"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages, Extension
from distutils import spawn
# To use a consistent encoding
from codecs import open
import os
import glob
import shutil
import platform
import sys
# For debugging, set the below to True. Run with (sth like): LD_PRELOAD='/usr/lib64/gcc/x86_64-pc-linux-gnu/9.2.0/libasan.so.5.0.0' python ...
use_asan = False
here = os.path.abspath(os.path.dirname(__file__))
# Get the long description from the relevant file
#with open(path.join(here, 'DESCRIPTION.rst'), encoding='utf-8') as f:
# long_description = f.read()
def get_cflags():
if 'windows' in platform.system().lower():
# Assuming MSVC, probably Anaconda
return ["/O2", "/std:c++17"]
if use_asan:
return '-O0 -g -DISOSPEC_DEBUG -std=c++17 -fsanitize=address'.split()
return '-mtune=native -march=native -O3 -std=c++17'.split()
cmodule = Extension('IsoSpecCppPy',
sources = ['IsoSpec++/python-build.cpp'],
extra_compile_args = get_cflags(),
extra_link_args = '-fsanitize=address'.split() if use_asan else []
)
setup_args = {
#setup(
'name': 'IsoSpecPy',
# Versions should comply with PEP440. For a discussion on single-sourcing
# the version across setup.py and the project code, see
# https://packaging.python.org/en/latest/single_source_version.html
'version': '2.2.1',
'description': 'Python interface to IsoSpec++ isotopic envelope calculator library',
'long_description': 'Python interface to IsoSpec++ isotopic envelope calculator library',
# The project's main homepage.
'url': 'http://matteolacki.github.io/IsoSpec/',
# Author details
'author': 'Mateusz Lacki & Michal Startek',
'author_email': 'matteo.lacki@gmail.com',
# Choose your license
'license': '2-clause BSD',
# See https://pypi.python.org/pypi?%3Aaction=list_classifiers
'classifiers' : [
# How mature is this project? Common values are
# 3 - Alpha
# 4 - Beta
# 5 - Production/Stable
'Development Status :: 5 - Production/Stable',
# Indicate who your project is intended for
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering :: Chemistry',
# Pick your license as you wish (should match "license" above)
'License :: OSI Approved :: BSD License',
# Specify the Python versions you support here. In particular, ensure
# that you indicate whether you support Python 2, Python 3 or both.
'Programming Language :: Python :: 2',
'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3',
'Programming Language :: Python :: 3.2',
'Programming Language :: Python :: 3.3',
'Programming Language :: Python :: 3.4',
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: 3.7',
'Programming Language :: Python :: 3.8',
'Programming Language :: Python :: 3.9',
],
# What does your project relate to?
'keywords' : 'isotopic envelope mass spectrometry',
# You can just specify the packages manually here if your project is
# simple. Or you can use find_packages().
'packages' : ['IsoSpecPy'],#find_packages(),
# List run-time dependencies here. These will be installed by pip when
# your project is installed. For an analysis of "install_requires" vs pip's
# requirements files see:
# https://packaging.python.org/en/latest/requirements.html
'install_requires' : ['cffi'],
'zip_safe' : False,
# List additional groups of dependencies here (e.g. development
# dependencies). You can install these using the following syntax,
# for example:
# $ pip install -e .[dev,test]
'extras_require' : {
'test': ["pytest", "numpy"]
},
# If there are data files included in your packages that need to be
# installed, specify them here. If using Python 2.6 or less, then these
# have to be included in MANIFEST.in as well.
'package_data' : {},
# Although 'package_data' is the preferred approach, in some case you may
# need to place data files outside of your packages. See:
# http://docs.python.org/3.4/distutils/setupscript.html#installing-additional-files # noqa
# In this case, 'data_file' will be installed into '<sys.prefix>/my_data'
'data_files' : [], #[('my_data', ['data/data_file'])],
# To provide executable scripts, use entry points in preference to the
# "scripts" keyword. Entry points provide cross-platform support and allow
# pip to create the appropriate form of executable for the target platform.
# entry_points={
# 'console_scripts': [
# 'sample=sample:main',
# ],
# },
'ext_modules' : [cmodule],
}
if 'cygwin' in platform.system().lower():
try:
import cffi
except ImportError:
print("You appear to be using CYGWIN, and CFFI was not found. Please use the Cygwin installer to install the cffi-python package for the appropriate Python version.")
