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setup.py
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setup.py
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try:
import setuptools
from setuptools import setup
from setuptools import Extension
except ImportError:
from distutils.core import setup
from distutils.extension import Extension
import numpy
import sys, os, subprocess, warnings, re
from Cython.Distutils import build_ext
found_omp = True
def set_omp_false():
global found_omp
found_omp = False
## Modify this to make the output of the compilation tests more verbose
silent_tests = not (("verbose" in sys.argv)
or ("-verbose" in sys.argv)
or ("--verbose" in sys.argv))
## Workaround for python<=3.9 on windows
try:
EXIT_SUCCESS = os.EX_OK
except AttributeError:
EXIT_SUCCESS = 0
## https://stackoverflow.com/questions/724664/python-distutils-how-to-get-a-compiler-that-is-going-to-be-used
class build_ext_subclass( build_ext ):
def build_extensions(self):
if self.compiler.compiler_type == 'msvc':
for e in self.extensions:
e.extra_compile_args += ['/O2', '/openmp', '/GL', '/fp:fast']
else:
if not self.check_for_variable_dont_set_march() and not self.check_cflags_contain_arch():
self.add_march_native()
self.add_openmp_linkage()
self.add_no_math_errno()
self.add_no_trapping_math()
self.add_ffp_contract_fast()
self.add_O3()
self.add_std_c99()
self.add_link_time_optimization()
# for e in self.extensions:
# e.extra_compile_args += ['-O3', '-fopenmp', '-march=native', '-std=c99']
# e.extra_link_args += ['-fopenmp']
# e.extra_compile_args += ["-fsanitize=address", "-static-libasan", "-ggdb"]
# e.extra_link_args += ["-fsanitize=address", "-static-libasan"]
# e.extra_compile_args += ["-ggdb"]
build_ext.build_extensions(self)
def check_cflags_contain_arch(self):
if "CFLAGS" in os.environ:
arch_list = [
"-march", "-mcpu", "-mtune", "-msse", "-msse2", "-msse3",
"-mssse3", "-msse4", "-msse4a", "-msse4.1", "-msse4.2",
"-mavx", "-mavx2", "-mavx512"
]
for flag in arch_list:
if flag in os.environ["CFLAGS"]:
return True
return False
def check_for_variable_dont_set_march(self):
return "DONT_SET_MARCH" in os.environ
def add_march_native(self):
args_march_native = ["-march=native", "-mcpu=native"]
for arg_march_native in args_march_native:
if self.test_supports_compile_arg(arg_march_native):
for e in self.extensions:
e.extra_compile_args.append(arg_march_native)
break
def add_link_time_optimization(self):
args_lto = ["-flto=auto", "-flto"]
for arg_lto in args_lto:
if self.test_supports_compile_arg(arg_lto):
for e in self.extensions:
e.extra_compile_args.append(arg_lto)
e.extra_link_args.append(arg_lto)
break
def add_no_math_errno(self):
arg_fnme = "-fno-math-errno"
if self.test_supports_compile_arg(arg_fnme):
for e in self.extensions:
e.extra_compile_args.append(arg_fnme)
e.extra_link_args.append(arg_fnme)
def add_no_trapping_math(self):
arg_fntm = "-fno-trapping-math"
if self.test_supports_compile_arg(arg_fntm):
for e in self.extensions:
e.extra_compile_args.append(arg_fntm)
e.extra_link_args.append(arg_fntm)
def add_ffp_contract_fast(self):
arg_ffpc = "-ffp-contract=fast"
if self.test_supports_compile_arg(arg_ffpc):
for e in self.extensions:
e.extra_compile_args.append(arg_ffpc)
e.extra_link_args.append(arg_ffpc)
def add_O3(self):
arg_O3 = "-O3"
if self.test_supports_compile_arg(arg_O3):
for e in self.extensions:
e.extra_compile_args.append(arg_O3)
e.extra_link_args.append(arg_O3)
def add_std_c99(self):
arg_std_c99 = "-std=c99"
if self.test_supports_compile_arg(arg_std_c99):
for e in self.extensions:
e.extra_compile_args.append(arg_std_c99)
e.extra_link_args.append(arg_std_c99)
def add_openmp_linkage(self):
arg_omp1 = "-fopenmp"
arg_omp2 = "-fopenmp=libomp"
args_omp3 = ["-fopenmp=libomp", "-lomp"]
arg_omp4 = "-qopenmp"
arg_omp5 = "-xopenmp"
is_apple = sys.platform[:3].lower() == "dar"
args_apple_omp = ["-Xclang", "-fopenmp", "-lomp"]
args_apple_omp2 = ["-Xclang", "-fopenmp", "-L/usr/local/lib", "-lomp", "-I/usr/local/include"]
has_brew_omp = False
if is_apple:
try:
res_brew_pref = subprocess.run(["brew", "--prefix", "libomp"], capture_output=True)
