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setup.py
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setup.py
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import sys, platform
if sys.version_info[0] < 2 or sys.version_info[1] < 4:
print >> sys.stderr, "ERROR: bx-python requires python 2.4 or greater"
sys.exit()
# Automatically download setuptools if not available
from ez_setup import use_setuptools
use_setuptools()
from setuptools import *
from glob import glob
try:
import numpy
have_numpy = True
except:
have_numpy = False
def main():
setup( name = "bx-python",
version = "0.5.0.1",
py_modules = [ 'psyco_full' ],
packages = find_packages( 'lib' ),
package_dir = { '': 'lib' },
package_data = { '': ['*.ps'] },
scripts = glob( "scripts/*.py" ),
ext_modules = get_extension_modules(),
test_suite = 'nose.collector',
setup_requires = ['nose>=0.10.4'],
author = "Ajish George, based on bx-python by James Taylor, Bob Harris, David King, Brent Pedersen, and others",
author_email = "james@jamestaylor.org",
description = "Tools for manipulating biological data, particularly multiple sequence alignments",
url = "http://bx-python.trac.bx.psu.edu",
zip_safe = False,
dependency_links = [],
cmdclass=command_classes )
# ---- Commands -------------------------------------------------------------
from distutils.core import Command
# Use build_ext from Cython
command_classes = {}
# Use build_ext from Cython if found
try:
import Cython.Distutils
command_classes['build_ext'] = Cython.Distutils.build_ext
except:
pass
# Use epydoc if found
try:
import pkg_resources
pkg_resources.require( "epydoc" )
import epydoc.cli, sys, os, os.path
# Create command class to build API documentation
class BuildAPIDocs( Command ):
user_options = []
def initialize_options( self ):
pass
def finalize_options( self ):
pass
def run( self ):
# Save working directory and args
old_argv = sys.argv
old_cwd = os.getcwd()
# Build command line for Epydoc
sys.argv = """epydoc.py bx --verbose --html --simple-term
--exclude=._
--exclude=_tests
--docformat=reStructuredText
--output=../doc/docbuild/html/apidoc""".split()
# Make output directory
if not os.path.exists( "./doc/docbuild/html/apidoc" ):
os.mkdir( "./doc/docbuild/html/apidoc" )
# Move to lib directory (so bx package is in current directory)
os.chdir( "./lib" )
# Invoke epydoc
epydoc.cli.cli()
# Restore args and working directory
sys.argv = old_argv
os.chdir( old_cwd )
# Add to extra_commands
command_classes['build_apidocs'] = BuildAPIDocs
except:
pass
# ---- Extension Modules ----------------------------------------------------
def get_extension_modules():
extensions = []
# 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" ] ) )
# 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 wiggle format
extensions.append( Extension( "bx.arrays.bed", [ "lib/bx/arrays/bed.pyx" ] ) )
# Reading UCSC wiggle format
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()