"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)

Copyright (C) 2004-2017 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,

Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.

Permission to use, modify, and distribute this software is given under the
terms of the PySceS (BSD style) license. See LICENSE.txt that came with
this distribution for specifics.

NO WARRANTY IS EXPRESSED OR IMPLIED.  USE AT YOUR OWN RISK.
Brett G. Olivier
"""

from version import __version__

__doc__ = """
            PySCeS: the Python Simulator for Cellular Systems
            -------------------------------------------------
            PySCeS is developed by the Triple-J Group for Molecular Cell Physiology
            in order to try model and understand the complex processes and systems
            which make up the living cell. PySCeS features, amongst other things:

            - A text based Model Description Language.
            - A structural analysis module.
            - Integrators for time simulation
            - Non-linear solvers for steady-state analysis
            - A module for performing Metabolic Control Analysis
            - A bifurcation module for systems which exhibit multiple steady states
            - A variety of extra utilites for parameter scans, data output and plotting.
            - A dynamic module loading framework.
            - SBML import and export capability.
            """

import os, time
import PyscesConfig
import PyscesParse
import PyscesLink as link
import codeutil
import PyscesSED as SED

from PyscesUtils import str2bool
from PyscesModelMap import ModelMap

#TODO get rid unused imports
from PyscesWeb import PyscesHTML
html = PyscesHTML()

DEBUG = False

inipath = None
lpath = None
install_dir = None
output_dir = None
model_dir = None
pitcon_switch = False
nleq2_switch = False
__USE_MATPLOTLIB__ = True
__MATPLOTLIB_BACKEND__ = 'TKagg'
__USE_GNUPLOT__ = False
__SILENT_START__ = False

extra_dll_dir = os.path.join(os.path.dirname(__file__), '.libs')
if os.path.isdir(extra_dll_dir):
    os.environ["PATH"] += os.pathsep + extra_dll_dir

if os.sys.platform == 'win32':
    __PyscesConfigDefault = PyscesConfig.__DefaultWin
else:
    __PyscesConfigDefault = PyscesConfig.__DefaultPosix

if DEBUG: print time.strftime('1-%H:%M:%S')

eggdir = 'pysces-%s-py%s.%s-%s.egg' %(__version__, os.sys.version_info[0],\
os.sys.version_info[1], os.sys.platform)
for path in os.sys.path:
    chkPath = path.split(os.path.sep)[-1]
    if chkPath == 'pysces' and path != os.getcwd():
        install_dir = path
        inipath = os.path.join(install_dir, 'pyscfg.ini')
        break
    elif chkPath == eggdir:
        install_dir = os.path.join(path, 'pysces')
        inipath = os.path.join(install_dir, 'pyscfg.ini')
        break
if inipath == None:
    for k in os.sys.path_importer_cache:
        if k.split(os.path.sep)[-1] == 'pysces':
            install_dir = k
            inipath = os.path.join(install_dir, 'pyscfg.ini')
            break
        elif k.split(os.path.sep)[-1] == eggdir:
            install_dir = os.path.join(path, 'pysces')
            inipath = os.path.join(install_dir, 'pyscfg.ini')
            break
del eggdir
if DEBUG: print time.strftime('2-%H:%M:%S')

try:
    __config_dict = PyscesConfig.ReadConfig(inipath, config=__PyscesConfigDefault)
except Exception, ex:
    print ex
    print 'Cwd', os.getcwd()
    print '\nWARNING: Cannot read pyscfg.ini using default values\n'
    __config_dict = __PyscesConfigDefault

# Read config
for key in __config_dict:
    if key == 'pitcon':
        pitcon_switch = str2bool(__config_dict[key])
    elif key == 'nleq2':
        nleq2_switch = str2bool(__config_dict[key])
    elif key == 'matplotlib':
        __USE_MATPLOTLIB__ = str2bool(__config_dict[key])
    elif key == 'matplotlib_backend':
        __MATPLOTLIB_BACKEND__ = __config_dict[key]
    elif key == 'gnuplot':
        __USE_GNUPLOT__ = str2bool(__config_dict[key])
    elif key == 'gnuplot_dir':
        GNUPLOT_DIR = __config_dict[key]
        if GNUPLOT_DIR == 'None':
            GNUPLOT_DIR = None
    elif key == 'silentstart':
        __SILENT_START__ = str2bool(__config_dict[key])
assert inipath != None, '\nNo configuration file found'

if DEBUG: print time.strftime('3-%H:%M:%S')

