141 lines
4.3 KiB
Python
Executable File
141 lines
4.3 KiB
Python
Executable File
import glob
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import os
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import sys
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import re
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import subprocess
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from distutils import log
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from distutils.core import setup
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from distutils.core import Extension
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from distutils.sysconfig import get_python_lib
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import os.path
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from distutils import log
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from distutils.extension import Extension
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sys.path.append(os.path.abspath("python"))
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def findPackage(root,base=None):
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modules=[]
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if base is None:
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base=[]
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for module in (os.path.basename(os.path.dirname(x))
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for x in glob.glob(os.path.join(root,'*','__init__.py'))):
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modules.append('.'.join(base+[module]))
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modules.extend(findPackage(os.path.join(root,module),base+[module]))
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return modules
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def RunMake():
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log.info("Build the build/cobject directory")
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try:
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os.mkdir("build")
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except OSError:
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pass
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try:
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os.mkdir("build/cobject")
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except OSError:
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pass
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oldwd = os.getcwd()
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os.chdir("build/cobject")
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install_clibdir_option="-DPYTHONLIB:STRING='%s'" % get_python_lib()
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log.info("Run CMake")
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subprocess.call(['cmake', install_clibdir_option, '../../src'])
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log.info("Compile the shared C library")
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subprocess.call(['make','install']) # temporary fix but should be in src
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os.chdir(oldwd)
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#def install_dependencies(deps):
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# for r in deps:
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# log.info("Installing dependency : %s" %r)
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# subprocess.call(['pip','install',r])
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PACKAGE = "OBITools3"
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VERSION = "0.0.6"
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AUTHOR = 'Eric Coissac'
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EMAIL = 'eric@metabarcoding.org'
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URL = "http://metabarcoding.org/obitools3"
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LICENSE = "CeCILL-V2"
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DESCRIPTION = "Tools and library for DNA metabarcoding",
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PYTHONMIN = '3.7'
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SRC = 'python'
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CSRC = 'src'
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REQUIRES = ['Cython>=0.24',
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'Sphinx>=1.2.0',
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'ipython>=3.0.0',
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'breathe>=4.0.0'
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]
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os.environ['CFLAGS'] = '-O3 -Wall -I "src" -I "src/libecoPCR" -I "src/libjson"'
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#install_dependencies(REQUIRES)
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RunMake()
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from Cython.Build import cythonize
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cython_src = [x for x in glob.iglob('python/obitools3/**/*.pyx',
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recursive=True
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)
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]
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#with open(os.path.join(os.path.dirname(__file__), 'README.rst')) as f:
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# readme = f.read()
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cython_ext = [Extension('.'.join([os.path.dirname(x).replace("python/",""),
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os.path.splitext(os.path.basename(x))[0]]).replace('/','.'),
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[x],
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library_dirs=[get_python_lib()],
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include_dirs=["src","src/libecoPCR","src/libjson"],
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libraries=["cobitools3"],
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runtime_library_dirs=[get_python_lib()],
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extra_compile_args=['-msse2',
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'-Wno-unused-function',
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'-Wmissing-braces',
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'-Wchar-subscripts',
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'-fPIC'
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],
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extra_link_args=["-Wl,-rpath,"+get_python_lib(),
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"-L"+get_python_lib()
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]
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)
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for x in cython_src
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]
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xx = cythonize(cython_ext,
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language_level=3,
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annotate=True,
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build_dir="build")
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#, include_path=["src","src/libecoPCR","src/libjson"]
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classifiers=['Development Status :: 1 - Planning',
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'Environment :: Console',
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'Intended Audience :: Science/Research',
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'License :: Other/Proprietary License',
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'Operating System :: Unix',
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'Programming Language :: Python :: 3',
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'Programming Language :: C',
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'Topic :: Scientific/Engineering :: Bio-Informatics',
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'Topic :: Utilities',
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]
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setup(name=PACKAGE,
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description=DESCRIPTION,
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classifiers=classifiers,
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version=VERSION,
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author=AUTHOR,
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author_email=EMAIL,
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license=LICENSE,
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url=URL,
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ext_modules=xx,
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packages = findPackage('python'),
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package_dir = {"" : "python"},
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scripts = ['scripts/obi']
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)
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