import glob

import sys

import os

import subprocess

import re

########################################################################

#######################################################################

## Check for dependencies

##

## Is there a way to do this more elegantly?

## 1. Run "pip install numpy"

## 2. Wrap inside functions (works for numpy/pysam, but not cython)

try:

import numpy

except ImportError:

raise ImportError("the CGAT code collection requires numpy to be installed before running setup.py (pip install numpy)" )

try:

import Cython

except ImportError:

raise ImportError("the CGAT code collection requires cython to be installed before running setup.py (pip install cython)" )

try:

import pysam

except ImportError:

raise ImportError("the CGAT code collection requires pysam to be installed before running setup.py (pip install pysam)" )

########################################################################

########################################################################

## Import setuptools

## Use existing setuptools, otherwise try ez_setup.

try:

import setuptools

except ImportError:

## try to get via ez_setup

## ez_setup did not work on all machines tested as

## it uses curl with https protocol, which is not

## enabled in ScientificLinux

import ez_setup

ez_setup.use_setuptools()

from setuptools import setup, find_packages, Extension

from distutils.version import LooseVersion, StrictVersion

if LooseVersion( setuptools.__version__ ) < LooseVersion( '1.1' ):

raise ImportError("the CGAT code collection requires setuptools 1.1 higher")

from Cython.Distutils import build_ext

########################################################################

########################################################################

IS_OSX = sys.platform == 'darwin'

########################################################################

########################################################################

# collect CGAT version

sys.path.insert( 0, "scripts")

import version

version = version.__version__

###############################################################

###############################################################

# Check for external dependencies

#

# Not exhaustive, simply execute a representative tool from a toolkit.

external_dependencies = (

("wigToBigWig", "UCSC tools", 255),

("bedtools", "bedtools", 0 ),

)

for tool, toolkit, expected in external_dependencies:

try:

from subprocess import DEVNULL # py3k

except ImportError:

import os

DEVNULL = open(os.devnull, 'wb')

try:

retcode = subprocess.call( tool, shell = True, stdout=DEVNULL, stderr=DEVNULL )

except OSError, msg:

print( "WARNING: depency check for %s failed: %s" % (toolkit, msg ) )

# UCSC tools return 255 when called without arguments

if retcode != expected:

print ( "WARNING: depency check for %s(%s) failed, error %i" % \

(toolkit, tool, retcode ) )

###############################################################

###############################################################

# Define dependencies

#

# Perform a CGAT Code Collection Installation

INSTALL_CGAT_CODE_COLLECTION = True

major, minor1, minor2, s, tmp = sys.version_info

if major==3:

raise SystemExit("""CGAT is not fully python3 compatible""")

if (major==2 and minor1<7) or major<2:

raise SystemExit("""CGAT requires Python 2.7 or later.""")

#####################################################################

#####################################################################

## Code to install dependencies from a repository

#####################################################################

## Modified from http://stackoverflow.com/a/9125399

#####################################################################

def which(program):

return None

REPO_REQUIREMENT = re.compile(r'^-e (?P<link>(?P<vcs>git|svn|hg|bzr).+#egg=(?P<package>.+)-(?P<version>\d(?:\.\d)*))$')

HTTPS_REQUIREMENT = re.compile(r'^-e (?P<link>.*).+#(?P<package>.+)-(?P<version>\d(?:\.\d)*)$')

install_requires = []

dependency_links = []

for requirement in (l.strip() for l in open('requires.txt') if not l.startswith("#")):

match = REPO_REQUIREMENT.match(requirement)

if match:

assert which(match.group('vcs')) is not None, \

"VCS '%(vcs)s' must be installed in order to install %(link)s" % match.groupdict()

install_requires.append("%(package)s==%(version)s" % match.groupdict())

dependency_links.append(match.group('link'))

continue

if requirement.startswith("https"):

install_requires.append(requirement)

continue

match = HTTPS_REQUIREMENT.match(requirement)

if match:

install_requires.append("%(package)s>=%(version)s" % match.groupdict())

dependency_links.append(match.group('link'))

continue

install_requires.append(requirement)

if major==2:

install_requires.extend( [ 'web.py>=0.37',

'xlwt>=0.7.4',

'matplotlib-venn>=0.5' ] )

elif major==3:

pass

import os

import re

if INSTALL_CGAT_CODE_COLLECTION:

cgat_packages= find_packages( exclude=["CGATPipelines*", "scripts*"])

else:

cgat_packages= find_packages( exclude=["scripts*"])

# rename scripts to CGATScripts

cgat_packages.append("CGATScripts")

cgat_package_dirs = {'CGAT': 'CGAT',

'CGATScripts': 'scripts',

'CGATPipelines': 'CGATPipelines'}

##########################################################

##########################################################

# Classifiers

classifiers="""

"""

##########################################################

##########################################################

## Extensions

# Connected components cython extension

Components = Extension(

)

# Nested containment lists

NCL = Extension(

)

# Nubiscan motif mapping

#Nubiscan = Extension(

# "CGAT.Nubiscan.cnubiscan",

# [ 'CGAT/Nubiscan/cnubiscan.pyx'],

# library_dirs=[],

# libraries=[],

# include_dirs = [numpy.get_include()],

# language="c",

# )

# Automatically build script extensions

pyx_files = glob.glob( "scripts/*.pyx" )

script_extensions = []

pysam_dirname = os.path.dirname( pysam.__file__ )

include_dirs = [ numpy.get_include() ] + pysam.get_include()

if IS_OSX:

# linking against bundles does no work (and apparently is not needed)

# within OS X

extra_link_args = []

else:

extra_link_args = [ os.path.join( pysam_dirname, "csamtools.so")]

for pyx_file in pyx_files:

script_name = os.path.basename( pyx_file )

script_prefix = script_name[:-4]

script_extensions.append(

Extension( "CGAT.%s" % (script_prefix),

sources = [pyx_file],

extra_link_args = extra_link_args,

include_dirs = include_dirs,

define_macros = pysam.get_defines() )

)

setup(## package information

name = 'CGAT',

version= version,

description = 'CGAT : the Computational Genomics Analysis Toolkit',

author = 'Andreas Heger',

author_email = 'andreas.heger@gmail.com',

license = "BSD",

platforms = ["any",],

keywords="computational genomics",

long_description='CGAT : the Computational Genomics Analysis Toolkit',

classifiers = filter(None, classifiers.split("\n")),

url="http://www.cgat.org/cgat/Tools/",

## package contents

packages = cgat_packages,

package_dir= cgat_package_dirs,

# package_data = { 'CGATScripts' : ['./scripts/*.py', './scripts/*.pyx',

# './scripts/*.pyxbld', './scripts/*.pl' ],

# },

include_package_data = True,

entry_points = {

'console_scripts': ['cgat = CGATScripts.cgat:main' ]

},

## dependencies

install_requires=install_requires,

dependency_links=dependency_links,

## extension modules

ext_modules=[Components, NCL] + script_extensions,

cmdclass = {'build_ext': build_ext},

## other options

zip_safe = False,

test_suite = "tests",

)