From 0e2e0297c8d85045e25a1bfdf3635805225a90d8 Mon Sep 17 00:00:00 2001
From: Bradley Ellert <bellert@dwavesys.com>
Date: Thu, 1 Mar 2018 16:54:02 -0800
Subject: [PATCH 1/7] Finish minimize_energy --> MinimizeEnergy

Change in __all__
---
 dwave_embedding_utilities.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dwave_embedding_utilities.py b/dwave_embedding_utilities.py
index 55e53cf..0014ab4 100644
--- a/dwave_embedding_utilities.py
+++ b/dwave_embedding_utilities.py
@@ -99,7 +99,7 @@ def itervalues(d):
 __all__ = ['target_to_source', 'chain_break_frequency', 'embed_ising',
            'edgelist_to_adjacency',
            'unembed_samples',
-           'discard', 'majority_vote', 'weighted_random', 'minimize_energy',
+           'discard', 'majority_vote', 'weighted_random', 'MinimizeEnergy',
            'chain_to_quadratic']
 
 __version__ = '0.3.0'

From afdeb7927d92f015e8b60348e885937aa781aa7d Mon Sep 17 00:00:00 2001
From: Bradley Ellert <bellert@dwavesys.com>
Date: Fri, 2 Mar 2018 10:46:14 -0800
Subject: [PATCH 2/7] Move to dwave.embedding.utilities

---
 .coveragerc                                         |  2 +-
 docs/conf.py                                        | 10 +++++-----
 dwave/__init__.py                                   |  2 ++
 dwave/embedding/__init__.py                         |  2 ++
 dwave/embedding/utilities/__init__.py               |  8 ++++++++
 dwave/embedding/utilities/package_info.py           |  4 ++++
 .../embedding/utilities/utilities.py                |  0
 setup.py                                            | 13 ++++++++++++-
 tests/test_embedding_utilities.py                   |  2 +-
 9 files changed, 35 insertions(+), 8 deletions(-)
 create mode 100644 dwave/__init__.py
 create mode 100644 dwave/embedding/__init__.py
 create mode 100644 dwave/embedding/utilities/__init__.py
 create mode 100644 dwave/embedding/utilities/package_info.py
 rename dwave_embedding_utilities.py => dwave/embedding/utilities/utilities.py (100%)

diff --git a/.coveragerc b/.coveragerc
index ac51b5c..4d00f14 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,4 +1,4 @@
 [run]
 # omit virtualenv and test files
 omit = venv/*, */tests/*
-source=dwave_embedding_utilities
+source=dwave
diff --git a/docs/conf.py b/docs/conf.py
index e79c9c3..cbddcde 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -63,11 +63,11 @@
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
-import dwave_embedding_utilities
+import dwave.embedding.utilities.utilities
 # The short X.Y version.
-version = dwave_embedding_utilities.__version__
+version = dwave.embedding.utilities.package_info.__version__
 # The full version, including alpha/beta/rc tags.
-release = dwave_embedding_utilities.__version__
+release = dwave.embedding.utilities.package_info.__version__
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -89,9 +89,9 @@
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = True
 
-modindex_common_prefix = ['dwave_embedding_utilities.']
+modindex_common_prefix = ['dwave.embedding.utilities.']
 
-doctest_global_setup = "from dwave_embedding_utilities import *"
+doctest_global_setup = "from dwave.embedding.utilities import *"
 
