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import json
import os
import shutil
import subprocess
import sys
import tempfile
import warnings
from distutils.ccompiler import new_compiler
from distutils.dep_util import newer_group
from distutils.errors import DistutilsExecError, DistutilsSetupError
from distutils.sysconfig import customize_compiler, get_config_vars
from setuptools import Extension
from setuptools.command.build_ext import build_ext as _build_ext
################################################################################
# Detection of compiler capabilities
################################################################################
class CompilerDetection:
# Necessary for OSX. See https://github.com/mdtraj/mdtraj/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):
self.disable_openmp = disable_openmp
self._is_initialized = False
def initialize(self):
if self._is_initialized:
return
cc = new_compiler()
customize_compiler(cc)
self.msvc = cc.compiler_type == "msvc"
self._print_compiler_version(cc)
if self.disable_openmp:
self.openmp_enabled = False
else:
self.openmp_enabled, openmp_needs_gomp = self._detect_openmp()
self.sse2_enabled = self._detect_sse2() if not self.msvc else True
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.neon_enabled = self._detect_neon() if not self.msvc else False
if self.msvc:
self.compiler_args_sse2 = ["/arch:SSE2"]
elif self.sse2_enabled:
self.compiler_args_sse2 = ["-msse2"]
else:
self.compiler_args_sse2 = []
self.compiler_args_sse3 = ["-mssse3"] if (self.sse3_enabled and not self.msvc) else []
self.compiler_args_neon = []
self.compiler_args_warn = (
["-Wno-unused-function", "-Wno-unreachable-code", "-Wno-sign-compare"] if not self.msvc else []
)
if self.neon_enabled:
self.compiler_args_sse2 = []
self.compiler_args_sse3 = []
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 os.environ.get("MDTRAJ_BUILD_DISABLE_INTRINSICS") == "1":
self.disable_intrinsics = True
print("Env var MDTRAJ_BUILD_DISABLE_INTRINSICS set")
else:
self.disable_intrinsics = False
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", "--std=c++11"]
print()
self._is_initialized = True
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 = f"""
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('{json.dumps(funcname)}')
INCLUDE = json.loads('{json.dumps(include)}')
LIBRARIES = json.loads('{json.dumps(libraries or [])}')
EXTRA_POSTARGS = json.loads('{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(f"Attempting to autodetect {feature:6} support...", end=" ")
def _print_support_end(self, feature, status):
if status is True:
print(f"Compiler supports {feature}")
else:
print(f"Did not detect {feature} support")
def _detect_openmp(self):
self._print_support_start("OpenMP")
extra_postargs = ["/openmp"] if self.msvc else ["-fopenmp"]
args = dict(extra_postargs=extra_postargs, include="<omp.h>")
hasopenmp = self.hasfunction("omp_get_num_threads()", **args)
needs_gomp = False
if not hasopenmp:
hasopenmp = self.hasfunction(
"omp_get_num_threads()",
libraries=["gomp"],
**args,
)
needs_gomp = hasopenmp
self._print_support_end("OpenMP", hasopenmp)
return hasopenmp, needs_gomp
def _detect_sse2(self):
"Does this compiler support SSE2 intrinsics?"
self._print_support_start("SSE2")
result = self.hasfunction(
"__m128d v; _mm_add_pd(v,v)",
include="<immintrin.h>", # Possibly emmintrin.h
extra_postargs=["-msse2"],
)
self._print_support_end("SSE2", result)
return result
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
def _detect_neon(self):
"""Does this compiler support NEON intrinsics (ARM64)"""
self._print_support_start("NEON")
result = self.hasfunction(
"int16x4_t acc = vdup_n_s16(0);",
include="<arm_neon.h>",
)
self._print_support_end("NEON", 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 copy_same_file_pass(source, destination):
try:
# Try to copy
shutil.copy(source, destination)
except shutil.SameFileError:
# Ignore the error
pass
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 copy_extensions_to_source(self):
_extensions = self.extensions
self.extensions = [e for e in _extensions if not isinstance(e, StaticLibrary)]
_build_ext.copy_extensions_to_source(self)
self.extensions = _extensions
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(
f"in 'ext_modules' option (extension '{ext.name}'), "
"'sources' must be present and must be "
"a list of source filenames",
)
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:]
# 1. copy to build directory
# 1. copy to src tree for develop mode
# 1. catch errors because we're running in editable mode
import re
src_tree_output_dir = re.match(".*build.*(mdtraj.*)", output_dir)
try:
# This might fail if no match in editable mode.
src_tree_output_dir = src_tree_output_dir.group(1)
if not os.path.exists(src_tree_output_dir):
os.makedirs(src_tree_output_dir)
except AttributeError:
src_tree_output_dir = output_dir
if not os.path.exists(output_dir):
# necessary for windows
os.makedirs(output_dir)
assert os.path.isdir(src_tree_output_dir)
self.compiler.create_static_lib(
objects,
output_libname=libname,
output_dir=output_dir,
target_lang=language,
)
lib_path = self.compiler.library_filename(libname, output_dir=output_dir)
copy_same_file_pass(lib_path, src_tree_output_dir)
for item in ext.export_include:
copy_same_file_pass(item, src_tree_output_dir)
copy_same_file_pass(item, output_dir)
def get_ext_filename(self, ext_name):
filename = _build_ext.get_ext_filename(self, ext_name)
try:
exts = [e for e in self.extensions if ext_name in {e.name, e.name.split(".")[-1]}]
ext = exts[0]
if isinstance(ext, StaticLibrary):
if new_compiler().compiler_type == "msvc":
return filename.split(".")[0] + ".lib"
else:
return filename.split(".")[0] + ".a"
except Exception as e: # noqa
pass
return filename
def parse_setuppy_commands():
"""Check the commands and respond appropriately.
Return a boolean value for whether or not to run the build or not (avoid
parsing Cython and template files if False).
Adopted from scipy setup
"""
args = sys.argv[1:]
if not args:
# User forgot to give an argument probably, let setuptools handle that.
return True
info_commands = [
"--help-commands",
"--name",
"--version",
"-V",
"--fullname",
"--author",
"--author-email",
"--maintainer",
"--maintainer-email",
"--contact",
"--contact-email",
"--url",
"--license",
"--description",
"--long-description",
"--platforms",
"--classifiers",
"--keywords",
"--provides",
"--requires",
"--obsoletes",
]
for command in info_commands:
if command in args:
return False
# Note that 'alias', 'saveopts' and 'setopt' commands also seem to work
# fine as they are, but are usually used together with one of the commands
# below and not standalone. Hence they're not added to good_commands.
good_commands = (
"develop",
"sdist",
"build",
"build_ext",
"build_py",
"build_clib",
"build_scripts",
"bdist_wheel",
"bdist_rpm",
"bdist_wininst",
"bdist_msi",
"bdist_mpkg",
"build_sphinx",
)
for command in good_commands:
if command in args:
return True
# The following commands are supported, but we need to show more
# useful messages to the user
if "install" in args:
return True
if "--help" in args or "-h" in sys.argv[1]:
return False
# Commands that do more than print info, but also don't need Cython and
# template parsing.
other_commands = ["egg_info", "install_egg_info", "rotate"]
for command in other_commands:
if command in args:
return False
# If we got here, we didn't detect what setup.py command was given
warnings.warn(
"Unrecognized setuptools command ('{}'), proceeding with "
"generating Cython sources and expanding templates".format(
" ".join(sys.argv[1:]),
),
)
return True
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