diff --git a/GPy/kern/__init__.py b/GPy/kern/__init__.py index dd0cfa25..f8f7d016 100644 --- a/GPy/kern/__init__.py +++ b/GPy/kern/__init__.py @@ -1,31 +1,31 @@ """ Kernel module the kernels to sit in. -.. automodule:: GPy.kern.src +.. automodule:: .src :members: :private-members: """ -from . import _src as src -from ._src.kern import Kern -from ._src.rbf import RBF -from ._src.linear import Linear, LinearFull -from ._src.static import Bias, White, Fixed -from ._src.brownian import Brownian -from ._src.stationary import Exponential, OU, Matern32, Matern52, ExpQuad, RatQuad, Cosine -from ._src.mlp import MLP -from ._src.periodic import PeriodicExponential, PeriodicMatern32, PeriodicMatern52 -from ._src.standard_periodic import StdPeriodic -from ._src.independent_outputs import IndependentOutputs, Hierarchical -from ._src.coregionalize import Coregionalize -from ._src.ODE_UY import ODE_UY -from ._src.ODE_UYC import ODE_UYC -from ._src.ODE_st import ODE_st -from ._src.ODE_t import ODE_t -from ._src.poly import Poly -from ._src.eq_ode2 import EQ_ODE2 -from ._src.trunclinear import TruncLinear,TruncLinear_inf -from ._src.splitKern import SplitKern,DEtime -from ._src.splitKern import DEtime as DiffGenomeKern -from ._src.spline import Spline -from ._src.eq_ode2 import EQ_ODE2 -from ._src.basis_funcs import LinearSlopeBasisFuncKernel, BasisFuncKernel, ChangePointBasisFuncKernel, DomainKernel \ No newline at end of file +from .src.kern import Kern +from .src.add import Add +from .src.prod import Prod +from .src.rbf import RBF +from .src.linear import Linear, LinearFull +from .src.static import Bias, White, Fixed +from .src.brownian import Brownian +from .src.stationary import Exponential, OU, Matern32, Matern52, ExpQuad, RatQuad, Cosine +from .src.mlp import MLP +from .src.periodic import PeriodicExponential, PeriodicMatern32, PeriodicMatern52 +from .src.standard_periodic import StdPeriodic +from .src.independent_outputs import IndependentOutputs, Hierarchical +from .src.coregionalize import Coregionalize +from .src.ODE_UY import ODE_UY +from .src.ODE_UYC import ODE_UYC +from .src.ODE_st import ODE_st +from .src.ODE_t import ODE_t +from .src.poly import Poly +from .src.eq_ode2 import EQ_ODE2 +from .src.trunclinear import TruncLinear,TruncLinear_inf +from .src.splitKern import SplitKern,DEtime +from .src.splitKern import DEtime as DiffGenomeKern +from .src.spline import Spline +from .src.basis_funcs import LinearSlopeBasisFuncKernel, BasisFuncKernel, ChangePointBasisFuncKernel, DomainKernel \ No newline at end of file diff --git a/GPy/kern/_src/__init__.py b/GPy/kern/_src/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/GPy/kern/_src/ODE_UY.py b/GPy/kern/src/ODE_UY.py similarity index 100% rename from GPy/kern/_src/ODE_UY.py rename to GPy/kern/src/ODE_UY.py index 9c9b47be..ae9c4574 100644 --- a/GPy/kern/_src/ODE_UY.py +++ b/GPy/kern/src/ODE_UY.py @@ -2,10 +2,10 @@ # Licensed under the BSD 3-clause license (see LICENSE.txt) from .kern import Kern +from .independent_outputs import index_to_slices from ...core.parameterization import Param from ...core.parameterization.transformations import Logexp import numpy as np -from .independent_outputs import index_to_slices