"""Setup settings for distutils.

You can get debug build with command:
python2.2 setup.py debug build
"""
import sys,time




print sys.argv

common_compile_args=["-Wall"]
if len(sys.argv)>1:
    if sys.argv[1]=='debug':
        common_compile_args=["-O0","-fno-inline","-Wall","-g","-UNDEBUG","-DEXTRADEBUG"]#,"-DDEBUG_OUTPUT","-DSUBOPTDEBUG"]
        print "Using debug settings"
        del sys.argv[1]
    elif sys.argv[1]=='profile':
        common_compile_args=["-pg"]
        print "Using profiling settings"
        del sys.argv[1]
    elif sys.argv[1]=='lite_debug':
        common_compile_args=["-g","-Wall","-O0","-D_GLIBCXX_DEBUG"]
        print "Using light debug settings"
        del sys.argv[1]


from distutils.core import setup, Extension


#alignCompileArgs = ["-Wall","-g","-UNDEBUG","-DEXTRADEBUG"]
#alignCompileArgs = ["-fno-inline","-Wall","-g","-UNDEBUG"]
#alignCompileArgs = ["-g","-Wall","-O3"]
alignCompileArgs = []

#Save memory if the matrix would be larger than 512MB
alignCompileArgs = ["-DSAVE_MEM","-DSAVE_MEM_LIMIT=536870912","-DOUTPUTFREQ=10000000","-DSILENTPROGRESS"]

if 0:
    print "No alignment score decrease allowed"
    alignCompileArgs.append("-DNO_SCORE_DECREASE")
alignLibs=[]


commonLibs=[]
alignLibDirs=[]
compileLibs=[]



extra_data=[]

from glob import glob
if sys.platform=='win32':
    try:
        import py2exe
        SDKdir=r"C:\Windows\system32"
        PythonDir=r"D:\Program Files\Python24\\"
        
        extra_data.append((r"tcl\tix8.1",[x for x in glob(PythonDir+r"\tcl\tix8.1\*") if x[-7:] not in ("bitmaps",".1\\pref")]))
        extra_data.append((r"tcl\tix8.1\bitmaps",glob(PythonDir+r"\tcl\tix8.1\bitmaps\*")))
        extra_data.append((r"tcl\tix8.1\pref",glob(PythonDir+r"\tcl\tix8.1\pref\*")))
        extra_data.append((".",glob(PythonDir+r"\DLLs\tix*.dll")+[SDKdir+r"\msvcr71.dll",SDKdir+r"\msvcp71.dll"]))
    except ImportError:
        pass
    common_compile_args.extend([r"/O2", r"/IC:\Program Files\Microsoft Visual Studio .NET\Vc7\include",\
                                r"/IC:\Program Files\Microsoft Visual C++ Toolkit 2003\include"])
    alignCompileArgs.extend([r"/DHAS_NO_TRUNC"])
    pass
else:
    commonLibs.extend(["stdc++"])
    #common_compile_args.extend([r"-O3", r"-Wall"])
    try:
        import gzip
        print "Looks like you have zlib! (It's a bad thing if you don't)"
        alignCompileArgs.extend(["-Isrc/gzstream","-DHAVE_GZSTREAM=1"])
        alignLibDirs.append("src/gzstream")
        alignLibs.extend(["gzstream","z","m"])

        libgzSrcs= ["src/gzstream/gzstream.C"]
        compileLibs.append(('gzstream',
                         {'sources':libgzSrcs,
                          'include_dirs':['./src/gzstream/'
                                          ],
                          'macros':[]},
                         ))

    except ImportError:
        print "Looks like you don't have zlib! You will not be able to use gzip:ed files in alignment"
        pass





modMatrix = Extension('eellib._c_matrix',
                    libraries = commonLibs,
                    sources = ['src/_c_matrix.cc'],
                    extra_compile_args = common_compile_args+["-DSEQ_BUFFER_SIZE=5000000","-DLARGE_AFFY_DELTA=0.0","-DMAX_SNP_COUNT=7","-DSCANNING_WINDOW_SIZE=6"],
                    extra_link_args = [])




modAlign = Extension('eellib.align',
                     library_dirs = alignLibDirs,
                     libraries = commonLibs+alignLibs,
                     sources = ['src/align.cc'],
                     extra_compile_args=alignCompileArgs+common_compile_args,
                     extra_link_args = [])

modAlignedCols=Extension('eellib.alignedCols',
                         library_dirs = alignLibDirs,
                         libraries = commonLibs+alignLibs,
                         sources = ['src/alignedCols.cc' ],
                         extra_compile_args=alignCompileArgs+common_compile_args,
                         extra_link_args = [])
                         

modDist = Extension("eellib.editdist",
                    sources = ["src/editdist.c"],
                    extra_compile_args = common_compile_args
                    )


modMultiAlign = Extension('eellib.multiAlign',
                          library_dirs = alignLibDirs,
                          libraries = commonLibs+alignLibs,
                          sources = ['src/multiAlign.cc'],
                          extra_compile_args=alignCompileArgs+common_compile_args,
                          extra_link_args = [])

modShortMultiAlign = Extension('eellib.shortMultiAlign',
                          library_dirs = alignLibDirs,
                          libraries = commonLibs+alignLibs,
                          sources = ['src/shortMultiAlign.cc'],
                          extra_compile_args=alignCompileArgs+common_compile_args,
                          extra_link_args = [])

modMultiFromPairwise = Extension('eellib.multiFromPairwise',
                          library_dirs = alignLibDirs,
                          libraries = commonLibs+alignLibs,
                          sources = ['src/multiFromPairwise.cc'],
                          extra_compile_args=alignCompileArgs+common_compile_args,
                          extra_link_args = [])

modTreeMultiAlign = Extension('eellib.treeMultiAlign',
                          library_dirs = alignLibDirs,
                          libraries = commonLibs+alignLibs,
                          sources = ['src/treeMultiAlign.cc'],
                          extra_compile_args=alignCompileArgs+common_compile_args,
                          extra_link_args = [])


#ext_modList= [modMatrix,modAlignedCols,modAlign,modDist]
#ext_modList= [modMatrix,modAlignedCols,modAlign,modMultiAlign,modDist]
#ext_modList= [modMatrix,modAlignedCols,modAlign,modMultiAlign,modShortMultiAlign,modMultiFromPairwise,modDist]
ext_modList= [modMatrix,modAlignedCols,modAlign,modMultiAlign,modShortMultiAlign,modMultiFromPairwise,modTreeMultiAlign,modDist]

setup (name = 'EEL',
       version = time.strftime("%y%m%d"),#'2.0pre4',
       url = "http://www.cs.helsinki.fi/u/kpalin/",
       author = "Kimmo Palin, Matthias Berg, Pasi Rastas",
       author_email = "kimmo.palin@helsinki.fi",
       maintainer = "Kimmo Palin",
       maintainer_email = "kimmo.palin@helsinki.fi",
       license = "GPL (see file COPYING)",
       description = 'A software tool for locating enhancer elements from genomic sequence',
       ext_modules = ext_modList,
       libraries= compileLibs,
       packages = ["eellib"],
       scripts = [ "eel"],
       console = [ "eel"],
       data_files=extra_data)