setup.py

#! /usr/bin/env python3

import os
import re
import sys
import sysconfig
import platform
import subprocess

from distutils.version import LooseVersion
from setuptools import setup, Extension, find_packages
from setuptools.command.build_ext import build_ext
from setuptools.command.test import test as TestCommand
from shutil import copyfile, copymode

PROJECT_NAME = "pinetree"
VERSION = "0.4.1"

class CMakeExtension(Extension):
    def __init__(self, name, sourcedir=''):
        Extension.__init__(self, name, sources=[])
        self.sourcedir = os.path.abspath(sourcedir)

class CMakeBuild(build_ext):
    def run(self):
        try:
            out = subprocess.check_output(['cmake', '--version'])
        except:
            print("\nPinetree requires CMake to build and install.\n")
            print(
                "To install CMake, run: \n\npython3 -m pip install cmake\n\nInstallation failed. ")
            sys.exit(1)

        if platform.system() == "Windows":
            cmake_version = LooseVersion(re.search(r'version\s*([\d.]+)',
                                                   out.decode()).group(1))
            if cmake_version < '3.1.0':
                raise RuntimeError("CMake >= 3.1.0 is required on Windows")

        for ext in self.extensions:
            self.build_extension(ext)

    def build_extension(self, ext):
        extdir = os.path.abspath(
            os.path.dirname(self.get_ext_fullpath(ext.name)))
        cmake_args = ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=' + extdir,
                      '-DPYTHON_EXECUTABLE=' + sys.executable]

        cfg = 'Debug' if self.debug else 'Release'
        build_args = ['--config', cfg]

        if platform.system() == "Windows":
            cmake_args += ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_{}={}'.format(
                cfg.upper(),
                extdir)]
            if sys.maxsize > 2**32:
                cmake_args += ['-A', 'x64']
            build_args += ['--', '/m']
        else:
            cmake_args += ['-DCMAKE_BUILD_TYPE=' + cfg]
            build_args += ['--', '-j2']

        # uncomment for openMP support

        #if platform.system() == "Darwin": # force compile with gcc instead of clang
        #    cmake_args += ["-DCMAKE_C_COMPILER=gcc-14", "-DCMAKE_CXX_COMPILER=g++-14"]

        env = os.environ.copy()
        env['CXXFLAGS'] = '{} -DVERSION_INFO=\\"{}\\"'.format(
            env.get('CXXFLAGS', ''),
            self.distribution.get_version())
        if not os.path.exists(self.build_temp):
            os.makedirs(self.build_temp)
        
        subprocess.check_call(['cmake', ext.sourcedir] + cmake_args,
                              cwd=self.build_temp, env=env)
        subprocess.check_call(['cmake', '--build', '.'] + build_args,
                              cwd=self.build_temp)
        test_bin = os.path.join(self.build_temp, PROJECT_NAME + '_test')
        if platform.system() != "Windows":
            self.copy_test_file(test_bin)
        print()  # Add an empty line for cleaner output

    def copy_test_file(self, src_file):
        '''
        Copy ``src_file`` to `tests/bin` directory, ensuring parent directory 
        exists. Messages like `creating directory /path/to/package` and
        `copying directory /src/path/to/package -> path/to/package` are 
        displayed on standard output. Adapted from scikit-build.
        '''
        # Create directory if needed
        dest_dir = os.path.join(os.path.dirname(
            os.path.abspath(__file__)), 'tests', 'bin')
        if dest_dir != "" and not os.path.exists(dest_dir):
            print("creating directory {}".format(dest_dir))
            os.makedirs(dest_dir)

        # Copy file
        dest_file = os.path.join(dest_dir, os.path.basename(src_file))
        print("copying {} -> {}".format(src_file, dest_file))
        copyfile(src_file, dest_file)
        copymode(src_file, dest_file)



with open('README.md', encoding='utf-8') as f:
    readme = f.read()

with open('LICENSE') as f:
    license = f.read()


setup(
    name=PROJECT_NAME,
    version=VERSION,
    description='stochastic simulation of gene expression with site-specific translation rates',
    long_description=readme,
    long_description_content_type='text/markdown',
    author='Benjamin Jack',
    author_email='benjamin.r.jack@gmail.com',
    url='https://github.com/clauswilke/' + PROJECT_NAME,
    download_url='https://github.com/clauswilke/' + PROJECT_NAME + '/archive/v' + VERSION + '.tar.gz',
    license='MIT',
    keywords=['gene', 'codon', 'transcription',
              'translation', 'biology', 'stochastic'],
    packages=find_packages('src'),
    package_dir={'': 'src'},
    ext_modules=[CMakeExtension(PROJECT_NAME + '/core')],
    cmdclass=dict(build_ext=CMakeBuild),
    zip_safe=False,
    test_suite='tests'
)