from __future__ import print_function, absolute_import
import os
import sys
import json
import string
import shutil
import subprocess
import tempfile
from distutils.dep_util import newer_group
from distutils.core import Extension
from distutils.errors import DistutilsExecError
from distutils.ccompiler import new_compiler
from distutils.sysconfig import customize_compiler, get_config_vars
from distutils.command.build_ext import build_ext as _build_ext
def find_packages():
"""Find all of assaytools's python packages.
Adapted from IPython's setupbase.py. Copyright IPython
contributors, licensed under the BSD license.
"""
packages = ['assaytools.scripts']
for dir,subdirs,files in os.walk('AssayTools'):
package = dir.replace(os.path.sep, '.')
if '__init__.py' not in files:
# not a package
continue
packages.append(package.replace('AssayTools', 'assaytools'))
return packages
################################################################################
# Detection of compiler capabilities
################################################################################
class CompilerDetection(object):
# Necessary for OSX. See https://github.com/assaytools/assaytools/issues/576
# The problem is that distutils.sysconfig.customize_compiler()
# is necessary to properly invoke the correct compiler for this class
# (otherwise the CC env variable isn't respected). Unfortunately,
# distutils.sysconfig.customize_compiler() DIES on OSX unless some
# appropriate initialization routines have been called. This line
# has a side effect of calling those initialzation routes, and is therefor
# necessary for OSX, even though we don't use the result.
_DONT_REMOVE_ME = get_config_vars()
def __init__(self, disable_openmp):
cc = new_compiler()
customize_compiler(cc)
self.msvc = cc.compiler_type == 'msvc'
self._print_compiler_version(cc)
if disable_openmp:
self.openmp_enabled = False
else:
self.openmp_enabled, openmp_needs_gomp = self._detect_openmp()
self.sse3_enabled = self._detect_sse3() if not self.msvc else True
self.sse41_enabled = self._detect_sse41() if not self.msvc else True
self.compiler_args_sse2 = ['-msse2'] if not self.msvc else ['/arch:SSE2']
self.compiler_args_sse3 = ['-mssse3'] if (self.sse3_enabled and not self.msvc) else []
self.compiler_args_sse41, self.define_macros_sse41 = [], []
if self.sse41_enabled:
self.define_macros_sse41 = [('__SSE4__', 1), ('__SSE4_1__', 1)]
if not self.msvc:
self.compiler_args_sse41 = ['-msse4']
if self.openmp_enabled:
self.compiler_libraries_openmp = []
if self.msvc:
self.compiler_args_openmp = ['/openmp']
else:
self.compiler_args_openmp = ['-fopenmp']
if openmp_needs_gomp:
self.compiler_libraries_openmp = ['gomp']
else:
self.compiler_libraries_openmp = []
self.compiler_args_openmp = []
if self.msvc:
self.compiler_args_opt = ['/O2']
else:
self.compiler_args_opt = ['-O3', '-funroll-loops']
print()
def _print_compiler_version(self, cc):
print("C compiler:")
try:
if self.msvc:
if not cc.initialized:
cc.initialize()
cc.spawn([cc.cc])
else:
cc.spawn([cc.compiler[0]] + ['-v'])
except DistutilsExecError:
pass
def hasfunction(self, funcname, include=None, libraries=None, extra_postargs=None):
# running in a separate subshell lets us prevent unwanted stdout/stderr
part1 = '''
from __future__ import print_function
import os
import json
from distutils.ccompiler import new_compiler
from distutils.sysconfig import customize_compiler, get_config_vars
FUNCNAME = json.loads('%(funcname)s')
INCLUDE = json.loads('%(include)s')
LIBRARIES = json.loads('%(libraries)s')
EXTRA_POSTARGS = json.loads('%(extra_postargs)s')
''' % {
'funcname': json.dumps(funcname),
'include': json.dumps(include),
'libraries': json.dumps(libraries or []),
'extra_postargs': json.dumps(extra_postargs)}
part2 = '''
get_config_vars() # DON'T REMOVE ME
cc = new_compiler()
customize_compiler(cc)
for library in LIBRARIES:
cc.add_library(library)
status = 0
try:
with open('func.c', 'w') as f:
if INCLUDE is not None:
f.write('#include %s\\n' % INCLUDE)
f.write('int main(void) {\\n')
f.write(' %s;\\n' % FUNCNAME)
f.write('}\\n')
objects = cc.compile(['func.c'], output_dir='.',
extra_postargs=EXTRA_POSTARGS)
cc.link_executable(objects, 'a.out')
except Exception as e:
status = 1
exit(status)
'''
tmpdir = tempfile.mkdtemp(prefix='hasfunction-')
try:
curdir = os.path.abspath(os.curdir)
os.chdir(tmpdir)
with open('script.py', 'w') as f:
f.write(part1 + part2)
proc = subprocess.Popen(
[sys.executable, 'script.py'],
stderr=subprocess.PIPE, stdout=subprocess.PIPE)
proc.communicate()
status = proc.wait()
finally:
os.chdir(curdir)
shutil.rmtree(tmpdir)
return status == 0
def _print_support_start(self, feature):
print('Attempting to autodetect {0:6} support...'.format(feature), end=' ')
def _print_support_end(self, feature, status):
if status is True:
print('Compiler supports {0}'.format(feature))
else:
print('Did not detect {0} support'.format(feature))
def _detect_openmp(self):
self._print_support_start('OpenMP')
hasopenmp = self.hasfunction('omp_get_num_threads()', extra_postargs=['-fopenmp', '/openmp'])
needs_gomp = hasopenmp
if not hasopenmp:
hasopenmp = self.hasfunction('omp_get_num_threads()', libraries=['gomp'])
needs_gomp = hasopenmp
self._print_support_end('OpenMP', hasopenmp)
return hasopenmp, needs_gomp
def _detect_sse3(self):
"Does this compiler support SSE3 intrinsics?"