class ODE_UY(Kern): def __init__(self, input_dim, variance_U=3., variance_Y=1., lengthscale_U=1., lengthscale_Y=1., active_dims=None, name='ode_uy'): diff --git a/GPy/kern/_src/ODE_UYC.py b/GPy/kern/src/ODE_UYC.py similarity index 100% rename from GPy/kern/_src/ODE_UYC.py rename to GPy/kern/src/ODE_UYC.py diff --git a/GPy/kern/_src/ODE_st.py b/GPy/kern/src/ODE_st.py similarity index 100% rename from GPy/kern/_src/ODE_st.py rename to GPy/kern/src/ODE_st.py diff --git a/GPy/kern/_src/ODE_t.py b/GPy/kern/src/ODE_t.py similarity index 100% rename from GPy/kern/_src/ODE_t.py rename to GPy/kern/src/ODE_t.py diff --git a/GPy/kern/src/__init__.py b/GPy/kern/src/__init__.py new file mode 100644 index 00000000..d90842ca --- /dev/null +++ b/GPy/kern/src/__init__.py @@ -0,0 +1 @@ +from . import psi_comp \ No newline at end of file diff --git a/GPy/kern/_src/add.py b/GPy/kern/src/add.py similarity index 100% rename from GPy/kern/_src/add.py rename to GPy/kern/src/add.py diff --git a/GPy/kern/_src/basis_funcs.py b/GPy/kern/src/basis_funcs.py similarity index 100% rename from GPy/kern/_src/basis_funcs.py rename to GPy/kern/src/basis_funcs.py index dc21a687..3d644af2 100644 --- a/GPy/kern/_src/basis_funcs.py +++ b/GPy/kern/src/basis_funcs.py @@ -1,9 +1,9 @@ # #Copyright (c) 2012, Max Zwiessele (see AUTHORS.txt). # Licensed under the BSD 3-clause license (see LICENSE.txt) +import numpy as np from .kern import Kern from ...core.parameterization.param import Param from ...core.parameterization.transformations import Logexp -import numpy as np from ...util.caching import Cache_this from ...util.linalg import tdot, mdot diff --git a/GPy/kern/_src/brownian.py b/GPy/kern/src/brownian.py similarity index 100% rename from GPy/kern/_src/brownian.py rename to GPy/kern/src/brownian.py diff --git a/GPy/kern/_src/coregionalize.py b/GPy/kern/src/coregionalize.py similarity index 100% rename from GPy/kern/_src/coregionalize.py rename to GPy/kern/src/coregionalize.py diff --git a/GPy/kern/_src/coregionalize_cython.c b/GPy/kern/src/coregionalize_cython.c similarity index 100% rename from GPy/kern/_src/coregionalize_cython.c rename to GPy/kern/src/coregionalize_cython.c diff --git a/GPy/kern/_src/coregionalize_cython.pyx b/GPy/kern/src/coregionalize_cython.pyx similarity index 100% rename from GPy/kern/_src/coregionalize_cython.pyx rename to GPy/kern/src/coregionalize_cython.pyx diff --git a/GPy/kern/_src/eq_ode2.py b/GPy/kern/src/eq_ode2.py similarity index 100% rename from GPy/kern/_src/eq_ode2.py rename to GPy/kern/src/eq_ode2.py diff --git a/GPy/kern/_src/independent_outputs.py b/GPy/kern/src/independent_outputs.py similarity index 99% rename from GPy/kern/_src/independent_outputs.py rename to GPy/kern/src/independent_outputs.py index e9c575bf..5fd22b15 100644 --- a/GPy/kern/_src/independent_outputs.py +++ b/GPy/kern/src/independent_outputs.py @@ -2,7 +2,7 @@ # Licensed under the BSD 3-clause license (see LICENSE.txt) -from .kern import Kern, CombinationKernel +from .kern import CombinationKernel import numpy as np import itertools diff --git a/GPy/kern/_src/kern.py b/GPy/kern/src/kern.py similarity index 97% rename from GPy/kern/_src/kern.py rename to GPy/kern/src/kern.py index 8bc053a4..19e98b89 