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setup.py
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setup.py
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from setuptools import setup, find_packages # Always prefer setuptools over distutils
from distutils.core import Extension
from codecs import open # To use a consistent encoding
from os import path
import glob
here = path.abspath(path.dirname(__file__))
# Get the long description from the relevant file
with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
readme = f.read()
#d2s_src_dir = path.join(path.join('Fred2', 'Distance2Self'), 'src')
#d2s_module = Extension('Fred2.d2s',
# define_macros=[('MAJOR_VERSION', '1'),
# ('MINOR_VERSION', '0')],
# include_dirs=[d2s_src_dir],
# libraries=['boost_serialization', 'boost_python'],
# #library_dirs = ['/usr/local/lib'],
# depends=[path.join(d2s_src_dir, 'distance2self.hpp')],
# sources=[path.join(d2s_src_dir, 'distance2self.cpp')])
#data_files = list()
# directories = glob.glob('Fred2/Data/svms/*/')
# for directory in directories:
# files = glob.glob(directory + '*')
# data_files.append((directory, files))
#directories = glob.glob('Fred2/Data/examples/')
#for directory in directories:
# files = glob.glob(directory + '*')
# data_files.append((directory, files))
#
# d2s_files = glob.glob(d2s_dir + "src/" + '*')
#data_files.append((d2s_dir + "src/", d2s_files))
#for packaging files must be in a package (with init) and listed in package_data
# package-externals can be included with data_files,
# and there is a bug in patternmatching http://bugs.python.org/issue19286
# install unclear for data_files
setup(
name='Fred2',
# Version:
version='2.0.1',
description='A Framework for Epitope Detection and Vaccine Design',
long_description=readme,
# The project's main homepage.
url='https://github.com/Fred-2/Fred2',
# Author details
author='Benjamin Schubert, Mathias Walzer',
author_email='schubert@informatik.uni-tuebingen.de, walzer@informatik.uni-tuebingen.de',
# Choose your license
license='BSD',
# See https://pypi.python.org/pypi?%3Aaction=list_classifiers
classifiers=[
# How mature is this project? Common values are
# 3 - Alpha
# 4 - Beta
# 5 - Production/Stable
'Development Status :: 4 - Beta',
# Indicate who your project is intended for
'Intended Audience :: Biologists, Pharmacologist, Developer',
'Topic :: Immunoinformatics :: Prediction Tools',
# The license as you wish (should match "license" above)
'License :: OSI Approved :: BSD License',
# The supported Python versions (other than development version were
# not yet tested. Especially we should check for Python 3 support
'Programming Language :: Python :: 2',
'Programming Language :: Python :: 2.7',
],
# What FRED2 relates to:
keywords='epitope prediction MHC FRED development',
# Specify packages via find_packages() and exclude the tests and
# documentation:
packages=find_packages(),
#packages=find_packages(exclude=['Fred2.test', 'Fred2.doc', 'Fred2.tutorials']),
# If there are data files included in your packages that need to be
# installed, specify them here. If using Python 2.6 or less, then these
# have to be included in MANIFEST.in as well.
#include_package_data=True,
package_data={
'Fred2.Data.examples': ['*.*'],
'Fred2.Data.svms.svmtap': ['*'],
'Fred2.Data.svms.svmhc': ['*'],
'Fred2.Data.svms.unitope': ['*'],
#'Fred2.Distance2Self': ['src/*'], #does not get installed, because the src folder is no package folder - compiles ok
},
#package_data is a lie: http://stackoverflow.com/questions/7522250/how-to-include-package-data-with-setuptools-distribute
# 'package_data' is used to also install non package data files
# see http://docs.python.org/3.4/distutils/setupscript.html#installing-additional-files
# example:
#data_files=data_files,
# Entry points provide cross-platform support and allow
# pip to create the appropriate form of executable for the target platform.
# IMPORTANT: script names need to be in lower case ! ! ! (otherwise
# deinstallation does not work)
#entry_points={
# 'console_scripts': [
# 'epitopeprediction=Fred2.Apps.EpitopePrediction:main',
# ],
#},
#ext_modules=[helloworld_module],
#ext_modules=[d2s_module],
# Run-time dependencies. (will be installed by pip when FRED2 is installed)
install_requires=['setuptools>=18.2', 'pandas', 'pyomo>=4.0','svmlight', 'MySQL-python >= 1.2.4', 'biopython', 'pyVCF'],
)