setup.py

import sys
import traceback
import os
import platform

from setuptools import setup, Extension as _Extension, find_packages

from distutils.command.build_ext import build_ext
from distutils.errors import (CCompilerError, DistutilsExecError,
                              DistutilsPlatformError)


def has_option(name):
    try:
        sys.argv.remove('--%s' % name)
        return True
    except ValueError:
        pass
    # allow passing all cmd line options also as environment variables
    env_val = os.getenv(name.upper().replace('-', '_'), 'false').lower()
    if env_val == "true":
        return True
    return False


include_diagnostics = has_option("include-diagnostics")
force_cythonize = has_option("force-cythonize")
no_openmp = has_option('no-openmp')
debug_symbols = has_option("debug")


with_openmp = not no_openmp


def configure_openmp(ext):
    # http://www.microsoft.com/en-us/download/confirmation.aspx?id=2092 was required.
    if os.name == 'nt' and with_openmp:
        ext.extra_compile_args.append("/openmp")
    elif platform.system() == 'Darwin':
        pass
    elif with_openmp:
        ext.extra_compile_args.append("-fopenmp")
        ext.extra_link_args.append("-fopenmp")


def Extension(*args, **kwargs):
    ext = _Extension(*args, **kwargs)
    if debug_symbols:
        if os.name == 'nt':
            ext.extra_compile_args.append("-Zi")
            ext.extra_compile_args.append("-Ox")
            ext.extra_link_args.append("-debug:full")
        else:
            ext.extra_compile_args.append("-g3")
            ext.extra_compile_args.append("-O0")
    # ext.extra_compile_args.append("/fsanitize=address")
    return ext

def OpenMPExtension(*args, **kwargs):
    ext = Extension(*args, **kwargs)
    configure_openmp(ext)
    return ext