 
 # -- Options for HTML output ----------------------------------------------
diff --git a/dwave/__init__.py b/dwave/__init__.py
new file mode 100644
index 0000000..bb61062
--- /dev/null
+++ b/dwave/__init__.py
@@ -0,0 +1,2 @@
+import pkgutil
+__path__ = pkgutil.extend_path(__path__, __name__)
diff --git a/dwave/embedding/__init__.py b/dwave/embedding/__init__.py
new file mode 100644
index 0000000..bb61062
--- /dev/null
+++ b/dwave/embedding/__init__.py
@@ -0,0 +1,2 @@
+import pkgutil
+__path__ = pkgutil.extend_path(__path__, __name__)
diff --git a/dwave/embedding/utilities/__init__.py b/dwave/embedding/utilities/__init__.py
new file mode 100644
index 0000000..df00fd9
--- /dev/null
+++ b/dwave/embedding/utilities/__init__.py
@@ -0,0 +1,8 @@
+from __future__ import absolute_import
+
+from dwave.embedding.utilities.package_info import __version__, __author__, __authoremail__, __description__
+
+# for each module in this package, import __all__
+
+from dwave.embedding.utilities.utilities import *
+import dwave.embedding.utilities.utilities
diff --git a/dwave/embedding/utilities/package_info.py b/dwave/embedding/utilities/package_info.py
new file mode 100644
index 0000000..5059d59
--- /dev/null
+++ b/dwave/embedding/utilities/package_info.py
@@ -0,0 +1,4 @@
+__version__ = '0.3.0'
+__author__ = 'D-Wave Systems Inc.'
+__authoremail__ = 'acondello@dwavesys.com'
+__description__ = 'Utilities to manage embedding for the D-Wave System'
diff --git a/dwave_embedding_utilities.py b/dwave/embedding/utilities/utilities.py
similarity index 100%
rename from dwave_embedding_utilities.py
rename to dwave/embedding/utilities/utilities.py
diff --git a/setup.py b/setup.py
index 126a70d..c00c9e7 100644
--- a/setup.py
+++ b/setup.py
@@ -1,7 +1,18 @@
+import sys
+import os
 from setuptools import setup
 
-from dwave_embedding_utilities import __version__, __author__, __description__, __authoremail__
+# add __version__, __author__, __authoremail__, __description__ to this namespace
+_PY2 = sys.version_info.major == 2
 
+# change directories so this works when called from other locations. Useful in build systems.
+setup_folder_loc = os.path.dirname(os.path.abspath(__file__))
+os.chdir(setup_folder_loc)
+
+if _PY2:
+    execfile(os.path.join(".", "dwave", "embedding", "utilities", "package_info.py"))
+else:
+    exec(open(os.path.join(".", "dwave", "embedding", "utilities", "package_info.py")).read())
 
 setup(
     name='dwave_embedding_utilities',
diff --git a/tests/test_embedding_utilities.py b/tests/test_embedding_utilities.py
index dc0580d..496e36f 100644
--- a/tests/test_embedding_utilities.py
+++ b/tests/test_embedding_utilities.py
@@ -6,7 +6,7 @@
 import dwave_networkx as dnx
 import dimod
 
-import dwave_embedding_utilities as eutil
+import dwave.embedding.utilities as eutil
 
 
 class TestTargetToSource(unittest.TestCase):

From 2be6edff26c3b0ff9b615b9eb8b951ba72baef17 Mon Sep 17 00:00:00 2001
From: Bradley Ellert <bellert@dwavesys.com>
Date: Fri, 2 Mar 2018 11:24:43 -0800
Subject: [PATCH 3/7] Tidy requirements

---
 docs/requirements.txt  |  2 ++
 requirements.txt       |  2 --
 setup.py               | 29 ++++++++++++++++++++++++-----
 tests/requirements.txt |  4 ++++
 4 files changed, 30 insertions(+), 7 deletions(-)
 create mode 100644 docs/requirements.txt
 create mode 100644 tests/requirements.txt

diff --git a/docs/requirements.txt b/docs/requirements.txt
new file mode 100644
index 0000000..8213302
--- /dev/null
+++ b/docs/requirements.txt
@@ -0,0 +1,2 @@
+sphinx
+sphinx_rtd_theme
diff --git a/requirements.txt b/requirements.txt
index 6a33fb9..8171964 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,3 @@
 dimod==0.5.0
 dwave_networkx==0.6.0
 networkx==2.0
-
-coveralls
\ No newline at end of file
diff --git a/setup.py b/setup.py
index c00c9e7..1812f6d 100644
--- a/setup.py
+++ b/setup.py
@@ -2,17 +2,31 @@
 import os
 from setuptools import setup
 
