rst deleted file mode 100644 index 273658b7..00000000 --- a/doc/source/GPy.inference.mcmc.rst +++ /dev/null @@ -1,30 +0,0 @@ -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: diff --git a/doc/source/GPy.inference.optimization.rst b/doc/source/GPy.inference.optimization.rst deleted file mode 100644 index f5f2a930..00000000 --- a/doc/source/GPy.inference.optimization.rst +++ /dev/null @@ -1,54 +0,0 @@ -GPy.inference.optimization package -================================== - -Submodules ----------- - -GPy.inference.optimization.conjugate_gradient_descent module ------------------------------------------------------------- - -.. automodule:: GPy.inference.optimization.conjugate_gradient_descent - :members: - :undoc-members: - :show-inheritance: - -GPy.inference.optimization.gradient_descent_update_rules module ---------------------------------------------------------------- - -.. automodule:: GPy.inference.optimization.gradient_descent_update_rules - :members: - :undoc-members: - :show-inheritance: - -GPy.inference.optimization.optimization module ----------------------------------------------- - -.. automodule:: GPy.inference.optimization.optimization - :members: - :undoc-members: - :show-inheritance: - -GPy.inference.optimization.scg module -------------------------------------- - -.. automodule:: GPy.inference.optimization.scg - :members: - :undoc-members: - :show-inheritance: - -GPy.inference.optimization.stochastics module ---------------------------------------------- - -.. automodule:: GPy.inference.optimization.stochastics - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: GPy.inference.optimization - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/GPy.inference.rst b/doc/source/GPy.inference.rst deleted file mode 100644 index 235f804b..00000000 --- a/doc/source/GPy.inference.rst +++ /dev/null @@ -1,19 +0,0 @@ -GPy.inference package -===================== - -Subpackages ------------ - -.. toctree:: - - GPy.inference.latent_function_inference - GPy.inference.mcmc - GPy.inference.optimization - -Module contents ---------------- - -.. automodule:: GPy.inference - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/GPy.kern.rst b/doc/source/GPy.kern.rst deleted file mode 100644 index bb61443b..00000000 --- a/doc/source/GPy.kern.rst +++ /dev/null @@ -1,17 +0,0 @@ -GPy.kern package -================ - -Subpackages ------------ - -.. toctree:: - - GPy.kern.src - -Module contents ---------------- - -.. automodule:: GPy.kern - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/GPy.kern.src.psi_comp.rst b/doc/source/GPy.kern.src.psi_comp.rst deleted file mode 100644 index dfa3c270..00000000 --- a/doc/source/GPy.kern.src.psi_comp.rst +++ /dev/null @@ -1,70 +0,0 @@ -GPy.kern.src.psi_comp package -============================= - -Submodules ----------- - -GPy.kern.src.psi_comp.gaussherm module --------------------------------------- - -.. automodule:: GPy.kern.src.psi_comp.gaussherm - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.psi_comp.linear_psi_comp module --------------------------------------------- - -.. automodule:: GPy.kern.src.psi_comp.linear_psi_comp - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.psi_comp.rbf_psi_comp module ------------------------------------------ - -.. automodule:: GPy.kern.src.psi_comp.rbf_psi_comp - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.psi_comp.rbf_psi_gpucomp module --------------------------------------------- - -.. automodule:: GPy.kern.src.psi_comp.rbf_psi_gpucomp - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.psi_comp.sslinear_psi_comp module ----------------------------------------------- - -.. automodule:: GPy.kern.src.psi_comp.sslinear_psi_comp - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.psi_comp.ssrbf_psi_comp module -------------------------------------------- - -.. automodule:: GPy.kern.src.psi_comp.ssrbf_psi_comp - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.psi_comp.ssrbf_psi_gpucomp module ----------------------------------------------- - -.. automodule:: GPy.kern.src.psi_comp.ssrbf_psi_gpucomp - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: GPy.kern.src.psi_comp - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/GPy.kern.src.rst b/doc/source/GPy.kern.src.rst deleted file mode 100644 index ccbc3f99..00000000 --- a/doc/source/GPy.kern.src.rst +++ /dev/null @@ -1,237 +0,0 @@ -GPy.kern.src package -==================== - -Subpackages ------------ - -.. toctree:: - - GPy.kern.src.psi_comp - -Submodules ----------- - -GPy.kern.src.ODE_UY module --------------------------- - -.. automodule:: GPy.kern.src.ODE_UY - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.ODE_UYC