258 lines
8.5 KiB
Python
258 lines
8.5 KiB
Python
#! /usr/bin/env python
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#
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# Install script
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#
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#
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try:
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from setuptools.core import setup
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except ImportError:
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from distutils.core import setup
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from distutils.extension import Extension
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from distutils.util import convert_path
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from distutils import log
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from distutils.dep_util import newer
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from distutils import sysconfig
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try:
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from Cython.Distutils import build_ext as ori_build_ext
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from Cython.Compiler import Main
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has_cython=True
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except ImportError:
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from distutils.command.build_ext import build_ext as ori_build_ext
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has_cython=False
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from distutils.command.build_scripts import build_scripts as ori_build_scripts
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from distutils.command.build_scripts import first_line_re
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from distutils.command.install_scripts import install_scripts as ori_install_scripts
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from stat import ST_MODE
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import os
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import os.path
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import re, sys
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import glob
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from os import path
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class install_scripts(ori_install_scripts):
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def remove_deprecated_script(self):
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for f in DEPRECATED_SCRIPTS:
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try:
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ff = os.path.join(self.install_dir,f)
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os.unlink(ff)
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log.info('Removing deprecated unix command : %s (file : %s)' % (f,ff))
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ff = os.path.join(self.build_dir,f)
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os.unlink(ff)
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except:
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log.info('Unix command %s is not present' % f)
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pass
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def run(self):
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self.remove_deprecated_script()
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ori_install_scripts.run(self)
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class build_ext(ori_build_ext):
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def modifyDocScripts(self):
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print >>open("doc/sphinx/build_dir.txt","w"),self.build_lib
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def run(self):
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self.modifyDocScripts()
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ori_build_ext.run(self)
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class build_scripts(ori_build_scripts):
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def copy_scripts (self):
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"""Copy each script listed in 'self.scripts'; if it's marked as a
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Python script in the Unix way (first line matches 'first_line_re',
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ie. starts with "\#!" and contains "python"), then adjust the first
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line to refer to the current Python interpreter as we copy.
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"""
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self.mkpath(self.build_dir)
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rawbuild_dir = os.path.join(os.path.dirname(self.build_dir),'raw_scripts')
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self.mkpath(rawbuild_dir)
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outfiles = []
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for script in self.scripts:
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adjust = 0
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script = convert_path(script)
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outfile = os.path.join(self.build_dir, os.path.splitext(os.path.basename(script))[0])
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rawoutfile = os.path.join(rawbuild_dir, os.path.basename(script))
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outfiles.append(outfile)
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if not self.force and not newer(script, outfile):
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log.debug("not copying %s (up-to-date)", script)
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continue
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# Always open the file, but ignore failures in dry-run mode --
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# that way, we'll get accurate feedback if we can read the
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# script.
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try:
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f = open(script, "r")
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except IOError:
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if not self.dry_run:
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raise
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f = None
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else:
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first_line = f.readline()
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if not first_line:
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self.warn("%s is an empty file (skipping)" % script)
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continue
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match = first_line_re.match(first_line)
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if match:
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adjust = 1
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post_interp = match.group(1) or ''
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log.info("Store the raw script %s -> %s", script,rawoutfile)
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self.copy_file(script, rawoutfile)
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if adjust:
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log.info("copying and adjusting %s -> %s", script,
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self.build_dir)
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if not self.dry_run:
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outf = open(outfile, "w")
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if not sysconfig.python_build:
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outf.write("#!%s%s\n" %
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(self.executable,
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post_interp))
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else:
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outf.write("#!%s%s\n" %
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(os.path.join(
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sysconfig.get_config_var("BINDIR"),
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"python%s%s" % (sysconfig.get_config_var("VERSION"),
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sysconfig.get_config_var("EXE"))),
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post_interp))
