import platform import sys if sys.version_info < (2, 6): sys.exit("ERROR: bx-python requires Python 2.6 or greater") elif sys.version_info > (3, ) and sys.version_info < (3, 3): sys.exit("ERROR: bx-python requires Python 3.3 or greater") try: from setuptools import setup, find_packages except ImportError: print >> sys.stderr, "ERROR: setuptools not installed. Please report this bug as instructed on https://bugs.debian.org/cgi-bin/pkgreport.cgi?package=python-bx" sys.exit() from setuptools import * from glob import glob def main(): metadata = \ dict( name = "bx-python", version = "0.8.2", setup_requires=['numpy', 'cython'], install_requires=['numpy', 'six'], py_modules = [ 'psyco_full' ], package_dir = { '': 'lib' }, package_data = { '': ['*.ps'] }, scripts = glob( "scripts/*.py" ), test_suite = 'nose.collector', tests_require = ['nose','python-lzo'], author = "James Taylor, Bob Harris, David King, Brent Pedersen, Kanwei Li, and others", author_email = "james@jamestaylor.org", description = "Tools for manipulating biological data, particularly multiple sequence alignments", url = "https://github.com/bxlab/bx-python", license = "MIT", classifiers = [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Operating System :: POSIX", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.6", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Software Development :: Libraries :: Python Modules" ], zip_safe = False, dependency_links = [], cmdclass=command_classes ) numpy = None try: import numpy # Suppress numpy tests numpy.test = None except: pass if len(sys.argv) >= 2 and ('--help' in sys.argv[1:] or sys.argv[1] in ('--help-commands', 'egg_info', '--version', 'clean')): # For these actions, NumPy is not required. # # They are required to succeed without Numpy for example when # pip is used to install when Numpy is not yet present in # the system. pass else: if numpy is None: raise Exception( "numpy must be installed to build" ) metadata['packages'] = find_packages( 'lib' ) metadata['ext_modules'] = get_extension_modules( numpy_include=numpy.get_include() ) setup(**metadata) # ---- Commands ------------------------------------------------------------- from distutils.core import Command # Use build_ext from Cython if found command_classes = {} try: import Cython.Distutils command_classes['build_ext'] = Cython.Distutils.build_ext except: pass # Run 2to3 builder if we're on Python 3.x, from # http://wiki.python.org/moin/PortingPythonToPy3k try: from distutils.command.build_py import build_py_2to3 as build_py except ImportError: # 2.x from distutils.command.build_py import build_py command_classes['build_py'] = build_py # 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 ---------------------------------------------------- # # suppress C++ #warning, e.g., to silence NumPy deprecation warnings: # from functools import partial # _Extension = Extension # Extension = partial(_Extension, extra_compile_args=["-Wno-cpp"]) def get_extension_modules( numpy_include=None ): 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" ] ) ) # 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"] ) ) extensions.append( Extension( "bx.motif._pwm", [ "lib/bx/motif/_pwm.pyx" ], include_dirs=[numpy_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_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_include] ) ) extensions.append( Extension( "bx.bbi.bigwig_file", [ "lib/bx/bbi/bigwig_file.pyx" ], include_dirs=[numpy_include] ) ) extensions.append( Extension( "bx.bbi.bigbed_file", [ "lib/bx/bbi/bigbed_file.pyx" ], include_dirs=[numpy_include] ) ) # EPO and Chain arithmetics and IO speedups extensions.append( Extension( "bx.align._epo", [ "lib/bx/align/_epo.pyx" ], include_dirs=[numpy_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" ], include_dirs=["src"] ) ) # 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 if __name__ == "__main__": main()