100644 --- a/GPy/kern/_src/kern.py +++ b/GPy/kern/src/kern.py @@ -3,9 +3,9 @@ import sys import numpy as np from ...core.parameterization.parameterized import Parameterized -from .kernel_slice_operations import KernCallsViaSlicerMeta +from ...core.parameterization.observable_array import ObsAr from ...util.caching import Cache_this -from GPy.core.parameterization.observable_array import ObsAr +from .kernel_slice_operations import KernCallsViaSlicerMeta from functools import reduce import six @@ -198,15 +198,6 @@ class Kern(Parameterized): from ...plotting.matplot_dep import kernel_plots kernel_plots.plot(self, x, fignum, ax, title, plot_limits, resolution, **mpl_kwargs) - def plot_ARD(self, *args, **kw): - """ - See :class:`~GPy.plotting.matplot_dep.kernel_plots` - """ - import sys - assert "matplotlib" in sys.modules, "matplotlib package has not been imported." - from ...plotting.matplot_dep import kernel_plots - return kernel_plots.plot_ARD(self,*args,**kw) - def input_sensitivity(self, summarize=True): """ Returns the sensitivity for each dimension of this kernel. diff --git a/GPy/kern/_src/kernel_slice_operations.py b/GPy/kern/src/kernel_slice_operations.py similarity index 100% rename from GPy/kern/_src/kernel_slice_operations.py rename to GPy/kern/src/kernel_slice_operations.py diff --git a/GPy/kern/_src/linear.py b/GPy/kern/src/linear.py similarity index 99% rename from GPy/kern/_src/linear.py rename to GPy/kern/src/linear.py index b743fdf0..25f6299d 100644 --- a/GPy/kern/_src/linear.py +++ b/GPy/kern/src/linear.py @@ -8,7 +8,6 @@ from ...util.linalg import tdot from ...core.parameterization import Param from ...core.parameterization.transformations import Logexp from ...util.caching import Cache_this -from ...util.config import * from .psi_comp import PSICOMP_Linear class Linear(Kern): diff --git a/GPy/kern/_src/mlp.py b/GPy/kern/src/mlp.py similarity index 99% rename from GPy/kern/_src/mlp.py rename to GPy/kern/src/mlp.py index 40a8d2d7..8f9a276c 100644 --- a/GPy/kern/_src/mlp.py +++ b/GPy/kern/src/mlp.py @@ -5,7 +5,6 @@ from .kern import Kern from ...core.parameterization import Param from ...core.parameterization.transformations import Logexp import numpy as np -from ...util.linalg import tdot from ...util.caching import Cache_this four_over_tau = 2./np.pi diff --git a/GPy/kern/_src/periodic.py b/GPy/kern/src/periodic.py similarity index 99% rename from GPy/kern/_src/periodic.py rename to GPy/kern/src/periodic.py index 014909ef..4c4d2234 100644 --- a/GPy/kern/_src/periodic.py +++ b/GPy/kern/src/periodic.py @@ -8,7 +8,6 @@ from ...util.linalg import mdot from ...util.decorators import silence_errors from ...core.parameterization.param import Param from ...core.parameterization.transformations import Logexp -from functools import reduce class Periodic(Kern): def __init__(self, input_dim, variance, lengthscale, period, n_freq, lower, upper, active_dims, name): diff --git a/GPy/kern/_src/poly.py b/GPy/kern/src/poly.py similarity index 100% rename from GPy/kern/_src/poly.py rename to GPy/kern/src/poly.py diff --git a/GPy/kern/_src/prod.py b/GPy/kern/src/prod.py similarity index 100% rename from GPy/kern/_src/prod.py rename to GPy/kern/src/prod.py diff --git a/GPy/kern/_src/psi_comp/__init__.py b/GPy/kern/src/psi_comp/__init__.py similarity index 93% rename from GPy/kern/_src/psi_comp/__init__.py rename to GPy/kern/src/psi_comp/__init__.py index 5cee363d..55780473 100644 --- a/GPy/kern/_src/psi_comp/__init__.py +++ b/GPy/kern/src/psi_comp/__init__.py @@ -2,13 +2,9 @@ # Licensed under the BSD 3-clause license (see LICENSE.txt) from ....core.parameterization.parameter_core import Pickleable -from GPy.util.caching import Cache_this +from ....util.caching import Cache_this from ....core.parameterization import variational -from . import rbf_psi_comp -from . import ssrbf_psi_comp -from . import sslinear_psi_comp -from . import linear_psi_comp - +#from linear_psi_comp import LINEAr class PSICOMP(Pickleable): @@ -22,6 +18,7 @@ class PSICOMP(Pickleable): pass from .gaussherm import PSICOMP_GH +from . import rbf_psi_comp, linear_psi_comp, ssrbf_psi_comp, sslinear_psi_comp class PSICOMP_RBF(PSICOMP): @Cache_this(limit=10, ignore_args=(0,)) @@ -67,3 +64,5 @@ class PSICOMP_Linear(PSICOMP): raise ValueError("unknown distriubtion received for psi-statistics") +from . import ssrbf_psi_gpucomp +from rbf_psi_gpucomp import PSICOMP_RBF_GPU diff --git a/GPy/kern/_src/psi_comp/gaussherm.py b/GPy/kern/src/psi_comp/gaussherm.py similarity index 98% rename from GPy/kern/_src/psi_comp/gaussherm.py rename to GPy/kern/src/psi_comp/gaussherm.py index be4856b4..35eab724 100644 --- a/GPy/kern/_src/psi_comp/gaussherm.py +++ b/GPy/kern/src/psi_comp/gaussherm.py @@ -8,10 +8,12 @@ An approximated psi-statistics implementation based on Gauss-Hermite Quadrature import numpy as np from ....core.parameterization import Param -from GPy.util.caching import Cache_this +from ....util.caching import Cache_this from ....util.linalg import tdot from . import PSICOMP + + class PSICOMP_GH(PSICOMP): def __init__(self, degree=5, cache_K=True): diff --git a/GPy/kern/_src/psi_comp/linear_psi_comp.py b/GPy/kern/src/psi_comp/linear_psi_comp.py similarity index 100% rename from GPy/kern/_src/psi_comp/linear_psi_comp.py rename to GPy/kern/src/psi_comp/linear_psi_comp.py diff --git a/GPy/kern/_src/psi_comp/rbf_psi_comp.py b/GPy/kern/src/psi_comp/rbf_psi_comp.py similarity index 100% rename from GPy/kern/_src/psi_comp/rbf_psi_comp.py rename to GPy/kern/src/psi_comp/rbf_psi_comp.py diff --git a/GPy/kern/_src/psi_comp/rbf_psi_gpucomp.py b/GPy/kern/src/psi_comp/rbf_psi_gpucomp.py similarity index 99% rename from GPy/kern/_src/psi_comp/rbf_psi_gpucomp.py rename to GPy/kern/src/psi_comp/rbf_psi_gpucomp.py index e2a5c7d1..50945db6 100644 --- a/GPy/kern/_src/psi_comp/rbf_psi_gpucomp.py +++ b/GPy/kern/src/psi_comp/rbf_psi_gpucomp.py @@ -235,7 +235,6 @@ gpu_code = """ class PSICOMP_RBF_GPU(PSICOMP_RBF): def __init__(self, threadnum=256, blocknum=30, GPU_direct=False): - from . import PSICOMP_RBF self.fall_back = PSICOMP_RBF() from pycuda.compiler import SourceModule diff --git a/GPy/kern/_src/psi_comp/sslinear_psi_comp.py b/GPy/kern/src/psi_comp/sslinear_psi_comp.py similarity index 100% rename from GPy/kern/_src/psi_comp/sslinear_psi_comp.py rename to GPy/kern/src/psi_comp/sslinear_psi_comp.py diff --git a/GPy/kern/_src/psi_comp/ssrbf_psi_comp.py b/GPy/kern/src/psi_comp/ssrbf_psi_comp.py