def make_extensions():
    is_ci = bool(os.getenv("CI", ""))
    try:
        import numpy
    except ImportError:
        print("Installation requires `numpy`")
        raise
    try:
        import brainpy
    except ImportError:
        print("Installation requires `brainpy`, install with `python -m pip install brain-isotopic-distribution`")
        raise
    try:
        import ms_peak_picker
    except ImportError:
        print("Installation requires `ms_peak_picker`")
        raise
    macros = []
    try:
        from Cython.Build import cythonize
        cython_directives = {
            'embedsignature': True,
            "profile": include_diagnostics
        }
        if include_diagnostics:
            macros.append(("CYTHON_TRACE_NOGIL", "1"))
        if is_ci and include_diagnostics:
            cython_directives['linetrace'] = True
        extensions = cythonize([
            Extension(name='ms_deisotope._c.scoring', sources=["src/ms_deisotope/_c/scoring.pyx"],
                      include_dirs=[brainpy.get_include(), ms_peak_picker.get_include(), numpy.get_include()]),
            Extension(name='ms_deisotope._c.averagine', sources=["src/ms_deisotope/_c/averagine.pyx"],
                      include_dirs=[brainpy.get_include()], define_macros=macros),
            Extension(name='ms_deisotope._c.deconvoluter_base', sources=["src/ms_deisotope/_c/deconvoluter_base.pyx"],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include()], define_macros=macros),
            Extension(name='ms_deisotope._c.peak_set', sources=["src/ms_deisotope/_c/peak_set.pyx"],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include()]),
            Extension(name='ms_deisotope._c.feature_map.lcms_feature', sources=[
                      "src/ms_deisotope/_c/feature_map/lcms_feature.pyx"],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include()],
                      define_macros=macros),
            Extension(name='ms_deisotope._c.feature_map.feature_processor', sources=[
                      "src/ms_deisotope/_c/feature_map/feature_processor.pyx"],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include(), brainpy.get_include()],
                      define_macros=macros),
            Extension(name='ms_deisotope._c.feature_map.feature_map', sources=[
                      "src/ms_deisotope/_c/feature_map/feature_map.pyx"],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include(), brainpy.get_include()],
                      define_macros=macros),
            Extension(name='ms_deisotope._c.feature_map.feature_fit', sources=[
                      "src/ms_deisotope/_c/feature_map/feature_fit.pyx"],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include(), brainpy.get_include()],
                      define_macros=macros),
            Extension(name='ms_deisotope._c.feature_map.shape_fitter', sources=[
                      "src/ms_deisotope/_c/feature_map/shape_fitter.pyx"],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include(), brainpy.get_include()],
                      define_macros=macros),
            Extension(name='ms_deisotope._c.feature_map.profile_transform', sources=[
                      "src/ms_deisotope/_c/feature_map/profile_transform.pyx"],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include(), brainpy.get_include()],
                      define_macros=macros),
            Extension(name='ms_deisotope._c.feature_map.dependence_network', sources=[
                      "src/ms_deisotope/_c/feature_map/dependence_network.pyx"],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include()],
                      define_macros=macros),
            Extension(name='ms_deisotope._c.utils', sources=["src/ms_deisotope/_c/utils.pyx"],
                      include_dirs=[brainpy.get_include(), ms_peak_picker.get_include(), numpy.get_include()]),
            Extension(name='ms_deisotope._c.peak_dependency_network.intervals',
                      sources=['src/ms_deisotope/_c/peak_dependency_network/intervals.pyx'],
                      include_dirs=[numpy.get_include()], define_macros=macros),
            Extension(name='ms_deisotope._c.peak_dependency_network.subgraph',
                      sources=['src/ms_deisotope/_c/peak_dependency_network/subgraph.pyx'],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include()], define_macros=macros),
            Extension(name='ms_deisotope._c.peak_dependency_network.peak_network',
                      sources=['src/ms_deisotope/_c/peak_dependency_network/peak_network.pyx'],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include()], define_macros=macros),
            Extension(name='ms_deisotope._c.spectrum_graph',
                      sources=['src/ms_deisotope/_c/spectrum_graph.pyx'],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include()], define_macros=macros),
            Extension(name='ms_deisotope._c.feature_map.feature_graph',
                      sources=['src/ms_deisotope/_c/feature_map/feature_graph.pyx'],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include()], define_macros=macros),
            OpenMPExtension(
                name='ms_deisotope._c.similarity_methods', sources=["src/ms_deisotope/_c/similarity_methods.pyx"],
                include_dirs=[brainpy.get_include(), ms_peak_picker.get_include(), numpy.get_include()]),
            Extension(
                name='ms_deisotope._c.units', sources=["src/ms_deisotope/_c/units.pyx"],
                include_dirs=[]),
        ],
        compiler_directives=cython_directives,
        emit_linenums=True,
        force=force_cythonize)
    except ImportError:
        extensions = ([
            Extension(name='ms_deisotope._c.scoring', sources=["src/ms_deisotope/_c/scoring.c"],
                      include_dirs=[brainpy.get_include(), ms_peak_picker.get_include(), numpy.get_include()]),
            Extension(name='ms_deisotope._c.averagine', sources=["src/ms_deisotope/_c/averagine.c"],
                      include_dirs=[brainpy.get_include()]),
            Extension(name='ms_deisotope._c.deconvoluter_base', sources=["src/ms_deisotope/_c/deconvoluter_base.c"],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include()]),
            Extension(name='ms_deisotope._c.peak_set', sources=["src/ms_deisotope/_c/peak_set.c"],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include()]),
            Extension(name='ms_deisotope._c.feature_map.lcms_feature', sources=[
                      "src/ms_deisotope/_c/feature_map/lcms_feature.c"],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include()]),
            Extension(name='ms_deisotope._c.feature_map.feature_processor', sources=[
                      "src/ms_deisotope/_c/feature_map/feature_processor.c"],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include(), brainpy.get_include()]),
            Extension(name='ms_deisotope._c.feature_map.feature_map', sources=[
                      "src/ms_deisotope/_c/feature_map/feature_map.c"],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include(), brainpy.get_include()]),
            Extension(name='ms_deisotope._c.feature_map.feature_fit', sources=[
                      "src/ms_deisotope/_c/feature_map/feature_fit.c"],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include(), brainpy.get_include()]),
            Extension(name='ms_deisotope._c.feature_map.shape_fitter', sources=[
                      "src/ms_deisotope/_c/feature_map/shape_fitter.c"],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include(), brainpy.get_include()],
                      define_macros=macros),
            Extension(name='ms_deisotope._c.feature_map.profile_transform', sources=[
                      "src/ms_deisotope/_c/feature_map/profile_transform.c"],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include(), brainpy.get_include()]),
            Extension(name='ms_deisotope._c.feature_map.dependence_network', sources=[
                      "src/ms_deisotope/_c/feature_map/dependence_network.c"],
                      include_dirs=[
                          numpy.get_include(), ms_peak_picker.get_include()],
                      define_macros=macros),
            Extension(name='ms_deisotope._c.utils', sources=["src/ms_deisotope/_c/utils.c"],
                      include_dirs=[brainpy.get_include(), ms_peak_picker.get_include(), numpy.get_include()]),
            Extension(name='ms_deisotope._c.peak_dependency_network.intervals',
                      sources=['src/ms_deisotope/_c/peak_dependency_network/intervals.c'],
                      include_dirs=[numpy.get_include()], define_macros=macros),
            Extension(name='ms_deisotope._c.peak_dependency_network.subgraph',
                      sources=['src/ms_deisotope/_c/peak_dependency_network/subgraph.c'],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include()], define_macros=macros),
            Extension(name='ms_deisotope._c.peak_dependency_network.peak_network',
                      sources=['src/ms_deisotope/_c/peak_dependency_network/peak_network.c'],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include()], define_macros=macros),
            Extension(name='ms_deisotope._c.spectrum_graph',
                      sources=['src/ms_deisotope/_c/spectrum_graph.c'],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include()], define_macros=macros),
            Extension(name='ms_deisotope._c.feature_map.feature_graph',
                      sources=['src/ms_deisotope/_c/feature_map/feature_graph.c'],
                      include_dirs=[numpy.get_include(), ms_peak_picker.get_include()], define_macros=macros),
            OpenMPExtension(
                name='ms_deisotope._c.similarity_methods', sources=["src/ms_deisotope/_c/similarity_methods.c"],
                include_dirs=[brainpy.get_include(), ms_peak_picker.get_include(), numpy.get_include()]),
            Extension(
                name='ms_deisotope._c.units', sources=["src/ms_deisotope/_c/units.c"],
                include_dirs=[]),
        ])
    return extensions


