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"""
Build cutadapt.
"""
import sys
import os.path
from setuptools import setup, Extension
from distutils.version import LooseVersion
from distutils.command.sdist import sdist as _sdist
from distutils.command.build_ext import build_ext as _build_ext
import versioneer
MIN_CYTHON_VERSION = '0.23.2'
if sys.version_info < (2, 6):
sys.stdout.write("At least Python 2.6 is required.\n")
sys.exit(1)
def out_of_date(extensions):
"""
Check whether any pyx source is newer than the corresponding generated
C source or whether any C source is missing.
"""
for extension in extensions:
for pyx in extension.sources:
path, ext = os.path.splitext(pyx)
if ext not in ('.pyx', '.py'):
continue
if extension.language == 'c++':
csource = path + '.cpp'
else:
csource = path + '.c'
# When comparing modification times, allow five seconds slack:
# If the installation is being run from pip, modification
# times are not preserved and therefore depends on the order in
# which files were unpacked.
if not os.path.exists(csource) or (
os.path.getmtime(pyx) > os.path.getmtime(csource) + 5):
return True
return False
def no_cythonize(extensions, **_ignore):
"""
Change file extensions from .pyx to .c or .cpp.
Copied from Cython documentation
"""
for extension in extensions:
sources = []
for sfile in extension.sources:
path, ext = os.path.splitext(sfile)
if ext in ('.pyx', '.py'):
if extension.language == 'c++':
ext = '.cpp'
else:
ext = '.c'
sfile = path + ext
sources.append(sfile)
extension.sources[:] = sources
def check_cython_version():
"""Exit if Cython was not found or is too old"""
try:
from Cython import __version__ as cyversion
except ImportError:
sys.stdout.write(
"ERROR: Cython is not installed. Install at least Cython version " +
str(MIN_CYTHON_VERSION) + " to continue.\n")
sys.exit(1)
if LooseVersion(cyversion) < LooseVersion(MIN_CYTHON_VERSION):
sys.stdout.write(
"ERROR: Your Cython is at version '" + str(cyversion) +
"', but at least version " + str(MIN_CYTHON_VERSION) + " is required.\n")
sys.exit(1)
extensions = [
Extension('cutadapt._align', sources=['cutadapt/_align.pyx']),
Extension('cutadapt._qualtrim', sources=['cutadapt/_qualtrim.pyx']),
Extension('cutadapt._seqio', sources=['cutadapt/_seqio.pyx']),
]
cmdclass = versioneer.get_cmdclass()
versioneer_build_ext = cmdclass.get('build_ext', _build_ext)
versioneer_sdist = cmdclass.get('sdist', _sdist)
class build_ext(versioneer_build_ext):
def run(self):
# If we encounter a PKG-INFO file, then this is likely a .tar.gz/.zip
# file retrieved from PyPI that already includes the pre-cythonized
# extension modules, and then we do not need to run cythonize().
if os.path.exists('PKG-INFO'):
no_cythonize(extensions)
else:
# Otherwise, this is a 'developer copy' of the code, and then the
# only sensible thing is to require Cython to be installed.
check_cython_version()
from Cython.Build import cythonize
self.extensions = cythonize(self.extensions)
versioneer_build_ext.run(self)
class sdist(versioneer_sdist):
def run(self):
# Make sure the compiled Cython files in the distribution are up-to-date
from Cython.Build import cythonize
check_cython_version()
cythonize(extensions)
versioneer_sdist.run(self)
cmdclass['build_ext'] = build_ext
cmdclass['sdist'] = sdist
with open('README.rst', 'rb') as f:
long_description = f.read().decode('utf8')
setup(
name = 'cutadapt',
version = versioneer.get_version(),
author = 'Marcel Martin',
author_email = 'marcel.martin@scilifelab.se',
url = 'https://cutadapt.readthedocs.io/',
description = 'trim adapters from high-throughput sequencing reads',
long_description = long_description,
license = 'MIT',
cmdclass = cmdclass,
ext_modules = extensions,
packages = ['cutadapt', 'cutadapt.scripts'],
install_requires = ['xopen>=0.1.0'],
entry_points = {'console_scripts': ['cutadapt = cutadapt.scripts.cutadapt:main']},
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Natural Language :: English",
"Programming Language :: Cython",
"Programming Language :: Python :: 2.7",
"Programming Language :: Python :: 3",
"Topic :: Scientific/Engineering :: Bio-Informatics"
]
)
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