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#!/usr/bin/env python
# -*- coding: utf-8 -*-
import io
import os
import re
import glob
from setuptools import find_packages, setup
from setuptools.extension import Extension
try:
from Cython.Distutils import build_ext as _build_ext
from Cython.Build import cythonize
except ImportError:
raise ImportError('Cython is now required to build the extension modules.')
def _read(*parts, **kwargs):
filepath = os.path.join(os.path.dirname(__file__), *parts)
encoding = kwargs.pop("encoding", "utf-8")
with io.open(filepath, encoding=encoding) as fh:
text = fh.read()
return text
def get_version():
version = re.search(
r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
_read("pairtools", "__init__.py"),
re.MULTILINE,
).group(1)
return version
def get_ext_modules():
ext = ".pyx"
src_files = glob.glob(
#os.path.join(os.path.dirname(__file__), "pairtools", "lib", "*" + ext)
os.path.join("pairtools", "lib", "*" + ext)
)
ext_modules = []
for src_file in src_files:
name = "pairtools.lib." + os.path.splitext(os.path.basename(src_file))[0]
if 'pysam' in name:
import pysam
ext_modules.append(
Extension(
name,
[src_file],
extra_link_args=pysam.get_libraries(),
include_dirs=pysam.get_include(),
define_macros=pysam.get_defines(),
)
)
elif "regions" in name:
ext_modules.append(
Extension(
name,
[src_file],
language="c++",
)
)
else:
ext_modules.append(Extension(name, [src_file]))
ext_modules = cythonize(ext_modules) # , annotate=True
return ext_modules
class build_ext(_build_ext):
# Extension module build configuration
def finalize_options(self):
_build_ext.finalize_options(self)
# Fix to work with bootstrapped numpy installation
# http://stackoverflow.com/a/21621689/579416
# Prevent numpy from thinking it is still in its setup process:
#__builtins__.__NUMPY_SETUP__ = False
import numpy
self.include_dirs.append(numpy.get_include())
def run(self):
# Import numpy here, only when headers are needed
import numpy
# Add numpy headers to include_dirs
self.include_dirs.append(numpy.get_include())
# Call original build_ext command
_build_ext.run(self)
setup(
version=get_version(),
ext_modules=get_ext_modules(),
cmdclass={"build_ext": build_ext},
zip_safe=False,
# entry_points={
# "console_scripts": [
# "pairtools = pairtools.cli:cli",
# ]
# },
packages=find_packages(),
)
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