setup.py

from setuptools import setup, Extension
from Cython.Build import cythonize
from Cython.Compiler import Options
import numpy

# These are optional
Options.docstrings = True
Options.annotate = False

# Modules to be compiled and include_dirs when necessary
extensions = [
    # Extension(
    #     "pyctmctree.inpyranoid_c",
    #     ["src/pyctmctree/inpyranoid_c.pyx"],
    # ),
    Extension(
        "chromatinhd.loaders.fragments_helpers",
            ["src/chromatinhd/loaders/fragments_helpers.pyx"],
            include_dirs=[numpy.get_include()],
            py_limited_api=True,
    ),
        Extension(
            "chromatinhd.data.motifscan.scan_helpers",
            ["src/chromatinhd/data/motifscan/scan_helpers.pyx"],
            include_dirs=[numpy.get_include()],
            py_limited_api=True,
        ),
]


# This is the function that is executed
setup(
    name='chromatinhd',  # Required

    # A list of compiler Directives is available at
    # https://cython.readthedocs.io/en/latest/src/userguide/source_files_and_compilation.html#compiler-directives

    # external to be compiled
    ext_modules = cythonize(extensions, compiler_directives={"language_level": 3, "profile": False}),
)