mirror of
https://github.com/SheffieldML/GPy.git
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Merge branch 'devel' into paramz
Conflicts: GPy/core/parameterization/parameter_core.py GPy/testing/pickle_tests.py
This commit is contained in:
mzwiessele
commit
5d605277bc
9 changed files with 58 additions and 38 deletions
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@ -39,18 +39,28 @@ def load(file_or_path):
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:param file_name: path/to/file.pickle
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"""
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# This is the pickling pain when changing _src -> src
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try:
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import cPickle as pickle
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if isinstance(file_or_path, basestring):
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with open(file_or_path, 'rb') as f:
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m = pickle.load(f)
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else:
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m = pickle.load(file_or_path)
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except:
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import pickle
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if isinstance(file_or_path, str):
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with open(file_or_path, 'rb') as f:
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m = pickle.load(f)
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else:
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m = pickle.load(file_or_path)
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try:
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import cPickle as pickle
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if isinstance(file_or_path, basestring):
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with open(file_or_path, 'rb') as f:
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m = pickle.load(f)
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else:
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m = pickle.load(file_or_path)
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except:
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import pickle
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if isinstance(file_or_path, str):
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with open(file_or_path, 'rb') as f:
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m = pickle.load(f)
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else:
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m = pickle.load(file_or_path)
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except ImportError:
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import sys
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import inspect
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sys.modules['GPy.kern._src'] = kern.src
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for name, module in inspect.getmembers(kern.src):
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if not name.startswith('_'):
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sys.modules['GPy.kern._src.{}'.format(name)] = module
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m = load(file_or_path)
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return m
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@ -13,6 +13,7 @@ def change_plotting_library(lib):
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if lib == 'matplotlib':
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import matplotlib
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from .matplot_dep.plot_definitions import MatplotlibPlots
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from .matplot_dep import visualize, mapping_plots, priors_plots, ssgplvm, svig_plots, variational_plots, img_plots
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current_lib[0] = MatplotlibPlots()
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if lib == 'plotly':
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import plotly
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@ -22,10 +23,11 @@ def change_plotting_library(lib):
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current_lib[0] = None
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#===========================================================================
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except (ImportError, NameError):
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raise
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config.set('plotting', 'library', 'none')
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import warnings
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warnings.warn(ImportWarning("{} not available, install newest version of {} for plotting".format(lib, lib)))
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from ..util.config import config
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lib = config.get('plotting', 'library')
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change_plotting_library(lib)
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@ -275,7 +275,7 @@ def get_x_y_var(model):
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and Y the outputs
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If (X, X_variance, Y) is given, this just returns.
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:returns: (X, X_variance, Y)
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"""
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# model given
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@ -285,7 +285,10 @@ def get_x_y_var(model):
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else:
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X = model.X.values
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X_variance = None
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Y = model.Y.values
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try:
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Y = model.Y.values
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except AttributeError:
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Y = model.Y
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if sparse.issparse(Y): Y = Y.todense().view(np.ndarray)
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return X, X_variance, Y
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@ -7,7 +7,6 @@ try:
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from matplotlib import pyplot as pb
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except:
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pass
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from .base_plots import x_frame1D, x_frame2D
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def plot_mapping(self, plot_limits=None, which_data='all', which_parts='all', resolution=None, levels=20, samples=0, fignum=None, ax=None, fixed_inputs=[], linecol=Tango.colorsHex['darkBlue']):
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@ -52,6 +51,7 @@ def plot_mapping(self, plot_limits=None, which_data='all', which_parts='all', re
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ax = fig.add_subplot(111)
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plotdims = self.input_dim - len(fixed_inputs)
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from ..gpy_plot.plot_util import x_frame1D, x_frame2D
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if plotdims == 1:
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@ -94,7 +94,7 @@ def plot_SpikeSlab(parameterized, fignum=None, ax=None, colors=None, side_by_sid
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a.set_xticklabels('')
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# binary prob plot
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a = fig.add_subplot(*sub2)
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a.bar(x,gamma[:,i],bottom=0.,linewidth=0,width=1.0,align='center')
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a.bar(x,gamma[:,i],bottom=0.,linewidth=1.,width=1.0,align='center')
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a.set_xlim(x.min(), x.max())
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a.set_ylim([0.,1.])
