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setup.py
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import os
import re
import sys
from setuptools import setup, find_packages
__pkg_name__ = 'fast5_research'
__author__ = 'cwright'
__description__ = 'ONT Research .fast5 read/write API.'
# Use readme as long description and say its github-flavour markdown
from os import path
this_directory = path.abspath(path.dirname(__file__))
kwargs = {'encoding':'utf-8'} if sys.version_info.major == 3 else {}
with open(path.join(this_directory, 'README.md'), **kwargs) as f:
__long_description__ = f.read()
__long_description_content_type__ = 'text/markdown'
# Get the version number from __init__.py
verstrline = open(os.path.join(__pkg_name__, '__init__.py'), 'r').read()
vsre = r"^__version__ = ['\"]([^'\"]*)['\"]"
mo = re.search(vsre, verstrline, re.M)
if mo:
__version__ = mo.group(1)
else:
raise RuntimeError('Unable to find version string in "{}/__init__.py".'.format(__pkg_name__))
dir_path = os.path.dirname(__file__)
with open(os.path.join(dir_path, 'requirements.txt')) as fh:
install_requires = [
r.split('#')[0].strip()
for r in fh.read().splitlines() if not r.strip().startswith('#')
]
extra_requires={}
py2only_requirements = ['futures']
if len(py2only_requirements) > 0:
extra_requires[':python_version == "2.7"'] = []
for requirement in py2only_requirements:
install_requires.remove(requirement)
extra_requires[':python_version == "2.7"'].append(requirement)
setup(
name=__pkg_name__,
version=__version__,
url='https://github.com/nanoporetech/{}'.format(__pkg_name__),
author=__author__,
author_email='{}@nanoporetech.com'.format(__author__),
description=__description__,
long_description=__long_description__,
long_description_content_type=__long_description_content_type__,
entry_points={
'console_scripts': [
'index_reads = {}.extract:build_read_index'.format(__pkg_name__),
'extract_reads = {}.extract:extract_reads'.format(__pkg_name__),
'read_summary = {}.extract:extract_read_summary'.format(__pkg_name__),
'filter_reads = {}.extract:filter_multi_reads'.format(__pkg_name__),
'filter_from_bam = {}.extract:filter_file_from_bam'.format(__pkg_name__),
]
},
license='Mozilla Public License 2.0',
dependency_links=[],
install_requires=install_requires,
tests_require=['nose>=1.3.7'].extend(install_requires),
extras_require=extra_requires,
packages=find_packages(exclude=['*.test', '*.test.*', 'test.*', 'test']),
package_data={},
zip_safe=True,
classifiers=[
'Development Status :: 4 - Beta',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)',
'Natural Language :: English',
'Programming Language :: Python',
'Topic :: Software Development :: Libraries :: Python Modules',
'Topic :: Scientific/Engineering :: Bio-Informatics'
],
keywords='ONT Research fast5 API',
)