setup.py

"""Description
Setup script for RSeQC  -- Comprehensive QC package for RNA-seq data
Copyright (c) 2012 Liguo Wang <wangliguo78@gmail.com>
This code is free software; you can redistribute it and/or modify it
under the terms of the Artistic License (see the file COPYING included
with the distribution).
"""

from distribute_setup import use_setuptools
use_setuptools()
from setuptools import *

import sys, os, glob, platform
from distutils.core import setup
from setuptools import *

try:
	import numpy
	have_numpy = True
except ImportError:
	have_numpy = False

#try:
#	import pysam
#	have_pysam = True
#except ImportError:
#	have_pysam = False
have_pysam = False	

#try:
#	import bx
#	have_bx = True
#except ImportError:
#	have_bx = False	
have_bx = False	

if sys.version_info[0] != 2 or sys.version_info[1] < 7:
	print >> sys.stderr, "ERROR: RSeQC requires Python 2.7"
	sys.exit()
	
IS_PYTHON3 = sys.version_info[0] >= 3	

cmdclass = {}

try:
	from Cython.Distutils import build_ext
	cmdclass = { 'build_ext' : build_ext }
except:
	pass


def main():
	setup(  name = "RSeQC",
            version = "2.4",
            packages = find_packages( 'lib' ),
            package_dir = { '': 'lib' },
            package_data = { '': ['*.ps'] },
            scripts = glob.glob( "scripts/*.py"),
            ext_modules = get_extension_modules(),
            py_modules = [ 'psyco_full' ],
            test_suite = 'nose.collector',
            setup_requires = ['nose>=0.10.4','cython>=0.12'],
            author = "Liguo Wang",
			author_email ="wangliguo78@gmail.com",
			platforms = ['Linux','MacOS'],
			requires = ['cython (>=0.17)'],
			install_requires = ['cython>=0.17',], 
            description = "RNA-seq QC Package",
            url = "http://rseqc.sourceforge.net/",
            zip_safe = False,
            dependency_links = [],
			classifiers=[
              'Development Status :: 1 - productive',
              'Environment :: Console',
              'Intended Audience :: Developers',
              'License :: GPL',
              'Operating System :: MacOS :: MacOS X',
              'Operating System :: POSIX',
              'Programming Language :: Python',
              ],

            cmdclass=cmdclass )

# ---- Extension Modules ----------------------------------------------------

def get_extension_modules():
	extensions = []
	
	
	# install pysam if it doesn't exist
	if not have_pysam:
		csamtools_sources = [ "lib/pysam/csamtools.pyx" ]
		tabix_sources = [ "lib/pysam/ctabix.pyx" ]
		tabproxies_sources = ["lib/pysam/TabProxies.pyx" ]
		cvcf_sources = ["lib/pysam/cvcf.pyx" ]
		os_c_files = []
		include_os = []	
		extensions.append(Extension(
    		"pysam.csamtools",              
			csamtools_sources + [ "lib/pysam/%s" % x for x in ("pysam_util.c", )] +\
			glob.glob( os.path.join( "lib/samtools", "*.pysam.c" )) +\
			os_c_files + \
			glob.glob( os.path.join( "lib/samtools", "*", "*.pysam.c" ) ),
			library_dirs=[],
			include_dirs=[ "lib/samtools", "lib/pysam" ] + include_os,
			libraries=[ "z", ],
			language="c",
			define_macros = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')], 
		))

		extensions.append(Extension(
			"pysam.ctabix",                   
			tabix_sources + [ "lib/pysam/%s" % x for x in ( "tabix_util.c", )] +\
			os_c_files + \
			glob.glob( os.path.join( "lib/tabix", "*.pysam.c" ) ),
			library_dirs=[],
			include_dirs=[ "lib/tabix", "lib/pysam" ] + include_os,
			libraries=[ "z", ],
			language="c",
			define_macros = [('_FILE_OFFSET_BITS','64'),
                     ('_USE_KNETFILE','')], 
		))

		extensions.append(Extension(
			"pysam.TabProxies",               
			tabproxies_sources + os_c_files,
			library_dirs=[],
			include_dirs= include_os,
			libraries=[ "z", ],
			language="c",
		))

		extensions.append(Extension(
			"pysam.cvcf",                   
			cvcf_sources + os_c_files,
			library_dirs=[],
			include_dirs= ["lib/tabix",] + include_os,
			libraries=[ "z", ],
			language="c",
		))
	
	if not have_bx:
		# Bitsets
		extensions.append( Extension( "bx.bitset",
                                  [ "lib/bx/bitset.pyx", 
                                    "src/binBits.c",
                                    "src/kent/bits.c",
                                    "src/kent/common.c" ],
                                  include_dirs=[ "src/kent", "src"] ) )
		# Interval intersection
		extensions.append( Extension( "bx.intervals.intersection", [ "lib/bx/intervals/intersection.pyx" ] ) )
		# Alignment object speedups
		extensions.append( Extension( "bx.align._core", [ "lib/bx/align/_core.pyx" ] ) )
		# NIB reading speedups
		extensions.append( Extension( "bx.seq._nib", [ "lib/bx/seq/_nib.pyx" ] ) )
		# 2bit reading speedups
		extensions.append( Extension( "bx.seq._twobit", [ "lib/bx/seq/_twobit.pyx" ] ) )
		# Translation if character / integer strings 
		extensions.append( Extension( "bx._seqmapping", [ "lib/bx/_seqmapping.pyx" ] ) )
		# BGZF
		extensions.append( Extension( "bx.misc.bgzf",
                                  [ "lib/bx/misc/bgzf.pyx", "src/samtools/bgzf.c" ],
                                  include_dirs=[ "src/samtools"],
                                  libraries=['z'] ) )
    
