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BoPengBoPeng
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restore original simuOpt design
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‎CMakeLists.txt‎

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@@ -555,7 +555,6 @@ install(FILES
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src/simuPOP/utils.py
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src/simuPOP/demography.py
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src/simuPOP/sampling.py
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src/simuPOP/simuOpt.py
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DESTINATION simuPOP
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)
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‎simuOpt.py‎

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#!/usr/bin/env python
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"""
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Backward compatibility stub for simuOpt module.
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DEPRECATED: Please use 'from simuPOP.simuOpt import setOptions' instead.
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This import path will be removed in a future version.
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"""
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#
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# $File: simuOpt.py $
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# $LastChangedDate$
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# $Rev$
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#
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# This file is part of simuPOP, a forward-time population genetics
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# simulation environment. Please visit https://github.com/BoPeng/simuPOP
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# for details.
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#
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# Copyright (C) 2004 - 2010 Bo Peng (Bo.Peng@bcm.edu)
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#
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# This program is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with this program. If not, see <http://www.gnu.org/licenses/>.
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#
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import warnings
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'''
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Module ``simuOpt`` provides a function ``simuOpt.setOptions`` to control which
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simuPOP module to load, and how it is loaded, and a class ``simuOpt.Params``
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that helps users manage simulation parameters.
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warnings.warn(
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"Importing 'simuOpt' directly is deprecated. "
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"Please use 'from simuPOP.simuOpt import setOptions' instead. "
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"This import path will be removed in a future version.",
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DeprecationWarning,
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stacklevel=2
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)
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When simuPOP is loaded, it checkes a few environmental variables
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(``SIMUOPTIMIZED``, ``SIMUALLELETYPE``, and ``SIMUDEBUG``) to determine which
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simuPOP module to load, and how to load it. More options can be set using the
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``simuOpt.setOptions`` function. For example, you can suppress the banner
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message when simuPOP is loaded and require a minimal version of simuPOP for
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your script. simuPOP recognize the following commandline arguments
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from simuPOP.simuOpt import *
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``--optimized``
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Load the optimized version of a simuPOP module.
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``--gui=None|batch|interactive|True|wxPython|Tkinter``
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Whether or not use a graphical toolkit and which one to use.
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``--gui=batch`` is usually used to run a script in batch mode (do not start
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a parameter input dialog and use all default values unless a parameter is
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specified from command line or a configuraiton file. If
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``--gui=interactive``, an interactive shell will be used to solicit input
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from users. Otherwise, simuPOP will try to use a graphical parameter input
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dialog, and falls to an interactive mode when no graphical Toolkit is
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available. Please refer to parameter ``gui`` for ``simuOpt.setOptions``
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for details.
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class ``params.Params`` provides a powerful way to handle commandline
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arguments. Briefly speaking, a ``Params`` object can be created from a list
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of parameter specification dictionaries. The parameters are then become
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attributes of this object. A number of functions are provided to determine
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values of these parameters using commandline arguments, a configuration
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file, or a parameter input dialog (using ``Tkinter`` or ``wxPython``).
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Values of these parameters can be accessed as attributes, or extracted
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as a list or a dictionary. Note that the ``Params.getParam`` function
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automatically handles the following commandline arguments.
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``-h`` or ``--help``
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Print usage message.
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``--config=configFile``
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Read parameters from a configuration file *configFile*.
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'''
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__all__ = [
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'simuOptions',
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'setOptions'
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]
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import os, sys, re, time, textwrap
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#
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# simuOptions that will be checked when simuPOP is loaded. This structure
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# can be changed by function setOptions
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#
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simuOptions = {
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'Optimized': False,
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'AlleleType': 'short',
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'Debug': [],
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'Quiet': False,
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'Version': None,
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'Revision': None,
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'GUI': True,
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'Plotter': None,
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'NumThreads': 1,
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}