similarity index 100% rename from GPy/kern/_src/psi_comp/ssrbf_psi_comp.py rename to GPy/kern/src/psi_comp/ssrbf_psi_comp.py diff --git a/GPy/kern/_src/psi_comp/ssrbf_psi_gpucomp.py b/GPy/kern/src/psi_comp/ssrbf_psi_gpucomp.py similarity index 100% rename from GPy/kern/_src/psi_comp/ssrbf_psi_gpucomp.py rename to GPy/kern/src/psi_comp/ssrbf_psi_gpucomp.py diff --git a/GPy/kern/_src/rbf.py b/GPy/kern/src/rbf.py similarity index 95% rename from GPy/kern/_src/rbf.py rename to GPy/kern/src/rbf.py index f4fb2ad5..3607bea9 100644 --- a/GPy/kern/_src/rbf.py +++ b/GPy/kern/src/rbf.py @@ -4,11 +4,9 @@ import numpy as np from .stationary import Stationary -from .psi_comp import PSICOMP_RBF -from .psi_comp.rbf_psi_gpucomp import PSICOMP_RBF_GPU -from ...util.config import * +from .psi_comp import PSICOMP_RBF, PSICOMP_RBF_GPU from ...core import Param -from GPy.core.parameterization.transformations import Logexp +from ...core.parameterization.transformations import Logexp class RBF(Stationary): """ diff --git a/GPy/kern/_src/spline.py b/GPy/kern/src/spline.py similarity index 99% rename from GPy/kern/_src/spline.py rename to GPy/kern/src/spline.py index 233cf7e8..c1b28764 100644 --- a/GPy/kern/_src/spline.py +++ b/GPy/kern/src/spline.py @@ -5,6 +5,7 @@ import numpy as np from .kern import Kern from ...core.parameterization import Param from ...core.parameterization.transformations import Logexp + class Spline(Kern): """ Linear spline kernel. You need to specify 2 parameters: the variance and c. diff --git a/GPy/kern/_src/splitKern.py b/GPy/kern/src/splitKern.py similarity index 98% rename from GPy/kern/_src/splitKern.py rename to GPy/kern/src/splitKern.py index c131dcd8..324178d4 100644 --- a/GPy/kern/_src/splitKern.py +++ b/GPy/kern/src/splitKern.py @@ -3,7 +3,7 @@ A new kernel """ import numpy as np -from .kern import Kern,CombinationKernel +from .kern import Kern, CombinationKernel from .independent_outputs import index_to_slices import itertools @@ -13,7 +13,7 @@ class DEtime(Kern): self.idx_p = idx_p self.index_dim=index_dim self.kern = SplitKern(kernel,Xp, index_dim=index_dim) - super(DiffGenomeKern, self).__init__(input_dim=kernel.input_dim+1, active_dims=None, name=name) + super(DEtime, self).__init__(input_dim=kernel.input_dim+1, active_dims=None, name=name) self.add_parameter(self.kern) def K(self, X, X2=None): diff --git a/GPy/kern/_src/standard_periodic.py b/GPy/kern/src/standard_periodic.py similarity index 100% rename from GPy/kern/_src/standard_periodic.py rename to GPy/kern/src/standard_periodic.py diff --git a/GPy/kern/_src/static.py b/GPy/kern/src/static.py similarity index 100% rename from GPy/kern/_src/static.py rename to GPy/kern/src/static.py diff --git a/GPy/kern/_src/stationary.py b/GPy/kern/src/stationary.py similarity index 100% rename from GPy/kern/_src/stationary.py rename to GPy/kern/src/stationary.py diff --git a/GPy/kern/_src/stationary_cython.c b/GPy/kern/src/stationary_cython.c similarity index 100% rename from GPy/kern/_src/stationary_cython.c rename to GPy/kern/src/stationary_cython.c diff --git a/GPy/kern/_src/stationary_cython.pyx b/GPy/kern/src/stationary_cython.pyx similarity index 100% rename from GPy/kern/_src/stationary_cython.pyx