setup.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# (c) The James Hutton Institute 2017-2019
# (c) University of Strathclyde 2019
# Author: Leighton Pritchard
#
# Contact:
# leighton.pritchard@strath.ac.uk
#
# Leighton Pritchard,
# Strathclyde Institute for Pharmacy and Biomedical Sciences,
# Cathedral Street,
# Glasgow,
# G1 1XQ
# Scotland,
# UK
#
# The MIT License
#
# Copyright (c) 2017-2019 The James Hutton Institute
# Copyright (c) 2019 University of Strathclyde
#
# 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.
"""Distribution setup."""

import sys
import re
import setuptools

from pathlib import Path

try:
    import distribute_setup

    distribute_setup.use_setuptools()
except ImportError:
    pass

# Get long description from README.md
with Path("README.md").open("r") as dfh:
    long_description = dfh.read()  # pylint: disable=C0103

# parse version from package/module without importing or
# evaluating the code
with Path("pyani/__init__.py").open() as ifh:
    for line in ifh:
        # The escaping/use of quotes in the re.search() below can be treacherous
        match = re.search(r'^__version__ = "(?P<version>[^"]+)"$', line)
        if match:
            version = match.group("version")
            break

if sys.version_info <= (3, 6):
    sys.stderr.write("ERROR: pyani requires Python 3.7 or above...exiting.\n")
    sys.exit(1)

setuptools.setup(
    name="pyani",
    version=version,
    author="Leighton Pritchard",
    author_email="leighton.pritchard@strath.ac.uk",
    description="".join(
        [
            (
                "pyani provides a package and script for calculation of genome-scale average nucleotide identity."
            )
        ]
    ),
    long_description=long_description,
    long_description_content_type="text/markdown",
    license="MIT",
    keywords="genome bioinformatics sequence taxonomy",
    platforms="Posix; MacOS X",
    url="http://widdowquinn.github.io/pyani/",  # project home page
    download_url="https://github.com/widdowquinn/pyani/releases",
    scripts=[],
    entry_points={
        "console_scripts": [
            "pyani = pyani.scripts.pyani_script:run_main",
            "average_nucleotide_identity.py = pyani.scripts.average_nucleotide_identity:run_main",
            "delta_filter_wrapper.py = pyani.scripts.delta_filter_wrapper:run_main",
            "genbank_get_genomes_by_taxon.py = pyani.scripts.genbank_get_genomes_by_taxon:run_main",
        ]
    },
    packages=setuptools.find_packages(),
    package_data={"pyani": ["tests/test_JSpecies/*.tab"]},
    include_package_date=True,
    install_requires=[
        "biopython",
        "matplotlib",
        "namedlist",
        "networkx",
        "pandas",
        "scipy",
        "seaborn",
        "sqlalchemy",
        "tqdm",
    ],
    classifiers=[
        "Development Status :: 4 - Beta",
        "Environment :: Console",
        "Intended Audience :: Science/Research",
        "License :: OSI Approved :: MIT License",
        "Natural Language :: English",
        "Operating System :: MacOS :: MacOS X",
        "Operating System :: POSIX :: Linux",
        "Programming Language :: Python",
        "Programming Language :: Python :: 3",
        "Programming Language :: Python :: 3.7",
        "Programming Language :: Python :: 3.8",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
    ],
)