		# The following extensions won't (currently) compile on windows
		if platform.system() not in ( 'Microsoft', 'Windows' ):
        
			# Interval clustering                
			extensions.append( Extension( "bx.intervals.cluster",
                                  [ "lib/bx/intervals/cluster.pyx", 
                                    "src/cluster.c"],
                                  include_dirs=["src"] ) )
			# Position weight matrices
			extensions.append( Extension( "bx.pwm._position_weight_matrix",
                                  [ "lib/bx/pwm/_position_weight_matrix.pyx", "src/pwm_utils.c" ],
                                  include_dirs=["src"]  ) )
 	
			if have_numpy:
				extensions.append( Extension( "bx.motif._pwm", [ "lib/bx/motif/_pwm.pyx" ], 
                                          include_dirs=[numpy.get_include()] ) )
            
				# Sparse arrays with summaries organized as trees on disk
				extensions.append( Extension( "bx.arrays.array_tree", [ "lib/bx/arrays/array_tree.pyx" ], include_dirs=[numpy.get_include()] ) )  
        
				# Reading UCSC "big binary index" files
				extensions.append( Extension( "bx.bbi.bpt_file", [ "lib/bx/bbi/bpt_file.pyx" ] ) )
				extensions.append( Extension( "bx.bbi.cirtree_file", [ "lib/bx/bbi/cirtree_file.pyx" ] ) )
				extensions.append( Extension( "bx.bbi.bbi_file", [ "lib/bx/bbi/bbi_file.pyx" ], include_dirs=[numpy.get_include()] ) )
				extensions.append( Extension( "bx.bbi.bigwig_file", [ "lib/bx/bbi/bigwig_file.pyx" ], include_dirs=[numpy.get_include()] ) )
				extensions.append( Extension( "bx.bbi.bigbed_file", [ "lib/bx/bbi/bigbed_file.pyx" ], include_dirs=[numpy.get_include()] ) )
	
			# Reading UCSC bed and wiggle formats
			extensions.append( Extension( "bx.arrays.bed", [ "lib/bx/arrays/bed.pyx" ] ) )
			extensions.append( Extension( "bx.arrays.wiggle", [ "lib/bx/arrays/wiggle.pyx" ] ) )
	
	
			# CpG masking
			extensions.append( Extension( "bx.align.sitemask._cpg", \
                                      [ "lib/bx/align/sitemask/_cpg.pyx", 
                                        "lib/bx/align/sitemask/find_cpg.c" ] ) )
        
			# Counting n-grams in integer strings
			extensions.append( Extension( "bx.intseq.ngramcount", [ "lib/bx/intseq/ngramcount.pyx" ] ) )
	
			# Seekable access to bzip2 files
			extensions.append( Extension( "bx.misc._seekbzip2", 
                                      [ "lib/bx/misc/_seekbzip2.pyx",
                                        "src/bunzip/micro-bunzip.c" ],
                                      include_dirs=[ "src/bunzip" ] ) )
	return extensions     
 
# ---- Monkey patches -------------------------------------------------------

def monkey_patch_doctest():
    #
    # Doctest and coverage don't get along, so we need to create
    # a monkeypatch that will replace the part of doctest that
    # interferes with coverage reports.
    #
    # The monkeypatch is based on this zope patch:
    # http://svn.zope.org/Zope3/trunk/src/zope/testing/doctest.py?rev=28679&r1=28703&r2=28705
    #
	try:
		import doctest
		_orp = doctest._OutputRedirectingPdb
		class NoseOutputRedirectingPdb(_orp):
			def __init__(self, out):
				self.__debugger_used = False
				_orp.__init__(self, out)

			def set_trace(self):
				self.__debugger_used = True
				_orp.set_trace(self)

			def set_continue(self):
				# Calling set_continue unconditionally would break unit test coverage
				# reporting, as Bdb.set_continue calls sys.settrace(None).
				if self.__debugger_used:
					_orp.set_continue(self)
		doctest._OutputRedirectingPdb = NoseOutputRedirectingPdb
	except:
		pass

def monkey_patch_numpy():
	# Numpy pushes its tests into every importers namespace, yeccch.
	try:
		import numpy
		numpy.test = None
	except:
		pass


if __name__ == "__main__":
	monkey_patch_doctest()
	if have_numpy:
		monkey_patch_numpy()
	main()