setup.py

import numpy as np
import yaml
import os
import platform

from setuptools import setup, find_packages
from pybind11.setup_helpers import Pybind11Extension, build_ext

with open('environment.yml') as f:
	required = yaml.safe_load(f.read())['dependencies'][-1]['pip']

is_arm = platform.machine() == 'arm64' or 'arm64' in os.getenv('ARCHFLAGS', '')
is_apple = platform.system() == 'Darwin'
is_windows = platform.system() == 'Windows'

if not is_arm:
	required.append('cpufeature==0.2.0')

sources = ['pyalign/algorithm/module.cpp']

script_dir = os.path.abspath(os.path.dirname(__file__))
include_dirs = [np.get_include(), script_dir]

if is_windows:
	include_dirs.append('deps/xtensor_prefix/include')


def mk_ext(name, arch=None, cpu=None):
	extra_compile_args = []
	extra_link_args = []

	is_sanitize = os.environ.get('PYALIGN_SANITIZE_ADDRESS', False)

	if is_sanitize:
		is_debug_build = True
	else:
		is_debug_build = os.environ.get('PYALIGN_DEBUG_BUILD', False)

	if is_windows:
		if arch == 'haswell':
			extra_compile_args.append('/arch:AVX2')
		if is_debug_build:
			extra_compile_args.append('/DEBUG')
		else:
			extra_compile_args.append('/O2')
	else:
		if is_debug_build:
			extra_compile_args.append('-O0')
			extra_compile_args.append('-g')
		else:
			extra_compile_args.append('-O3')

		extra_compile_args.extend(['-ftemplate-backtrace-limit=0'])
		if arch is not None:
			extra_compile_args.append(f'-march={arch}')
		if cpu is not None:
			extra_compile_args.append(f'-mcpu={cpu}')

	if is_sanitize:
		extra_compile_args.append('-fsanitize=address')
		extra_compile_args.append('-fno-omit-frame-pointer')
		extra_compile_args.append('-fno-optimize-sibling-calls')
		extra_link_args.append('-fsanitize=address')

	return Pybind11Extension(
		f'pyalign.algorithm.{name}.algorithm',
		sources,
		cxx_std=17,
		include_dirs=include_dirs,
		extra_compile_args=extra_compile_args,
		extra_link_args=extra_link_args,
	)


ext_modules = []

if os.environ.get('PYALIGN_PREBUILT_MARCH'):
	ext_modules.append(mk_ext('generic'))
	if is_apple and is_arm:
		ext_modules.append(mk_ext('apple_m1', cpu='apple-m1'))
	elif not is_arm:
		ext_modules.append(mk_ext('intel_avx2', arch='haswell'))
elif is_apple and is_arm:
	ext_modules.append(mk_ext('apple_m1', cpu='apple-m1'))
else:
	ext_modules.append(mk_ext('native', arch='native'))

with open('README.md') as f:
	long_description = f.read()

exec(open('pyalign/_version.py').read())

setup(
	name='pyalign',
	version=__version__,
	packages=find_packages(
		include=[
			'pyalign',
			'pyalign.algorithm',
			'pyalign.problems',
			'pyalign.gaps',
			'pyalign.io',
			'pyalign.tests',
		]
	),
	python_requires='>=3.7',
	license='MIT',
	author='Bernhard Liebl',
	author_email='liebl@informatik.uni-leipzig.de',
	url='https://github.com/poke1024/pyalign',
	ext_modules=ext_modules,
	cmdclass={'build_ext': build_ext},
	install_requires=required,
	description='Fast and Versatile Alignments for Python',
	long_description=long_description,
	long_description_content_type='text/markdown',
	# include_package_data=True,
)