"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
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.
Authors: Brett G. Olivier and Johann M. Rohwer (see CONTRIBUTORS.md for details)
"""
from __future__ import division, print_function
from __future__ import absolute_import
from __future__ import unicode_literals
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.
Authors: Brett G. Olivier and Johann M. Rohwer (see CONTRIBUTORS.md for details)
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.
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
"""
import os
import time
from importlib import util
from . import PyscesConfig
from . import PyscesParse
from . import PyscesLink as link
from . import PyscesSED as SED
from .PyscesUtils import str2bool
from .PyscesModelMap import ModelMap
from .version import current_version_tuple
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.sys.platform == 'win32' and os.path.isdir(extra_dll_dir):
os.environ["PATH"] += os.pathsep + extra_dll_dir
if hasattr(os, 'add_dll_directory'):
os.add_dll_directory(extra_dll_dir)
__PyscesConfigDefault = PyscesConfig.__DefaultConfig
if DEBUG:
print(time.strftime('1-%H:%M:%S'))
install_dir = os.path.dirname(util.find_spec('pysces').origin)
inipath = os.path.join(install_dir, 'pyscfg.ini')
if DEBUG:
print(time.strftime('2-%H:%M:%S'))
try:
__config_dict = PyscesConfig.ReadConfig(inipath, config=__PyscesConfigDefault)
except Exception as ex:
if DEBUG:
print(ex)
if not __SILENT_START__:
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])
elif key == 'change_dir_on_start':
__CHGDIR_ON_START__ = str2bool(__config_dict[key])
elif key == 'custom_datatype':
__CUSTOM_DATATYPE__ = __config_dict[key]
if __CUSTOM_DATATYPE__ == 'None':
__CUSTOM_DATATYPE__ = None
assert inipath != None, '\nNo configuration file found'
if DEBUG:
print(time.strftime('3-%H:%M:%S'))
__userdict = None
# search for legacy Windows Pysces directory location
if os.sys.platform == 'win32' and 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.__DefaultConfigUsr,
)
else:
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.__DefaultConfigUsr,
)
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.__DefaultConfigUsr,
section='Pysces',
)
__userdict = PyscesConfig.ReadConfig(
os.path.join(os.path.expanduser('~'), 'Pysces', '.pys_usercfg.ini'),
PyscesConfig.__DefaultConfigUsr,
)
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])
elif key == 'change_dir_on_start':
__CHGDIR_ON_START__ = str2bool(__userdict[key])
elif key == 'custom_datatype':
__CUSTOM_DATATYPE__ = __userdict[key]
if __CUSTOM_DATATYPE__ == 'None':
__CUSTOM_DATATYPE__ = None
assert output_dir != None, '\nNo output directory defined'
assert model_dir != None, '\nNo model 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:
from . import PyscesInterfaces
interface = PyscesInterfaces.Core2interfaces()
except Exception as ex:
if DEBUG:
print(ex)
if not __SILENT_START__:
print('INFO: pysces.interface.* not available')
interface = None
# initialise pysces.plt.*
from . 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 as ex:
if not __SILENT_START__:
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):
if not __SILENT_START__:
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 as ex:
if not __SILENT_START__:
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:
from .pitcon import pitcon as pitcon
if not __SILENT_START__:
print('Continuation routines available')
except Exception as ex:
try:
os.environ['path'] = '%s;%s' % (
os.path.join(install_dir, 'win32'),
os.environ['path'],
)
from .pitcon import pitcon as pitcon
if not __SILENT_START__:
print('Continuation routines available')
except Exception as ex:
