Restructure the code folders.

gpflow/core/compilable.py

@@ -0,0 +1,114 @@
+# Copyright 2017 Artem Artemev @awav
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import abc
+import enum
+import inspect
+
+
+# TODO(@awav): Introducing global variable is not best idea for managing compilation, but
+# necessary for context manager support.
+# Inspect approach works well, except that I have a concern that it can be slow when
+# nesting is too deep and it doesn't work well with context managers, because the code which
+# is run inside `with` statement doesn't have an access to the frame which caused it.
+
+class AutoBuildStatus(enum.Enum):
+    """
+    This enum class is used for safe marking current status for global and local
+    autobuild settings. It must never be used outside of the project.
+    """
+    __autobuild_enabled_global__ = True
+
+    BUILD = 1
+    IGNORE = 2
+    FOLLOW = 3
+
+
+class AutoBuild(abc.ABCMeta):
+    """
+    AutoBuild meta class is used for change behavior of all its `compilable` decendants.
+    Whenever an object defined with this metaclass is created - the build and initialization
+    methods of compilable interface are called immediately after object's __init__ function.
+    """
+    _autobuild_arg = 'autobuild'
+
+    def __new__(mcs, name, bases, namespace, **kwargs):
+        new_cls = super(AutoBuild, mcs).__new__(mcs, name, bases, namespace, **kwargs)
+        origin_init = new_cls.__init__
+        def __init__(self, *args, **kwargs):
+            autobuild = kwargs.pop(AutoBuild._autobuild_arg, True)
+            __execute_autobuild__ = AutoBuildStatus.BUILD if autobuild else AutoBuildStatus.IGNORE
+            tag = '__execute_autobuild__'
+            frame = inspect.currentframe().f_back
+            while autobuild and frame:
+                if isinstance(frame.f_locals.get(tag, None), AutoBuildStatus):
+                    __execute_autobuild__ = AutoBuildStatus.FOLLOW
+                    break
+                frame = frame.f_back
+            origin_init(self, *args, **kwargs)
+            autobuild_on = __execute_autobuild__ == AutoBuildStatus.BUILD
+            global_autobuild_on = AutoBuildStatus.__autobuild_enabled_global__
+            if autobuild_on and global_autobuild_on:
+                self.build()
+                self.initialize(force=True)
+        setattr(new_cls, '__init__', __init__)
+        return new_cls
+
+
+class Build(enum.Enum):
+    YES = 1
+    NO = 0  # pylint: disable=C0103
+    NOT_COMPATIBLE_GRAPH = None
+
+
+class ICompilable(metaclass=AutoBuild):
+    @abc.abstractproperty
+    def graph(self):
+        raise NotImplementedError()
+
+    @abc.abstractproperty
+    def feeds(self):
+        raise NotImplementedError()
+
+    @abc.abstractproperty
+    def initializables(self):
+        raise NotImplementedError()
+
+    @abc.abstractproperty
+    def initializable_feeds(self):
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def build(self):
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def initialize(self, session=None, force=False):
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def compile(self, session=None):
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def is_built(self, graph):
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def clear(self):
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def _build(self):
+        raise NotImplementedError()

gpflow/core/errors.py

@@ -0,0 +1,16 @@
+# Copyright 2017 Artem Artemev @awav
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+class GPflowError(Exception):
+    pass

setup.py

@@ -40,7 +40,6 @@
     dependencies.append('tensorflow>={0}'.format(min_tf_version))
 
 packages = find_packages('.')
-packages.remove('testing')
 
 setup(name='gpflow',
       version=verstr,
@@ -54,7 +53,7 @@
       install_requires=dependencies,
       package_data={'gpflow': ['gpflow/gpflowrc']},
       include_package_data=True,
-      test_suite='testing',
+      test_suite='tests',
       extras_require={'tensorflow with gpu': ['tensorflow-gpu>=1.0.0'],
                       'Export parameters as pandas dataframes': ['pandas>=0.18.1']},
       classifiers=['License :: OSI Approved :: Apache Software License',

testing/test_autoflow.py → tests/test_autoflow.py

@@ -1,4 +1,3 @@
-import unittest
 import tensorflow as tf
 
 import numpy as np
@@ -195,3 +194,7 @@ def test(self):
             likelihood=gpflow.likelihoods.Gaussian(), Z=Z)
         model.compile()
         model.compute_log_likelihood()
+
+
+if __name__ == '__main__':
+    tf.test.main()

testing/test_conditionals.py → tests/test_conditionals.py

@@ -1,6 +1,3 @@
-from __future__ import print_function
-import unittest
-
 import tensorflow as tf
 
 import numpy as np
@@ -103,7 +100,7 @@ def test_whiten(self):
         with self.test_context() as sess:
             Xs, X, F, k, num_data, feed_dict = self.prepare()
             k.compile(session=sess)
-            
+
             K = k.K(X) + tf.eye(num_data, dtype=settings.np_float) * 1e-6
             L = tf.cholesky(K)
             V = tf.matrix_triangular_solve(L, F, lower=True)
@@ -151,5 +148,5 @@ def test_whiten(self):
             assert_allclose(var_difference, 0, atol=4)
 
 
-if __name__ == "__main__":
-    unittest.main()
+if __name__ == '__main__':
+    tf.test.main()

testing/test_config.py → tests/test_config.py

@@ -1,7 +1,6 @@
 
 # pylint: disable=W0212
 
-import unittest
 import os
 import tensorflow as tf
 import gpflow
@@ -78,5 +77,5 @@ def testContextManager(self):
         gpflow.settings.verbosity.hmc_verb = orig
 
