setup.py

import pathlib, setuptools, sys, os, re
import setuptools.command.develop
import setuptools.command.install
import setuptools.command.egg_info
import subprocess

## right now it uses "local" copy of biomcmc but also needs system global-wide one (cant copy to sys.path)
## I'll end up installing biomcmc with autotools and setup.py only when needed

min_version = (3, 6)

if sys.version_info < min_version:
    error = """
Python {0} or above is required.

Make sure you have an up-to-date pip installed.  
""".format('.'.join(str(n) for n in min_version)), sys.exit(error)

base_dir = pathlib.Path(__file__).parent.resolve()
readme_file  = base_dir/"README.md"
build_path   = f"{base_dir}/build_setup"
biomcmc_path = f"{build_path}/biomcmc-lib"

# first line of configure.ac is "AC_INIT([tauari_c], [0.0.1], [leomrtns@gmail.com]"
version_txt = open(f"{base_dir}/configure.ac").readline()  
version_txt = re.findall(r'\[(.*?)\]',version_txt)[1] 

# Eval the version file to get __version__; avoids importing our own package
with readme_file.open(encoding = "utf-8") as f: long_description = f.read()

if not os.path.exists(biomcmc_path): # developers can have their own links (without submodule)
    source = f"{base_dir}/submodules/biomcmc-lib/"
    if not os.path.exists(source):
        sys.exit(f"Tauari:: No '{source}' found;\n You must download this repository with 'git clone --recursive' or add biomcmc-lib by hand to {biomcmc_path}")
    print (f"Tauari:: Creating a link '{biomcmc_path}' pointing to '{source}'")
    os.symlink(source, biomcmc_path)

def biomc2_compilation (options = ""):     
    if not os.path.isfile(f"{build_path}/lib/tauari_c.so"):
        subprocess.call(f"../configure --prefix={build_path} {options}".split(), cwd=build_path) # --program-prefix=PREFIX 
        subprocess.call(f"make".split(), cwd=build_path)
        subprocess.call(f"make install".split(), cwd=build_path) # tauari_c.so* will be installed in {build_path}

class PrePostDevelopCompile(setuptools.command.develop.develop):
    """pre- and post-compilation for development mode (only pre- currently)"""
    def run(self):
        biomc2_compilation("--enable-debug")
        setuptools.command.develop.develop.run(self) # run() after chec k_call means pre-install
class PrePostInstallCompile(setuptools.command.install.install):
    """Pre- and post-compilation for installation mode (only pre- currently)"""
    def run(self):
        biomc2_compilation()
        setuptools.command.install.install.run(self)
class PrePostEggInfoCompile(setuptools.command.egg_info.egg_info):
    """Pre- and post-compilation for installation mode (only pre- currently)"""
    def run(self):
        biomc2_compilation()
        setuptools.command.egg_info.egg_info.run(self)

setuptools.setup(
    name = "tauari",
    version = version_txt,
    author = "Leonardo de Oliveira Martins",
    author_email = "Leonardo.de-Oliveira-Martins@quadram.ac.uk",
    description = "Python bindings for biomcmc-lib, a C library for phylogenetics",
    long_description = long_description,
    long_description_content_type = "text/markdown",
    keywords = "phylogenetics",
    url = "https://github.com/quadram-institute-bioscience",
    project_urls = {
        "Source": "https://github.com/quadram-institute-bioscience",
    },
    packages = setuptools.find_packages(),
#    package_dir = {'tauari':"build_setup/lib"}, # copy to site-packages/tauari 
    package_data = {'tauari': ["build_setup/lib/tauari_c.so*"]},      # relative paths to setup.py only 
    data_files = [("", ["LICENSE"])],
    python_requires = '>={}'.format('.'.join(str(n) for n in min_version)),
    license='GPLv3+',
    install_requires=[
        'treeswift >= 1.0',
        'biopython >= 1.70'
       ],
    classifiers = [
        "Development Status :: 2 - Pre-Alpha",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
        "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
        "Programming Language :: Python :: 3",
        "Programming Language :: Python :: 3.6"
        "Programming Language :: Python :: 3.7",
        "Programming Language :: Python :: 3.8",
    ],
    # Install a "tauari" program which calls tauari.__main__.main()
    # entry_points = { "console_scripts": ["tauari = tauari.tauari:main"]},
    # ext_modules = [module_c], 
    cmdclass={
        'develop':  PrePostDevelopCompile,
        'install':  PrePostInstallCompile,
        'egg_info':  PrePostEggInfoCompile,
    } 
)