gistfile1.py

# -*- coding: utf-8 -*-
from __future__ import print_function
try:
    from setuptools import setup, find_packages, Extension
except ImportError:
    from distutils.core import setup, Extension
    def find_packages():
        return ['treeCl']
try:
    from Cython.Distutils import build_ext
except ImportError:
    print('You don\'t seem to have Cython installed.')
    print('Cython and Numpy are required for the')
    print('installation process, all other dependencies')
    print('will be installed automatically.')
    print('Install Cython [and Numpy] and try again.')
    import sys
    sys.exit()

try:
    from numpy import get_include as numpy_get_include
except ImportError:
    print('You don\'t seem to have Numpy installed.')
    print('Numpy and Cython are required for the')
    print('installation process, all other dependencies')
    print('will be installed automatically.')
    print('Install Numpy [and Cython] and try again.')
    import sys
    sys.exit()

VERSION='1.0.0'

logo = """
═══════════ ╔═╗┬
┌┬┐┬─┐┌─┐┌─┐║  │
 │ ├┬┘├┤ ├┤ ╚═╝┴─┘
 ┴ ┴└─└─┘└─┘╭─────
┈┈┈┈┈┈┄┄┄┄┄─┤  ╭──
   V{0:s}   ╰──┤
══════════════ ╰──
""".format(VERSION)

print(logo)

# extensions = [
#     Extension(name='tree_collection',
#         sources=[
#             'extensions/tree_collection/cython/py_wrapper.pyx',
#             'extensions/tree_collection/src/ProblemParser.cc',
#             'extensions/tree_collection/src/MinSqTree.cc',
#             'extensions/tree_collection/src/newick.cc',
#         ],
#         language='c++',
#     ),
#     # Extension(name='evrot_extensions',
#     #     sources=['extensions/evrot/evrot_extensions.c'],
#     #     language='c',
#     #     include_dirs=[numpy_get_include()]
#     # ),
# ]

setup(name = "treeCl",
    version=VERSION,
    author='Kevin Gori',
    author_email='kgori@ebi.ac.uk',
    description='Phylogenetic Clustering Package',
    url='https://github.com/kgori/treeCl.git',
    packages=find_packages(),
    include_package_data=True,
    package_data={
        'treeCl': ['software_interfaces/gtp.jar']
    },
    scripts=[
        'bin/simulator',
        'bin/treeCl',
        'bin/seqconvert',
        'bin/bootstrap',
    ],
    install_requires=[
        'biopython',
        'bsub',
        'cython',
        'dendropy',
        'fastcluster',
        'ggplot',
        'matplotlib',
        'numpy',
        'progressbar-latest',
        'scipy',
        'pandas',
        'scikit-learn',
    ],
    # cmdclass = { 'build_ext': build_ext},
    # ext_modules = extensions,
)