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setup.py
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setup.py
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try:
from setuptools import setup
from setuptools.extension import Extension
except ImportError:
from distutils.core import setup
from distutils.extension import Extension
import numpy as np
import ctypes
from Cython.Distutils import build_ext
from sys import platform
import sys, os, subprocess, warnings, re
from os import environ
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
## For debugging
if "--asan" in sys.argv:
ADD_ASAN = True
sys.argv.remove("--asan")
else:
ADD_ASAN = False
if "--ggdb" in sys.argv:
ADD_GGDB = True
sys.argv.remove("--ggdb")
else:
ADD_GGDB = False
## 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):
is_msvc = self.compiler.compiler_type == "msvc"
is_clang = hasattr(self.compiler, 'compiler_cxx') and ("clang++" in self.compiler.compiler_cxx)
is_windows = sys.platform[:3] == "win"
is_mingw = (is_windows and
(self.compiler.compiler_type.lower()
in ["mingw32", "mingw64", "mingw", "msys", "msys2", "gcc", "g++"]))
no_ld = "NO_LONG_DOUBLE" in os.environ
has_robinmap = os.path.exists("src/robinmap/include/tsl")
if is_msvc:
for e in self.extensions:
e.extra_compile_args = ['/openmp', '/O2', '/GL', '/std:c++14', '/fp:except-', '/wd4244', '/wd4267', '/wd4018', '/wd5030']
e.define_macros += [("NO_LONG_DOUBLE", None)]
if has_robinmap:
e.define_macros += [("_USE_ROBIN_MAP", None)]
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_restrict_qualifier()
self.add_O3()
self.add_no_math_errno()
self.add_no_trapping_math()
if not is_mingw:
self.add_highest_supported_cxx_standard()
if not is_windows:
self.add_link_time_optimization()
for e in self.extensions:
if is_mingw:
e.extra_compile_args += ['-std=gnu++14']
if np.iinfo(ctypes.c_size_t).max >= (2**64 - 1):
e.define_macros += [("_FILE_OFFSET_BITS", 64)]
if has_robinmap:
e.define_macros += [("_USE_ROBIN_MAP", None)]
if is_windows or no_ld:
e.define_macros += [("NO_LONG_DOUBLE", None)]
if ADD_ASAN and not is_msvc:
# run this with `LD_PRELOAD=libasan.so python script.py`
for e in self.extensions:
if not is_clang:
e.extra_compile_args += ["-fsanitize=address", "-static-libasan", "-ggdb"]
else:
e.extra_compile_args += ["-fsanitize=address", "-static-libsan", "-ggdb"]
elif ADD_GGDB and not is_msvc:
for e in self.extensions:
e.extra_compile_args += ["-ggdb"]
build_ext.build_extensions(self)
def check_cflags_contain_arch(self):
if ("CFLAGS" in os.environ) or ("CXXFLAGS" in os.environ):
has_cflags = "CFLAGS" in os.environ
has_cxxflags = "CXXFLAGS" 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 has_cflags and flag in os.environ["CFLAGS"]:
return True
if has_cxxflags and flag in os.environ["CXXFLAGS"]:
return True
return False
def check_for_variable_dont_set_march(self):
return "DONT_SET_MARCH" in os.environ
def add_march_native(self):
is_apple = sys.platform[:3].lower() == "dar"
args_march_native = ["-march=native", "-mcpu=native"]
for arg_march_native in args_march_native:
if self.test_supports_compile_arg(arg_march_native, with_c_comp=is_apple):
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_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 add_O3(self):
O3 = "-O3"
if self.test_supports_compile_arg(O3):
for e in self.extensions:
e.extra_compile_args.append(O3)
def add_highest_supported_cxx_standard(self):
args_cxx_std = ["-std=c++17", "-std=gnu++14", "-std=c++11"]
set_standard = False
for arg_cxx_std in args_cxx_std:
if self.test_supports_compile_arg(arg_cxx_std):
for e in self.extensions:
e.extra_compile_args.append(arg_cxx_std)
set_standard = True
break
if not set_standard:
msg = "\n\n\nWarning: compiler does not support C++11, compilation/installation of "
msg += "'isotree' might fail without it.\n\n\n"
warnings.warn(msg)
# Note: in apple systems, it somehow might end up triggering the arguments with
# the C compiler instead of the CXX compiler. What's worse, sometimes this compiler
# thinks it's building for aarch64 even when executed in amd64.
def test_supports_compile_arg(self, comm, with_omp=False, with_c_comp=False):
is_supported = False
try:
if not hasattr(self.compiler, "compiler_cxx"):
return False
if not isinstance(comm, list):
comm = [comm]
print("--- Checking compiler support for option '%s'" % " ".join(comm))
fname = "isotree_compiler_testing.cpp"
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_cxx, list):
cmd = list(self.compiler.compiler_cxx)
else:
cmd = self.compiler.compiler_cxx
except Exception:
cmd = self.compiler.compiler_cxx
if with_c_comp:
if not isinstance(self.compiler.compiler, list):
cmd0 = list(self.compiler.compiler)
else:
cmd0 = 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)
if is_supported and with_c_comp:
val = subprocess.run(cmd0 + 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
def add_restrict_qualifier(self):
supports_restrict = False
try:
if not hasattr(self.compiler, "compiler_cxx"):
return None
print("--- Checking compiler support for '__restrict' qualifier")
fname = "isotree_compiler_testing.cpp"
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_cxx, list):
cmd = list(self.compiler.compiler_cxx)
else:
cmd = self.compiler.compiler_cxx
except Exception:
cmd = self.compiler.compiler_cxx
try:
with open(fname, "w") as ftest:
ftest.write(u"int main(int argc, char**argv) {double *__restrict x = 0; return 0;}\n")
val = subprocess.run(cmd + comm + [fname], capture_output=silent_tests).returncode
is_supported = (val == EXIT_SUCCESS)
except Exception:
return None
except Exception:
pass
try:
os.remove(fname)
except Exception:
pass
if supports_restrict:
for e in self.extensions:
e.define_macros += [("SUPPORTS_RESTRICT", "1")]
setup(
name = "isotree",
packages = ["isotree"],
version = '0.6.1-4',
description = 'Isolation-Based Outlier Detection, Distance, and NA imputation',
author = 'David Cortes',
url = 'https://github.com/david-cortes/isotree',
keywords = ['isolation-forest', 'anomaly', 'outlier'],
cmdclass = {'build_ext': build_ext_subclass},
ext_modules = [Extension(
"isotree._cpp_interface",
sources=["isotree/cpp_interface.pyx",
"src/indexer.cpp",
"src/merge_models.cpp", "src/subset_models.cpp",
"src/serialize.cpp", "src/sql.cpp",
"src/formatted_exporters.cpp"],
include_dirs=[np.get_include(), ".", "./src"],
language="c++",
install_requires = ["numpy", "pandas>=0.24.0", "cython", "scipy"],
define_macros = [("_USE_XOSHIRO", None),
("NDEBUG", None),
("_FOR_PYTHON", None),
("CYTHON_EXTERN_C", 'extern "C"')]
)]
)
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 isotree'.\n"
warnings.warn(omp_msg)