Camoco/setup.py at master · LinkageIO/Camoco · GitHub

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#!/usr/bin/env python3

from setuptools import setup, find_packages, Extension

import os
import io
import re
import sys

try:
    import numpy
except ModuleNotFoundError as e:
    #raise ModuleNotFoundError(
    print(
        "Please install numpy before installing Camoco,"
    )
    sys.exit(1)

def read(*names, **kwargs):
    with io.open(
        os.path.join(os.path.dirname(__file__), *names),
        encoding=kwargs.get("encoding", "utf8")
    ) as fp:
        return fp.read()

def find_version(*file_paths):
    version_file = read(*file_paths)
    version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
                              version_file, re.M)
    if version_match:
        return version_match.group(1)
    raise RuntimeError("Unable to find version string.")

pccup = Extension(
    'camoco.PCCUP',
    sources=['camoco/PCCUP.pyx'],
    include_dirs=[numpy.get_include()]
)
refgendist = Extension(
    'camoco.RefGenDist',
    sources=['camoco/RefGenDist.pyx'],
    include_dirs=[numpy.get_include()]
)

# Check if running Windows or OSX
if (
    not sys.platform.startswith('linux')
    and int(os.environ.get('CAMOCO_FORCE_INSTALL',default='0')) != 1
    ):
    print(
        "Sorry! Camoco is not currently supported on non-linux systems "
        "If you would like to proceed with installation please set the "
        "ENV variable 'CAMOCO_FORCE_INSTALL' to '1'"
    )
    sys.exit(1)

setup(
    name = 'camoco',
    version = find_version('camoco','__init__.py'),
    packages = find_packages(),
    scripts = [
        'camoco/cli/camoco'
    ],
    ext_modules = [pccup,refgendist],
    cmdclass = {
    },
    package_data = {
        '':['*.cyx']
    },
    python_requires='>=3.8',
    setup_requires = [
        # Setuptools 18.0 properly handles Cython extensions.
        'setuptools>=18.0',
        'numpy>=1.14.5',
        'cython>=0.29.10',
    ],
    install_requires = [
        'minus80>=1.0.0',
        'cython>=0.29.10',
        'igraph==0.1.11',
        'pyyaml>=5.1.1',
        'matplotlib>=3.1.0',
        'numpy>=1.16.4',
        'scipy>=1.2.1',
        'pandas==0.23.4',
        'fa2>=0.3.5',
        'scikit-learn>=0.21.2',
        'statsmodels>=0.8.0',
        'termcolor>=1.1.0',
        'powerlaw>=1.4.6',
        'flask==2.3.2',
        'markov-clustering>=0.0.6.dev0',
        'fastcluster>=1.1.25',
        'bcolz>=1.2.1',
        'psutil>=5.6.3',
        'odo>=0.5.0',
        'blaze>=0.10.1'
    ],
    extras_require={
        'docs' : [
            'ipython>=6.5.0',
            'matplotlib>=2.2.3',
            'numpydoc',
            'sphinx_materialdesign_theme',
            'sphinx_rtd_theme',
            'sphinxcontrib-programoutput'
        ]
    },
    dependency_links = [
        #'git+https://github.com/LinkageIO/Minus80'
        #'git+https://github.com/rogerbinns/apsw'
    ],
    include_package_data=True,
    author = 'Rob Schaefer',
    author_email = 'rob@linkage.io',
    description = 'Library for Co-Analysis of Molecular Componenets.',
    license = "Copyright Linkage Analytics 2017, Available under the MIT License",
    url = 'https://github.com/schae234/camoco'
)