module ---------------------------- - -.. automodule:: GPy.kern.src.ODE_UYC - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.ODE_st module --------------------------- - -.. automodule:: GPy.kern.src.ODE_st - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.ODE_t module -------------------------- - -.. automodule:: GPy.kern.src.ODE_t - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.add module ------------------------ - -.. automodule:: GPy.kern.src.add - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.basis_funcs module -------------------------------- - -.. automodule:: GPy.kern.src.basis_funcs - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.brownian module ----------------------------- - -.. automodule:: GPy.kern.src.brownian - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.coregionalize module ---------------------------------- - -.. automodule:: GPy.kern.src.coregionalize - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.coregionalize_cython module ----------------------------------------- - -.. automodule:: GPy.kern.src.coregionalize_cython - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.eq_ode2 module ---------------------------- - -.. automodule:: GPy.kern.src.eq_ode2 - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.independent_outputs module ---------------------------------------- - -.. automodule:: GPy.kern.src.independent_outputs - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.kern module ------------------------- - -.. automodule:: GPy.kern.src.kern - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.kernel_slice_operations module -------------------------------------------- - -.. automodule:: GPy.kern.src.kernel_slice_operations - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.linear module --------------------------- - -.. automodule:: GPy.kern.src.linear - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.mlp module ------------------------ - -.. automodule:: GPy.kern.src.mlp - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.periodic module ----------------------------- - -.. automodule:: GPy.kern.src.periodic - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.poly module ------------------------- - -.. automodule:: GPy.kern.src.poly - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.prod module ------------------------- - -.. automodule:: GPy.kern.src.prod - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.rbf module ------------------------ - -.. automodule:: GPy.kern.src.rbf - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.spline module --------------------------- - -.. automodule:: GPy.kern.src.spline - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.splitKern module ------------------------------ - -.. automodule:: GPy.kern.src.splitKern - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.standard_periodic module -------------------------------------- - -.. automodule:: GPy.kern.src.standard_periodic - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.static module --------------------------- - -.. automodule:: GPy.kern.src.static - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.stationary module ------------------------------- - -.. automodule:: GPy.kern.src.stationary - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.stationary_cython module -------------------------------------- - -.. automodule:: GPy.kern.src.stationary_cython - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.symbolic module ----------------------------- - -.. automodule:: GPy.kern.src.symbolic - :members: - :undoc-members: - :show-inheritance: - -GPy.kern.src.trunclinear module -------------------------------- - -.. automodule:: GPy.kern.src.trunclinear - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: GPy.kern.src - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/GPy.likelihoods.rst b/doc/source/GPy.likelihoods.rst deleted file mode 100644 index 15d1952b..00000000 --- a/doc/source/GPy.likelihoods.rst +++ /dev/null @@ -1,94 +0,0 @@ -GPy.likelihoods package -======================= - -Submodules ----------- - -GPy.likelihoods.bernoulli module --------------------------------- - -.. automodule:: GPy.likelihoods.bernoulli - :members: - :undoc-members: - :show-inheritance: - -GPy.likelihoods.binomial module -------------------------------- - -.. automodule:: GPy.likelihoods.binomial - :members: - :undoc-members: - :show-inheritance: - -GPy.likelihoods.exponential module ----------------------------------- - -.. automodule:: GPy.likelihoods.exponential - :members: - :undoc-members: - :show-inheritance: - -GPy.likelihoods.gamma module ----------------------------- - -.. automodule:: GPy.likelihoods.gamma - :members: - :undoc-members: - :show-inheritance: - -GPy.likelihoods.gaussian module -------------------------------- - -.. automodule:: GPy.likelihoods.gaussian - :members: - :undoc-members: - :show-inheritance: - -GPy.likelihoods.likelihood module ---------------------------------- - -.. automodule:: GPy.likelihoods.likelihood - :members: - :undoc-members: - :show-inheritance: - -GPy.likelihoods.link_functions module -------------------------------------- - -.. automodule:: GPy.likelihoods.link_functions - :members: - :undoc-members: - :show-inheritance: - -GPy.likelihoods.mixed_noise module ----------------------------------- - -.. automodule:: GPy.likelihoods.mixed_noise - :members: - :undoc-members: - :show-inheritance: - -GPy.likelihoods.poisson module ------------------------------- - -.. automodule:: GPy.likelihoods.poisson - :members: - :undoc-members: - :show-inheritance: - -GPy.likelihoods.student_t module --------------------------------- - -.. automodule:: GPy.likelihoods.student_t - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: GPy.likelihoods - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/GPy.mappings.rst b/doc/source/GPy.mappings.rst deleted file mode 100644 index dad16d34..00000000 --- a/doc/source/GPy.mappings.rst +++ /dev/null @@ -1,78 +0,0 @@ -GPy.mappings package -==================== - -Submodules ----------- - -GPy.mappings.additive module ----------------------------- - -.. automodule:: GPy.mappings.additive - :members: - :undoc-members: - :show-inheritance: - -GPy.mappings.compound module ----------------------------- - -.. automodule:: GPy.mappings.compound - :members: - :undoc-members: - :show-inheritance: - -GPy.mappings.constant module ----------------------------- - -.. automodule:: GPy.mappings.constant - :members: - :undoc-members: - :show-inheritance: - -GPy.mappings.identity module ----------------------------- - -.. automodule:: GPy.mappings.identity - :members: - :undoc-members: - :show-inheritance: - -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: - -GPy.mappings.piecewise_linear module ------------------------------------- - -.. automodule:: GPy.mappings.piecewise_linear - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: GPy.mappings - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/GPy.models.rst b/doc/source/GPy.models.rst deleted file mode 100644 index e65b4fb0..00000000 --- a/doc/source/GPy.models.rst +++ /dev/null @@ -1,198 +0,0 @@ -GPy.models package -================== - -Submodules ----------- - -GPy.models.bayesian_gplvm module --------------------------------- - -.. automodule:: GPy.models.bayesian_gplvm - :members: - :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 -------------------------- - -.. automodule:: GPy.models.bcgplvm - :members: - :undoc-members: - :show-inheritance: - -GPy.models.dpgplvm module -------------------------- - -.. automodule:: GPy.models.dpgplvm - :members: - :undoc-members: - :show-inheritance: - -GPy.models.gp_classification module ------------------------------------ - -.. automodule:: GPy.models.gp_classification - :members: - :undoc-members: - :show-inheritance: - -GPy.models.gp_coregionalized_regression module ----------------------------------------------- - -.. automodule:: GPy.models.gp_coregionalized_regression - :members: - :undoc-members: - :show-inheritance: - -GPy.models.gp_heteroscedastic_regression module ------------------------------------------------ - -.. automodule:: GPy.models.gp_heteroscedastic_regression - :members: - :undoc-members: - :show-inheritance: - -GPy.models.gp_kronecker_gaussian_regression module --------------------------------------------------- - -.. automodule:: GPy.models.gp_kronecker_gaussian_regression - :members: - :undoc-members: - :show-inheritance: - -GPy.models.gp_regression module -------------------------------- - -.. automodule:: GPy.models.gp_regression - :members: - :undoc-members: - :show-inheritance: - -GPy.models.gp_var_gauss module ------------------------------- - -.. automodule:: GPy.models.gp_var_gauss - :members: - :undoc-members: - :show-inheritance: - -GPy.models.gplvm module ------------------------ - -.. 