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release 0.9.3
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‎LICENSE.txt

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Copyright (c) 2004-2015, Brett G. Olivier, Johann M. Rohwer and Jan-Hendrik S. Hofmeyr
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Copyright (c) 2004-2016, Brett G. Olivier, Johann M. Rohwer and Jan-Hendrik S. Hofmeyr
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All rights reserved.
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Redistribution and use in source and binary forms, with or without

‎MANIFEST

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@@ -32,6 +32,10 @@ D:\code-git\pysces\pysces\pscmodels\pysces_test_branch1.psc
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D:\code-git\pysces\pysces\pscmodels\pysces_test_linear1.psc
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D:\code-git\pysces\pysces\pscmodels\pysces_test_moiety1.psc
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D:\code-git\pysces\pysces\pscmodels\pysces_test_pitcon.psc
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D:\code-git\pysces\pysces\win32\libgcc_s_seh-1.dll
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D:\code-git\pysces\pysces\win32\libgfortran-3.dll
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D:\code-git\pysces\pysces\win32\libquadmath-0.dll
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D:\code-git\pysces\pysces\win32\libwinpthread-1.dll
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pysces\PyscesConfig.py
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pysces\PyscesContrib.py
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pysces\PyscesContribUser.py

‎pysces/PyscesConfig.py

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"""
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PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
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Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
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Copyright (C) 2004-2016 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
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Brett G. Olivier ([email protected])
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Triple-J Group for Molecular Cell Physiology

‎pysces/PyscesContrib.py

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"""
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PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
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Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
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Copyright (C) 2004-2016 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
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Brett G. Olivier ([email protected])
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Triple-J Group for Molecular Cell Physiology

‎pysces/PyscesContribUser.py

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"""
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PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
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Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
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Copyright (C) 2004-2016 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
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Brett G. Olivier ([email protected])
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Triple-J Group for Molecular Cell Physiology

‎pysces/PyscesInterfaces.py

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"""
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PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
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Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
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Copyright (C) 2004-2016 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
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Brett G. Olivier ([email protected])
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Triple-J Group for Molecular Cell Physiology

‎pysces/PyscesJWSParse.py

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"""
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PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
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Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
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Copyright (C) 2004-2016 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
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Brett G. Olivier ([email protected])
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Triple-J Group for Molecular Cell Physiology

‎pysces/PyscesLink.py

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"""
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PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
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Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
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Copyright (C) 2004-2016 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
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Brett G. Olivier ([email protected])
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Triple-J Group for Molecular Cell Physiology

‎pysces/PyscesMiniModel.py

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"""
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PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
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Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
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Copyright (C) 2004-2016 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
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Brett G. Olivier ([email protected])
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Triple-J Group for Molecular Cell Physiology

‎pysces/PyscesModel.py

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"""
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PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
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Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
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Copyright (C) 2004-2016 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
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Brett G. Olivier ([email protected])
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Triple-J Group for Molecular Cell Physiology
@@ -2670,7 +2670,7 @@ def InitialiseOldFunctions(self):
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#print '\nInitializing init function ...'
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#print self._Function_init
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try:
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self.ReloadInitFunc()
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except Exception, e:
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Recompile and execute the user initialisations (!I) as defined in the PSC input file.
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and in mod.__InitFuncs__.
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UPDATE 2015: can now be used to define InitialAssignments (no need for self.* prefix in input file)
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Arguments:
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None
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"""
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def topolgical_sort(graph_unsorted):
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"""
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Repeatedly go through all of the nodes in the graph, moving each of
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can be moved once all the nodes its edges point to, have been moved
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from the unsorted graph onto the sorted one.
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"""
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# This is the list we'll return, that stores each node/edges pair
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# in topological order.
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graph_sorted = []
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# Convert the unsorted graph into a hash table. This gives us
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# constant-time lookup for checking if edges are unresolved, and
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# for removing nodes from the unsorted graph.
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graph_unsorted = dict(graph_unsorted)
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# Run until the unsorted graph is empty.
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while graph_unsorted:
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# Go through each of the node/edges pairs in the unsorted
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# graph. If a set of edges doesn't contain any nodes that
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# haven't been resolved, that is, that are still in the
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acyclic = True
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del graph_unsorted[node]
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graph_sorted.append((node, edges))
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if not acyclic:
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# Uh oh, we've passed through all the unsorted nodes and
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# weren't able to resolve any of them, which means there
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# are nodes with cyclic edges that will never be resolved,
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# so we bail out with an error.
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raise RuntimeError("A cyclic dependency occurred")
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return graph_sorted
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return graph_sorted
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simpleAss = []
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exprsAss = []
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symbolsX = []
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if s_ not in symbolsX:
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symbolsX.append(s_)
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if init not in symbolsX:
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symbolsX.append(init)
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symbolsX.append(init)
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functions = InfixParser.functions
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code_string = 'self.%s = %s' % (init, InfixParser.output)
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xcode = compile(code_string, '_InitAss_', 'exec')
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self.scan_res = numpy.zeros((len(range1),len(self.scan_out)+1))
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else:
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self.scan_res = numpy.array(result)
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@property
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def scan(self):
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if self._scan is None and self.scan_res is not None:

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