__userdict = None
if os.sys.platform != 'win32':
    if os.path.exists(os.path.join(os.path.expanduser('~'),'Pysces','.pys_usercfg.ini')):
        __userdict = PyscesConfig.ReadConfig(os.path.join(os.path.expanduser('~'),'Pysces','.pys_usercfg.ini'), PyscesConfig.__DefaultPosixUsr)
    else:
        if not os.path.exists(os.path.join(os.path.expanduser('~'),'Pysces')):
            os.makedirs(os.path.join(os.path.expanduser('~'),'Pysces'))
        PyscesConfig.WriteConfig(os.path.join(os.path.expanduser('~'),'Pysces','.pys_usercfg.ini'),config=PyscesConfig.__DefaultPosixUsr, section='Pysces')
        __userdict = PyscesConfig.ReadConfig(os.path.join(os.path.expanduser('~'),'Pysces','.pys_usercfg.ini'), PyscesConfig.__DefaultPosixUsr)
else:
    if os.path.exists(os.path.join(os.getenv('HOMEDRIVE')+os.path.sep,'Pysces','.pys_usercfg.ini')):
        __userdict = PyscesConfig.ReadConfig(os.path.join(os.getenv('HOMEDRIVE')+os.path.sep,'Pysces','.pys_usercfg.ini'), PyscesConfig.__DefaultWinUsr)
    else:
        if not os.path.exists(os.path.join(os.getenv('HOMEDRIVE')+os.path.sep,'Pysces')):
            os.makedirs(os.path.join(os.getenv('HOMEDRIVE')+os.path.sep,'Pysces'))
        PyscesConfig.WriteConfig(os.path.join(os.getenv('HOMEDRIVE')+os.path.sep,'Pysces','.pys_usercfg.ini'), config=PyscesConfig.__DefaultWinUsr, section='Pysces')
        __userdict = PyscesConfig.ReadConfig(os.path.join(os.getenv('HOMEDRIVE')+os.path.sep,'Pysces','.pys_usercfg.ini'), PyscesConfig.__DefaultWinUsr)
for key in __userdict:
    if key == 'output_dir':
        output_dir = __userdict[key]
        if not os.path.exists(__userdict[key]):
            os.makedirs(__userdict[key])
    elif key == 'model_dir':
        model_dir = __userdict[key]
        if not os.path.exists(__userdict[key]):
            os.makedirs(__userdict[key])
    elif key == 'matplotlib':
        __USE_MATPLOTLIB__ = str2bool(__userdict[key])
    elif key == 'matplotlib_backend':
        __MATPLOTLIB_BACKEND__ = __userdict[key]
    elif key == 'gnuplot':
        __USE_GNUPLOT__ = str2bool(__userdict[key])
    elif key == 'gnuplot_dir':
        GNUPLOT_DIR = __userdict[key]
        if GNUPLOT_DIR == 'None':
            GNUPLOT_DIR = None
    elif key == 'silentstart':
        __SILENT_START__ = str2bool(__userdict[key])
assert output_dir != None, '\nNo output directory defined'
assert model_dir != None, '\nNo output directory defined'

# following is to get the full path when .pys_usercfg.ini specifies CWD as follows:
# output_dir = ./
backup_dir = os.getcwd()
os.chdir(output_dir)
output_dir = os.getcwd()
os.chdir(backup_dir)
os.chdir(model_dir)
model_dir = os.getcwd()
os.chdir(backup_dir)

del PyscesConfig

if DEBUG: print time.strftime('4-%H:%M:%S')

# initialise pysces.interface.*
try:
    import PyscesInterfaces
    interface = PyscesInterfaces.Core2interfaces()
except Exception, ex:
    print 'INFO: pysces.interface.* not available'
    print ex
    interface = None