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.one_vs_all_classification module -------------------------------------------- - -.. automodule:: GPy.models.one_vs_all_classification - :members: - :undoc-members: - :show-inheritance: - -GPy.models.one_vs_all_sparse_classification module --------------------------------------------------- - -.. automodule:: GPy.models.one_vs_all_sparse_classification - :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_coregionalized_regression module ------------------------------------------------------ - -.. automodule:: GPy.models.sparse_gp_coregionalized_regression - :members: - :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_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.ss_gplvm module --------------------------- - -.. automodule:: GPy.models.ss_gplvm - :members: - :undoc-members: - :show-inheritance: - -GPy.models.ss_mrd module ------------------------- - -.. automodule:: GPy.models.ss_mrd - :members: - :undoc-members: - :show-inheritance: - -GPy.models.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/source/GPy.plotting.gpy_plot.rst b/doc/source/GPy.plotting.gpy_plot.rst deleted file mode 100644 index 8391cd3a..00000000 --- a/doc/source/GPy.plotting.gpy_plot.rst +++ /dev/null @@ -1,62 +0,0 @@ -GPy.plotting.gpy_plot package -============================= - -Submodules ----------- - -GPy.plotting.gpy_plot.data_plots module ---------------------------------------- - -.. automodule:: GPy.plotting.gpy_plot.data_plots - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.gpy_plot.gp_plots module -------------------------------------- - -.. automodule:: GPy.plotting.gpy_plot.gp_plots - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.gpy_plot.inference_plots module --------------------------------------------- - -.. automodule:: GPy.plotting.gpy_plot.inference_plots - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.gpy_plot.kernel_plots module ------------------------------------------ - -.. automodule:: GPy.plotting.gpy_plot.kernel_plots - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.gpy_plot.latent_plots module ------------------------------------------ - -.. automodule:: GPy.plotting.gpy_plot.latent_plots - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.gpy_plot.plot_util module --------------------------------------- - -.. automodule:: GPy.plotting.gpy_plot.plot_util - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: GPy.plotting.gpy_plot - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/GPy.plotting.matplot_dep.controllers.rst b/doc/source/GPy.plotting.matplot_dep.controllers.rst deleted file mode 100644 index 239f8e79..00000000 --- a/doc/source/GPy.plotting.matplot_dep.controllers.rst +++ /dev/null @@ -1,30 +0,0 @@ -GPy.plotting.matplot_dep.controllers package -============================================ - -Submodules ----------- - -GPy.plotting.matplot_dep.controllers.axis_event_controller module ------------------------------------------------------------------ - -.. automodule:: GPy.plotting.matplot_dep.controllers.axis_event_controller - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.matplot_dep.controllers.imshow_controller module -------------------------------------------------------------- - -.. automodule:: GPy.plotting.matplot_dep.controllers.imshow_controller - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: GPy.plotting.matplot_dep.controllers - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/GPy.plotting.matplot_dep.rst b/doc/source/GPy.plotting.matplot_dep.rst deleted file mode 100644 index 9521d9e6..00000000 --- a/doc/source/GPy.plotting.matplot_dep.rst +++ /dev/null @@ -1,117 +0,0 @@ -GPy.plotting.matplot_dep package -================================ - -Subpackages ------------ - -.. toctree:: - - GPy.plotting.matplot_dep.controllers - -Submodules ----------- - -GPy.plotting.matplot_dep.defaults module ----------------------------------------- - -.. automodule:: GPy.plotting.matplot_dep.defaults - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.matplot_dep.img_plots module ------------------------------------------ - -.. automodule:: GPy.plotting.matplot_dep.img_plots - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.matplot_dep.kernel_plots module --------------------------------------------- - -.. automodule:: GPy.plotting.matplot_dep.kernel_plots - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.matplot_dep.mapping_plots module ---------------------------------------------- - -.. automodule:: GPy.plotting.matplot_dep.mapping_plots - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.matplot_dep.maps module ------------------------------------- - -.. automodule:: GPy.plotting.matplot_dep.maps - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.matplot_dep.plot_definitions module ------------------------------------------------- - -.. automodule:: GPy.plotting.matplot_dep.plot_definitions - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.matplot_dep.priors_plots module --------------------------------------------- - -.. automodule:: GPy.plotting.matplot_dep.priors_plots - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.matplot_dep.ssgplvm module ---------------------------------------- - -.. automodule:: GPy.plotting.matplot_dep.ssgplvm - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.matplot_dep.svig_plots module ------------------------------------------- - -.. automodule:: GPy.plotting.matplot_dep.svig_plots - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.matplot_dep.util module ------------------------------------- - -.. automodule:: GPy.plotting.matplot_dep.util - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.matplot_dep.variational_plots module -------------------------------------------------- - -.. automodule:: GPy.plotting.matplot_dep.variational_plots - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.matplot_dep.visualize module ------------------------------------------ - -.. automodule:: GPy.plotting.matplot_dep.visualize - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: GPy.plotting.matplot_dep - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/GPy.plotting.plotly_dep.rst b/doc/source/GPy.plotting.plotly_dep.rst deleted file mode 100644 index 52642e49..00000000 --- a/doc/source/GPy.plotting.plotly_dep.rst +++ /dev/null @@ -1,30 +0,0 @@ -GPy.plotting.plotly_dep package -=============================== - -Submodules ----------- - -GPy.plotting.plotly_dep.defaults module ---------------------------------------- - -.. automodule:: GPy.plotting.plotly_dep.defaults - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.plotly_dep.plot_definitions module ------------------------------------------------ - -.. automodule:: GPy.plotting.plotly_dep.plot_definitions - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: GPy.plotting.plotly_dep - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/GPy.plotting.rst b/doc/source/GPy.plotting.rst deleted file mode 100644 index 33c39c93..00000000 --- a/doc/source/GPy.plotting.rst +++ /dev/null @@ -1,39 +0,0 @@ -GPy.plotting package -==================== - -Subpackages ------------ - -.. toctree:: - - GPy.plotting.gpy_plot - GPy.plotting.matplot_dep - GPy.plotting.plotly_dep - -Submodules ----------- - -GPy.plotting.Tango module -------------------------- - -.. automodule:: GPy.plotting.Tango - :members: - :undoc-members: - :show-inheritance: - -GPy.plotting.abstract_plotting_library module ---------------------------------------------- - -.. automodule:: GPy.plotting.abstract_plotting_library - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: GPy.plotting - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/GPy.rst b/doc/source/GPy.rst deleted file mode 100644 index 9be6dbec..00000000 --- a/doc/source/GPy.rst +++ /dev/null @@ -1,26 +0,0 @@ -GPy package -=========== - -Subpackages ------------ - -.. toctree:: - - GPy.core - GPy.examples - GPy.inference - GPy.kern - GPy.likelihoods - GPy.mappings - GPy.models - GPy.plotting - GPy.testing - GPy.util - -Module contents ---------------- - -.. automodule:: GPy - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/GPy.testing.rst b/doc/source/GPy.testing.rst deleted file mode 100644 index a10c3d18..00000000 --- a/doc/source/GPy.testing.rst +++ /dev/null @@ -1,206 +0,0 @@ -GPy.testing package -=================== - -Submodules ----------- - -GPy.testing.bgplvm_minibatch_tests module ------------------------------------------ - -.. automodule:: GPy.testing.bgplvm_minibatch_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.cacher_tests module -------------------------------- - -.. automodule:: GPy.testing.cacher_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.cython_tests module -------------------------------- - -.. automodule:: GPy.testing.cython_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.examples_tests module ---------------------------------- - -.. automodule:: GPy.testing.examples_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.fitc module ------------------------ - -.. automodule:: GPy.testing.fitc - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.gp_tests module ---------------------------- - -.. automodule:: GPy.testing.gp_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.index_operations_tests module ------------------------------------------ - -.. automodule:: GPy.testing.index_operations_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.inference_tests module ----------------------------------- - -.. automodule:: GPy.testing.inference_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.kernel_tests module -------------------------------- - -.. automodule:: GPy.testing.kernel_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.likelihood_tests module ------------------------------------ - -.. automodule:: GPy.testing.likelihood_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.linalg_test module ------------------------------- - -.. automodule:: GPy.testing.linalg_test - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.link_function_tests module --------------------------------------- - -.. automodule:: GPy.testing.link_function_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.mapping_tests module --------------------------------- - -.. automodule:: GPy.testing.mapping_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.meanfunc_tests module ---------------------------------- - -.. automodule:: GPy.testing.meanfunc_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.misc_tests module ------------------------------ - -.. automodule:: GPy.testing.misc_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.model_tests module ------------------------------- - -.. automodule:: GPy.testing.model_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.mpi_tests module ----------------------------- - -.. automodule:: GPy.testing.mpi_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.observable_tests module ------------------------------------ - -.. automodule:: GPy.testing.observable_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.parameterized_tests module --------------------------------------- - -.. automodule:: GPy.testing.parameterized_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.pickle_tests module -------------------------------- - -.. automodule:: GPy.testing.pickle_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.plotting_tests module ---------------------------------- - -.. automodule:: GPy.testing.plotting_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.prior_tests module ------------------------------- - -.. automodule:: GPy.testing.prior_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.rv_transformation_tests module ------------------------------------------- - -.. automodule:: GPy.testing.rv_transformation_tests - :members: - :undoc-members: - :show-inheritance: - -GPy.testing.svgp_tests module ------------------------------ - -.. automodule:: GPy.testing.svgp_tests - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: GPy.testing - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/GPy.util.rst b/doc/source/GPy.util.rst deleted file mode 100644 index 354a3cce..00000000 --- a/doc/source/GPy.util.rst +++ /dev/null @@ -1,238 +0,0 @@ -GPy.util package -================ - -Submodules ----------- - -GPy.util.block_matrices module ------------------------------- - -.. automodule:: GPy.util.block_matrices - :members: - :undoc-members: - :show-inheritance: - -GPy.util.caching module ------------------------ - -.. automodule:: GPy.util.caching - :members: - :undoc-members: - :show-inheritance: - -GPy.util.choleskies module --------------------------- - -.. automodule:: GPy.util.choleskies - :members: - :undoc-members: - :show-inheritance: - -GPy.util.choleskies_cython module ---------------------------------- - -.. automodule:: GPy.util.choleskies_cython - :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.debug module ---------------------- - -.. automodule:: GPy.util.debug - :members: - :undoc-members: - :show-inheritance: - -GPy.util.decorators module --------------------------- - -.. automodule:: GPy.util.decorators - :members: - :undoc-members: - :show-inheritance: - -GPy.util.diag module --------------------- - -.. automodule:: GPy.util.diag - :members: - :undoc-members: - :show-inheritance: - -GPy.util.functions module -------------------------- - -.. automodule:: GPy.util.functions - :members: - :undoc-members: - :show-inheritance: - -GPy.util.gpu_init module ------------------------- - -.. automodule:: GPy.util.gpu_init - :members: - :undoc-members: - :show-inheritance: - -GPy.util.initialization module ------------------------------- - -.. automodule:: GPy.util.initialization - :members: - :undoc-members: - :show-inheritance: - -GPy.util.linalg module ----------------------- - -.. automodule:: GPy.util.linalg - :members: - :undoc-members: - :show-inheritance: - -GPy.util.linalg_cython module ------------------------------ - -.. automodule:: GPy.util.linalg_cython - :members: - :undoc-members: - :show-inheritance: - -GPy.util.linalg_gpu module --------------------------- - -.. automodule:: GPy.util.linalg_gpu - :members: - :undoc-members: - :show-inheritance: - -GPy.util.ln_diff_erfs module ----------------------------- - -.. automodule:: GPy.util.ln_diff_erfs - :members: - :undoc-members: - :show-inheritance: - -GPy.util.misc module --------------------- - -.. 