[ADAM-1691] Move bdgenomics.adam to use a namespace package.

Resolves #1691.

adam-python/Makefile

@@ -32,7 +32,7 @@ The 'clean' target undoes the effect of 'develop'.
 
 The 'test' target runs ADAM's unit tests. Set the 'tests' variable to run a particular test, e.g.
 
-	make test tests=src/adam/test/sort/sortTest.py::SortTest::testSort
+	make test tests=bdgenomics/adam/test/sort/sortTest.py::SortTest::testSort
 
 The 'pypi' target publishes the current commit of ADAM to PyPI after enforcing that the working
 copy and the index are clean, and tagging it as an unstable .dev build.
@@ -46,7 +46,7 @@ help:
 SHELL=bash
 python=python2.7
 pip=pip
-tests=src
+tests=bdgenomics
 extras=
 adam_version:=$(shell $(python) version.py)
 sdist_name:=adam-$(adam_version).tar.gz
@@ -62,7 +62,7 @@ develop:
 	$(pip) install -e .$(extras)
 clean_develop:
 	- $(pip) uninstall -y adam
-	- rm -rf src/*.egg-info
+	- rm -rf bdgenomics/*.egg-info
 
 sdist: dist/$(sdist_name)
 dist/$(sdist_name):

adam-python/src/bdgenomics/adam/__init__.py → adam-python/bdgenomics/__init__.py

@@ -1,17 +1,16 @@
-#
 # Licensed to Big Data Genomics (BDG) under one
 # or more contributor license agreements.  See the NOTICE file
 # distributed with this work for additional information
 # regarding copyright ownership.  The BDG licenses this file
 # to you 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.
-#
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)

adam-python/setup.py

@@ -27,6 +27,4 @@
     author_email='fnothaft@berkeley.edu',
     url="https://github.com/bdgenomics/adam",
     install_requires=[],
-    package_dir={'': 'src'},
-    packages=find_packages(where='src',
-                           exclude=['*.test.*']))
+    packages=find_packages(exclude=['*.test.*']))