setup.py

from setuptools import setup
import shutil
import os
import sys
import subprocess

# remove the dist folder first if exists
if os.path.exists("dist"):
    shutil.rmtree("dist")

VERSION = "1.1.24"


with open("README.md") as f:
    long_description = f.read()


def write_version_py(filename="SigProfilerExtractor/version.py"):
    # Copied from numpy setup.py
    cnt = """
# THIS FILE IS GENERATED FROM SIGPROFILEREXTRACTOR SETUP.PY
short_version = '%(version)s'
version = '%(version)s'
Update = 'Upgrade v1.1.24: Add input processing to SigProfilerExtractor'
    
    """
    fh = open(filename, "w")
    fh.write(
        cnt
        % {
            "version": VERSION,
        }
    )
    fh.close()


requirements = [
    "scipy>=1.6.3",
    "torch>=1.8.1",
    "numpy>=1.21.2",
    "pandas>=1.2.4",
    "nimfa>=1.1.0",
    "SigProfilerMatrixGenerator>=1.2.25",
    "sigProfilerPlotting>=1.3.22",
    "SigProfilerAssignment>=0.1.4",
    "pillow",
    "statsmodels>=0.9.0",
    "scikit-learn>=0.24.2",
    "psutil>=5.6.1",
    "reportlab>=3.5.42",
    "PyPDF2>=1.26.0",
]

operating_system = sys.platform
print(operating_system)
if operating_system in ["win32", "cygwin", "windows"]:
    requirements.remove("matplotlib>=3.3.0")
    requirements.remove("torch==1.5.1")
    print("Trying to install pytorch!")
    code = 1
    try:
        code = subprocess.call(
            [
                "pip",
                "install",
                "torch===1.5.1+cpu",
                "-f",
                "https://download.pytorch.org/whl/torch_stable.html",
            ]
        )
        if code != 0:
            raise Exception("Torch  instalation failed !")
    except:
        try:
            code = subprocess.call(
                [
                    "pip3",
                    "install",
                    "torch===1.5.1+cpu",
                    "-f",
                    "https://download.pytorch.org/whl/torch_stable.html",
                ]
            )
            if code != 0:
                raise Exception("Torch instalation failed !")
        except:
            print(
                "Failed to install pytorch, please install pytorch manually be following the simple instructions over at: https://pytorch.org/get-started/locally/"
            )
    if code == 0:
        print(
            "Successfully installed pytorch version! (If you need the GPU version, please install it manually, checkout the mindsdb docs and the pytroch docs if you need help)"
        )


write_version_py()
setup(
    name="SigProfilerExtractor",
    version=VERSION,
    description="Extracts mutational signatures from mutational catalogues",
    long_description=long_description,
    long_description_content_type="text/markdown",  # This is important!
    url="https://github.com/AlexandrovLab/SigProfilerExtractor.git",
    author="S Mishu Ashiqul Islam",
    author_email="m0islam@ucsd.edu",
    license="UCSD",
    packages=["SigProfilerExtractor"],
    install_requires=requirements,
    include_package_data=True,
    zip_safe=False,
)