Change back to use setup.py only instead of setup.cfg and setup.py du…

…e to non-py files are not included in distribution

setup.py

@@ -1,5 +1,57 @@
-#!/usr/bin/env python
-import setuptools
+import sys
+import os
+from setuptools import setup, find_packages
 
-if __name__ == '__main__':
-    setuptools.setup()
+
+# read the contents of your README file
+this_directory = os.path.abspath(os.path.dirname(__file__))
+with open(os.path.join(this_directory, 'README.md')) as f:
+    long_description = f.read()
+
+
+def get_version(relpath):
+    '''Read version info from a file without importing it'''
+    for line in open(os.path.join(os.path.dirname(__file__), relpath)):
+        if '__version__' in line:
+            v = line.strip().split('=', 1)[1]
+            v = v.strip().strip('"\' ')
+            return v
+        else:
+            sys.stderr.write('*** No version info found..\n')
+            return ''
+
+setup(
+    name='virsorter',
+    version='2.2',
+    url='https://github.com/jiarong/VirSorter2',
+    license='GPL-2',
+    author='Jiarong Guo',
+    author_email='guojiaro@gmail.com',
+    description=('VirSorter2: A multi-classifier, expert-guided approach to '
+        'detect diverse DNA and RNA virus genomes'),
+    long_description=long_description,
+    long_description_content_type='text/markdown',
+    packages=['virsorter'],
+    # use MANIFEST.in instead
+    #package_data={
+    #    #'': ["virsorter/*", ]  
+    #    # include anything under virsorter; 
+    #    'virsorter': ['*']
+    #},
+    # include_package_data flag controls whether non-python files 
+    #  distributed in the sdist AND existing in a package 
+    #  (directory with __init__.py) install to the site-packages location. 
+    #  So in order for non-python files to install with your code 
+    #  they need to a) be in the sdist (controlled by MANIFEST.in) and 
+    #  b) exist inside an installable python package.
+    include_package_data=True,  # include all files in MANIFEST.in
+    data_files=[],
+    zip_safe=False,
+    install_requires= [], # install via conda instead
+    entry_points={
+          'console_scripts': [
+              'virsorter = virsorter.virsorter:cli'
+          ]
+    },
+    classifiers=["Topic :: Scientific/Engineering :: Bioinformatics"],
+)