if res_brew_pref.returncode == EXIT_SUCCESS:
brew_omp_prefix = res_brew_pref.stdout.decode().strip()
args_apple_omp3 = ["-Xclang", "-fopenmp", f"-L{brew_omp_prefix}/lib", "-lomp", f"-I{brew_omp_prefix}/include"]
has_brew_omp = True
except Exception as e:
pass
if self.test_supports_compile_arg(arg_omp1, with_omp=True):
for e in self.extensions:
e.extra_compile_args.append(arg_omp1)
e.extra_link_args.append(arg_omp1)
elif is_apple and self.test_supports_compile_arg(args_apple_omp, with_omp=True):
for e in self.extensions:
e.extra_compile_args += ["-Xclang", "-fopenmp"]
e.extra_link_args += ["-lomp"]
elif is_apple and self.test_supports_compile_arg(args_apple_omp2, with_omp=True):
for e in self.extensions:
e.extra_compile_args += ["-Xclang", "-fopenmp"]
e.extra_link_args += ["-L/usr/local/lib", "-lomp"]
e.include_dirs += ["/usr/local/include"]
elif is_apple and has_brew_omp and self.test_supports_compile_arg(args_apple_omp3, with_omp=True):
for e in self.extensions:
e.extra_compile_args += ["-Xclang", "-fopenmp"]
e.extra_link_args += [f"-L{brew_omp_prefix}/lib", "-lomp"]
e.include_dirs += [f"{brew_omp_prefix}/include"]
elif self.test_supports_compile_arg(arg_omp2, with_omp=True):
for e in self.extensions:
e.extra_compile_args += ["-fopenmp=libomp"]
e.extra_link_args += ["-fopenmp"]
elif self.test_supports_compile_arg(args_omp3, with_omp=True):
for e in self.extensions:
e.extra_compile_args += ["-fopenmp=libomp"]
e.extra_link_args += ["-fopenmp", "-lomp"]
elif self.test_supports_compile_arg(arg_omp4, with_omp=True):
for e in self.extensions:
e.extra_compile_args.append(arg_omp4)
e.extra_link_args.append(arg_omp4)
elif self.test_supports_compile_arg(arg_omp5, with_omp=True):
for e in self.extensions:
e.extra_compile_args.append(arg_omp5)
e.extra_link_args.append(arg_omp5)
else:
set_omp_false()
def test_supports_compile_arg(self, comm, with_omp=False):
is_supported = False
try:
if not hasattr(self.compiler, "compiler"):
return False
if not isinstance(comm, list):
comm = [comm]
print("--- Checking compiler support for option '%s'" % " ".join(comm))
fname = "poismf_compiler_testing.c"
with open(fname, "w") as ftest:
ftest.write(u"int main(int argc, char**argv) {return 0;}\n")
try:
if not isinstance(self.compiler.compiler, list):
cmd = list(self.compiler.compiler)
else:
cmd = self.compiler.compiler
except Exception:
cmd = self.compiler.compiler
if with_omp:
with open(fname, "w") as ftest:
ftest.write(u"#include <omp.h>\nint main(int argc, char**argv) {return 0;}\n")
try:
val = subprocess.run(cmd + comm + [fname], capture_output=silent_tests).returncode
is_supported = (val == EXIT_SUCCESS)
except Exception:
is_supported = False
except Exception:
pass
try:
os.remove(fname)
except Exception:
pass
return is_supported
setup(
name = "poismf",
packages = ["poismf"],
author = 'David Cortes',
url = 'https://github.com/david-cortes/poismf',
version = '0.4.0-10',
install_requires = ['numpy', 'pandas>=0.24', 'cython', 'scipy'],
description = 'Fast and memory-efficient Poisson factorization for sparse count matrices',
cmdclass = {'build_ext': build_ext_subclass},
ext_modules = [
Extension("poismf.c_funs_double",
sources=["poismf/cfuns_double.pyx",
"src/poismf.c", "src/topN.c", "src/pred.c",
"src/nonnegcg.c", "src/tnc.c"],
include_dirs=[numpy.get_include(), "src/"],
define_macros = [
("_FOR_PYTHON", None),
("NDEBUG", None),
]),
Extension("poismf.c_funs_float",
sources=["poismf/cfuns_float.pyx",
"src/poismf.c", "src/topN.c", "src/pred.c",
"src/nonnegcg.c", "src/tnc.c"],
include_dirs=[numpy.get_include(), "src/"],
define_macros = [
("_FOR_PYTHON", None),
("NDEBUG", None),
("USE_FLOAT", None),
])
]
)
if not found_omp:
omp_msg = "\n\n\nCould not detect OpenMP. Package will be built without multi-threading capabilities. "
omp_msg += " To enable multi-threading, first install OpenMP"
if (sys.platform[:3] == "dar"):
omp_msg += " - for macOS: 'brew install libomp'\n"
else:
omp_msg += " modules for your compiler. "
omp_msg += "Then reinstall this package from scratch: 'pip install --upgrade --no-deps --force-reinstall poismf'.\n"
warnings.warn(omp_msg)