forked from fabriziocosta/EDeN
/
setup.py
executable file
·140 lines (123 loc) · 4.04 KB
/
setup.py
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#!/usr/bin/env python
from __future__ import absolute_import
from __future__ import print_function
import os
import sys
import subprocess
import re
from setuptools import setup
from setuptools.command.sdist import sdist as _sdist
from setuptools.command.install import install as _install
VERSION_PY = """
# This file is originally generated from Git information by running 'setup.py
# version'. Distribution tarballs contain a pre-generated copy of this file.
__version__ = '%s'
"""
def update_version_py():
if not os.path.isdir(".git"):
print("This does not appear to be a Git repository.")
return
try:
p = subprocess.Popen(["git", "describe",
"--tags", "--always"],
stdout=subprocess.PIPE)
except EnvironmentError:
print("unable to run git, leaving eden/_version.py alone")
return
stdout = p.communicate()[0]
if p.returncode != 0:
print("unable to run git, leaving eden/_version.py alone")
return
ver = stdout.strip()
f = open("eden/_version.py", "w")
f.write(VERSION_PY % ver)
f.close()
print("set eden/_version.py to '%s'" % ver)
def get_version():
try:
f = open("eden/_version.py")
except EnvironmentError:
return None
for line in f.readlines():
mo = re.match("__version__ = '([^']+)'", line)
if mo:
ver = mo.group(1)
return ver
return None
class sdist(_sdist):
def run(self):
update_version_py()
self.distribution.metadata.version = get_version()
return _sdist.run(self)
class install(_install):
def run(self):
_install.run(self)
def checkProgramIsInstalled(self, program, args, where_to_download,
affected_tools):
try:
subprocess.Popen([program, args], stderr=subprocess.PIPE, stdout=subprocess.PIPE)
return True
except EnvironmentError:
# handle file not found error.
# the config file is installed in:
msg = "\n**{0} not found. This " \
"program is needed for the following "\
"tools to work properly:\n"\
" {1}\n"\
"{0} can be downloaded from here:\n " \
" {2}\n".format(program, affected_tools,
where_to_download)
sys.stderr.write(msg)
except Exception as e:
sys.stderr.write("Error: {}".format(e))
setup(
name='eden',
version=get_version(),
author='Fabrizio Costa',
author_email='graph-eden@googlegroups.com',
packages=['eden',
'eden.display',
'eden.io',
],
scripts=['bin/model',
'bin/motif',
'bin/location_predictor',
'bin/motif_display.py',
],
include_package_data=True,
package_data={},
url='http://pypi.python.org/pypi/eden/',
license='LICENSE',
description='The Explicit Decomposition with Neighborhoods (EDeN) is a decompositional kernel \
based on the Neighborhood Subgraph Pairwise Distance Kernel (NSPDK) that can be used to induce \
an explicit feature representation for graphs. This in turn allows the adoption of machine learning\
algorithm to perform supervised and unsupervised learning task in a scalable way (e.g. fast\
stochastic gradient descent methods in classification).',
long_description=open('README.md').read(),
install_requires=[
"cvxopt",
"cvxpy",
"dill",
"esmre",
"flake8",
"joblib",
"matplotlib",
"mpld3",
"networkx <= 1.10",
"nose",
"numpy >= 1.8.0",
"openbabel",
"pandas",
"pybedtools>=0.6.6",
"pymf",
"reportlab",
"requests",
"scikit-learn >= 0.17.0",
"scikit-neuralnetwork",
"scipy >= 0.14.0",
"scripttest",
"theano",
"weblogo"
],
cmdclass={'sdist': sdist, 'install': install}
)