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try:
from setuptools import setup, Extension
except ImportError:
from distutils.core import setup
from distutils.extension import Extension
import sys, platform
import subprocess
sys.path.append('python')
extra_compile_args = ['-DHAVE_KALLOC']
# extra_link_args= ['-lminimap2'] # FIXME: this is ignored :-(
extra_objects = ['libminimap2.a']
include_dirs = ["."]
arch = subprocess.run(["dpkg-architecture", "-qDEB_HOST_ARCH"], capture_output=True, text=True).stdout.strip()
if arch in ["aarch64", "arm64"]:
extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-DUSE_SIMDE', '-D__SSE2__', '-DSIMDE_ENABLE_NATIVE_ALIASES', '-fopenmp-simd', '-O3', '-DSIMDE_ENABLE_OPENMP'])
elif arch != "amd64":
extra_compile_args.extend(['-DKSW_SSE2_ONLY', '-DUSE_SIMDE', '-DSIMDE_ENABLE_NATIVE_ALIASES', '-fopenmp-simd', '-O3', '-DSIMDE_ENABLE_OPENMP'])
def readme():
with open('python/README.rst') as f:
return f.read()
setup(
name = 'mappy',
version = '2.27',
url = 'https://github.com/lh3/minimap2',
description = 'Minimap2 python binding',
long_description = readme(),
author = 'Heng Li',
author_email = 'lh3@me.com',
license = 'MIT',
keywords = 'sequence-alignment',
scripts = ['python/minimap2.py'],
ext_modules = [Extension('mappy',
sources = ['python/mappy.pyx', 'align.c', 'bseq.c', 'lchain.c', 'seed.c', 'format.c', 'hit.c', 'index.c', 'pe.c', 'options.c',
'ksw2_extd2_sse.c', 'ksw2_exts2_sse.c', 'ksw2_extz2_sse.c', 'ksw2_ll_sse.c',
'kalloc.c', 'kthread.c', 'map.c', 'misc.c', 'sdust.c', 'sketch.c', 'esterr.c', 'splitidx.c'],
depends = ['minimap.h', 'bseq.h', 'kalloc.h', 'kdq.h', 'khash.h', 'kseq.h', 'ksort.h',
'ksw2.h', 'kthread.h', 'kvec.h', 'mmpriv.h', 'sdust.h',
'python/cmappy.h', 'python/cmappy.pxd'],
extra_compile_args = extra_compile_args,
include_dirs = include_dirs,
libraries = ['z', 'm', 'pthread'])],
classifiers = [
'Development Status :: 5 - Production/Stable',
'License :: OSI Approved :: MIT License',
'Operating System :: POSIX',
'Programming Language :: C',
'Programming Language :: Cython',
'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3',
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering :: Bio-Informatics'],
setup_requires=["cython"])
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