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# Optimized: command line option --optimized or environmental variable SIMUOPTIMIZED
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if '--optimized' in sys.argv or os.getenv('SIMUOPTIMIZED') is not None:
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simuOptions['Optimized'] = True
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# AlleleType: from environmental variable SIMUALLELETYPE
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if os.getenv('SIMUALLELETYPE') in ['short', 'long', 'binary', 'mutant', 'lineage']:
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simuOptions['AlleleType'] = os.getenv('SIMUALLELETYPE')
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elif os.getenv('SIMUALLELETYPE') is not None:
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print('Environmental variable SIMUALLELETYPE can only be short, long, binary, mutant, or lineage.')
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# Debug: from environmental variable SIMUDEBUG
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if os.getenv('SIMUDEBUG') is not None:
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simuOptions['Debug'].extend(os.getenv('SIMUDEBUG').split(','))
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# openMP number of threads
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if os.getenv('OMP_NUM_THREADS') is not None:
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try:
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simuOptions['NumThreads'] = int(os.getenv('OMP_NUM_THREADS'))
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except:
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print('Ignoring invalid value for environmental variable OMP_NUM_THREADS')
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# GUI: from environmental variable SIMUGUI
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if os.getenv('SIMUGUI') is not None:
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_gui = os.getenv('SIMUGUI')
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elif '--gui' in sys.argv:
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if sys.argv[-1] == '--gui':
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raise ValueError('An value is expected for command line option --gui')
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_gui = sys.argv[sys.argv.index('--gui') + 1]
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elif True in [x.startswith('--gui=') for x in sys.argv]:
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_gui = sys.argv[[x.startswith('--gui=') for x in sys.argv].index(True)][len('--gui='):]
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else:
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_gui = None
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if _gui in ['True', 'true', '1']:
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simuOptions['GUI'] = True
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elif _gui in ['False', 'false', '0']:
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simuOptions['GUI'] = False
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elif _gui in ['wxPython', 'Tkinter', 'batch', 'interactive']:
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simuOptions['GUI'] = _gui
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elif _gui is not None:
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print("Invalid value '%s' for environmental variable SIMUGUI or commandline option --gui." % _gui)
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def setOptions(alleleType=None, optimized=None, gui=None, quiet=None,
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debug=None, version=None, revision=None, numThreads=None, plotter=None):
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'''Set options before simuPOP is loaded to control which simuPOP module to
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load, and how the module should be loaded.
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alleleType
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Use the standard, binary,long or mutant allele version of the simuPOP
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module if ``alleleType`` is set to 'short', 'binary', 'long', 'mutant',
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or 'lineage' respectively. If this parameter is not set, this function
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will try to get its value from environmental variable ``SIMUALLELETYPE``.
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The standard (short) module will be used if the environmental variable
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is not defined.
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optimized
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Load the optimized version of a module if this parameter is set to
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``True`` and the standard version if it is set to ``False``. If this
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parameter is not set (``None``), the optimized version will be used
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if environmental variable ``SIMUOPTIMIZED`` is defined. The standard
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version will be used otherwise.
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gui
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Whether or not use graphical user interfaces, which graphical toolkit
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to use and how to process parameters in non-GUI mode. If this parameter
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is ``None`` (default), this function will check environmental variable
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``SIMUGUI`` or commandline option ``--gui`` for a value, and assume
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``True`` if such an option is unavailable. If ``gui=True``, simuPOP
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will use ``wxPython``-based dialogs if ``wxPython`` is available, and
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use ``Tkinter``-based dialogs if ``Tkinter`` is available and use an
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interactive shell if no graphical toolkit is available.
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``gui='Tkinter'`` or ``'wxPython'`` can be used to specify the
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graphical toolkit to use. If ``gui='interactive'``, a simuPOP script
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prompt users to input values of parameters. If ``gui='batch'``,
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default values of unspecified parameters will be used. In any case,
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commandline arguments and a configuration file specified by parameter
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--config will be processed. This option is usually left to ``None`` so
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that the same script can be run in both GUI and batch mode using
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commandline option ``--gui``.
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plotter
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(Deprecated)
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quiet
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If set to ``True``, suppress the banner message when a simuPOP module
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is loaded.
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debug
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A list of debug code (as string) that will be turned on when simuPOP
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is loaded. If this parameter is not set, a list of comma separated
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debug code specified in environmental variable ``SIMUDEBUG``, if
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available, will be used. Note that setting ``debug=[]`` will remove
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any debug code that might have been by variable ``SIMUDEBUG``.
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version
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A version string (e.g. 1.0.0) indicating the required version number
