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import os, platform, sys
try:
from setuptools import setup, Extension
except ImportError:
from distutils.core import setup
from distutils.extension import Extension
simde = ['-DUSE_SIMDE', '-DSIMDE_ENABLE_NATIVE_ALIASES']
if platform.system() == "Darwin":
# note: see https://github.com/pypa/wheel/issues/406
simd_flag = ['-march=native', '-D__AVX2__', '-mmacosx-version-min=10.9']
if platform.machine() in ["aarch64", "arm64"]:
os.environ['_PYTHON_HOST_PLATFORM'] = "macosx-10.9-arm64"
os.environ['ARCHFLAGS'] = "-arch arm64"
else:
os.environ['_PYTHON_HOST_PLATFORM'] = "macosx-10.9-x86_64"
os.environ['ARCHFLAGS'] = "-arch x86_64"
else:
if platform.machine() in ["aarch64", "arm64"]:
simd_flag = ['-march=armv8-a+simd', '-D__AVX2__']
elif platform.machine() in ["aarch32"]:
simd_flag = ['-march=armv8-a+simd', '-mfpu=auto -D__AVX2__']
else:
simd_flag=['-march=native']
if os.getenv('SSE4', False):
simd_flag=['-msse4.1']
elif os.getenv('SSE2', False):
simd_flag=['-msse2']
elif os.getenv('AVX2', False):
simd_flag=['-mavx2']
#elif os.getenv('AVX512F', False):
# simd_flag='-mavx512f'
#elif os.getenv('AVX512BW', False):
# simd_flag='-mavx512bw'
src_dir = 'src/'
inc_dir = 'include/'
sources = [
'abpoa_align.c', 'abpoa_graph.c', 'abpoa_output.c', 'abpoa_plot.c', 'abpoa_seed.c', 'abpoa_seq.c',
'kalloc.c', 'kstring.c',
'simd_abpoa_align.c', 'simd_check.c',
'utils.c']
depends = [
'abpoa.h', 'abpoa_align.h', 'abpoa_graph.h', 'abpoa_output.h', 'abpoa_seed.h', 'abpoa_seq.h',
'kalloc.h', 'khash.h', 'kdq.h', 'kseq.h', 'ksort.h', 'kstring.h', 'kvec.h',
'simd_abpoa_align.h', 'simd_instruction.h',
'utils.h']
module_src = 'python/pyabpoa.pyx'
module_dep = 'python/cabpoa.pxd'
long_description = open('python/README.md').read()
setup(
# Information
name = "pyabpoa",
description = "pyabpoa: SIMD-based partial order alignment using adaptive band",
long_description = long_description,
long_description_content_type="text/markdown",
version = "1.5.1",
url = "https://github.com/yangao07/abPOA",
author = "Yan Gao",
author_email = "gaoy1@chop.edu",
license = "MIT",
keywords = "multiple-sequence-alignment partial-order-graph-alignment",
setup_requires=["cython"],
# Build instructions
ext_modules = [
Extension(
"pyabpoa",
sources=[module_src] + [src_dir + x for x in sources],
include_dirs=[inc_dir],
depends=[module_dep] + [src_dir + x for x in depends],
libraries=['z', 'm', 'pthread'],
# extra_compile_args=['-O3', '-Wno-error=declaration-after-statement', '-D __DEBUG__'] + simde + simd_flag
extra_compile_args=['-O3', '-Wno-misleading-indentation', '-Wno-error=declaration-after-statement'] + simde
)]
)
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