diff --git a/GPy/core/gp.py b/GPy/core/gp.py index 3252ac08..5110e9a5 100644 --- a/GPy/core/gp.py +++ b/GPy/core/gp.py @@ -4,11 +4,11 @@ import numpy as np import sys from .. import kern -from model import Model -from parameterization import ObsAr +from .model import Model +from .parameterization import ObsAr from .. import likelihoods from ..inference.latent_function_inference import exact_gaussian_inference, expectation_propagation -from parameterization.variational import VariationalPosterior +from .parameterization.variational import VariationalPosterior import logging from GPy.util.normalizer import MeanNorm diff --git a/GPy/core/mapping.py b/GPy/core/mapping.py index 111fec6f..163db0c9 100644 --- a/GPy/core/mapping.py +++ b/GPy/core/mapping.py @@ -2,7 +2,7 @@ # Licensed under the BSD 3-clause license (see LICENSE.txt) import sys -from parameterization import Parameterized +from .parameterization import Parameterized import numpy as np class Mapping(Parameterized): @@ -74,7 +74,7 @@ class Bijective_mapping(Mapping): """Inverse mapping from output domain of the function to the inputs.""" raise NotImplementedError -from model import Model +from .model import Model class Mapping_check_model(Model): """ diff --git a/GPy/core/model.py b/GPy/core/model.py index c63a29e5..8eb34f33 100644 --- a/GPy/core/model.py +++ b/GPy/core/model.py @@ -5,7 +5,7 @@ from .. import likelihoods from ..inference import optimization from ..util.misc import opt_wrapper -from parameterization import Parameterized +from .parameterization import Parameterized import multiprocessing as mp import numpy as np from numpy.linalg.linalg import LinAlgError diff --git a/GPy/core/parameterization/index_operations.py b/GPy/core/parameterization/index_operations.py index 61c82da1..e5273e55 100644 --- a/GPy/core/parameterization/index_operations.py +++ b/GPy/core/parameterization/index_operations.py @@ -3,7 +3,7 @@ import numpy from numpy.lib.function_base import vectorize -from lists_and_dicts import IntArrayDict +from .lists_and_dicts import IntArrayDict def extract_properties_to_index(index, props): prop_index = dict() diff --git a/GPy/core/parameterization/lists_and_dicts.py b/GPy/core/parameterization/lists_and_dicts.py index 5afbb8ed..626603ec 100644 --- a/GPy/core/parameterization/lists_and_dicts.py +++ b/GPy/core/parameterization/lists_and_dicts.py @@ -75,7 +75,7 @@ class ObserverList(object): def __str__(self): from . import ObsAr, Param - from parameter_core import Parameterizable + from .parameter_core import Parameterizable ret = [] curr_p = None diff --git a/GPy/core/parameterization/observable.py b/GPy/core/parameterization/observable.py index 8a85c6ca..0836b5d6 100644 --- a/GPy/core/parameterization/observable.py +++ b/GPy/core/parameterization/observable.py @@ -12,7 +12,7 @@ class Observable(object): """ def __init__(self, *args, **kwargs): super(Observable, self).__init__() - from lists_and_dicts import ObserverList + from .lists_and_dicts import ObserverList self.observers = ObserverList() self._update_on = True diff --git a/GPy/core/parameterization/observable_array.py b/GPy/core/parameterization/observable_array.py index 271fe7b9..c6fea497 100644 --- a/GPy/core/parameterization/observable_array.py +++ b/GPy/core/parameterization/observable_array.py @@ -3,8 +3,8 @@ import numpy as np -from parameter_core import Pickleable -from observable import Observable +from .parameter_core import Pickleable +from .observable import Observable class ObsAr(np.ndarray, Pickleable, Observable): """ @@ -39,7 +39,7 @@ class ObsAr(np.ndarray, Pickleable, Observable): return self.view(np.ndarray) def copy(self): - from lists_and_dicts import ObserverList + from .lists_and_dicts import ObserverList memo = {} memo[id(self)] = self memo[id(self.observers)] = ObserverList() diff --git a/GPy/core/parameterization/param.py b/GPy/core/parameterization/param.py index 1246bc18..fbbb59ed 100644 --- a/GPy/core/parameterization/param.py +++ b/GPy/core/parameterization/param.py @@ -4,8 +4,8 @@ import itertools import numpy np = numpy -from parameter_core import Parameterizable, adjust_name_for_printing, Pickleable -from observable_array import ObsAr +from .parameter_core import Parameterizable, adjust_name_for_printing, Pickleable +from .observable_array import ObsAr ###### printing __constraints_name__ = "Constraint" @@ -156,7 +156,7 @@ class