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for the simuPOP module to be loaded. simuPOP will fail to load if the
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installed version is older than the required version.
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revision
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Obsolete with the introduction of parameter version.
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numThreads
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Number of Threads that will be used to execute a simuPOP script. The
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values can be a positive number (number of threads) or 0 (all available
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cores of the computer, or whatever number set by environmental variable
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``OMP_NUM_THREADS``). If this parameter is not set, the number of
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threads will be set to 1, or a value set by environmental variable
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``OMP_NUM_THREADS``.
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'''
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# if the module has already been imported, check which module
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# was imported
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try:
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_imported = sys.modules['simuPOP'].moduleInfo()
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except Exception as e:
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_imported = {}
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# Allele type
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if alleleType in ['long', 'binary', 'short', 'mutant', 'lineage']:
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# if simuPOP has been imported and re-imported with a different module name
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# the existing module will be used so moduleInfo() will return a different
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# module type from what is specified in simuOptions.
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if _imported and _imported['alleleType'] != alleleType:
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raise ImportError(('simuPOP has already been imported with allele type %s (%s) and cannot be '
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're-imported with allele type %s. Please make sure you import module simuOpt before '
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'any simuPOP module is imported.') % (
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_imported['alleleType'], ('optimized' if _imported['optimized'] else 'standard'),
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alleleType))
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simuOptions['AlleleType'] = alleleType
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elif alleleType is not None:
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raise TypeError('Parameter alleleType can be either short, long, binary, mutant or lineage.')
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# Optimized
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if optimized in [True, False]:
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# if simuPOP has been imported and re-imported with a different module name
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# the existing module will be used so moduleInfo() will return a different
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# module type from what is specified in simuOptions.
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if _imported and _imported['optimized'] != optimized:
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raise ImportError(('simuPOP has already been imported with allele type %s (%s) and cannot be '
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're-imported in %s mode. Please make sure you import module simuOpt before '
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'any simuPOP module is imported.') % (
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_imported['alleleType'], ('optimized' if _imported['optimized'] else 'standard'),
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'optimized' if optimized else 'standard'))
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simuOptions['Optimized'] = optimized
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elif optimized is not None:
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raise TypeError('Parameter optimized can be either True or False.')
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# Graphical toolkit
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if gui in [True, False, 'wxPython', 'Tkinter', 'batch']:
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simuOptions['GUI'] = gui
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elif gui is not None:
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raise TypeError('Parameter gui can be True/False, wxPython or Tkinter.')
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# Quiet
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if quiet in [True, False]:
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simuOptions['Quiet'] = quiet
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elif quiet is not None:
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raise TypeError('Parameter quiet can be either True or False.')
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# Debug
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if debug is not None:
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if type(debug) == str:
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simuOptions['Debug'] = [debug]
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else:
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simuOptions['Debug'] = debug
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# Version
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if type(version) == str:
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try:
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major, minor, release = [int(x) for x in re.sub('\D', ' ', version).split()]
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except:
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print('Invalid version string %s' % simuOptions['Version'])
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simuOptions['Version'] = version
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elif version is not None:
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raise TypeError('A version string is expected for parameter version.')
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# Revision
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if type(revision) == int:
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simuOptions['Revision'] = revision
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elif revision is not None:
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raise TypeError('A revision number is expected for parameter revision.')
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# NumThreads
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if type(numThreads) == int:
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simuOptions['NumThreads'] = numThreads
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elif numThreads is not None:
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raise TypeError('An integer number is expected for parameter numThreads.')
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if plotter is not None:
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sys.stderr.write('WARNING: plotter option is deprecated because of the removal of rpy/rpy2 support\n')

‎src/simuPOP/__init__.py‎

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]
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# get options
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from .simuOpt import simuOptions
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from simuOpt import simuOptions
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import os, sys, re
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if simuOptions['Optimized']:

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