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Revert #868 and use the old setup.py

This commit is contained in:
Heng Li 2023-04-29 11:48:41 -04:00
parent 4483f89ee5
commit f8d46a7a30
1 changed files with 21 additions and 31 deletions
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52
setup.py
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@ -1,37 +1,26 @@
try: try:
from setuptools import setup, Extension from setuptools import setup, Extension
from setuptools.command.build_ext import build_ext
except ImportError: except ImportError:
from distutils.core import setup from distutils.core import setup
from distutils.extension import Extension from distutils.extension import Extension
from distutils.command.build_ext import build_ext
import sys, platform, subprocess import sys, platform
sys.path.append('python')
extra_compile_args = ['-DHAVE_KALLOC']
include_dirs = ["."]
if platform.machine() in ["aarch64", "arm64"]:
include_dirs.append("sse2neon/")
extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__'])
else:
extra_compile_args.append('-msse4.1') # WARNING: ancient x86_64 CPUs don't have SSE4
def readme(): def readme():
with open('python/README.rst') as f: with open('python/README.rst') as f:
return f.read() return f.read()
class LibMM2Build(build_ext):
# Uses Makefile to build library, avoids duplicating logic
# determining which objects to compile but does require
# end users to have Make (since precompiled wheels are not
# distributed on PyPI).
def run(self):
def compile_libminimap2(*args, **kwargs):
cmd = ['make', 'libminimap2.a'] + list(args)
subprocess.check_call(cmd)
options = []
if platform.machine() in ["aarch64", "arm64"]:
options = ["arm_neon=1", "aarch64=1"]
self.execute(
compile_libminimap2, options,
'Compiling libminimap2 using Makefile')
build_ext.run(self)
setup( setup(
name = 'mappy', name = 'mappy',
version = '2.25', version = '2.25',
@ -43,15 +32,16 @@ setup(
license = 'MIT', license = 'MIT',
keywords = 'sequence-alignment', keywords = 'sequence-alignment',
scripts = ['python/minimap2.py'], scripts = ['python/minimap2.py'],
cmdclass = {'build_ext': LibMM2Build}, ext_modules = [Extension('mappy',
ext_modules = [ sources = ['python/mappy.pyx', 'align.c', 'bseq.c', 'lchain.c', 'seed.c', 'format.c', 'hit.c', 'index.c', 'pe.c', 'options.c',
Extension( 'ksw2_extd2_sse.c', 'ksw2_exts2_sse.c', 'ksw2_extz2_sse.c', 'ksw2_ll_sse.c',
'mappy', 'kalloc.c', 'kthread.c', 'map.c', 'misc.c', 'sdust.c', 'sketch.c', 'esterr.c', 'splitidx.c'],
sources = ['python/mappy.pyx'], depends = ['minimap.h', 'bseq.h', 'kalloc.h', 'kdq.h', 'khash.h', 'kseq.h', 'ksort.h',
depends = ['python/cmappy.h', 'python/cmappy.pxd'], 'ksw2.h', 'kthread.h', 'kvec.h', 'mmpriv.h', 'sdust.h',
include_dirs = ['.'], 'python/cmappy.h', 'python/cmappy.pxd'],
extra_objects = ['libminimap2.a'], extra_compile_args = extra_compile_args,
libraries = ['z', 'm', 'pthread'])], include_dirs = include_dirs,
libraries = ['z', 'm', 'pthread'])],
classifiers = [ classifiers = [
'Development Status :: 5 - Production/Stable', 'Development Status :: 5 - Production/Stable',
'License :: OSI Approved :: MIT License', 'License :: OSI Approved :: MIT License',