setup.py

from setuptools import setup, find_packages
import sys, os, json, urllib, subprocess
import shutil, tarfile, zipfile

# Utility function for Mac idiosyncracy
def get_folder (arch):
    for fname in arch.getnames():
        if (fname.startswith('._')):
            continue
        else:
            break
    print(fname)
    return(fname)

subprocess.check_call([sys.executable, "-m", "pip", "install", "numpy"])
import urllib.request
import itertools as itt

with open(os.path.join(*["bionetgen", "assets", "VERSION"]), "r") as f:
    vfile = f.read()
VERSION = ".".join(vfile.split()[:3])

#### BNG DOWNLOAD START ####
# Handle BNG download and inclusion

# get re-downloaded json to avoid GH rate exceeded issues
# with testing and/or multiple people installing
# within the same hour
ghapi_plist = ["bionetgen", "assets", "ghapi.json"]
with open(os.path.join(*ghapi_plist), "r") as f:
    rls_json = json.load(f)
# write BNG version tag to use later in banner
bng_version_tag = rls_json["tag_name"]
with open("bionetgen/assets/BNGVERSION", "w") as f:
    f.write(bng_version_tag)
# get assets
assets = rls_json["assets"]
for asset in assets:
    browser_url = asset["browser_download_url"]
    if "linux" in browser_url:
        linux_url = browser_url
    elif "mac" in browser_url:
        mac_url = browser_url
    elif ("win" in browser_url and "tgz" in browser_url) or (
        "win" in browser_url and "tar.gz" in browser_url
    ):
        windows_url = browser_url

# next download and place the appropriate files

bng_downloaded = False
for iurl, bng_url in enumerate([linux_url, mac_url, windows_url]):
    # this lists the stuff in bng distribution
    # to move in our python package
    if iurl < 2:
        to_move = [
            ["BNG2.pl"],
            ["bin", "NFsim"],
            ["bin", "run_network"],
            ["bin", "sundials-config"],
            ["Perl2"],
            ["VERSION"],
        ]
    elif iurl == 2:
        to_move = [
            ["BNG2.pl"],
            ["bin", "NFsim.exe"],
            ["bin", "run_network.exe"],
            ["bin", "sundials-config"],
            ["Perl2"],
            ["VERSION"],
            ["bin", "cyggcc_s-seh-1.dll"],
            ["bin", "cygstdc++-6.dll"],
            ["bin", "cygwin1.dll"],
            ["bin", "cygz.dll"],
            ["bin", "cygzstd-1.dll"],
            ["bin", "libgcc_s_seh-1.dll"],
            ["bin", "libstdc++-6.dll"],
            ["bin", "libwinpthread-1.dll"],
        ]
    # import file and download libraries
    ext = bng_url.split(".")[-1]
    fname = "bng.{}".format(ext)
    # download bng distro
    print(bng_url, fname)
    urllib.request.urlretrieve(bng_url, fname)
    # file extension dependent actions, tar for
    # mac and linux, zip for windows
    if iurl < 2:
        # if "tgz" == ext or "gz" == etx:
        bng_arch = tarfile.open(fname)
        # Find containing folder of the archive.
        # On macs may need to skip first item because
        # filesystem makes shadow files with `._` prepended.
        fold_name = get_folder(bng_arch)
        bng_arch.extractall()
        # make sure bionetgen/bng exists
        if iurl == 0:
            bng_path_to_move = "bionetgen/bng-linux"
        elif iurl == 1:
            bng_path_to_move = "bionetgen/bng-mac"

        if os.path.isdir(bng_path_to_move):
            shutil.rmtree(bng_path_to_move)
        os.mkdir(bng_path_to_move)
        os.mkdir(os.path.join(bng_path_to_move, "bin"))
        # move items in
        for item in to_move:
            item_list = [fold_name] + item
            item_path = list(
                itt.accumulate(item_list, lambda x, y: os.path.join(x, y))
            )[-1]
            to_move_item = [bng_path_to_move] + item
            to_move_path = list(
                itt.accumulate(to_move_item, lambda x, y: os.path.join(x, y))
            )[-1]
            shutil.move(item_path, to_move_path)
        # we got bionetgen in
        bng_downloaded = True
        # Done unpacking, remove useless files
        bng_arch.close()
        os.remove(fname)
        shutil.rmtree(fold_name)
    if iurl == 2:
        # elif "zip" == etx:
        # TODO: handle zip/windows case
        # bng_arch = zipfile.Zipfile(fname)
        # fold_name = bng_arch.namelist()[0]
        # bng_arch.extractall()
        bng_arch = tarfile.open(fname)
        fold_name = get_folder(bng_arch)
        bng_arch.extractall()
        # bng folder
        if iurl == 2:
            bng_path_to_move = "bionetgen/bng-win"

        if os.path.isdir(bng_path_to_move):
            shutil.rmtree(bng_path_to_move)
        os.mkdir(bng_path_to_move)
        os.mkdir(os.path.join(bng_path_to_move, "bin"))
        # move items in
        for item in to_move:
            item_list = [fold_name] + item
            item_path = list(
                itt.accumulate(item_list, lambda x, y: os.path.join(x, y))
            )[-1]
            to_move_item = [bng_path_to_move] + item[:-1]
            to_move_path = list(
                itt.accumulate(to_move_item, lambda x, y: os.path.join(x, y))
            )[-1]
            shutil.move(item_path, to_move_path)
        # we got bionetgen in
        bng_downloaded = True
        # Done unpacking, remove useless files
        bng_arch.close()
        os.remove(fname)
        shutil.rmtree(fold_name)

# if bng_downloaded:
#     # TODO: only add if not there
#     with open("MANIFEST.in", "a") as f:
#         f.write("recursive-include bionetgen/bng-linux *\n")
#         f.write("recursive-include bionetgen/bng-mac *\n")
#         f.write("recursive-include bionetgen/bng-win *\n")
#### BNG DOWNLOAD DONE ####

with open("README.md", "r") as f:
    LONG_DESCRIPTION = f.read()

setup(
    name="bionetgen",
    version=VERSION,
    description="A simple CLI and library for the BioNetGen modeling language",
    long_description=LONG_DESCRIPTION,
    long_description_content_type="text/markdown",
    author="Ali Sinan Saglam, Alex DiBiasi, and James R. Faeder",
    author_email="bionetgen.main@gmail.com",
    url="https://github.com/RuleWorld/PyBioNetGen",
    license="MIT",
    packages=find_packages(exclude=["ez_setup", "tests*"]),
    package_data={"bionetgen": ["bng*/*", "assets/*"]},
    zip_safe=False,
    include_package_data=True,
    entry_points="""
        [console_scripts]
        bionetgen = bionetgen.main:main
    """,
    install_requires=[
        "cement",
        "nbopen",
        "numpy",
        "pyyaml",
        "colorlog",
        "xmltodict",
        "seaborn",
        "libroadrunner",
        "sympy",
        "lxml",
        "networkx",
        "python-libsbml",
        "pylru",
        "pyparsing",
    ],
)