# initialise pysces.plt.*
import PyscesPlot2
gplt = None
mplt = None
if __USE_MATPLOTLIB__:
    try:
        mplt = PyscesPlot2.MatplotlibUPI(work_dir=output_dir, backend=__MATPLOTLIB_BACKEND__)
        if not __SILENT_START__:
            print 'Matplotlib interface loaded (pysces.plt.m)'
    except Exception, ex:
        print 'Matplotlib interface not available'
        if DEBUG: print ex
        __USE_MATPLOTLIB__ = False
if __USE_GNUPLOT__:
    if GNUPLOT_DIR == None or not os.path.exists(GNUPLOT_DIR):
        print '''GnuPlot has been enabled but the path to the executable has
not been defined (or does not exist). Please set the "gnuplot_dir" key
in your pyscfg.ini file.
        '''
    else:
        try:
            if DEBUG: print GNUPLOT_DIR
            gplt = PyscesPlot2.GnuPlotUPI(work_dir=output_dir, gnuplot_dir=GNUPLOT_DIR)
            if not __SILENT_START__:
                print 'GnuPlot interface loaded (pysces.plt.g)'
        except Exception, ex:
            print 'GnuPlot interface not available'
            if DEBUG: print ex
            __USE_GNUPLOT__ = False

plt = None
if __USE_MATPLOTLIB__ or __USE_GNUPLOT__:
    plt = PyscesPlot2.PyscesUPI()
if __USE_MATPLOTLIB__ and not __USE_GNUPLOT__:
    plt.p_setInterface('matplotlib', mplt)
elif __USE_GNUPLOT__ and not __USE_MATPLOTLIB__:
    plt.p_setInterface('gnuplot', gplt)
elif __USE_GNUPLOT__ and __USE_MATPLOTLIB__:
    plt.p_setInterface('matplotlib', mplt)
    plt.p_setInterface('gnuplot', gplt)
    plt.p_deactivateInterface('gnuplot')

if DEBUG: print time.strftime('5-%H:%M:%S')

alt_import = False
alt_import_pitcon = False
alt_import_nleq2 = False
if os.sys.platform == 'win32':
    if pitcon_switch:
        os.sys.path.append(os.path.join(install_dir,'pitcon'))
        try:
            import pitcon.pitcon as pitcon
            if not __SILENT_START__:
                print 'Continuation routines available'
        except Exception, ex:
            try:
                os.environ['path'] = '%s;%s' % (os.path.join(install_dir,'win32'), os.environ['path'])
                import pitcon.pitcon as pitcon
                if not __SILENT_START__:
                    print 'Continuation routines available'
            except Exception, ex:
                #print 'Attempting alternate pitcon import ...'
                #alt_import = True
                #alt_import_pitcon = True
                print ex
                print 'INFO: Pitcon import failed: continuation not available'


    if nleq2_switch:
        os.sys.path.append(os.path.join(install_dir,'nleq2'))
        try:
            import nleq2.nleq2 as nleq2
            if not __SILENT_START__:
                print 'NLEQ2 routines available'
        except Exception, ex:
            try:
                os.environ['path'] = '%s;%s' % (os.path.join(install_dir,'win32'), os.environ['path'])
                import nleq2.nleq2 as nleq2
                if not __SILENT_START__:
                    print 'NLEQ2 routines available'
            except Exception, ex:
                #print 'Attempting alternate nleq2 import ...'
                #alt_import = True
                #alt_import_nleq2 = True
                print ex
                print 'INFO: NLEQ2 import failed: option not available'
else:
    if pitcon_switch:
        os.sys.path.append(os.path.join(install_dir,'pitcon'))
        try:
            import pitcon.pitcon as pitcon
            if not __SILENT_START__:
                print 'Pitcon routines available'
        except Exception, ex:
            #print ex
            alt_import = True
            alt_import_pitcon = True

            print 'Attempting alternate pitcon import ...'
    if nleq2_switch:
        os.sys.path.append(os.path.join(install_dir,'nleq2'))
        try:
            import nleq2.nleq2 as nleq2
            if not __SILENT_START__:
                print 'NLEQ2 routines available'
        except Exception, ex:
            #print ex
            alt_import = True
            alt_import_nleq2 = True
            print 'Attempting alternate nleq2 import ...'

