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# ----------------------------------------------------------------------------
# Copyright (c) 2016-2017, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from setuptools import setup, find_packages
from setuptools.extension import Extension
from setuptools.command.build_ext import build_ext as build_ext_orig
import numpy as np
import subprocess
import os
import sys
PREFIX = os.environ.get('PREFIX', "")
base = ["cython >= 0.26", "biom-format", "numpy", "h5py >= 3.3.0",
"scikit-bio >= 0.5.8", "iow"]
test = ["nose", "flake8"]
all_deps = base + test
# https://stackoverflow.com/a/33308902/379593
if sys.platform == 'darwin':
os.environ['MACOSX_DEPLOYMENT_TARGET'] = '10.12'
def compile_ssu():
"""Clean and compile the SSU binary"""
to_link = ["unifrac/task_parameters.hpp",
"unifrac/api.hpp",
"unifrac/status_enum.hpp"]
# clean the target
cmd = ["rm", "-f"] + to_link
ret = subprocess.call(cmd)
if ret != 0:
raise Exception('Error removing temp unifrac files!')
for f in to_link:
# link to files from conda
cmd = ["ln", "-s", '/usr/include/' + f,
"unifrac/"]
ret = subprocess.call(cmd)
if ret != 0:
raise Exception('Error removing linking unifrac files!')
class build_ext(build_ext_orig):
"""Pre-installation for any time an Extension is built"""
def run(self):
self.run_compile_ssu()
super().run()
def run_compile_ssu(self):
self.execute(compile_ssu, [], 'Compiling SSU')
if sys.platform == "darwin":
LINK_ARGS = ['-Wl,' + os.environ.get('CONDA_PREFIX') +
'/lib/libssu.so']
else:
LINK_ARGS = []
COMPILE_ARGS = []
if 'CONDA_PREFIX' in os.environ:
CONDA_INCLUDES = [os.environ.get('CONDA_PREFIX') + '/include']
else:
CONDA_INCLUDES = []
USE_CYTHON = os.environ.get('USE_CYTHON', True)
ext = '.pyx' if USE_CYTHON else '.cpp'
extensions = [Extension("unifrac._api",
sources=["unifrac/_api" + ext],
extra_link_args=LINK_ARGS,
extra_compile_args=COMPILE_ARGS,
include_dirs=([np.get_include()] +
CONDA_INCLUDES),
libraries=['ssu'])]
if USE_CYTHON:
from Cython.Build import cythonize
extensions = cythonize(extensions)
with open('README.md') as f:
long_description = f.read()
setup(
name="unifrac",
version="1.2.0",
packages=find_packages(),
author="Daniel McDonald",
license='BSD-3-Clause',
author_email="wasade@gmail.com",
url="https://github.com/biocore/unifrac",
description="High performance phylogenetic diversity calculations",
long_description=long_description,
long_description_content_type='text/markdown',
ext_modules=extensions,
install_requires=base,
extras_require={'test': test, 'all': all_deps},
cmdclass={'build_ext': build_ext},
package_data={
'unifrac.tests': ['data/*', ]}
)
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