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outf.writelines(f.readlines())
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outf.close()
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if f:
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f.close()
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else:
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if f:
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f.close()
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self.copy_file(script, outfile)
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if os.name == 'posix':
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for file in outfiles:
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if self.dry_run:
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log.info("changing mode of %s", file)
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else:
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oldmode = os.stat(file)[ST_MODE] & 07777
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newmode = (oldmode | 0555) & 07777
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if newmode != oldmode:
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log.info("changing mode of %s from %o to %o",
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file, oldmode, newmode)
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os.chmod(file, newmode)
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class build_filters(build_scripts):
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pass
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def findPackage(root,base=None):
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modules=[]
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if base is None:
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base=[]
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for module in (path.basename(path.dirname(x))
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for x in glob.glob(path.join(root,'*','__init__.py'))):
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modules.append('.'.join(base+[module]))
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modules.extend(findPackage(path.join(root,module),base+[module]))
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return modules
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def findCython(root,base=None,pyrexs=None):
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modules=[]
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pyrexs=[]
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#o=dict(Main.default_options)
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pyopt=Main.CompilationOptions(Main.default_options)
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#print dir(pyopt)
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Main.__dict__['context'] = Main.Context(pyopt.include_path, {})
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if base is None:
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base=[]
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for module in (path.basename(path.dirname(x))
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for x in glob.glob(path.join(root,'*','__init__.py'))):
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for pyrex in glob.glob(path.join(root,module,'*.pyx')):
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pyrexs.append(Extension('.'.join(base+[module,path.splitext(path.basename(pyrex))[0]]),[pyrex]))
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pyrexs[-1].sources.extend(glob.glob(os.path.splitext(pyrex)[0]+'.ext.*.c'))
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print pyrexs[-1].sources
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Main.compile([pyrex],timestamps=True,recursion=True)
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pyrexs.extend(findCython(path.join(root,module),base+[module]))
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return pyrexs
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def findC(root,base=None,pyrexs=None):
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modules=[]
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pyrexs=[]
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if base is None:
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base=[]
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for module in (path.basename(path.dirname(x))
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for x in glob.glob(path.join(root,'*','__init__.py'))):
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for pyrex in glob.glob(path.join(root,module,'*.c')):
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if '.ext.' not in pyrex:
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pyrexs.append(Extension('.'.join(base+[module,path.splitext(path.basename(pyrex))[0]]),[pyrex]))
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pyrexs[-1].sources.extend(glob.glob(os.path.splitext(pyrex)[0]+'.ext.*.c'))
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print pyrexs[-1].sources
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pyrexs.extend(findC(path.join(root,module),base+[module]))
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return pyrexs
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#sys.path.insert(0,"src")
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#from obitools.version import version as obiversion
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#sys.path.pop(0)
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VERSION = "1.0.beta"
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AUTHOR = 'Eric Coissac'
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EMAIL = 'eric@coissac.eu'
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URL = 'www.grenoble.prabi.fr/trac/OBITools'
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LICENSE = 'CeCILL-V2'
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SRC = 'src'
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FILTERSRC = 'textwrangler/filter'
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SCRIPTS = glob.glob('%s/*.py' % SRC)
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FILTERS = glob.glob('%s/*.py' % FILTERSRC)
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DEPRECATED_SCRIPTS=["fastaComplement", "fastaUniq","fasta2tab","fastaAnnotate",
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"fastaSample","fastaGrep","fastaCount","fastaLength",
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"fastaHead","fastaTail","fastaSplit","fastaStrand",
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"fastaLocate","solexaPairEnd","ecoTag","obijoinpairedend"
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]
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def rootname(x):
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return os.path.splitext(x.sources[0])[0]
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if has_cython:
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EXTENTION=findCython(SRC)
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CEXTENTION=findC(SRC)
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cython_ext = set(rootname(x) for x in EXTENTION)
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EXTENTION.extend(x for x in CEXTENTION if rootname(x) not in cython_ext)
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else:
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EXTENTION=findC(SRC)
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#SCRIPTS.append('src/fastaComplement')
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setup(name="OBITools",
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description="Scripts and library for sequence analysis",
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version=VERSION,
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author=AUTHOR,
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author_email=EMAIL,
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license=LICENSE,
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url=URL,
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scripts=SCRIPTS,
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package_dir = {'': SRC},
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packages=findPackage(SRC),
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cmdclass = {'build_ext': build_ext,'build_scripts':build_scripts, 'install_scripts':install_scripts},
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requires=['Cython (>=0.16)'],
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zip_safe = False,
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ext_modules=EXTENTION)
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