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#!/usr/bin/python3
from setuptools import setup
from distutils.command.build import build as _build
from distutils.errors import CompileError
from distutils import sysconfig
import os, re, sys
from glob import glob
from os.path import join, dirname as up
def die(msg):
print(msg)
sys.exit(1)
def str_version(tpl):
return ".".join(map(str, tpl))
def configure():
"""
Look up the dependencies
- Python.h
- numpy headers
- boost headers (from configuration flag)
meanwhile, pass through any config-looking arguments (ex: --boost=...)
"""
# Python.h
python_inc = sysconfig.get_python_inc()
# Libpython
python_libdir = join(sysconfig.get_python_lib(standard_lib=True), "config")
python_lib = "python" + sysconfig.get_python_version()
if '--version' in sys.argv:
return "--version"
# numpy headers
try:
import numpy
numpy_inc = numpy.get_include()
except ImportError:
die("Requires numpy >= 1.6.0")
ccArgs = re.compile(r"^--(?:boost|swig|swig-lib)=?")
ccOpts = re.compile(r"^--(?:debug|c\+\+11|pbi|modules)$")
configArgs = []
for arg in sys.argv[:]:
if ccArgs.match(arg) or ccOpts.match(arg):
configArgs.append(arg)
sys.argv.remove(arg)
configArgs.append("--python-include=%s " % python_inc)
configArgs.append("--numpy-include=%s " % numpy_inc)
return " ".join(configArgs)
# This always has to be run, to remove extra arguments that will
# confuse setuptools otherwise
configuration = configure()
class build(_build):
"""
Build the native code using the Makefile, sidestepping
most of the horrors of Python packaging.
"""
def run(self):
error = os.system("./configure " + configuration)
if error:
raise CompileError("Failed to configure ConsensusCore build")
error = os.system("make python")
if error:
raise CompileError("Failed to compile or link ConsensusCore C++ code")
@staticmethod
def pythonBuildDirectory():
"""
Returns the directory where the build stashed the generated
Python module.
"""
#return os.popen("make --no-print-directory echo-python-build-directory").read().strip()
return "build/Python"
# HACK: "setup.py install" will fail if build hasn't been called yet,
# because setuptools attempts to scan the package directory before
# invoking the build---which will fail because the directory is
# created by the build. I consider this a bug in setuptools, and this
# is the least involved workaround I have found: inject "build" into
# the command line.
if "install" in sys.argv and not "build" in sys.argv:
installPos = sys.argv.index("install")
sys.argv.insert(installPos, "build")
setup(name="ConsensusCore",
version="1.0.2",
author="Pacific Biosciences",
author_email="devnet@pacificbiosciences.com",
url="http://www.github.com/PacificBiosciences/ConsensusCore",
description= \
"""A library for genomic consensus and variant calling""",
license=open("LICENSES").read(),
py_modules=["ConsensusCore"],
packages = [""],
package_dir={"": build.pythonBuildDirectory() },
# Smuggle the native library in as a data file
package_data={"": ["_ConsensusCore.so"]},
cmdclass={"build": build})
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