 
-if __name__ == "__main__":
-    unittest.main()
+if __name__ == '__main__':
+    tf.test.main()

testing/test_coregion.py → tests/test_coregion.py

@@ -1,6 +1,3 @@
-from __future__ import print_function
-import unittest
-
 import tensorflow as tf
 import numpy as np
 from numpy.testing import assert_allclose
@@ -162,4 +159,4 @@ def test_predicts(self):
 
 
 if __name__ == '__main__':
-    unittest.main()
+    tf.test.main()

testing/test_data_object.py → tests/test_data_object.py

@@ -1,8 +1,5 @@
-from __future__ import print_function
-import unittest
 import tensorflow as tf
 
-
 import numpy as np
 from numpy.testing import assert_array_equal
 
@@ -160,4 +157,4 @@ def test_vgp(self):
 
 
 if __name__ == '__main__':
-    unittest.main()
+    tf.test.main()

testing/test_ekerns.py → tests/test_ekerns.py

@@ -1,4 +1,3 @@
-import unittest
 import numpy as np
 import tensorflow as tf
 import gpflow
@@ -592,3 +591,7 @@ def test_cross_quad(self):
                          tfXcov: self.Xcov}
             a, b = session.run((tfa, tfb), feed_dict=feed_dict)
             _assert_pdeq(self, a, b)
+
+
+if __name__ == "__main__":
+    tf.test.main()

testing/test_gplvm.py → tests/test_gplvm.py

@@ -1,5 +1,4 @@
-from __future__ import print_function
-
+import tensorflow as tf
 import numpy as np
 
 import gpflow
@@ -164,4 +163,4 @@ def test_kernelsActiveDims(self):
 
 
 if __name__ == "__main__":
-    unittest.main()
+    tf.test.main()

testing/test_hmc.py → tests/test_hmc.py

@@ -1,13 +1,14 @@
-import gpflow
-import unittest
 import tensorflow as tf
 
+from nose.plugins.attrib import attr
+
 import numpy as np
-from numpy.testing import assert_almost_equal, assert_allclose
+from numpy.testing import assert_almost_equal
 
-from nose.plugins.attrib import attr
+import gpflow
 from gpflow.test_util import GPflowTestCase
 
+
 @attr(speed='slow')
 class SampleGaussianTest(GPflowTestCase):
     class Gauss(gpflow.models.Model):
@@ -174,5 +175,5 @@ def check_last_variables_state(self, m, samples):
             assert_almost_equal(last[col], params[col].read_value())
 
 
-if __name__ == "__main__":
-    unittest.main()
+if __name__ == '__main__':
+    tf.test.main()

testing/test_kerns.py → tests/test_kerns.py

@@ -1,6 +1,3 @@
-from __future__ import absolute_import, print_function
-
-import unittest
 import tensorflow as tf
 
 import numpy as np
@@ -568,4 +565,4 @@ def test_MLP(self):
 
 
 if __name__ == "__main__":
-    unittest.main()
+    tf.test.main()

testing/test_likelihoods.py → tests/test_likelihoods.py

@@ -1,4 +1,3 @@
-import unittest
 import six
 import tensorflow as tf
 
@@ -393,4 +392,4 @@ def test_likelihood_checks(self):
 
 
 if __name__ == "__main__":
-    unittest.main()
+    tf.test.main()

testing/test_mean_functions.py → tests/test_mean_functions.py

@@ -1,6 +1,5 @@
 import itertools
 import tensorflow as tf
-import unittest
 
 import numpy as np
 from numpy.testing import assert_allclose
@@ -381,4 +380,4 @@ def test(self):
 
 
 if __name__ == "__main__":
-    unittest.main()
+    tf.test.main()

testing/test_method_equivalence.py → tests/test_method_equivalence.py

@@ -12,7 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.from __future__ import print_function
 
-import unittest
 import tensorflow as tf
 
 from nose.plugins.attrib import attr
@@ -258,4 +257,4 @@ def test_few_inducing_points(self):
 
 
 if __name__ == '__main__':
-    unittest.main()
+    tf.test.main()

testing/test_methods.py → tests/test_methods.py

@@ -12,7 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.from __future__ import print_function
 
-import unittest
 import tensorflow as tf
 
 import numpy as np
@@ -304,4 +303,4 @@ def test_likelihoods_and_gradients(self):
 
 
 if __name__ == "__main__":
-    unittest.main()
+    tf.test.main()

testing/test_model.py → tests/test_model.py

@@ -12,9 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.from __future__ import print_function
 
-from __future__ import print_function
-
-import unittest
 import tensorflow as tf
 
 import numpy as np
@@ -276,4 +273,4 @@ def test_name(self):
 
 
 if __name__ == "__main__":
-    unittest.main()
+    tf.test.main()

testing/test_notebooks.py → tests/test_notebooks.py

@@ -1,7 +1,4 @@
-from __future__ import print_function
-
 import traceback
-import unittest
 import sys
 import time
 import os

testing/test_param.py → tests/test_param.py

@@ -14,8 +14,6 @@
 
 # pylint: disable=E1123
 
-import unittest
-
 import tensorflow as tf
 import numpy as np
 
@@ -241,7 +239,7 @@ def test_add_parameter_to_empty_parameterized(self):
                 self.m.b = gpflow.Param(20)
 
 
-class ParameterizedCompileTests(GPflowTestCase):
+class TestParameterizedCompile(GPflowTestCase):
     def setUp(self):
         self.test_graph = tf.Graph()
         with self.test_context() as session:
@@ -684,3 +682,6 @@ def _check_trainable_flag(m, assert_true, assert_false):
         if param.trainable:
             assert_bool = assert_true
         assert_bool(gpflow.misc.is_tensor_trainable(param.parameter_tensor))
+
+if __name__ == '__main__':
+    tf.test.main()