setup.py

from setuptools import setup, find_packages
from codecs import open
from os import path
import os
import re
import io


# Get version strip
def read(*names, **kwargs):
    with io.open(os.path.join(os.path.dirname(__file__), *names),
                 encoding=kwargs.get("encoding", "utf8")) as fp:
        return fp.read()


def find_version(*file_paths):
    version_file = read(*file_paths)
    version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
                              version_file, re.M)
    if version_match:
        return version_match.group(1)
    raise RuntimeError("Unable to find version string.")


here = path.abspath(path.dirname(__file__))

with open(path.join(here, 'README.md'), encoding='utf-8') as f:
    long_description = f.read()

setup(
    name="panaroo",
    version=find_version("panaroo/__init__.py"),
    author="Gerry Tonkin-Hill, Neil MacAlistair, Chris Ruis and Aaron Weimann",
    author_email="g.tonkinhill@gmail.com",
    description="A pangenome analysis pipeline",
    long_description=long_description,
    long_description_content_type="text/markdown",
    url="https://github.com/gtonkinhill/panaroo",
    install_requires=[
        'networkx', 'gffutils', 'BioPython', 'joblib', 'tqdm', 'edlib',
        'scipy', 'numpy', 'matplotlib', 'scikit-learn', 'plotly', 'dendropy',
        'intbitset', 'biocode'
    ],
    python_requires='>=3.6.0',
    packages=['panaroo'],
    keywords='pangenome roary bacteria',
    classifiers=[
        "Programming Language :: Python :: 3",
        "License :: OSI Approved :: MIT License",
        "Operating System :: OS Independent",
        'Development Status :: 4 - Beta',
        'Intended Audience :: Science/Research',
        'Topic :: Scientific/Engineering :: Bio-Informatics',
    ],
    entry_points={
        'console_scripts': [
            'panaroo = panaroo.__main__:main',
            'run_prokka = panaroo.run_prokka:main',
            'panaroo-qc = panaroo.generate_qc_plots:main',
            'panaroo-merge = panaroo.merge_graphs:main',
            'panaroo-plot-abundance = panaroo.generate_abundance_plots:main',
            'panaroo-spydrpick = panaroo.spydrpick:main',
            'panaroo-img = panaroo.estimate_img_params:main',
            'panaroo-fmg = panaroo.estimate_many_genes_params:main',
            'panaroo-msa = panaroo.post_run_alignment_gen:main',
            'panaroo-gene-neighbourhood = panaroo.get_neighborhood:main',
            'panaroo-integrate = panaroo.integrate:main',
            'panaroo-filter-pa = panaroo.filter_pa:main',
            'panaroo-generate-gffs = panaroo.post_run_gff_output:main',
            'panaroo-extract-gene = panaroo.extract_gene_fasta:main'
        ],
    },
)