Merge pull request #40 from phac-nml/sistr/updates-for-release

Sistr/updates for release

MANIFEST.in

@@ -3,4 +3,5 @@ include README.rst
 include MANIFEST.in
 include setup.py
 
-recursive-include sistr/data/ *.fasta *.txt *.csv *.msh
+include sistr/dbstatus.txt
+recursive-include sistr/data/ *

README.rst

@@ -7,8 +7,8 @@
 
 .. |pypi| image:: https://badge.fury.io/py/sistr-cmd.svg
     :target: https://pypi.python.org/pypi/sistr-cmd/
-.. |license| image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
-	:target: https://www.gnu.org/licenses/gpl-3.0
+.. |license| image:: https://img.shields.io/github/license/phac-nml/sistr_cmd
+	:target: https://www.apache.org/licenses/LICENSE-2.0
 .. |nbsp| unicode:: 0xA0 
    :trim:
 
@@ -552,4 +552,4 @@ License
 
 Copyright 2017 Public Health Agency of Canada
 
-Distributed under the GNU Public License version 3.0
+Distributed under the Apache 2.0 license.

setup.py

@@ -1,14 +1,11 @@
-import os
 from distutils.core import setup
 from setuptools import find_packages
-import sys
-sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
 from sistr.version import __version__
 
 classifiers = """
-Development Status :: 3 - Alpha
+Development Status :: 4 - Beta
 Environment :: Console
-License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+License :: OSI Approved :: Apache Software License
 Intended Audience :: Science/Research
 Topic :: Scientific/Engineering
 Topic :: Scientific/Engineering :: Bio-Informatics
@@ -21,33 +18,20 @@
 Operating System :: POSIX :: Linux
 """.strip().split('\n')
 
-def read(fname):
-    return open(os.path.join(os.path.dirname(__file__), fname)).read()
-
-exec(open('sistr/version.py').read())
-
 setup(
     name='sistr_cmd',
     version=__version__,
     packages=find_packages(exclude=['tests']),
-    url='https://github.com/peterk87/sistr_cmd',
-    license='GPLv3',
+    url='https://github.com/phac-nml/sistr_cmd',
+    license='Apache 2.0',
     author='Peter Kruczkiewicz',
     author_email='[email protected]',
     description=('Serovar predictions from Salmonella whole-genome sequence assemblies by determination of antigen gene'
                  'and cgMLST gene alleles using BLAST. Mash MinHash can also be used for serovar prediction.'),
     keywords='Salmonella serotyping genotyping cgMLST BLAST Mash MinHash',
     classifiers=classifiers,
     package_dir={'sistr':'sistr'},
-    package_data={'sistr': ['data/*.msh',
-                            'data/*.csv',
-                            'data/*.txt',
-                            'data/antigens/*.fasta',
-                            'data/cgmlst/*.fasta',
-                            'data/cgmlst/*.txt',
-                            'data/cgmlst/*.csv',
-                            'data/cgmlst/*.hdf'
-                            ]},
+    include_package_data=True,
     install_requires=[
         'numpy>=1.11.1',
         'pandas>=0.18.1',