Packaging fix: version has changed file location

Closes #209

MANIFEST.in

@@ -1,5 +1,4 @@
 include README.rst
-include VERSION
 include LICENSE
 include requirements.txt
 include requirements-rtd.txt

cellbender/__init__.py

@@ -0,0 +1 @@
+__version__ = '0.3.0'

cellbender/base_cli.py

@@ -10,16 +10,25 @@
 from abc import ABC, abstractmethod
 from typing import Dict
 import importlib
+import codecs
 
 # New tools should be added to this list.
 TOOL_NAME_LIST = ['remove-background']
 
 
+def read(rel_path):
+    here = os.path.abspath(os.path.dirname(__file__))
+    with codecs.open(os.path.join(here, rel_path), 'r') as fp:
+        return fp.read()
+
+
 def get_version() -> str:
-    """Version number is centrally located in the file called VERSION"""
-    with open(os.path.join(os.path.dirname(__file__), '..', 'VERSION')) as f:
-        version = f.read().strip()
-    return version
+    for line in read('__init__.py').splitlines():
+        if line.startswith('__version__'):
+            delim = '"' if '"' in line else "'"
+            return line.split(delim)[1]
+    else:
+        raise RuntimeError("Unable to find version string.")
 
 
 class AbstractCLI(ABC):

setup.py

@@ -2,9 +2,25 @@
 
 import os
 import setuptools
+import codecs
 from typing import List
 
 
+def read(rel_path):
+    here = os.path.abspath(os.path.dirname(__file__))
+    with codecs.open(os.path.join(here, rel_path), 'r') as fp:
+        return fp.read()
+
+
+def get_version() -> str:
+    for line in read('cellbender/__init__.py').splitlines():
+        if line.startswith('__version__'):
+            delim = '"' if '"' in line else "'"
+            return line.split(delim)[1]
+    else:
+        raise RuntimeError("Unable to find version string.")
+
+
 def readme() -> str:
     with open('README.rst') as f:
         return f.read()
@@ -28,13 +44,6 @@ def get_rtd_requirements() -> List[str]:
     return requirements
 
 
-def get_version() -> str:
-    """Version number is centrally located in the file called VERSION"""
-    with open('VERSION') as f:
-        version = f.read().strip()
-    return version
-
-
 setuptools.setup(
     name='cellbender',
     version=get_version(),