ext_errors = (CCompilerError, DistutilsExecError, DistutilsPlatformError)
if sys.platform == 'win32':
    # 2.6's distutils.msvc9compiler can raise an IOError when failing to
    # find the compiler
    ext_errors += (IOError,)


class BuildFailed(Exception):

    def __init__(self):
        self.cause = sys.exc_info()[1]  # work around py 2/3 different syntax

    def __str__(self):
        return str(self.cause)


class ve_build_ext(build_ext):
    # This class allows C extension building to fail.

    def run(self):
        try:
            build_ext.run(self)
        except DistutilsPlatformError:
            traceback.print_exc()
            raise BuildFailed()

    def build_extension(self, ext):
        try:
            build_ext.build_extension(self, ext)
        except ext_errors:
            traceback.print_exc()
            raise BuildFailed()
        except ValueError:
            # this can happen on Windows 64 bit, see Python issue 7511
            traceback.print_exc()
            if "'path'" in str(sys.exc_info()[1]):  # works with both py 2/3
                raise BuildFailed()
            raise


cmdclass = {}

cmdclass['build_ext'] = ve_build_ext


def status_msgs(*msgs):
    print('*' * 75)
    for msg in msgs:
        print(msg)
    print('*' * 75)


install_requires = [
    "numpy>=2.0.0; python_version >= '3.9'",
    "numpy; python_version < '3.9'",
    "scipy",
    "six",
    "dill",
    "ms_peak_picker >= 0.1.46",
    "brain-isotopic-distribution >= 1.5.8",
    "pyteomics >= 4.6.2",
    "lxml",
    "psims >= 1.3.0",
    "python-idzip >=0.3.2",
    "pyzstd",
]


extra_requires = {
    "com": [
        "comtypes"
    ],
    "net": [
        "pythonnet"
    ],
    "plot": [
        "matplotlib",
    ],
    "cli": [
        'click'
    ],
    'mzmlb': [
        'h5py',
        'hdf5plugin'
    ]
}


extra_requires['all'] = [dep for feature_reqs in extra_requires.values() for dep in feature_reqs]


def run_setup(include_cext=True):
    with open("src/ms_deisotope/version.py") as version_file:
        version = None
        for line in version_file.readlines():
            if "version = " in line:
                version = line.split(" = ")[1].replace("\"", "").strip()
                print("Version is: %r" % (version,))
                break
        else:
            print("Cannot determine version")

    try:
        with open("README.rst") as readme_file:
            long_description = readme_file.read()
    except Exception as e:
        print(e)
        long_description = ''

    setup(
        name='ms_deisotope',
        version=version,
        packages=find_packages(where='src'),
        package_dir={"": "src"},
        author=', '.join(["Joshua Klein"]),
        author_email=','.join(["jaklein@bu.edu"]),
        description='Access, Deisotope, and Charge Deconvolute Mass Spectra',
        long_description=long_description,
        ext_modules=make_extensions() if include_cext else None,
        cmdclass=cmdclass,
        entry_points={
            'console_scripts': [
                "ms-index = ms_deisotope.tools.indexing:main",
                "ms-view = ms_deisotope.tools.view:main",
                "ms-deisotope = ms_deisotope.tools.deisotoper.main:deisotope",
            ],
        },
        classifiers=[
            'Development Status :: 3 - Alpha',
            'Intended Audience :: Science/Research',
            'License :: OSI Approved :: Apache Software License',
            'Topic :: Scientific/Engineering :: Bio-Informatics'],
        install_requires=install_requires,
        extras_require=extra_requires,
        include_package_data=True,
        zip_safe=False,
        python_requires=">3.8",
        project_urls={
            'Documentation': 'https://mobiusklein.github.io/ms_deisotope',
            'Source Code': 'https://github.com/mobiusklein/ms_deisotope',
            'Issue Tracker': 'https://github.com/mobiusklein/ms_deisotope/issues',
            'Change Log': 'https://github.com/mobiusklein/ms_deisotope/blob/master/CHANGELOG.md'
        })


try:
    run_setup(True)
except Exception as exc:
    print(exc)
    traceback.print_exc()
    run_setup(False)

    status_msgs(
        "WARNING: The C extension could not be compiled, " +
        "speedups are not enabled.",
        "Plain-Python build succeeded."
    )