-# add __version__, __author__, __authoremail__, __description__ to this namespace
 _PY2 = sys.version_info.major == 2
 
-# change directories so this works when called from other locations. Useful in build systems.
+# Change directories so this works when called from other locations. Useful in build systems that build from source.
 setup_folder_loc = os.path.dirname(os.path.abspath(__file__))
 os.chdir(setup_folder_loc)
 
+# Add __version__, __author__, __authoremail__, __description__ to this namespace
+path_to_package_info = os.path.join('.', 'dwave', 'embedding', 'utilities', 'package_info.py')
 if _PY2:
-    execfile(os.path.join(".", "dwave", "embedding", "utilities", "package_info.py"))
+    execfile(path_to_package_info)
 else:
-    exec(open(os.path.join(".", "dwave", "embedding", "utilities", "package_info.py")).read())
+    exec(open(path_to_package_info).read())
+
+# These should be minimal requiments for the package to work, and avoid pinning dependencies unless required. See
+# https://packaging.python.org/discussions/install-requires-vs-requirements/
+install_requires = ['dimod>=0.5.0,<0.6.0',
+                    'dwave_networkx>=0.6.0,<0.7.0',
+                    'networkx>=2.0,<3.0']
+
+# Any extra requirements, to be used by pip install PACKAGENAME['keyname']
+extras_require = {}
+
+# The packages in this repo that are to be installed. Either list these explictly, or use setuptools.find_packages. If
+# the latter, take care to filter unwanted packages (e.g. tests)
+packages = ['dwave.embedding.utilities']
 
 setup(
     name='dwave_embedding_utilities',
@@ -20,7 +34,12 @@
     author=__author__,
     author_email=__authoremail__,
     description=__description__,
+    long_description=open('README.rst').read(),
     url='https://github.com/dwavesystems/dwave_embedding_utilities',
     license='Apache 2.0',
-    py_modules=['dwave_embedding_utilities']
+    packages=packages,
+    install_requires=install_requires,
+    extras_require=extras_require,
+    # Required to make this a namespace package. If this package is at lower level, include all packages above it.
+    namespace_packages=['dwave', 'dwave.embedding']
 )
diff --git a/tests/requirements.txt b/tests/requirements.txt
new file mode 100644
index 0000000..131c54e
--- /dev/null
+++ b/tests/requirements.txt
@@ -0,0 +1,4 @@
+-r ../requirements.txt
+
+coverage
+coveralls

From 2a91d6503e2687efe77fc624e55bdbbd9be6be81 Mon Sep 17 00:00:00 2001
From: Bradley Ellert <bellert@dwavesys.com>
Date: Fri, 2 Mar 2018 18:18:18 -0800
Subject: [PATCH 4/7] Fix setup to follow pypa example

https://github.com/pypa/sample-namespace-packages/tree/master/pkgutil
---
 setup.py | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/setup.py b/setup.py
index 1812f6d..f98b434 100644
--- a/setup.py
+++ b/setup.py
@@ -1,6 +1,6 @@
 import sys
 import os
-from setuptools import setup
+from setuptools import setup, find_packages
 
 _PY2 = sys.version_info.major == 2
 
@@ -24,10 +24,6 @@
 # Any extra requirements, to be used by pip install PACKAGENAME['keyname']
 extras_require = {}
 
-# The packages in this repo that are to be installed. Either list these explictly, or use setuptools.find_packages. If
-# the latter, take care to filter unwanted packages (e.g. tests)
-packages = ['dwave.embedding.utilities']
-
 setup(
     name='dwave_embedding_utilities',
     version=__version__,
@@ -37,9 +33,8 @@
     long_description=open('README.rst').read(),
     url='https://github.com/dwavesystems/dwave_embedding_utilities',
     license='Apache 2.0',
-    packages=packages,
+    packages=find_packages(exclude=['tests']),
     install_requires=install_requires,
     extras_require=extras_require,
-    # Required to make this a namespace package. If this package is at lower level, include all packages above it.
-    namespace_packages=['dwave', 'dwave.embedding']
+    zip_safe=False,
 )

