setup.py

# -*- coding: utf-8 -*-
import sys
import os
import os.path
from glob import glob

import setuptools
from distutils.core import setup, Extension
from distutils import sysconfig, spawn


import platform

build_asan = False

# If we're not on Windows, assume something POSIX-compatible (either Linux, OSX, *BSD or Cygwin) with a working gcc-like compiler
windows = platform.system() == "Windows"

# Dual-build: work-around for the fact that we have both C and C++ files in the extension, and sometimes need
# to split it into two. Windows and CYGWIN for now seems to need dual_build set to False, OSX to True, Linux seems fine
# with either setting.
dual_build = not windows

if platform.system() == "Windows":
    assert not build_asan
    dual_build = False
elif platform.system().startswith("CYGWIN"):
    dual_build = False


# native_build = "CIBUILDWHEEL" not in os.environ and 'darwin' not in platform.system().lower() and not 'aarch' in platform.machine().lower()
native_build = False  # For now, Ubuntu ships with GCC on which -march=native is broken... and it just fails in too many situations.

use_clang = (
    (not windows)
    and spawn.find_executable("clang++") != None
    and os.getenv("OPENTIMS_USE_DEFAULT_CXX") == None
)
# use_ccache = (not windows) and spawn.find_executable('ccache') != None and native_build
use_ccache = os.path.exists("./use_ccache")

# Prefer clang on UNIX if available
if use_clang:
    if use_ccache:
        os.environ["CXX"] = "ccache g++"
        os.environ["CC"] = "ccache gcc"
    else:
        os.environ["CXX"] = "clang++"
else:
    if use_ccache:
        os.environ["CXX"] = "ccache c++"
        os.environ["CC"] = "ccache cc"
    else:
        # leave defaults
        pass


def get_cflags(asan=False, warnings=True, std_flag=False):
    if windows:
        return ["/O2"]
    if asan:
        return "-Og -g -std=c++20 -fsanitize=address".split()
    res = ["-g", "-O3"]
    if std_flag:
        res.append("-std=c++20")
    if warnings:
        res.extend(["-Wall", "-Wextra"])
    if native_build:
        res.extend(["-march=native", "-mtune=native"])
    return res


cflags = get_cflags


class get_pybind_include(object):
    """Helper class to determine the pybind11 include path
    The purpose of this class is to postpone importing pybind11
    until it is actually installed, so that the ``get_include()``
    method can be invoked."""

    def __str__(self):
        try:
            import pybind11

            return pybind11.get_include()
        except ImportError:
            print(
                "pybind11 not found. Please either install it manually, or install via pip rather than through setuptools directly."
            )
            sys.exit(1)


if dual_build:
    ext_modules = [
        Extension(
            name="libopentims_support",
            sources=[
                os.path.join("opentims++", "sqlite", "sqlite3.c"),
                os.path.join("opentims++", "zstd", "zstddeclib.c"),
            ],
            extra_compile_args=get_cflags(asan=False, warnings=False, std_flag=False),
            libraries=[] if windows else "pthread dl".split(),
            include_dirs=[get_pybind_include()],
        ),
        Extension(
            name="opentimspy_cpp",
            sources=[
                os.path.join("opentims++", "opentims_pybind11.cpp"),
            ],
            extra_compile_args=get_cflags(asan=build_asan, std_flag=True),
            libraries=[] if windows else "pthread dl".split(),
            include_dirs=[get_pybind_include()],
            undef_macros=[] if not build_asan else ["NDEBUG"],
        ),
        Extension(
            name="libopentims_cpp",
            sources=[os.path.join("opentims++", "opentims_all.cpp")],
            extra_compile_args=get_cflags(asan=False, std_flag=True),
            libraries=[] if windows else "pthread dl".split(),
        ),
    ]
else:
    ext_modules = [
        Extension(
            name="opentimspy_cpp",
            sources=[
                os.path.join("opentims++", "sqlite", "sqlite3.c"),
                os.path.join("opentims++", "zstd", "zstddeclib.c"),
                os.path.join("opentims++", "opentims_pybind11.cpp"),
            ],
            extra_compile_args=get_cflags(asan=build_asan, std_flag=True),
            libraries="" if windows else "pthread dl".split(),
            include_dirs=[get_pybind_include()],
        ),
        Extension(
            name="libopentims_cpp",
            sources=[
                os.path.join("opentims++", "sqlite", "sqlite3.c"),
                os.path.join("opentims++", "zstd", "zstddeclib.c"),
                os.path.join("opentims++", "libopentims_py.cpp"),
            ],
            extra_compile_args=get_cflags(asan=False, std_flag=True),
            libraries=[] if windows else "pthread dl".split(),
        ),
    ]


setup(
    name="opentimspy",
    packages=["opentimspy"],
    version="1.0.16",
    author="Mateusz Krzysztof Łącki (MatteoLacki), Michał Startek (michalsta)",
    author_email="matteo.lacki@gmail.com, michal.startek@mimuw.edu.pl",
    description="opentimspy: An open-source parser of Bruker Tims Data File (.tdf).",
    long_description="opentimspy: An open-source parser of Bruker Tims Data File (.tdf).",
    keywords=["timsTOFpro", "Bruker TDF", "data science", "mass spectrometry"],
    classifiers=[
        "Development Status :: 4 - Beta",
        "Intended Audience :: Science/Research",
        "Topic :: Scientific/Engineering :: Chemistry",
        "Programming Language :: Python :: 3.6",
        "Programming Language :: Python :: 3.7",
        "Programming Language :: Python :: 3.8",
        "Programming Language :: Python :: 3.9",
    ],
    zip_safe=False,
    setup_requires=["pybind11"],
    install_requires=["pybind11", "numpy"],
    ext_modules=ext_modules,
    scripts=glob("scripts/*.py"),
    package_dir={"opentimspy": "opentimspy"},
    package_data={
        "opentimspy": ["opentims++/*.h", "opentims++/*/*.h", "opentims++/*.hpp"]
    },
    extras_require={"bruker_proprietary": ["opentims_bruker_bridge>=1.0.3"], "plotting":["matplotlib"]},
)