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simplify initial condition export and preserve parameter dependency #417

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merged 5 commits into from Feb 15, 2019
Merged

simplify initial condition export and preserve parameter dependency #417

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41e2d2c
simplify initial condition export and preserve parameter dependency
FFroehlich Feb 8, 2019
ccc9ed4
only encode initial expressions as symbolic entities in sbml
FFroehlich Feb 11, 2019
a2d40d8
also write parameter initial conditions as symbolic reference
FFroehlich Feb 11, 2019
3d96b3a
Merge branch 'master' into sbml_export_initial_conditions
FFroehlich Feb 12, 2019
8e0ca20
remove pytest cache files
FFroehlich Feb 12, 2019
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29 changes: 9 additions & 20 deletions pysb/export/sbml.py
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Expand Up @@ -8,6 +8,7 @@
import pysb.bng
from pysb.export import Exporter
from sympy.printing.mathml import MathMLPrinter
from sympy import Symbol
from xml.dom.minidom import Document
try:
import libsbml
Expand Down Expand Up @@ -168,21 +169,17 @@ def convert(self, level=(3, 2)):
_check(expr_rule.setMath(expr_mathml))

# Initial values/assignments
initial_concs = [0.0] * len(self.model.species)
fixed_species_idx = set()
for ic in self.model.initials:
sp_idx = self.model.get_species_index(ic.pattern)
if isinstance(ic.value, pysb.Expression):
ia = smodel.createInitialAssignment()
_check(ia)
_check(ia.setSymbol('__s{}'.format(sp_idx)))
init_mathml = self._sympy_to_sbmlast(ic.value)
_check(ia.setMath(init_mathml))
initial_concs[sp_idx] = None
else:
initial_concs[sp_idx] = ic.value.value
if ic.fixed:
fixed_species_idx.add(sp_idx)
ia = smodel.createInitialAssignment()
_check(ia)
_check(ia.setSymbol('__s{}'.format(sp_idx)))
init_mathml = self._sympy_to_sbmlast(Symbol(ic.value.name))
_check(ia.setMath(init_mathml))

if ic.fixed:
fixed_species_idx.add(sp_idx)

# Species
for i, s in enumerate(self.model.species):
Expand Down Expand Up @@ -210,18 +207,10 @@ def convert(self, level=(3, 2)):
_check(sp.setBoundaryCondition(i in fixed_species_idx))
_check(sp.setConstant(False))
_check(sp.setHasOnlySubstanceUnits(True))
if initial_concs[i] is not None:
_check(sp.setInitialAmount(initial_concs[i]))

# Parameters
params_only_initials = (self.model.parameters_initial_conditions() -
self.model.parameters_rules() -
self.model.parameters_compartments() -
self.model.parameters_expressions())

for i, param in enumerate(self.model.parameters):
if param in params_only_initials:
continue
p = smodel.createParameter()
_check(p)
_check(p.setId(param.name))
Expand Down