setup.py

import platform
from glob import glob

import numpy
from Cython.Distutils import build_ext
from setuptools import setup
from setuptools.extension import Extension

VERSION = "3.11.0"

NAME = "ms2pip"
LICENSE = "apache-2.0"
DESCRIPTION = "MS²PIP: MS² Peak Intensity Prediction"
AUTHOR = (
    "Sven Degroeve, Ralf Gabriels, Kevin Velghe, Ana Sílvia C. Silva, Arthur Declercq"
)
AUTHOR_EMAIL = "sven.degroeve@vib-ugent.be"
URL = "https://www.github.com/compomics/ms2pip_c"
PROJECT_URLS = {
    "Documentation": "http://compomics.github.io/projects/ms2pip_c",
    "Source": "https://github.com/compomics/ms2pip_c",
    "Tracker": "https://github.com/compomics/ms2pip_c/issues",
    "Web server": "https://iomics.ugent.be/ms2pip/",
    "Publication": "https://doi.org/10.1093/nar/gkz299/",
}
KEYWORDS = [
    "MS2PIP",
    "Proteomics",
    "peptides",
    "peak intensity prediction",
    "spectrum",
    "machine learning",
    "spectral library",
    "fasta2speclib",
]
CLASSIFIERS = [
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: Apache Software License",
    "Operating System :: POSIX :: Linux",
    "Programming Language :: Python :: 3 :: Only",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Development Status :: 5 - Production/Stable",
]
INSTALL_REQUIRES = [
    "biopython>=1.74,<2",
    "numpy>=1.16,<2",
    "pandas>=1,<2",
    "pyteomics>=3.5,<5",
    "tqdm>=4,<5",
    "tables>=3.4",
    "tomlkit>=0.5,<1",
    "sqlalchemy>=1.3,<2",
    "click>=7,<9",
    "xgboost>=1.3,<2",
    "matplotlib>=3.0",
    "spectrum-utils==0.3.5",
    "lxml>=4",
    "rich>=13",
    "pydantic>=1.10,<2",
]
PYTHON_REQUIRES = ">=3.7,<4"

with open("README.md", "r") as fh:
    LONG_DESCRIPTION = fh.read()

to_remove = [
    "ms2pip/cython_modules/ms2pip_pyx.c*",
    "ms2pip/cython_modules/ms2pip_pyx.so",
]
# _ = [[os.remove(f) for f in glob(pat)] for pat in to_remove]

# Large machine-written C model files require optimization to be disabled
compile_args = {
    "Linux": [
        "-O0",
        "-fno-var-tracking",
        "-Wno-unused-result",
        "-Wno-cpp",
        "-Wno-unused-function",
    ],
    "Darwin": [
        "-O0",
    ],
    "Windows": [
        "/Od",
        "/DEBUG",
        "/GL-",
        "/bigobj",
        "/wd4244",
    ],
}

extensions = [
    Extension(
        "ms2pip.cython_modules.ms2pip_pyx",
        sources=["ms2pip/cython_modules/ms2pip_pyx.pyx"] + glob("ms2pip/models/*/*.c"),
        extra_compile_args=compile_args[platform.system()],
    )
]

setup(
    name=NAME,
    version=VERSION,
    license=LICENSE,
    description=DESCRIPTION,
    long_description=LONG_DESCRIPTION,
    long_description_content_type="text/markdown",
    author=AUTHOR,
    author_email=AUTHOR_EMAIL,
    url=URL,
    project_urls=PROJECT_URLS,
    keywords=KEYWORDS,
    classifiers=CLASSIFIERS,
    packages=["ms2pip", "ms2pip.ms2pip_tools", "fasta2speclib"],
    include_package_data=True,
    entry_points={
        "console_scripts": [
            "ms2pip=ms2pip.__main__:main",
            "fasta2speclib=fasta2speclib.fasta2speclib:main",
            "ms2pip-single-prediction=ms2pip.single_prediction:_main",
        ],
    },
    install_requires=INSTALL_REQUIRES,
    python_requires=PYTHON_REQUIRES,
    ext_modules=extensions,
    include_dirs=[numpy.get_include()],
    cmdclass={"build_ext": build_ext},
)