Switched from distutils to setuptools and added entrypoint and some s…

…mall changes

pygwas/__init__.py

@@ -1,3 +1,3 @@
-__version__ = '0.1.0'
-__updated__ = "20.8.2014"
+__version__ = '0.1.1'
+__updated__ = "01.12.2014"
 __date__ = "20.8.2014"

pygwas/__main__.py

@@ -0,0 +1,9 @@
+#!/usr/bin/env python
+"""The main entry point. Invoke as `pygwas' or `python -m pygwas'.
+"""
+import sys
+from pygwas import main
+
+
+if __name__ == '__main__':
+    sys.exit(main())

pygwas/pygwas.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # coding: utf-8
 """
-    pygwas.pygwas
+    pygwas
     ~~~~~~~~~~~~~
 
     The main module for running Genome Wide Association studies
@@ -10,9 +10,8 @@
     :license: license_name, see LICENSE for more details
 """
 
-from __init__ import __version__,__updated__,__date__
-from argparse import ArgumentParser
-from argparse import RawDescriptionHelpFormatter
+from . import __version__,__updated__,__date__
+import argparse
 from core import kinship
 from core import gwas
 import logging, logging.config
@@ -56,7 +55,7 @@
 log = logging.getLogger()
 
 def get_parser(program_license,program_version_message):
-    parser = ArgumentParser(description=program_license, formatter_class=RawDescriptionHelpFormatter)
+    parser = argparse.ArgumentParser(description=program_license)
     parser.add_argument("-t", "--transformation", dest="transformation", help="Apply a transformation to the data. Default[None]", choices=["log", "sqrt", "exp", "sqr", "arcsin_sqrt", "box_cox"])
     parser.add_argument("-a", "--analysis_method", dest="analysis_method", help="analyis method to use",required=True,choices=["lm", "emma", "emmax", "kw", "ft", "emmax_anova", "lm_anova", "emmax_step", "lm_step","loc_glob_mm","amm"])
     parser.add_argument("-g", "--genotype", dest="genotype", help="genotype dataset to be used in the GWAS analysis (run with option -l to display list of available genotype datasets)", required=True, type=int,metavar="INTEGER" )
@@ -71,11 +70,10 @@ def get_parser(program_license,program_version_message):
 
 def main(): 
     '''Command line options.'''
-    program_name = os.path.basename(sys.argv[0])
     program_version = "v%s" % __version__
     program_build_date = str(__updated__)
     program_version_message = '%%(prog)s %s (%s)' % (program_version, program_build_date)
-    program_shortdesc = __import__('__main__').__doc__.split("\n")[1]
+    program_shortdesc = "The main module for running Genome Wide Association studies"
     program_license = '''%s
 
   Created by Ümit Seren on %s.
@@ -89,13 +87,12 @@ def main():
 
 USAGE
 ''' % (program_shortdesc, str(__date__))
-
+    # Process arguments
+    parser = get_parser(program_license,program_version_message)
+    args = vars(parser.parse_args())
     try:
-        # Process arguments
-        parser = get_parser(program_license,program_version_message)
-        args = parser.parse_args()
-        result = perform_gwas(args.file,args.analysis_method, args.genotype_folder,args.genotype,args.transformation,args.kinship)
-        result.save_as_hdf5(args.outputfile)
+        result = perform_gwas(args['file'],args['analysis_method'], args['genotype_folder'],args['genotype'],args['transformation'],args['kinship'])
+        result.save_as_hdf5(args['outputfile'])
         return 0
     except KeyboardInterrupt:
         ### handle keyboard interrupt ###

setup.cfg

@@ -0,0 +1,5 @@
+[bdist_wheel]
+# This flag says that the code is written to work on both Python 2 and Python
+# 3. If at all possible, it is good practice to do this. If you cannot, you
+# will need to generate wheels for each Python version that you support.
+universal=1

setup.py

@@ -1,18 +1,47 @@
-from distutils.core import setup
+from setuptools import setup, find_packages  # Always prefer setuptools over distutils
+from codecs import open  # To use a consistent encoding
+from os import path
+import pygwas
+
+here = path.abspath(path.dirname(__file__))
+
+# Get the long description from the relevant file
+with open(path.join(here, 'DESCRIPTION.rst'), encoding='utf-8') as f:
+    long_description = f.read()
 
 setup(
     name='PyGWAS',
-    version='0.1.0',
+    version=pygwas.__version__,
+    description='A GWAS library',
+    long_description=long_description,
+    url='https://github.com/pypa/pygwas',
     author='Uemit Seren',
-    author_email='[email protected]',
-    packages=['pygwas','pygwas.core'],
-    url='http://pypi.python.org/pypi/pygwas/',
-    license='LICENSE.txt',
-    description='GWAS library',
-    long_description=open('README.txt').read(),
+    author_email='[email protected]',
+    license='MIT',
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Developers',
+	'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'License :: OSI Approved :: MIT License',
+        'Programming Language :: Python :: 2',
+        'Programming Language :: Python :: 2.6',
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.2',
+        'Programming Language :: Python :: 3.3',
+        'Programming Language :: Python :: 3.4',
+    ],
+    keywords='GWAS',
+    packages=find_packages(exclude=['contrib', 'docs', 'tests*']),
     install_requires=[
         "numpy >=1.6.1",
         "scipy >=0.13.0",
         "h5py >=2.1.3",
+    ],
+    entry_points={
+        'console_scripts': [
+            'pygwas=pygwas.__main__:main',
         ],
-    )
+    },
+)
+