Param(Parameterizable, ObsAr): #=========================================================================== @property def is_fixed(self): - from transformations import __fixed__ + from .transformations import __fixed__ return self.constraints[__fixed__].size == self.size def _get_original(self, param): @@ -313,7 +313,7 @@ class ParamConcatenation(object): See :py:class:`GPy.core.parameter.Param` for more details on constraining. """ # self.params = params - from lists_and_dicts import ArrayList + from .lists_and_dicts import ArrayList self.params = ArrayList([]) for p in params: for p in p.flattened_parameters: diff --git a/GPy/core/parameterization/parameter_core.py b/GPy/core/parameterization/parameter_core.py index bee160b2..5baa81c8 100644 --- a/GPy/core/parameterization/parameter_core.py +++ b/GPy/core/parameterization/parameter_core.py @@ -13,11 +13,11 @@ Observable Pattern for patameterization """ -from transformations import Transformation,Logexp, NegativeLogexp, Logistic, __fixed__, FIXED, UNFIXED +from .transformations import Transformation,Logexp, NegativeLogexp, Logistic, __fixed__, FIXED, UNFIXED import numpy as np import re import logging -from updateable import Updateable +from .updateable import Updateable class HierarchyError(Exception): """ @@ -170,7 +170,7 @@ class Pickleable(object): def __setstate__(self, state): self.__dict__.update(state) - from lists_and_dicts import ObserverList + from .lists_and_dicts import ObserverList self.observers = ObserverList() self._setup_observers() self._optimizer_copy_transformed = False @@ -268,7 +268,7 @@ class Indexable(Nameable, Updateable): def __init__(self, name, default_constraint=None, *a, **kw): super(Indexable, self).__init__(name=name, *a, **kw) self._default_constraint_ = default_constraint - from index_operations import ParameterIndexOperations + from .index_operations import ParameterIndexOperations self.constraints = ParameterIndexOperations() self.priors = ParameterIndexOperations() if self._default_constraint_ is not None: @@ -310,7 +310,7 @@ class Indexable(Nameable, Updateable): that is an int array, containing the indexes for the flattened param inside this parameterized logic. """ - from param import ParamConcatenation + from .param import ParamConcatenation if isinstance(param, ParamConcatenation): return np.hstack((self._raveled_index_for(p) for p in param.params)) return param._raveled_index() + self._offset_for(param) @@ -407,7 +407,7 @@ class Indexable(Nameable, Updateable): repriorized = self.unset_priors() self._add_to_index_operations(self.priors, repriorized, prior, warning) - from domains import _REAL, _POSITIVE, _NEGATIVE + from .domains import _REAL, _POSITIVE, _NEGATIVE if prior.domain is _POSITIVE: self.constrain_positive(warning) elif prior.domain is _NEGATIVE: @@ -536,7 +536,7 @@ class Indexable(Nameable, Updateable): update the constraints and priors view, so that constraining is automized for the parent. """ - from index_operations import ParameterIndexOperationsView + from .index_operations import ParameterIndexOperationsView #if getattr(self, "_in_init_"): #import ipdb;ipdb.set_trace() #self.constraints.update(param.constraints, start) diff --git a/GPy/core/parameterization/parameterized.py b/GPy/core/parameterization/parameterized.py index 44173f58..6bdd8036 100644 --- a/GPy/core/parameterization/parameterized.py +++ b/GPy/core/parameterization/parameterized.py @@ -5,8 +5,8 @@ import numpy; np = numpy import itertools from re import compile, _pattern_type -from param import ParamConcatenation -from parameter_core import HierarchyError, Parameterizable, adjust_name_for_printing +from .param import ParamConcatenation +from .parameter_core import HierarchyError, Parameterizable, adjust_name_for_printing import logging from GPy.core.parameterization.index_operations import ParameterIndexOperationsView diff --git a/GPy/core/parameterization/priors.py b/GPy/core/parameterization/priors.py index 84b6357e..61835e28 100644 --- a/GPy/core/parameterization/priors.py +++ b/GPy/core/parameterization/priors.py @@ -5,7 +5,7 @@ import numpy as np from scipy.special import gammaln, digamma from ...util.linalg import pdinv -from domains import _REAL, _POSITIVE +from .domains import _REAL, _POSITIVE import warnings import weakref diff --git a/GPy/core/parameterization/ties_and_remappings.py b/GPy/core/parameterization/ties_and_remappings.py