setup.py

   1 #!/usr/bin/env python
   2 """
   3 Pygr
   4 ====
   5
   6 Pygr is an open source software project used to develop graph database
   7 interfaces for the popular Python language, with a strong emphasis
   8 on bioinformatics applications ranging from genome-wide analysis of
   9 alternative splicing patterns, to comparative genomics queries of
  10 multi-genome alignment data.
  11 """
  12
  13 import os, sys
  14
  15 try:
  16     from setuptools import setup, Extension
  17 except ImportError:
  18     print 'Setuptools not imported, falling back to distutils'
  19     from distutils.core import setup, Extension
  20
  21 def error(msg):
  22     "Fatal errors"
  23     print( '*** error %s' % msg )
  24     sys.exit()
  25
  26 import pygr
  27
  28 PYGR_NAME = "pygr"
  29 PYGR_VERSION = pygr.__version__
  30
  31 if sys.version_info < (2, 3):
  32     error( 'pygr requires python 2.3 or higher' )
  33
  34 CLASSIFIERS = """
  35 Development Status :: 5 - Production/Stable
  36 Operating System :: MacOS :: MacOS X
  37 Operating System :: Microsoft :: Windows :: Windows NT/2000
  38 Operating System :: OS Independent
  39 Operating System :: POSIX
  40 Operating System :: POSIX :: Linux
  41 Operating System :: Unix
  42 Programming Language :: Python
  43 Topic :: Scientific/Engineering
  44 Topic :: Scientific/Engineering :: Bio-Informatics
  45 """
  46
  47 # split into lines and filter empty ones
  48 CLASSIFIERS = filter(None, CLASSIFIERS.splitlines() )
  49
  50 # Setuptools should handle all this automatically
  51 if sys.modules.has_key('setuptools'):
  52     try:
  53         import pkg_resources
  54         pkg_resources.require('Pyrex>=0.9.8')
  55         ext = 'pyx'
  56     except pkg_resources.DistributionNotFound:
  57         ext = 'c'
  58     cmdclass = { }
  59 else:
  60 # if pyrex is not present try compiling the C files
  61     try:
  62         from Pyrex.Compiler.Version import version as PYREX_VERSION
  63         from Pyrex.Distutils import build_ext
  64         if PYREX_VERSION < "0.9.8":
  65             error ( "pyrex version >=0.9.8 required, found %s" % PYREX_VERSION )
  66         ext = 'pyx'
  67         cmdclass = { 'build_ext': build_ext }
  68     except ImportError, exc:
  69         ext = 'c'
  70         cmdclass = {}
  71
  72 # extension sources
  73 seqfmt_src = [ os.path.join('pygr', 'seqfmt.%s' % ext) ]
  74 cdict_src  = [ os.path.join('pygr', 'cgraph.c'),
  75               os.path.join('pygr', 'cdict.%s' % ext) ]
  76 nested_src = [ os.path.join('pygr', 'intervaldb.c'),
  77               os.path.join('pygr', 'cnestedlist.%s' % ext),
  78               os.path.join('pygr', 'apps', 'maf2nclist.c') ]
  79
  80 def main():
  81     setup(
  82         name = PYGR_NAME ,
  83         version= PYGR_VERSION,
  84         description = 'Pygr, a Python graph-database toolkit oriented primarily on bioinformatics applications',
  85         long_description = __doc__,
  86         author = "Christopher Lee",
  87         author_email='leec@chem.ucla.edu',
  88         url = 'http://code.google.com/p/pygr/',
  89         license = 'New BSD License',
  90         classifiers = CLASSIFIERS,
  91
  92         packages = [ 'pygr', 'pygr.apps' ],
  93
  94         ext_modules = [
  95             Extension( 'pygr.seqfmt', seqfmt_src ),
  96             Extension( 'pygr.cdict',  cdict_src ),
  97             Extension( 'pygr.cnestedlist', nested_src),
  98         ],
  99
 100         cmdclass = cmdclass,
 101      )
 102
 103 if __name__ == '__main__':
 104     main()