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pb.draw()
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BIN
GPy/testing/pickle_test.pickle
Normal file
BIN
GPy/testing/pickle_test.pickle
Normal file
Binary file not shown.
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@ -30,6 +30,12 @@ class ListDictTestCase(unittest.TestCase):
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np.testing.assert_array_equal(a1, a2)
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class Test(ListDictTestCase):
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def test_load_pickle(self):
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import os, GPy
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m = GPy.load(os.path.join(os.path.abspath(os.path.split(__file__)[0]), 'pickle_test.pickle'))
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self.assertTrue(m.checkgrad())
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self.assertEqual(m.log_likelihood(), -4.7351019830022087)
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def test_model(self):
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par = toy_model()
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pcopy = par.copy()
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@ -1,11 +1,7 @@
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include *.txt
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recursive-include doc *.txt
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include *.md
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recursive-include doc *.md
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include *.cfg
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recursive-include doc *.cfg
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include *.json
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recursive-include doc *.json
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recursive-include GPy *.c
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recursive-include GPy *.so
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recursive-include GPy *.pyx
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include GPy/testing/plotting_tests/baseline/*.png
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include GPy/testing/pickle_test.pickle
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31
setup.py
31
setup.py
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@ -7,21 +7,21 @@
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# Copyright (c) 2015, Max Zwiessele
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#
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# All rights reserved.
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#
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#
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# Redistribution and use in source and binary forms, with or without
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# modification, are permitted provided that the following conditions are met:
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#
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#
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# * Redistributions of source code must retain the above copyright notice, this
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# list of conditions and the following disclaimer.
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#
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#
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# * Redistributions in binary form must reproduce the above copyright notice,
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# this list of conditions and the following disclaimer in the documentation
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# and/or other materials provided with the distribution.
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#
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#
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# * Neither the name of GPy nor the names of its
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# contributors may be used to endorse or promote products derived from
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# this software without specific prior written permission.
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#
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#
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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@ -44,7 +44,7 @@ import codecs
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def read(fname):
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with codecs.open(fname, 'r', 'latin') as f:
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return f.read()
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def read_to_rst(fname):
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try:
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import pypandoc
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@ -102,32 +102,35 @@ setup(name = 'GPy',
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ext_modules = ext_mods,
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packages = ["GPy",
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"GPy.core",
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"GPy.core.parameterization",
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"GPy.core.parameterization",
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"GPy.kern",
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"GPy.kern.src",
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"GPy.kern.src.psi_comp",
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"GPy.kern.src.psi_comp",
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"GPy.models",
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"GPy.inference",
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"GPy.inference.optimization",
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"GPy.inference.mcmc",
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"GPy.inference.latent_function_inference",
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"GPy.likelihoods",
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"GPy.likelihoods",
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"GPy.mappings",
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"GPy.examples",
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"GPy.testing",
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"GPy.util",
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"GPy.util",
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"GPy.plotting",
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"GPy.plotting.gpy_plot",
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"GPy.plotting.matplot_dep",
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"GPy.plotting.matplot_dep",
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"GPy.plotting.matplot_dep.controllers",
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"GPy.plotting.plotly_dep",
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"GPy.plotting.plotly_dep",
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],
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package_dir={'GPy': 'GPy'},
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package_data = {'GPy': ['defaults.cfg', 'installation.cfg',
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'util/data_resources.json',
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'util/football_teams.json',
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'plotting/plotting_tests/baseline/*.png'
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'testing/plotting_tests/baseline/*.png'
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]},
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data_files=[('GPy/testing/plotting_tests/baseline', 'testing/plotting_tests/baseline/*.png'),
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('GPy/testing/', 'GPy/testing/pickle_test.pickle'),
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],
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include_package_data = True,
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py_modules = ['GPy.__init__'],
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test_suite = 'GPy.testing',
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@ -170,7 +173,7 @@ if not os.path.exists(user_file):
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if os.path.exists(old_user_file):
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# Move it to new location:
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print("GPy: Found old config file, moving to new location {}".format(user_file))
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os.rename(old_user_file, user_file)
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os.rename(old_user_file, user_file)
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else:
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# No config file exists, save informative stub to user config folder:
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print("GPy: Saving user configuration file to {}".format(user_file))
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