setup.py

#!/usr/bin/env python3

from setuptools import setup
import setuptools
from setuptools.command.install_lib import install_lib
import setuptools.command.build_py
import distutils.cmd
import os
import sys


executable_list = [
    "makeblastdb",
    "tandem",
    "tandem.exe",
    "qvality",
    "percolator",
    "percolator_2_08",
    "omssacl",
    "myrimatch_2_1_138",
    "myrimatch.exe",
    "MSAmanda.exe",
    "PepNovo_bin",
    "novor.bat",
    "novor.sh",
    "PepNovo.exe",
]

if sys.platform in ["win32"]:

    class my_install_lib(setuptools.command.install_lib.install_lib):
        pass

else:

    class my_install_lib(setuptools.command.install_lib.install_lib):
        def run(self):
            setuptools.command.install_lib.install_lib.run(self)
            for fn in self.get_outputs():
                if os.path.basename(fn) in executable_list:
                    # copied from setuptools source - make the binaries
                    # executable
                    mode = ((os.stat(fn).st_mode) | 0o555) & 0o7777
                    print("changing mode of %s to %o", fn, mode)
                    os.chmod(fn, mode)


def install_resources():
    working_directory = os.path.join(
        os.path.dirname(os.path.realpath(__file__)),
    )
    if os.path.exists(os.path.join(working_directory, "ursgal")) is False:
        print("Could not find ursgal directory")
        sys.exit(1)
    import ursgal

    uc = ursgal.UController()
    downloaded_zips = uc.download_resources(resources=["msgfplus_v2019_01_22"])
    if len(downloaded_zips) == 0:
        print("[ INFO ] No engines were downloaded, all should be available")
    else:
        print(
            "[ INFO ] Downloaded and installed {0} engine(s)".format(
                len(downloaded_zips)
            )
        )
        for engine, zip_file in downloaded_zips:
            print(
                "[ INFO ] Engine: {0} has been installed from {1}".format(
                    engine, zip_file
                )
            )


class BuildPyWithResources(setuptools.command.build_py.build_py):
    """Includes install_resources.py before the setuptools build"""

    def run(self):
        # self.run_command('install_resources')
        install_resources()
        setuptools.command.build_py.build_py.run(self)


class InstallResourcesCommand(distutils.cmd.Command):
    """Download resources from webpage and install into ursgal/resources"""

    description = "Download and install third party engines"
    user_options = []

    def initialize_options(self):
        return

    def finalize_options(self):
        return

    def run(self):
        """
        Download all resources from our webpage to ursgal/resources.

        """
        install_resources()


# We store our version number in a simple text file:
version_path = os.path.join(os.path.dirname(__file__), "ursgal", "version.txt")
with open(version_path, "r") as version_file:
    ursgal_version = version_file.read().strip()

with open("requirements/install_requires.txt") as req:
    requirements = req.readlines()

setup(
    name="ursgal",
    version=ursgal_version,
    packages=["ursgal"],
    package_dir={"ursgal": "ursgal"},
    description="ursgal",
    package_data={
        "ursgal": [
            "version.txt",
            "wrappers/*.py",
            "resources/*/*/*",
            "resources/*/*/*/*",
            "resources/*/*/*/*/*",
        ]
    },
    install_requires=requirements,
    long_description="Universal Python module combining common bottom-up proteomics tools for large-scale analysis",
    author="Lukas P. M. Kremer, Purevdulam Oyunchimeg, Johannes Barth, Stefan Schulze and Christian Fufezan",
    author_email="christian@fufezan.net",
    url="http://ursgal.github.com",
    license="Lesser GNU General Public License (LGPL)",
    platforms="any that supports python 3.5",
    classifiers=[
        "Development Status :: 4 - Beta",
        "Environment :: Console",
        "Intended Audience :: Education",
        "Intended Audience :: Science/Research",
        "Intended Audience :: Developers",
        "Operating System :: MacOS :: MacOS X",
        "Operating System :: Microsoft :: Windows",
        "Operating System :: POSIX",
        "Operating System :: POSIX :: SunOS/Solaris",
        "Operating System :: Unix",
        "Programming Language :: Python :: 3",
        "Programming Language :: Python :: 3.5",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
        "Topic :: Scientific/Engineering :: Chemistry",
        "Topic :: Scientific/Engineering :: Medical Science Apps.",
        "Topic :: Software Development :: Libraries :: Python Modules",
    ],
    cmdclass={
        "install_lib": my_install_lib,
        "build_py": BuildPyWithResources,
        "install_resources": InstallResourcesCommand,
    },
    entry_points={
        "console_scripts": ["ursgal-install-resources=ursgal.uinstaller:main"],
    },
    # scripts=['installer.py']
)