if DEBUG: print time.strftime('6-%H:%M:%S')

if alt_import:
    savedir = os.getcwd()
    for tpath in os.sys.path:
        if alt_import_pitcon:
            try:
                if os.path.exists(os.path.join(tpath,'pysces','pitcon')) and tpath != '':
                    os.chdir(os.path.join(tpath,'pysces','pitcon'))
                    import pitcon
                    if not __SILENT_START__:
                        print 'Continuation routines available (A)'
            except Exception, ex:
                print ex
                print 'INFO: Alternate pitcon import failed: continuation not available'
        if alt_import_nleq2:
            try:
                if os.path.exists(os.path.join(tpath,'pysces','nleq2')) and tpath != '':
                    os.chdir(os.path.join(tpath,'pysces','nleq2'))
                    import nleq2
                    if not __SILENT_START__:
                        print 'NLEQ2 routines available (A)'
            except Exception, ex:
                print ex
                nleq2_switch = False
                print 'INFO: Alternate NLEQ2 import failed: option not available'
    os.chdir(savedir)

if DEBUG: print time.strftime('7-%H:%M:%S')

def setWorkPath(path):
    """
    Sets the output or working directory.

     - *path* a path/subdirectory (will be created if it doesn't exist)

    """
    import pysces as P
    import os as O
    if not O.path.exists(path):
        O.makedirs(path)
    O.chdir(path)
    try:
        P.PyscesModel.OUTPUT_DIR = path
        P.output_dir = path
        if hasattr(P, 'plt') and hasattr(P.plt, 'm') and hasattr(P.plt.m, '__WORK_DIR__'):
            P.plt.m.__WORK_DIR__ = path
        if hasattr(P, 'plt') and hasattr(P.plt, 'g') and hasattr(P.plt.g, '__WORK_DIR__'):
            P.plt.g.__WORK_DIR__ = path
    except Exception, ex:
        print ex
        print 'Path change exception'
    del P, O



# This has to come at the end
from PyscesModel import PysMod as model
from PyscesModel import ScanDataObj as ScanDataObj
PyscesModel.interface = interface
from PyscesTest import PyscesTest as test
write = None
try:
    from PyscesUtils import WriteOutput
    write = WriteOutput()
    del WriteOutput
except ImportError, ex:
    pass

from PyscesScan import PITCONScanUtils, Scanner

try:
    from RateChar import RateChar
    if not __SILENT_START__:
        print "RateChar is available"
except Exception, ex:
    RateChar = None
    #print "RateChar not available"

# ParScanner import
try:
    from PyscesParScan import ParScanner
    if not __SILENT_START__:
        print "Parallel scanner is available"
except ImportError, ex:
    ParScanner = None
    print ex
    print "INFO: Parallel scanner not available"

if DEBUG: print time.strftime('9-%H:%M:%S')

if not __SILENT_START__:
    print '\nPySCeS environment\n******************'
    print 'pysces.model_dir = ' + model_dir
    print 'pysces.output_dir = ' + output_dir

    print '\n\n***********************************************************************'
    print '* Welcome to PySCeS (' + __version__ + ') - Python Simulator for Cellular Systems   *'
    print '*                http://pysces.sourceforge.net                        *'
    ##  print '*                       Somewhere In Time                             *'
    print '* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2017  *'
    print '* Triple-J Group for Molecular Cell Physiology                        *'
    print '* Stellenbosch University, ZA and VU University Amsterdam, NL         *'
    print '* PySCeS is distributed under the PySCeS (BSD style) licence, see     *'
    print '* LICENCE.txt (supplied with this release) for details                *'
    ##  print '*                 ** Read about PySCeS **                             *'
    print '* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046          *'
    print '***********************************************************************'

try:
    del os, key, gplt, mplt
except Exception, ex:
    print ex
    print '\n\nOops I did it again error ...\n\n'
if DEBUG: print time.strftime('10-%H:%M:%S')