rename to GPy/kern/src/stationary_cython.pyx diff --git a/GPy/kern/_src/stationary_utils.c b/GPy/kern/src/stationary_utils.c similarity index 100% rename from GPy/kern/_src/stationary_utils.c rename to GPy/kern/src/stationary_utils.c diff --git a/GPy/kern/_src/stationary_utils.h b/GPy/kern/src/stationary_utils.h similarity index 100% rename from GPy/kern/_src/stationary_utils.h rename to GPy/kern/src/stationary_utils.h diff --git a/GPy/kern/_src/symbolic.py b/GPy/kern/src/symbolic.py similarity index 98% rename from GPy/kern/_src/symbolic.py rename to GPy/kern/src/symbolic.py index c339893a..0d855bbb 100644 --- a/GPy/kern/_src/symbolic.py +++ b/GPy/kern/src/symbolic.py @@ -1,7 +1,7 @@ # Check Matthew Rocklin's blog post. import sympy as sym import numpy as np -from .kern import Kern +from GPy.kern.src import Kern from ...core.symbolic import Symbolic_core diff --git a/GPy/kern/_src/sympy_helpers.cpp b/GPy/kern/src/sympy_helpers.cpp similarity index 100% rename from GPy/kern/_src/sympy_helpers.cpp rename to GPy/kern/src/sympy_helpers.cpp diff --git a/GPy/kern/_src/sympy_helpers.h b/GPy/kern/src/sympy_helpers.h similarity index 100% rename from GPy/kern/_src/sympy_helpers.h rename to GPy/kern/src/sympy_helpers.h diff --git a/GPy/kern/_src/todo/ODE_1.py b/GPy/kern/src/todo/ODE_1.py similarity index 100% rename from GPy/kern/_src/todo/ODE_1.py rename to GPy/kern/src/todo/ODE_1.py diff --git a/GPy/kern/_src/todo/eq_ode1.py b/GPy/kern/src/todo/eq_ode1.py similarity index 100% rename from GPy/kern/_src/todo/eq_ode1.py rename to GPy/kern/src/todo/eq_ode1.py diff --git a/GPy/kern/_src/todo/finite_dimensional.py b/GPy/kern/src/todo/finite_dimensional.py similarity index 100% rename from GPy/kern/_src/todo/finite_dimensional.py rename to GPy/kern/src/todo/finite_dimensional.py diff --git a/GPy/kern/_src/todo/fixed.py b/GPy/kern/src/todo/fixed.py similarity index 100% rename from GPy/kern/_src/todo/fixed.py rename to GPy/kern/src/todo/fixed.py diff --git a/GPy/kern/_src/todo/gibbs.py b/GPy/kern/src/todo/gibbs.py similarity index 100% rename from GPy/kern/_src/todo/gibbs.py rename to GPy/kern/src/todo/gibbs.py diff --git a/GPy/kern/_src/todo/hetero.py b/GPy/kern/src/todo/hetero.py similarity index 100% rename from GPy/kern/_src/todo/hetero.py rename to GPy/kern/src/todo/hetero.py diff --git a/GPy/kern/_src/todo/odekern1.c b/GPy/kern/src/todo/odekern1.c similarity index 100% rename from GPy/kern/_src/todo/odekern1.c rename to GPy/kern/src/todo/odekern1.c diff --git a/GPy/kern/_src/todo/poly.py b/GPy/kern/src/todo/poly.py similarity index 100% rename from GPy/kern/_src/todo/poly.py rename to GPy/kern/src/todo/poly.py diff --git a/GPy/kern/_src/todo/rbf_inv.py b/GPy/kern/src/todo/rbf_inv.py similarity index 100% rename from GPy/kern/_src/todo/rbf_inv.py rename to GPy/kern/src/todo/rbf_inv.py diff --git a/GPy/kern/_src/todo/spline.py b/GPy/kern/src/todo/spline.py similarity index 100% rename from GPy/kern/_src/todo/spline.py rename to GPy/kern/src/todo/spline.py diff --git a/GPy/kern/_src/todo/symmetric.py b/GPy/kern/src/todo/symmetric.py similarity index 100% rename from GPy/kern/_src/todo/symmetric.py rename to GPy/kern/src/todo/symmetric.py diff --git