From 365006a92f016f24d877c06143c560a2e5220386 Mon Sep 17 00:00:00 2001
From: Bradley Ellert <bellert@dwavesys.com>
Date: Fri, 2 Mar 2018 18:19:40 -0800
Subject: [PATCH 5/7] Fix cyclic import

---
 dwave/__init__.py                     | 3 +--
 dwave/embedding/__init__.py           | 3 +--
 dwave/embedding/utilities/__init__.py | 3 ---
 3 files changed, 2 insertions(+), 7 deletions(-)

diff --git a/dwave/__init__.py b/dwave/__init__.py
index bb61062..69e3be5 100644
--- a/dwave/__init__.py
+++ b/dwave/__init__.py
@@ -1,2 +1 @@
-import pkgutil
-__path__ = pkgutil.extend_path(__path__, __name__)
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)
diff --git a/dwave/embedding/__init__.py b/dwave/embedding/__init__.py
index bb61062..69e3be5 100644
--- a/dwave/embedding/__init__.py
+++ b/dwave/embedding/__init__.py
@@ -1,2 +1 @@
-import pkgutil
-__path__ = pkgutil.extend_path(__path__, __name__)
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)
diff --git a/dwave/embedding/utilities/__init__.py b/dwave/embedding/utilities/__init__.py
index df00fd9..a802038 100644
--- a/dwave/embedding/utilities/__init__.py
+++ b/dwave/embedding/utilities/__init__.py
@@ -1,8 +1,5 @@
 from __future__ import absolute_import
 
-from dwave.embedding.utilities.package_info import __version__, __author__, __authoremail__, __description__
-
 # for each module in this package, import __all__
 
 from dwave.embedding.utilities.utilities import *
-import dwave.embedding.utilities.utilities

From 93a90b362aec65eeb7994f9134c5d5d89b8dccd6 Mon Sep 17 00:00:00 2001
From: Bradley Ellert <bellert@dwavesys.com>
Date: Mon, 5 Mar 2018 16:00:35 -0800
Subject: [PATCH 6/7] Install test requirements in Travis

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 5a9550e..acc6c9d 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -44,9 +44,9 @@ matrix:
           deploy:
 
 install:
-    - pip install -r requirements.txt
+    - pip install -r tests/requirements.txt
     - pip install .
-    
+
 script:
 - coverage run -m unittest discover
 

From 3260d11cf4c25a9ccc391a72e018ed0ea41ec3e6 Mon Sep 17 00:00:00 2001
From: Bradley Ellert <bellert@dwavesys.com>
Date: Mon, 5 Mar 2018 16:43:22 -0800
Subject: [PATCH 7/7] Change 'brew install python3' to 'brew upgrade python'

---
 .travis.yml | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index acc6c9d..4fb387d 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,6 +6,7 @@ matrix:
         #   sudo: required
         #   python: "nightly"
         #   env: TOXENV=pynightly
+        #   deploy:
         - os: linux
           sudo: required
           python: "3.6"
@@ -27,19 +28,20 @@ matrix:
           deploy:
         - os: osx
           language: generic
-          env: TOXENV=py27
+          env: TOXENV=py36
           before_install:
             - brew update
-            - virtualenv env -p python2
+            - brew upgrade python
+            - pip install virtualenv
+            - virtualenv env -p python
             - source env/bin/activate
           deploy:
         - os: osx
           language: generic
-          env: TOXENV=py36
+          env: TOXENV=py27
           before_install:
             - brew update
-            - brew install python3
-            - virtualenv env -p python3
+            - virtualenv env -p python2
             - source env/bin/activate
           deploy: