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#!/usr/bin/python3
#
# Copyright (c) 2013 Mikkel Schubert <MikkelSch@gmail.com>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
import codecs
import os
import sys
from setuptools import find_packages, setup
if sys.version_info < (3, 5):
sys.stderr.write("FATAL ERROR: ")
sys.stderr.write("PALEOMIX requires at least Python 3.5, but setup.py ")
sys.stderr.write("was run using Python %s.%s!\n" % sys.version_info[:2])
sys.exit(1)
def _get_version():
"""Retrieve version from current install directory."""
env = {}
with open(os.path.join("paleomix", "__init__.py")) as handle:
exec(handle.read(), env)
return env["__version__"]
def _get_readme():
"""Retrieves contents of README.rst, forcing UTF-8 encoding."""
with codecs.open("README.rst", encoding="utf-8") as handle:
return handle.read()
setup(
name="paleomix",
version=_get_version(),
description="Bioinformatics pipelines for HTS data",
long_description=_get_readme(),
url="https://github.com/MikkelSchubert/paleomix",
author="Mikkel Schubert",
author_email="MikkelSch@gmail.com",
license="MIT",
classifiers=[
"Development Status :: 5 - Production/Stable",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.5",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
],
keywords="pipeline bioinformatics hts phylogeny bam",
packages=find_packages(exclude=["misc", "tests"]),
install_requires=[
"coloredlogs>=10.0",
"configargparse>=0.13.0",
"pysam>=0.10.0",
"ruamel.yaml>=0.16.0",
"setproctitle>=1.1.0",
],
entry_points={"console_scripts": ["paleomix=paleomix.main:entry_point"]},
zip_safe=False,
include_package_data=True,
)
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