index a81b8d61..f0bb2d61 100644 --- a/GPy/core/parameterization/ties_and_remappings.py +++ b/GPy/core/parameterization/ties_and_remappings.py @@ -2,8 +2,8 @@ # Licensed under the BSD 3-clause license (see LICENSE.txt) import numpy as np -from parameterized import Parameterized -from param import Param +from .parameterized import Parameterized +from .param import Param class Remapping(Parameterized): def mapping(self): diff --git a/GPy/core/parameterization/transformations.py b/GPy/core/parameterization/transformations.py index d929b1d9..181c16e0 100644 --- a/GPy/core/parameterization/transformations.py +++ b/GPy/core/parameterization/transformations.py @@ -3,7 +3,7 @@ import numpy as np -from domains import _POSITIVE,_NEGATIVE, _BOUNDED +from .domains import _POSITIVE,_NEGATIVE, _BOUNDED import weakref import sys diff --git a/GPy/core/parameterization/updateable.py b/GPy/core/parameterization/updateable.py index 278ba8cd..86446fa0 100644 --- a/GPy/core/parameterization/updateable.py +++ b/GPy/core/parameterization/updateable.py @@ -3,7 +3,7 @@ Created on 11 Nov 2014 @author: maxz ''' -from observable import Observable +from .observable import Observable class Updateable(Observable): diff --git a/GPy/core/parameterization/variational.py b/GPy/core/parameterization/variational.py index 7cc5c99a..25efdc92 100644 --- a/GPy/core/parameterization/variational.py +++ b/GPy/core/parameterization/variational.py @@ -5,9 +5,9 @@ Created on 6 Nov 2013 ''' import numpy as np -from parameterized import Parameterized -from param import Param -from transformations import Logexp, Logistic,__fixed__ +from .parameterized import Parameterized +from .param import Param +from .transformations import Logexp, Logistic,__fixed__ from GPy.util.misc import param_to_array from GPy.util.caching import Cache_this diff --git a/GPy/core/sparse_gp.py b/GPy/core/sparse_gp.py index 9004c9c7..a9866f48 100644 --- a/GPy/core/sparse_gp.py +++ b/GPy/core/sparse_gp.py @@ -2,11 +2,11 @@ # Licensed under the BSD 3-clause license (see LICENSE.txt) import numpy as np -from gp import GP -from parameterization.param import Param +from .gp import GP +from .parameterization.param import Param from ..inference.latent_function_inference import var_dtc from .. import likelihoods -from parameterization.variational import VariationalPosterior, NormalPosterior +from .parameterization.variational import VariationalPosterior, NormalPosterior from ..util.linalg import mdot import logging diff --git a/GPy/core/sparse_gp_mpi.py b/GPy/core/sparse_gp_mpi.py index 15d3ad76..ac53d4ac 100644 --- a/GPy/core/sparse_gp_mpi.py +++ b/GPy/core/sparse_gp_mpi.py @@ -2,7 +2,7 @@ # Licensed under the BSD 3-clause license (see LICENSE.txt) import numpy as np -from sparse_gp import SparseGP +from .sparse_gp import SparseGP from numpy.linalg.linalg import LinAlgError from ..inference.latent_function_inference.var_dtc_parallel import update_gradients, VarDTC_minibatch diff --git a/GPy/core/svgp.py b/GPy/core/svgp.py index 603a64a5..9d74889a 100644 --- a/GPy/core/svgp.py +++ b/GPy/core/svgp.py @@ -3,8 +3,8 @@ import numpy as np from ..util import choleskies -from sparse_gp import SparseGP -from parameterization.param import Param +from .sparse_gp import SparseGP +from .parameterization.param import Param from ..inference.latent_function_inference import SVGP as svgp_inf diff --git a/GPy/likelihoods/bernoulli.py b/GPy/likelihoods/bernoulli.py index ff2ab30a..2c246042 100644 --- a/GPy/likelihoods/bernoulli.py +++ b/GPy/likelihoods/bernoulli.py @@ -3,8 +3,8 @@ import numpy as np from ..util.univariate_Gaussian import std_norm_pdf, std_norm_cdf -import link_functions -from likelihood import Likelihood +from . import link_functions +from .likelihood import Likelihood from scipy import stats class Bernoulli(Likelihood): diff --git a/GPy/likelihoods/exponential.py b/GPy/likelihoods/exponential.py index 8110c7d4..1df48412 100644 --- a/GPy/likelihoods/exponential.py +++ b/GPy/likelihoods/exponential.py @@ -5,8 +5,8 @@ import numpy as np from scipy import stats,special import scipy as sp -import link_functions -from likelihood import Likelihood +from . import link_functions +from .likelihood import Likelihood class Exponential(Likelihood): """ diff --git a/GPy/likelihoods/gamma.py b/GPy/likelihoods/gamma.py index c79e196c..c153bd1c 100644 --- a/GPy/likelihoods/gamma.py +++ b/GPy/likelihoods/gamma.py @@ -6,8 +6,8 @@ import numpy as np from scipy import stats,special import scipy as sp from ..core.parameterization import Param -import link_functions -from likelihood import Likelihood +from . import link_functions +from .likelihood import Likelihood class Gamma(Likelihood): """ diff --git a/GPy/likelihoods/gaussian.py b/GPy/likelihoods/gaussian.py index a6e5b7e0..8029eeba 100644 --- a/GPy/likelihoods/gaussian.py +++ b/GPy/likelihoods/gaussian.py @@ -13,8 +13,8 @@ James 11/12/13 import numpy as np from scipy import stats, special -import link_functions -from likelihood import Likelihood +from . import link_functions +from .likelihood import Likelihood from ..core.parameterization import Param from ..core.parameterization.transformations import Logexp from scipy import stats diff --git a/GPy/likelihoods/likelihood.py b/GPy/likelihoods/likelihood.py index 790c6ba4..33698eb2 100644 --- a/GPy/likelihoods/likelihood.py +++ b/GPy/likelihoods/likelihood.py @@ -4,7 +4,7 @@ import numpy as np from scipy import stats,special import scipy as sp -import link_functions +from . import link_functions from ..util.misc import chain_1, chain_2, chain_3 from scipy.integrate import quad import warnings diff --git a/GPy/likelihoods/mixed_noise.py b/GPy/likelihoods/mixed_noise.py index 8c56f45b..84b3001d 100644 --- a/GPy/likelihoods/mixed_noise.py +++ b/GPy/likelihoods/mixed_noise.py @@ -3,9 +3,9 @@ import numpy as np from scipy import stats, special -import link_functions -from likelihood import Likelihood -from gaussian import Gaussian +from . import link_functions +from .likelihood import Likelihood +from .gaussian import Gaussian from ..core.parameterization import Param from ..core.parameterization.transformations import Logexp from ..core.parameterization import Parameterized diff --git a/GPy/likelihoods/poisson.py b/GPy/likelihoods/poisson.py index ea9b2d10..d6c4334b 100644 --- a/GPy/likelihoods/poisson.py +++ b/GPy/likelihoods/poisson.py @@ -5,8 +5,8 @@ from __future__ import division import numpy as np from scipy import stats,special import scipy as sp -import link_functions -from likelihood import Likelihood +from . import link_functions +from .likelihood import Likelihood class Poisson(Likelihood): """ diff --git a/GPy/likelihoods/student_t.py b/GPy/likelihoods/student_t.py index 855f6b40..745ce9e8 100644 --- a/GPy/likelihoods/student_t.py +++ b/GPy/likelihoods/student_t.py @@ -4,10 +4,10 @@ import numpy as np from scipy import stats, special import scipy as sp -import link_functions +from . import link_functions from scipy import stats, integrate from scipy.special import gammaln, gamma -from likelihood import Likelihood +from .likelihood import Likelihood from ..core.parameterization import Param from ..core.parameterization.transformations import Logexp diff --git a/GPy/util/choleskies.py b/GPy/util/choleskies.py index 3f37fc3f..cc3a7f75 100644 --- a/GPy/util/choleskies.py +++ b/GPy/util/choleskies.py @@ -3,7 +3,7 @@ import numpy as np from scipy import weave -import linalg +from . import linalg def safe_root(N): diff --git a/GPy/util/datasets.py b/GPy/util/datasets.py index 254639a6..10835463 100644 --- a/GPy/util/datasets.py +++ b/GPy/util/datasets.py @@ -11,7 +11,7 @@ import datetime import json import re -from config import * +from .config import * ipython_available=True try: diff --git a/GPy/util/linalg.py b/GPy/util/linalg.py index b148f2f4..216a1050 100644 --- a/GPy/util/linalg.py +++ b/GPy/util/linalg.py @@ -13,7 +13,7 @@ from ctypes import byref, c_char, c_int, c_double # TODO import scipy import warnings import os -from config import config +from .config import config import logging _scipyversion = np.float64((scipy.__version__).split('.')[:2]) diff --git a/GPy/util/ln_diff_erfs.py b/GPy/util/ln_diff_erfs.py index bb9cfe03..582a4585 100644 --- a/GPy/util/ln_diff_erfs.py +++ b/GPy/util/ln_diff_erfs.py @@ -6,7 +6,7 @@ try: from scipy.special import erfcx, erf except ImportError: from scipy.special import erf - from erfcx import erfcx + from .erfcx import erfcx import numpy as np diff --git a/GPy/util/misc.py b/GPy/util/misc.py index bf37159d..1f746e19 100644 --- a/GPy/util/misc.py +++ b/GPy/util/misc.py @@ -2,7 +2,7 @@ # Licensed under the BSD 3-clause license (see LICENSE.txt) import numpy as np -from config import * +from .config import * def chain_1(df_dg, dg_dx): """