setup.py

from setuptools import setup, find_packages
from setuptools.command.build_py import build_py
import glob
import os
import pkg_resources

from cov_support import __version__, _program


setup(name='cov-support',
      version=__version__,
      packages=find_packages(),
      package_data={"cov_support":["data/*"]},
      scripts=["cov_support/scripts/Snakefile",
      "cov_support/scripts/process_data_download.smk",
      "cov_support/scripts/build_phylogeny.smk",
      "cov_support/scripts/train_pangoLEARN.smk",
      "cov_support/scripts/update_lineage_data.smk",
      "cov_support/scripts/prepare_package_data.smk",
      "cov_support/scripts/get_polytomy.py",
      "cov_support/scripts/get_basal_polytomy.py",
      "cov_support/scripts/get_masked_representatives.py",
      "cov_support/scripts/categorise_snps.py",
      "cov_support/scripts/find_all_snps.py",
      "cov_support/scripts/make_summary_table.py",
      "cov_support/scripts/lineage_distributions.R",
      "cov_support/scripts/utils/parse_data.py",
      "cov_support/scripts/utils/class_defs.py",
      "cov_support/scripts/utils/time_functions.py",
      "cov_support/scripts/update_web_pages.py"],
      install_requires=[
            "biopython>=1.70",
            "dendropy>=4.4.0",
            "pytools>=2020.1",
            'pandas>=1.0.1',
            'pysam>=0.15.4',
            "scipy>=1.4.1",
            "numpy>=1.13.3"
        ],
        description='annotated global cov-support builder',
        url='https://github.com/cov-lineages/cov-support',
        author='cov-lineages org',
        author_email='aine.otoole@ed.ac.uk',
        entry_points="""
        [console_scripts]
        {program} = cov_support.command:main
        """.format(program = _program),
        include_package_data=True,
        keywords=[],
        zip_safe=False)