setup.py

"""Build GRAFIMO
"""

from setuptools import setup, find_packages, Extension
from distutils.version import LooseVersion
from distutils.command.sdist import sdist as sd
from distutils.command.build_ext import build_ext as be

import sys

try:  # sphinx could not be available
    from sphinx.setup_command import BuildDoc
except ImportError:
    errmsg = "\n\nPlease install \"sphinx\" before installing GRAFIMO.\n"
    sys.stderr.write(errmsg)
    sys.exit(3)


if sys.version_info[:2] < (3,6): # python 3.7 is required
    """Check Python version.
    It must be >= 3.6
    """
    
    sys.stderr.write("Pyhton >= 3.6 is required to run GRAFIMO\n")
    sys.exit(1)

# read README file
encoding_arg={"encoding": "utf-8"} if sys.version_info[0] >= 3 else dict()
readmefile = "README.md"
with open(readmefile, **encoding_arg) as infile:
    long_description = infile.read()

# Cython code build
CYTHON_V_REQUIRED="0.28"  # minimum Cython version required

def check_cython():
    """Check Cython version
    """

    try:
        from Cython import __version__ as cyv
    except ImportError:
        sys.stderr.write(
            f"Cython not found on your machine. Install Cython >= {str(CYTHON_V_REQUIRED)}"
        )
        sys.exit(1)
    if LooseVersion(cyv) < LooseVersion(CYTHON_V_REQUIRED):
        sys.stderr.write(
            f"Found Cython v{str(cyv)}. Cython v{str(CYTHON_V_REQUIRED)} is required."
        )
        sys.exit(1)
extensions=[
    Extension("motif_processing", sources=["src/grafimo/motif_processing.pyx"]),
]

class BuildExt(be):

    def run(self):

        check_cython()
        from Cython.Build import cythonize
        self.extensions=cythonize(self.extensions)

        super().run()

class SDist(sd):

    def run(self):

        check_cython()
        from Cython.Build import cythonize
        cythonize(extensions)
        super().run()

name = "GRAFIMO"
version = "1.1.6"

# definition of setup()
setup(
      name="grafimo",
      version=version,
      author="Manuel Tognon",
      author_email="manu.tognon@gmail.com",
      url="https://github.com/pinellolab/GRAFIMO",
      description="GRAph-based Finding of Indivividual Motif Occurrences",
      long_description=long_description,
      long_description_content_type="text/markdown",
      license="MIT", 
      cmdclass={"build_ext": BuildExt, "sdist": SDist, "build_sphinx": BuildDoc},
      command_options={
          "build_sphinx": {
              "project":("setup.py", name),
              "version":("setup.py", version),
              "source_dir":("setup.py", "docs") 
          }
      },
      ext_modules=extensions,
      packages=find_packages("src"),
      package_dir={"":"src"},
      entry_points={"console_scripts":["grafimo = grafimo.__main__:main"]},
      install_requires=[
              "pandas>=0.24.2",
              "numpy>=1.16.4",
              "statsmodels>=0.11.0",
              "numba>=0.47",
              "sphinx>=3.5.2",
              "colorama"
        ],
      extras_require={
          "dev": ["Cython"]
      },
      python_requires=">=3.6",
      classifiers=[
        "Development Status :: 4 - Beta",
        "Environment :: Console",
        "Intended Audience :: Developers",
        "Intended Audience :: Science/Research",
        "License :: OSI Approved :: MIT License",
        "Operating System :: MacOS :: MacOS X",
        "Operating System :: POSIX :: Linux",
        "Natural Language :: English",
        "Programming Language :: Python :: 3",
        "Topic :: Scientific/Engineering :: Bio-Informatics"
    ],
)