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#!/usr/bin/env python
from distutils.core import setup
import sys, os, re, subprocess
__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2011, The Cogent Project"
__contributors__ = ["Peter Maxwell", "Gavin Huttley", "Matthew Wakefield",
"Greg Caporaso", "Daniel McDonald"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Peter Maxwell"
__email__ = "pm67nz@gmail.com"
__status__ = "Production"
# Check Python version, no point installing if unsupported version inplace
if sys.version_info < (2, 6):
py_version = ".".join([str(n) for n in sys.version_info])
raise RuntimeError("Python-2.6 or greater is required, Python-%s used." % py_version)
# Check Numpy version, no point installing if unsupported version inplace
try:
import numpy
except ImportError:
raise RuntimeError("Numpy required but not found.")
numpy_version = re.split("[^\d]", numpy.__version__)
numpy_version_info = tuple([int(i) for i in numpy_version if i.isdigit()])
if numpy_version_info < (1, 3):
raise RuntimeError("Numpy-1.3 is required, %s found." % numpy_version)
doc_imports_failed = False
try:
import sphinx
except ImportError:
doc_imports_failed = True
# A new command for predist, ie: pyrexc but no compile.
import distutils.ccompiler
class NullCompiler(distutils.ccompiler.CCompiler):
# this basically to stop pyrexc building binaries, just the .c files
executables = ()
def __init__(self, *args, **kw):
pass
def compile(self, *args, **kw):
return []
def link(self, *args, **kw):
pass
# Pyrex makes some messy C code so limit some warnings when we know how.
import distutils.sysconfig
if (distutils.sysconfig.get_config_var('CC') or '').startswith("gcc"):
pyrex_compile_options = ['-w']
else:
pyrex_compile_options = []
# On windows with no commandline probably means we want to build an installer.
if sys.platform == "win32" and len(sys.argv) < 2:
sys.argv[1:] = ["bdist_wininst"]
# Restructured Text -> HTML
def build_html():
if doc_imports_failed:
print "Failed to build html due to ImportErrors for sphinx"
return
cwd = os.getcwd()
os.chdir('doc')
subprocess.call(["make", "html"])
os.chdir(cwd)
print "Built index.html"
# Compiling Pyrex modules to .c and .so
include_path = os.path.join(os.getcwd(), 'include')
# find arrayobject.h on every system an alternative would be to put
# arrayobject.h into pycogent/include, but why ..
numpy_include_path = numpy.get_include()
distutils_extras = {"include_dirs": [include_path, numpy_include_path]}
try:
if 'DONT_USE_PYREX' in os.environ:
raise ImportError
from Cython.Compiler.Version import version
version = tuple([int(v) \
for v in re.split("[^\d]", version) if v.isdigit()])
if version < (0, 11, 2):
print "Your Cython version is too old"
raise ImportError
except ImportError:
print "No Cython, will compile from .c files"
for cmd in ['cython', 'pyrexc', 'predist']:
if cmd in sys.argv:
print "'%s' not available without Cython" % cmd
sys.exit(1)
from distutils.extension import Extension
pyrex_suffix = ".c"
else:
from Cython.Distutils import build_ext
from Cython.Distutils.extension import Extension
pyrex_suffix = ".pyx"
class build_wrappers(build_ext):
# for predist, make .c files
def run(self):
self.compiler = NullCompiler()
# skip build_ext.run() and thus ccompiler setup
build_ext.build_extensions(self)
class build_wrappers_and_html(build_wrappers):
def run(self):
build_wrappers.run(self)
build_html()
distutils_extras["cmdclass"] = {
'build_ext': build_ext,
'pyrexc': build_wrappers,
'cython': build_wrappers,
'predist': build_wrappers_and_html}
# predist python setup.py predist --inplace --force, this is in _darcs/prefs/prefs for instructing darcs predist to execute the subsequent, predist is a darcs word
# Save some repetitive typing. We have all compiled
# modules in place with their python siblings.
def CogentExtension(module_name, extra_compile_args=[], **kw):
path = module_name.replace('.', '/')
kw['extra_compile_args'] = pyrex_compile_options + extra_compile_args
if pyrex_suffix == '.pyx':
kw['pyrex_include_dirs'] = [include_path]
return Extension(module_name, [path + pyrex_suffix], **kw)
short_description = "COmparative GENomics Toolkit"
# This ends up displayed by the installer
long_description = """Cogent
A toolkit for statistical analysis of biological sequences.
Version %s.
""" % __version__
setup(
name="cogent",
version=__version__,
url="http://sourceforge.net/projects/pycogent",
author="Gavin Huttley, Rob Knight",
author_email="gavin.huttley@anu.edu.au, rob@spot.colorado.edu",
description=short_description,
long_description=long_description,
platforms=["any"],
license=["GPL"],
keywords=["biology", "genomics", "statistics", "phylogeny", "evolution",
"bioinformatics"],
classifiers=[
"Development Status :: 5 - Production/Stable",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: GNU General Public License (GPL)",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Software Development :: Libraries :: Python Modules",
"Operating System :: OS Independent",
],
packages=['cogent', 'cogent.align', 'cogent.align.weights', 'cogent.app',
'cogent.cluster', 'cogent.core', 'cogent.data', 'cogent.db',
'cogent.db.ensembl', 'cogent.draw',
'cogent.evolve', 'cogent.format', 'cogent.maths',
'cogent.maths.matrix', 'cogent.maths.stats',
'cogent.maths.stats.cai', 'cogent.maths.unifrac',
'cogent.maths.spatial', 'cogent.motif', 'cogent.parse',
'cogent.phylo', 'cogent.recalculation', 'cogent.seqsim',
'cogent.struct', 'cogent.util'],
ext_modules=[
CogentExtension("cogent.align._compare"),
CogentExtension("cogent.align._pairwise_seqs"),
CogentExtension("cogent.align._pairwise_pogs"),
CogentExtension("cogent.evolve._solved_models"),
CogentExtension("cogent.evolve._likelihood_tree"),
CogentExtension("cogent.evolve._pairwise_distance"),
CogentExtension("cogent.struct._asa"),
CogentExtension("cogent.struct._contact"),
CogentExtension("cogent.maths._period"),
CogentExtension("cogent.maths.spatial.ckd3"),
],
**distutils_extras
)
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