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# This file is based on https://github.com/pybind/python_example
# which is under a BSD-like license:
# https://github.com/pybind/python_example/blob/master/LICENSE
from setuptools import setup, Extension
from setuptools.command.build_ext import build_ext
from setuptools import distutils
import os
import sys
USE_SYSTEM_ZLIB = False
MIN_PYBIND_VER = '2.6.2'
def read_version_from_header():
with open('include/gemmi/version.hpp') as f:
for line in f:
if line.startswith('#define GEMMI_VERSION '):
return line.split()[2].strip('"dev')
__version__ = read_version_from_header()
class get_pybind_include(object):
"""Helper class to determine the pybind11 include path
The purpose of this class is to postpone importing pybind11
until it is actually installed, so that the ``get_include()``
method can be invoked. """
def __str__(self):
import pybind11
return pybind11.get_include()
if USE_SYSTEM_ZLIB:
zlib_library = 'z'
zlib_include_dirs = []
build_libs = []
else:
zlib_library = 'gemmi_zlib'
zlib_include_dirs = ['third_party/zlib']
zlib_files = ['third_party/zlib/%s.c' % name for name in
['adler32', 'crc32', 'gzlib', 'gzread', 'inflate',
'inftrees', 'inffast', 'zutil']]
zlib_macros = [('NO_GZCOMPRESS', '1')]
if os.name != 'nt':
zlib_macros += [('Z_HAVE_UNISTD_H', '1')]
build_libs = [('gemmi_zlib', {'sources': zlib_files,
'macros': zlib_macros})]
ext_modules = [
Extension('gemmi',
['python/%s.cpp' % name for name in
['gemmi', 'align', 'ccp4', 'chemcomp', 'cif', 'custom',
'elem', 'hkl', 'grid', 'meta', 'mol', 'monlib', 'mtz',
'read', 'recgrid', 'scaling', 'search', 'sf', 'sym',
'topo', 'unitcell', 'write']],
include_dirs=zlib_include_dirs + [
'include',
'third_party',
# Path to pybind11 headers
get_pybind_include(),
],
libraries=[zlib_library],
language='c++'),
]
# As of Python 3.6, CCompiler has a `has_flag` method.
# cf http://bugs.python.org/issue26689
def has_flag(compiler, flagname):
"""Return a boolean indicating whether a flag name is supported on
the specified compiler.
"""
import tempfile
with tempfile.NamedTemporaryFile('w', suffix='.cpp', delete=False) as f:
# Don't trigger -Wunused-parameter.
f.write('int main (int, char **) { return 0; }')
fname = f.name
try:
compiler.compile([fname], extra_postargs=[flagname])
except distutils.errors.CompileError:
return False
finally:
try:
os.remove(fname)
except OSError:
pass
return True
def cpp_flag(compiler):
"""Return the -std=c++[11/14/17] compiler flag.
The newer version is prefered over c++11 (when it is available).
"""
flags = ['-std=c++17', '-std=c++14', '-std=c++11']
# C++17 on Mac requires higher -mmacosx-version-min, skip it for now
if sys.platform == 'darwin':
flags.pop(0)
for flag in flags:
if has_flag(compiler, flag):
return flag
raise RuntimeError('Unsupported compiler -- at least C++11 support '
'is needed!')
class BuildExt(build_ext):
"""A custom build extension for adding compiler-specific options."""
c_opts = {
'msvc': ['/EHsc', '/D_CRT_SECURE_NO_WARNINGS'],
'unix': [],
}
l_opts = {
'msvc': [],
'unix': [],
}
if sys.platform == 'win32':
if sys.version_info[0] == 2:
# without these variables distutils insist on using VS 2008
os.environ['DISTUTILS_USE_SDK'] = '1'
os.environ['MSSdk'] = '1'
if sys.version_info[0] >= 3:
c_opts['msvc'].append('/D_UNICODE')
def build_extensions(self):
ct = self.compiler.compiler_type
opts = self.c_opts.get(ct, [])
link_opts = self.l_opts.get(ct, [])
if sys.platform == 'darwin':
darwin_opts = []
if 'MACOSX_DEPLOYMENT_TARGET' not in os.environ:
import platform
mac_ver = platform.mac_ver()
current_macos = tuple(int(x) for x in mac_ver[0].split(".")[:2])
if current_macos > (10, 9):
darwin_opts.append('-mmacosx-version-min=10.9')
if has_flag(self.compiler, '-stdlib=libc++'):
darwin_opts.append('-stdlib=libc++')
opts += darwin_opts
link_opts += darwin_opts
if ct == 'unix':
opts.append(cpp_flag(self.compiler))
if has_flag(self.compiler, '-fvisibility=hidden'):
opts.append('-fvisibility=hidden')
if has_flag(self.compiler, '-g0'):
opts.append('-g0')
if has_flag(self.compiler, '-Wl,-s'):
link_opts.append('-Wl,-s')
elif ct.startswith('mingw'):
#opts.append('-std=c++14')
opts.append(cpp_flag(self.compiler))
opts.append('-fvisibility=hidden')
opts.append('-g0')
link_opts.append('-Wl,-s')
for ext in self.extensions:
ext.define_macros = [('VERSION_INFO',
'"%s"' % self.distribution.get_version())]
ext.extra_compile_args = opts
ext.extra_link_args = link_opts
build_ext.build_extensions(self)
setup(
name='gemmi',
version=__version__,
author='Marcin Wojdyr',
author_email='wojdyr@gmail.com',
url='https://project-gemmi.github.io/',
description='library for structural biology',
long_description='''\
Library for macromolecular crystallography and structural bioinformatics.
For working with coordinate files (mmCIF, PDB, mmJSON),
refinement restraints (monomer library), electron density maps (CCP4),
and crystallographic reflection data (MTZ, SF-mmCIF). It understands
crystallographic symmetries, it knows how to switch between the real
and reciprocal space and it can do a few other things.
The setup.py script builds only Python extension.
Use cmake to build also a command-line program.
''',
long_description_content_type='text/plain',
libraries=build_libs,
ext_modules=ext_modules,
packages=['gemmi-examples'],
package_dir={'gemmi-examples': 'examples'},
install_requires=[],
setup_requires=['pybind11>=' + MIN_PYBIND_VER],
cmdclass={'build_ext': BuildExt},
zip_safe=False,
license='MPL-2.0', # or, at your option, LGPL-3.0
keywords=('structural bioinformatics, structural biology, crystallography,'
' CIF, mmCIF, PDB, CCP4, MTZ'),
classifiers=[
'Development Status :: 4 - Beta',
'Intended Audience :: Developers',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)',
'Topic :: Software Development :: Libraries :: Python Modules',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Topic :: Scientific/Engineering :: Chemistry',
'Programming Language :: C++',
'Programming Language :: Python',
],
)
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