self._print_support_start('SSE3')
result = self.hasfunction('__m128 v; _mm_hadd_ps(v,v)',
include='<pmmintrin.h>',
extra_postargs=['-msse3'])
self._print_support_end('SSE3', result)
return result
def _detect_sse41(self):
"Does this compiler support SSE4.1 intrinsics?"
self._print_support_start('SSE4.1')
result = self.hasfunction( '__m128 v; _mm_round_ps(v,0x00)',
include='<smmintrin.h>',
extra_postargs=['-msse4'])
self._print_support_end('SSE4.1', result)
return result
################################################################################
# Writing version control information to the module
################################################################################
def git_version():
# Return the git revision as a string
# copied from numpy setup.py
def _minimal_ext_cmd(cmd):
# construct minimal environment
env = {}
for k in ['SYSTEMROOT', 'PATH']:
v = os.environ.get(k)
if v is not None:
env[k] = v
# LANGUAGE is used on win32
env['LANGUAGE'] = 'C'
env['LANG'] = 'C'
env['LC_ALL'] = 'C'
out = subprocess.Popen(
cmd, stdout=subprocess.PIPE, env=env).communicate()[0]
return out
try:
out = _minimal_ext_cmd(['git', 'rev-parse', 'HEAD'])
GIT_REVISION = out.strip().decode('ascii')
except OSError:
GIT_REVISION = 'Unknown'
return GIT_REVISION
def write_version_py(VERSION, ISRELEASED, filename='AssayTools/version.py'):
cnt = """
# THIS FILE IS GENERATED FROM ASSAYTOOLS SETUP.PY
short_version = '%(version)s'
version = '%(version)s'
full_version = '%(full_version)s'
git_revision = '%(git_revision)s'
release = %(isrelease)s
if not release:
version = full_version
"""
# Adding the git rev number needs to be done inside write_version_py(),
# otherwise the import of numpy.version messes up the build under Python 3.
FULLVERSION = VERSION
if os.path.exists('.git'):
GIT_REVISION = git_version()
else:
GIT_REVISION = 'Unknown'
if not ISRELEASED:
FULLVERSION += '.dev-' + GIT_REVISION[:7]
a = open(filename, 'w')
try:
a.write(cnt % {'version': VERSION,
'full_version': FULLVERSION,
'git_revision': GIT_REVISION,
'isrelease': str(ISRELEASED)})
finally:
a.close()
class StaticLibrary(Extension):
def __init__(self, *args, **kwargs):
self.export_include = kwargs.pop('export_include', [])
Extension.__init__(self, *args, **kwargs)
class build_ext(_build_ext):
def build_extension(self, ext):
if isinstance(ext, StaticLibrary):
self.build_static_extension(ext)
else:
_build_ext.build_extension(self, ext)
def build_static_extension(self, ext):
from distutils import log
sources = ext.sources
if sources is None or not isinstance(sources, (list, tuple)):
raise DistutilsSetupError(
("in 'ext_modules' option (extension '%s'), " +
"'sources' must be present and must be " +
"a list of source filenames") % ext.name)
sources = list(sources)
ext_path = self.get_ext_fullpath(ext.name)
depends = sources + ext.depends
if not (self.force or newer_group(depends, ext_path, 'newer')):
log.debug("skipping '%s' extension (up-to-date)", ext.name)
return
else:
log.info("building '%s' extension", ext.name)
extra_args = ext.extra_compile_args or []
macros = ext.define_macros[:]
for undef in ext.undef_macros:
macros.append((undef,))
objects = self.compiler.compile(sources,
output_dir=self.build_temp,
macros=macros,
include_dirs=ext.include_dirs,
debug=self.debug,
extra_postargs=extra_args,
depends=ext.depends)
self._built_objects = objects[:]
if ext.extra_objects:
objects.extend(ext.extra_objects)
extra_args = ext.extra_link_args or []
language = ext.language or self.compiler.detect_language(sources)
libname = os.path.basename(ext_path).split(os.extsep)[0]
output_dir = os.path.dirname(ext_path)
if (self.compiler.static_lib_format.startswith('lib') and
libname.startswith('lib')):
libname = libname[3:]
if not os.path.exists(output_dir):
# necessary for windows
os.makedirs(output_dir)
self.compiler.create_static_lib(objects,
output_libname=libname,
output_dir=output_dir,
target_lang=language)
for item in ext.export_include:
shutil.copy(item, output_dir)