# print 'Attempting alternate pitcon import ...'
# alt_import = True
# alt_import_pitcon = True
if DEBUG:
print(ex)
if not __SILENT_START__:
print('INFO: Pitcon import failed: continuation not available')
if nleq2_switch:
os.sys.path.append(os.path.join(install_dir, 'nleq2'))
try:
from .nleq2 import nleq2 as nleq2
if not __SILENT_START__:
print('NLEQ2 routines available')
except Exception as ex:
try:
os.environ['path'] = '%s;%s' % (
os.path.join(install_dir, 'win32'),
os.environ['path'],
)
from .nleq2 import nleq2 as nleq2
if not __SILENT_START__:
print('NLEQ2 routines available')
except Exception as ex:
# print 'Attempting alternate nleq2 import ...'
# alt_import = True
# alt_import_nleq2 = True
if DEBUG:
print(ex)
if not __SILENT_START__:
print('INFO: NLEQ2 import failed: option not available')
else:
if pitcon_switch:
os.sys.path.append(os.path.join(install_dir, 'pitcon'))
try:
from .pitcon import pitcon as pitcon
if not __SILENT_START__:
print('Pitcon routines available')
except Exception as ex:
if DEBUG:
print(ex)
alt_import = True
alt_import_pitcon = True
if not __SILENT_START__:
print('Attempting alternate pitcon import ...')
if nleq2_switch:
os.sys.path.append(os.path.join(install_dir, 'nleq2'))
try:
from .nleq2 import nleq2 as nleq2
if not __SILENT_START__:
print('NLEQ2 routines available')
except Exception as ex:
if DEBUG:
print(ex)
alt_import = True
alt_import_nleq2 = True
if not __SILENT_START__:
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'))
from . import pitcon
if not __SILENT_START__:
print('Continuation routines available (A)')
except Exception as ex:
if DEBUG:
print(ex)
if not __SILENT_START__:
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'))
from . import nleq2
if not __SILENT_START__:
print('NLEQ2 routines available (A)')
except Exception as ex:
if DEBUG:
print(ex)
nleq2_switch = False
if not __SILENT_START__:
print('INFO: Alternate NLEQ2 import failed: option not available')
os.chdir(savedir)
if DEBUG:
print(time.strftime('7-%H:%M:%S'))
# check for libsbml
try:
import libsbml as SBML
if not __SILENT_START__:
print("SBML support available")
except ImportError as ex:
SBML = None
if DEBUG:
print(ex)
if not __SILENT_START__:
print("INFO: libSBML not installed, SBML support not available.")
# custom datatype for mod.sim and mod.scan
if __CUSTOM_DATATYPE__:
assert (
__CUSTOM_DATATYPE__ == 'pandas'
), f'Custom datatype {__CUSTOM_DATATYPE__} not supported, only pandas is supported.'
if not __SILENT_START__:
print('INFO: Custom datatype set to pandas.')
def _checkPandas():
try:
import pandas
return True
except ModuleNotFoundError:
print(
"""
Custom datatype set in configuration but pandas not installed. Install with:
pip install pandas or
conda install pandas
Unsetting custom datatype!
"""
)
return False
[docs]def enablePandas(var=True):
"""
Enable pandas data type globally per session for `mod.sim` and `mod.scan` objects.
- *var* if True, return pandas DataFrame, else numpy recarray
"""
if var and _checkPandas():
PyscesModel.__CUSTOM_DATATYPE__ = 'pandas'
print('Enabling pandas globally...')
else:
PyscesModel.__CUSTOM_DATATYPE__ = None
print('Disabling pandas globally...')
# This has to come at the end
from . import PyscesModel
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 as ex:
pass
from .PyscesScan import PITCONScanUtils, Scanner
try:
from .RateChar import RateChar
if not __SILENT_START__:
print("RateChar is available")
except Exception as ex:
RateChar = None
if DEBUG:
print(ex)
# print "RateChar not available"
# ParScanner import
try:
from .PyscesParScan import ParScanner
if not __SILENT_START__:
print("Parallel scanner is available")
except ImportError as ex:
ParScanner = None
if DEBUG:
print(ex)
if not __SILENT_START__:
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, 2004-2024 *')
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 as ex:
print(ex)
print('\n\nOops I did it again error ...\n\n')
if DEBUG:
print(time.strftime('10-%H:%M:%S'))