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"""
Created on 25/02/2013
@author: victor
"""
if __name__ == '__main__': # Compatibility with sphynx
from distutils.core import setup, Extension
import numpy
import distutils.sysconfig
import os
def read(fname):
return open(os.path.join(os.path.dirname(__file__), fname)).read()
setup(
name='pyProCT',
version='1.7.3',
description='pyProCT is an open source cluster analysis software especially adapted for jobs related with structural proteomics',
author='Victor Alejandro Gil Sepulveda',
author_email='victor.gil.sepulveda@gmail.com',
url='https://github.com/victor-gil-sepulveda/pyProCT',
license = 'LICENSE.txt',
long_description = read('README.rst'),
packages=[
'pyproct',
'pyproct.clustering',
'pyproct.clustering.algorithms',
'pyproct.clustering.algorithms.dbscan',
'pyproct.clustering.algorithms.dbscan.cython',
'pyproct.clustering.algorithms.gromos',
'pyproct.clustering.algorithms.hierarchical',
'pyproct.clustering.algorithms.kmedoids',
'pyproct.clustering.algorithms.random',
'pyproct.clustering.algorithms.spectral',
'pyproct.clustering.algorithms.spectral.cython',
'pyproct.clustering.evaluation',
'pyproct.clustering.evaluation.analysis',
'pyproct.clustering.evaluation.metrics',
'pyproct.clustering.evaluation.metrics.cython',
'pyproct.clustering.evaluation.metrics.cython.graph',
'pyproct.clustering.filtering',
'pyproct.clustering.protocol',
'pyproct.clustering.protocol.exploration',
'pyproct.clustering.protocol.refinement',
'pyproct.clustering.selection',
'pyproct.data',
'pyproct.data.handler',
'pyproct.data.handler.featurearray',
'pyproct.data.handler.protein',
'pyproct.data.matrix',
'pyproct.data.matrix.featurearray',
'pyproct.data.matrix.combination',
'pyproct.data.matrix.protein',
'pyproct.data.matrix.protein.cases',
'pyproct.data.matrix.protein.cases.rmsd',
'pyproct.data.matrix.protein.cases.euclidean',
'pyproct.driver',
'pyproct.driver.observer',
'pyproct.driver.results',
'pyproct.driver.scheduling',
'pyproct.driver.time',
'pyproct.driver.workspace',
'pyproct.postprocess',
'pyproct.postprocess.actions',
'pyproct.postprocess.actions.confSpaceComparison',
'pyproct.tools'
],
include_dirs = [numpy.get_include(),
distutils.sysconfig.get_python_inc()],
# ext_modules=[
# # Graph metrics
# Extension('pyproct.clustering.evaluation.metrics.cython.graph.nCut',[
# 'pyproct/clustering/evaluation/metrics/cython/graph/nCut.c'
# ], extra_compile_args=["-O3","-ffast-math"]),
# Extension('pyproct.clustering.evaluation.metrics.cython.graph.ratioCut',[
# 'pyproct/clustering/evaluation/metrics/cython/graph/ratioCut.c'
# ], extra_compile_args=["-O3","-ffast-math"]),
# Extension('pyproct.clustering.evaluation.metrics.cython.graph.minMaxCut',[
# 'pyproct/clustering/evaluation/metrics/cython/graph/minMaxCut.c'
# ], extra_compile_args=["-O3","-ffast-math"]),
# Extension('pyproct.clustering.evaluation.metrics.cython.graph.tools',[
# 'pyproct/clustering/evaluation/metrics/cython/graph/tools.c'
# ], extra_compile_args=["-O3","-ffast-math"]),
#
# # Other metrics
# Extension('pyproct.clustering.evaluation.metrics.cython.cohesion', [
# 'pyproct/clustering/evaluation/metrics/cython/cohesion.c'
# ], extra_compile_args=["-O3","-ffast-math"]),
# Extension('pyproct.clustering.evaluation.metrics.cython.silhouette',[
# 'pyproct/clustering/evaluation/metrics/cython/silhouette.c'
# ], extra_compile_args=["-O3","-ffast-math"]),
#
# # Algorithm tools
# Extension("pyproct.clustering.algorithms.dbscan.cython.cythonDbscanTools", [
# 'pyproct/clustering/algorithms/dbscan/cython/cythonDbscanTools.c'
# ],extra_compile_args=["-O3","-ffast-math"]),
# Extension("pyproct.clustering.algorithms.spectral.cython.spectralTools", [
# 'pyproct/clustering/algorithms/spectral/cython/spectralTools.c'
# ],extra_compile_args=["-O3","-ffast-math"])
# ],
install_requires=[
#"pyRMSD>=4.0.0",
#"pyScheduler>=0.1.0",
"fastcluster>=1.1.6",
"ProDy>=1.4.2",
"numpy>=1.6.1",
"scipy>=0.9.0",
"scikit-learn>=0.12",
"Pillow>=2.6.2",
"matplotlib>=1.1.1rc",
"mpi4py>=1.3"
]
)