cleaning up packaging

MANIFEST.in

@@ -1,3 +1,9 @@
+# description
+include README.rst
+
+# version
+include wc_sim/VERSION
+
 # license
 include LICENSE
 

README.md

@@ -1,4 +1,4 @@
-<!-- [![PyPI package](https://img.shields.io/pypi/v/wc_sim.svg)](https://pypi.python.org/pypi/wc_sim) -->
+[//]: # ( [![PyPI package](https://img.shields.io/pypi/v/wc_sim.svg)](https://pypi.python.org/pypi/wc_sim) )
 [![Documentation](https://img.shields.io/badge/docs-latest-brightgreen.svg)](http://code.karrlab.org)
 [![Test results](https://circleci.com/gh/KarrLab/wc_sim.svg?style=shield&circle-token=5f0ee7e437b91cbcac19a9b8526a7ea320ee61c7)](https://circleci.com/gh/KarrLab/wc_sim)
 [![Test coverage](https://coveralls.io/repos/github/KarrLab/wc_sim/badge.svg?t=EUFJ40)](https://coveralls.io/github/KarrLab/wc_sim)

examples/__init__.py

@@ -1 +0,0 @@
-__version__ = '0.0.1'

setup.cfg

@@ -1,6 +1,3 @@
-[metadata]
-description-file = README.rst
-
 [bdist_wheel]
 universal = 1
 

setup.py

@@ -3,7 +3,18 @@
 
 from setuptools import setup, find_packages
 from wc_utils.util.install import parse_requirements, install_dependencies
-import wc_sim
+import os
+
+# get long description
+if os.path.isfile('README.rst'):
+    with open('README.rst', 'r') as file:
+        long_description = file.read()
+else:
+    long_description = ''
+
+# get version
+with open('wc_sim/VERSION', 'r') as file:
+    version = file.read().strip()
 
 # parse dependencies and links from requirements.txt files
 with open('requirements.txt', 'r') as file:
@@ -18,24 +29,26 @@
 # install package
 setup(
     name="wc_sim",
-    version=wc_sim.__version__,
+    version=version,
     description="Sequential whole-cell model simulator",
+    long_description=long_description,
     url="https://github.com/KarrLab/wc_sim",
-    download_url='https://github.com/KarrLab/wc_sim/tarball/{}'.format(wc_sim.__version__),
+    download_url='https://github.com/KarrLab/wc_sim',
     author="Arthur Goldberg",
     author_email="[email protected]",
     license="MIT",
     keywords='whole-cell systems cell molecular biology',
     packages=find_packages(exclude=['tests', 'tests.*']),
     package_data={
         'wc_sim': [
+            'VERSION',
             'core/config/core.default.cfg',
             'core/config/core.schema.cfg',
             'core/config/debug.default.cfg',
             'multialgorithm/config/core.default.cfg',
             'multialgorithm/config/core.schema.cfg',
             'multialgorithm/config/debug.default.cfg',
-            'examples/config/debug.default.cfg',
+            'examples/config/debug.default.cfg',            
         ],
     },
     install_requires=install_requires,

tests/__init__.py

@@ -1 +1 @@
-__version__ = '0.0.1'
+

wc_sim/VERSION

@@ -0,0 +1 @@
+0.0.1

wc_sim/__init__.py

@@ -1 +1,5 @@
-__version__ = '0.0.1'
+import pkg_resources
+
+with open(pkg_resources.resource_filename('wc_sim', 'VERSION'), 'r') as file:
+    __version__ = file.read().strip()
+# :obj:`str`: version