a/GPy/kern/_src/trunclinear.py b/GPy/kern/src/trunclinear.py similarity index 99% rename from GPy/kern/_src/trunclinear.py rename to GPy/kern/src/trunclinear.py index af90c4a5..81d7376f 100644 --- a/GPy/kern/_src/trunclinear.py +++ b/GPy/kern/src/trunclinear.py @@ -7,7 +7,6 @@ from .kern import Kern from ...core.parameterization import Param from ...core.parameterization.transformations import Logexp from ...util.caching import Cache_this -from ...util.config import * class TruncLinear(Kern): """ diff --git a/GPy/models/ss_gplvm.py b/GPy/models/ss_gplvm.py index e0c3a4f2..4ccf58ac 100644 --- a/GPy/models/ss_gplvm.py +++ b/GPy/models/ss_gplvm.py @@ -9,7 +9,7 @@ from ..core.parameterization import Param from ..likelihoods import Gaussian from ..core.parameterization.variational import SpikeAndSlabPrior, SpikeAndSlabPosterior,VariationalPrior from ..inference.latent_function_inference.var_dtc_parallel import update_gradients, VarDTC_minibatch -from ..kern._src.psi_comp.ssrbf_psi_gpucomp import PSICOMP_SSRBF_GPU +from ..kern.src.psi_comp.ssrbf_psi_gpucomp import PSICOMP_SSRBF_GPU class IBPPosterior(SpikeAndSlabPosterior): ''' diff --git a/GPy/testing/pickle_tests.py b/GPy/testing/pickle_tests.py index ec9ea3c3..bf00055f 100644 --- a/GPy/testing/pickle_tests.py +++ b/GPy/testing/pickle_tests.py @@ -13,9 +13,9 @@ import tempfile from GPy.core.parameterization.param import Param from GPy.core.parameterization.observable_array import ObsAr from GPy.core.parameterization.priors import Gaussian -from GPy.kern._src.rbf import RBF -from GPy.kern._src.linear import Linear -from GPy.kern._src.static import Bias, White +from GPy.kern.src.rbf import RBF +from GPy.kern.src.linear import Linear +from GPy.kern.src.static import Bias, White from GPy.examples.dimensionality_reduction import mrd_simulation from GPy.core.parameterization.variational import NormalPosterior from GPy.models.gp_regression import GPRegression diff --git a/setup.py b/setup.py index 74ac7ecb..6715aa20 100644 --- a/setup.py +++ b/setup.py @@ -76,9 +76,9 @@ else: compile_flags = [ '-fopenmp', '-O3', ] link_args = ['-lgomp'] -ext_mods = [Extension(name='GPy.kern._src.stationary_cython', - sources=['GPy/kern/_src/stationary_cython.c', - 'GPy/kern/_src/stationary_utils.c'], +ext_mods = [Extension(name='GPy.kern.src.stationary_cython', + sources=['GPy/kern/src/stationary_cython.c', + 'GPy/kern/src/stationary_utils.c'], include_dirs=[np.get_include(),'.'], extra_compile_args=compile_flags, extra_link_args = link_args), @@ -91,8 +91,8 @@ ext_mods = [Extension(name='GPy.kern._src.stationary_cython', sources=['GPy/util/linalg_cython.c'], include_dirs=[np.get_include(),'.'], extra_compile_args=compile_flags), - Extension(name='GPy.kern._src.coregionalize_cython', - sources=['GPy/kern/_src/coregionalize_cython.c'], + Extension(name='GPy.kern.src.coregionalize_cython', + sources=['GPy/kern/src/coregionalize_cython.c'], include_dirs=[np.get_include(),'.'], extra_compile_args=compile_flags)] @@ -109,8 +109,8 @@ setup(name = 'GPy', "GPy.core", "GPy.core.parameterization", "GPy.kern", - "GPy.kern._src", - "GPy.kern._src.psi_comp", + "GPy.kern.src", + "GPy.kern.src.psi_comp", "GPy.models", "GPy.inference", "GPy.inference.optimization",