print("Installing CFFI using pip will most likely NOT work. This is *NOT* a bug in IsoSpecPy.")
sys.exit(1)
if spawn.find_executable('clang++') == None:
print("You appear to be using CYGWIN and clang++ executable was not found. Please install the clang++ package using Cygwin installer.")
sys.exit(1)
import distutils
import distutils.sysconfig
distutils.sysconfig.get_config_vars() # Precalculate the dict so we can...
distutils.sysconfig._config_vars['CFLAGS'] = "" # Nuke CFLAGS: they contain gcc stuff not supported by clang
from distutils.command.build_ext import build_ext
class build_ext_subclass(build_ext):
def get_libraries(self, ext):
return ext.libraries # Override default function which wants to link in libpython on Windows. We're using CFFI and don't need that.
setup_args['cmdclass'] = {'build_ext' : build_ext_subclass}
setup(**setup_args)
elif 'darwin' in platform.system().lower():
# Okay, so OSX is apparently horribly broken. On OSX the "g++" command can be nonexistent and stuff will be compiled with clang++,
# or g++ can be present and behave sanely, or it can be clang pretending to be g++ and behaving somewhat sanely, or it can be broken
# clang which needs extra commandline arguments to compile anything that imports stdlib headers. Because hey, it's absolutely normal
# that C++ compiler should require extra commandline args to compile a "Hello World" program, and of course those commandline options
# are incompatible with g++ it's pretending to be. Someone at Apple should be tarred and feathered for this. For now we will do
# some convoluted logic to try to find out experimentally whether "g++" really is g++, or is working clang or is broken clang, and
# which flags are needed to compile stuff. Setuptools don't make this easy to do as well...
#
# See https://github.com/mciach/wassersteinms/issues/1 for the rationale behind this.
from distutils.command.build_ext import build_ext
import subprocess
class build_ext_subclass(build_ext):
def build_extensions(self):
compiler_cmd = "g++" # sane default in case the next stuff crashes...
try:
compiler_cmd = self.compiler.compiler_cxx[0]
compiler_cmd = self.compiler.compiler_so_cxx[0]
except AttributeError:
pass
with open(os.devnull, 'w') as devnull:
def check_flags(flags_l):
cpp_hello_world = '''#include <iostream>
int main()
{
std::cout << "Hello World!" << std::endl;
};
'''
try:
proc = subprocess.Popen([compiler_cmd] + ["-x", "c++", "-fsyntax-only", "-"] + flags_l, stdin = subprocess.PIPE, stdout = devnull, stderr = devnull, universal_newlines = True)
proc.stdin.write(cpp_hello_world)
proc.stdin.flush()
proc.stdin.close()
ret = proc.wait()
except (OSError, IOError):
return False
print("Check flags:", ret == 0, flags_l)
return ret == 0
extra_flags = []
if check_flags([]):
pass
elif check_flags(["-stdlib=libc++"]):
extra_flags.append("-stdlib=libc++")
elif check_flags(["-stdlib=libstdc++"]):
extra_flags.append("-stdlib=libstdc++")
# Check flags, because OF COURSE OSX's clang masquerading as g++ doesn't support some of them
for flag in cmodule.extra_compile_args:
if check_flags(extra_flags + [flag]):
extra_flags.append(flag)
cmodule.extra_compile_args = extra_flags
# else just hope for the best, that is, that the compiler isn't broken...
try:
super(build_ext_subclass, self).build_extensions()
except TypeError: # which means we're on Python 2 and *of course* build_ext is an old-style class...
build_ext.build_extensions(self)
setup_args['cmdclass'] = {'build_ext' : build_ext_subclass}
setup(**setup_args)
else:
# Assuming sane UNIX with a working compiler.
setup(**setup_args)