# Copyright (C) 2015 UCSC Computational Genomics Lab

#

# Licensed under the Apache License, Version 2.0 (the "License");

# you may not use this file except in compliance with the License.

# You may obtain a copy of the License at

#

# http://www.apache.org/licenses/LICENSE-2.0

#

# Unless required by applicable law or agreed to in writing, software

# distributed under the License is distributed on an "AS IS" BASIS,

# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

# See the License for the specific language governing permissions and

# limitations under the License.

import sys

from version import version

from setuptools import find_packages, setup

kwargs = dict(

name='toil',

version=version,

description='Pipeline management software for clusters.',

author='Benedict Paten',

author_email='benedict@soe.usc.edu',

url="https://github.com/BD2KGenomics/toil",

install_requires=[

'bd2k-python-lib==1.13.dev14'],

tests_require=[

'mock==1.0.1',

'pytest==2.8.3'],

test_suite='toil',

extras_require={

'mesos': [

'psutil==3.0.1'],

'aws': [

'boto==2.38.0',

'cgcloud-lib==1.4a1.dev195' ],

'azure': [

'azure==1.0.3'],

'encryption': [

'pynacl==0.3.0'],

'cwl': [

'cwltool==1.0.20160425140546']},

package_dir={'': 'src'},

packages=find_packages('src', exclude=['*.test']),

entry_points={

'console_scripts': [

'toil = toil.utils.toilMain:main',

'_toil_worker = toil.worker:main',

'cwltoil = toil.cwl.cwltoil:main [cwl]',

'cwl-runner = toil.cwl.cwltoil:main [cwl]',

'_toil_mesos_executor = toil.batchSystems.mesos.executor:main [mesos]']})

from setuptools.command.test import test as TestCommand

class PyTest(TestCommand):

user_options = [('pytest-args=', 'a', "Arguments to pass to py.test")]

def initialize_options(self):

TestCommand.initialize_options(self)

self.pytest_args = []

def finalize_options(self):

TestCommand.finalize_options(self)

self.test_args = []

self.test_suite = True

def run_tests(self):

import pytest

# Sanitize command line arguments to avoid confusing Toil code attempting to parse them

sys.argv[1:] = []

errno = pytest.main(self.pytest_args)

sys.exit(errno)

kwargs['cmdclass'] = {'test': PyTest}

setup(**kwargs)