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.normalizer module --------------------------- - -.. automodule:: GPy.util.normalizer - :members: - :undoc-members: - :show-inheritance: - -GPy.util.parallel module ------------------------- - -.. automodule:: GPy.util.parallel - :members: - :undoc-members: - :show-inheritance: - -GPy.util.pca module -------------------- - -.. automodule:: GPy.util.pca - :members: - :undoc-members: - :show-inheritance: - -GPy.util.squashers module -------------------------- - -.. automodule:: GPy.util.squashers - :members: - :undoc-members: - :show-inheritance: - -GPy.util.subarray_and_sorting module ------------------------------------- - -.. automodule:: GPy.util.subarray_and_sorting - :members: - :undoc-members: - :show-inheritance: - -GPy.util.univariate_Gaussian module ------------------------------------ - -.. automodule:: GPy.util.univariate_Gaussian - :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/source/conf.py b/doc/source/conf.py index 0885c380..1f9c98b6 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -22,7 +22,7 @@ import shlex #for p in os.walk('../../GPy'): # sys.path.append(p[0]) sys.path.insert(0, os.path.abspath('../../')) -sys.path.insert(0, os.path.abspath('../../GPy/')) +#sys.path.insert(0, os.path.abspath('../../GPy/')) on_rtd = os.environ.get('READTHEDOCS', None) == 'True' @@ -82,7 +82,8 @@ MOCK_MODULES = ['scipy.linalg.blas', 'blas', 'scipy.optimize', 'scipy.optimize.l 'sympy', 'sympy.utilities.iterables', 'sympy.utilities.lambdify', 'sympy.utilities', 'sympy.utilities.codegen', 'sympy.core.cache', 'sympy.core', 'sympy.parsing', 'sympy.parsing.sympy_parser', - 'nose', 'nose.tools'] + 'nose', 'nose.tools' + ] autodoc_mock_imports = MOCK_MODULES # diff --git a/doc/source/requirements.txt b/doc/source/requirements.txt index d5f47c6b..dd3ba36f 100644 --- a/doc/source/requirements.txt +++ b/doc/source/requirements.txt @@ -1 +1 @@ -paramz +paramz \ No newline at end of file diff --git a/setup.cfg b/setup.cfg index 0d66c052..b38dbc60 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.0.3 +current_version = 1.0.5 tag = False commit = True diff --git a/setup.py b/setup.py index 6ad99e9c..17205504 100644 --- a/setup.py +++ b/setup.py @@ -57,7 +57,7 @@ def read_to_rst(fname): except ImportError: return read(fname) -#desc = read_to_rst('README.md') +desc = read('README.rst') version_dummy = {} exec(read('GPy/__version__.py'), version_dummy) @@ -143,7 +143,7 @@ setup(name = 'GPy', include_package_data = True, py_modules = ['GPy.__init__'], test_suite = 'GPy.testing', - #long_description=desc, + long_description=desc, install_requires=['numpy>=1.7', 'scipy>=0.16', 'six', 'paramz'], extras_require = {'docs':['sphinx'], 'optional':['mpi4py', @@ -176,23 +176,26 @@ home = os.getenv('HOME') or os.getenv('USERPROFILE') user_file = os.path.join(home,'.config', 'GPy', 'user.cfg') print("") -if not os.path.exists(user_file): - # Does an old config exist? - old_user_file = os.path.join(home,'.gpy_user.cfg') - if os.path.exists(old_user_file): - # Move it to new location: - print("GPy: Found old config file, moving to new location {}".format(user_file)) - if not os.path.exists(os.path.dirname(user_file)): - os.makedirs(os.path.dirname(user_file)) - os.rename(old_user_file, user_file) +try: + if not os.path.exists(user_file): + # Does an old config exist? + old_user_file = os.path.join(home,'.gpy_user.cfg') + if os.path.exists(old_user_file): + # Move it to new location: + print("GPy: Found old config file, moving to new location {}".format(user_file)) + if not os.path.exists(os.path.dirname(user_file)): + os.makedirs(os.path.dirname(user_file)) + os.rename(old_user_file, user_file) + else: + # No config file exists, save informative stub to user config folder: + print("GPy: Saving user configuration file to {}".format(user_file)) + if not os.path.exists(os.path.dirname(user_file)): + os.makedirs(os.path.dirname(user_file)) + with open(user_file, 'w') as f: + with open(local_file, 'r') as l: + tmp = l.read() + f.write(tmp) else: - # No config file exists, save informative stub to user config folder: - print("GPy: Saving user configuration file to {}".format(user_file)) - if not os.path.exists(os.path.dirname(user_file)): - os.makedirs(os.path.dirname(user_file)) - with open(user_file, 'w') as f: - with open(local_file, 'r') as l: - tmp = l.read() - f.write(tmp) -else: - print("GPy: User configuration file at location {}".format(user_file)) + print("GPy: User configuration file at location {}".format(user_file)) +except: + print("GPy: Could not write user configuration file {}".format(user_file)) \ No newline at end of file