Recent changes to bugs

#13 CVODE event triggered but not assigned in simple model

2013-06-03T14:24:54.083000Z

status: closed --> closed-fixed

#13 CVODE event triggered but not assigned in simple model

2013-06-03T14:24:18.902000Z

status: open --> closed
Group: -->

CVODE event triggered but not assigned in simple model

2013-04-03T14:42:08.064000Z

Bug submitted by Attila

https://sourceforge.net/p/pysces/discussion/938972/thread/0ddd3d65/#625a

CVODE event triggered but not assigned in simple model

2013-04-03T14:42:08.064000Z

Ticket 13 has been modified: CVODE event triggered but not assigned in simple model
Edited By: Brett (bgoli)
Status updated: u'closed' => u'closed-fixed'

CVODE event triggered but not assigned in simple model

2013-04-03T14:42:08.064000Z

Ticket 13 has been modified: CVODE event triggered but not assigned in simple model
Edited By: Brett (bgoli)
Status updated: u'open' => u'closed'

SBMl import fails when modifierSpeciesReference has sboTerm

2011-07-04T18:19:27Z

In any reaction, when a modifier is listed as:

SBML import works perfectly fine. However, as soon as an sboTerm is set, it fails:

PySCes should just ignore the sboTerm here and read the "species" attribute only. File with exact error attached.

Import of SBML that references "time" in event assgn fails

2011-07-04T18:08:22Z

I have an SBML file that uses:
<csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
(a) in an event trigger and (b) in an event assignment.

Converting the SBML to PSC and loading the resulting file works fine for (a) but (b) fails with the error in the file attached.

The event that causes the error is of the form:

<event id="event_1" name="time event">
<trigger>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<gt/>
<ci> parameter_31 </ci>
<cn> 3600 </cn>
</apply>
</math>
</trigger>
<listOfEventAssignments>
<eventAssignment variable="parameter_55">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
</apply>
</math>
</eventAssignment>
</listOfEventAssignments>
</event>

PSC import fails for models that have no reactions

2011-06-28T13:23:46Z

I have created a very simple model that should demonstrate species dilution by increasing compartment size. Therefore, I have defined one species, one event and no reactions.

Import of this model fails with:

/ebi/research/software/Linux_x86_64/opt/stow/python-2.6.1/lib/python2.6/site-packages/pysces/PyscesModel.pyc in Stoichiometry_Analyse(self, override, load)
1889 print '\nStoichiometric override active\n'
1890
-> 1891 assert len(self.nmatrix) > 0, '\nUnable to generate Stoichiometric Matrix! model has:\n%s reactions\n%s species\nwhat did you have in mind?\n' % (len(self.__reactions__), len(self.__species__))
1892
1893 ## self.__nmatrix__ = copy.copy(self.nmatrix)

The expected behaviour would be that a stoichiometric matrix of size 0 is allowed.

Fortran modules should be built as shared library

2011-06-28T09:05:50Z

On Archlinux (gfortran=4.6.0) and CentOS (gfortran=4.1.2), the Fortran libraries need to be built with the flag '-shared', otherwise they won't link due to the undefined main method.

This can be done by adding "extra_link_args=['-shared']" in setup.py for both pitcon and nleq2, cf. http://aur.archlinux.org/packages/python2-pysces/PKGBUILD

PITCON error

2009-12-08T12:57:02Z

Reported by Johann, using continuation with a specific model breaks PITCON.