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Local function export fixes, example model #464

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merged 3 commits into from Oct 16, 2019

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alubbock commented Oct 7, 2019

  • New localfunc.py example model, based on a BioNetGen example model
  • Fix export of models with local functions to SBML and StochKit
  • Show meaningful error messages when attempting to export models
    with local functions to cupSODA or Kappa
  • Fix local function parameter reads from BioNetGen when parameter
    is actually a constant expression, e.g. 2^2
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jmuhlich left a comment

Approved, but I did notice a couple of minor things.

I was going to suggest using the | operator instead of itertools.chain on the ComponentSets, but it doesn't make things much more readable and it's not very efficient. It might be worth optimizing those set operators in the future.

pysb/bng.py Outdated
p = pysb.core.Parameter(pname, pval, _export=False)
# Need to parse the value, since BNG considers some expressions
# to be "Constant", e.g. "2^2"
p = pysb.core.Parameter(pname, parse_bngl_expr(pval), _export=False)

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jmuhlich Oct 16, 2019

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Maybe hoist pval = parse_bngl_expr(pval) out of theif ptype ... block since we're doing it in both cases now. Up to you.

@@ -15,7 +15,7 @@
from pysb.pathfinder import get_path
import sympy
import collections

import itertools

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jmuhlich Oct 16, 2019

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This seems spurious.

alubbock added 3 commits Oct 7, 2019
Imported from the BioNetGen model localfunc.bngl
Fix export of models with local functions to SBML and StochKit.
Meaningful error messages with same models when exporting to
Kappa or cupSODA.

Fix local function parameter reads from BNG when parameter
is actually a constant expression, e.g. "2^2"
@alubbock alubbock force-pushed the alubbock:localfunc_example branch from ff5f0af to 717fdde Oct 16, 2019
@alubbock alubbock merged commit d74ba62 into pysb:master Oct 16, 2019
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@alubbock alubbock deleted the alubbock:localfunc_example branch Oct 16, 2019
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