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Fix SbmlModel.get_free_parameter_ids_with_values to handle InitialA… #248

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Merged
dweindl merged 2 commits into from
Mar 6, 2024
Merged

Fix SbmlModel.get_free_parameter_ids_with_values to handle InitialA… #248

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15d210a
Fix `SbmlModel.get_free_parameter_ids_with_values` to handle InitialA…
dweindl Mar 5, 2024
c47666d
float; omit non-numeric initial assignments
dweindl Mar 6, 2024
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34 changes: 33 additions & 1 deletion petab/models/sbml_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
from typing import Iterable, Optional, Tuple

import libsbml
import sympy as sp

from ..sbml import (
get_sbml_model,
Expand Down Expand Up @@ -103,10 +104,41 @@ def get_free_parameter_ids_with_values(
ar.getVariable() for ar in self.sbml_model.getListOfRules()
}

parser_settings = libsbml.L3ParserSettings(
self.sbml_model,
libsbml.L3P_PARSE_LOG_AS_LOG10,
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@dilpath dilpath Mar 5, 2024

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This is pretty unintuitive, to me it looks like this will convert log to log10, and I'm not sure if the libsbml docs make sense. e.g. this for L3P_PARSE_LOG_AS_ERROR

Collapse unary minuses where possible when parsing text-string formulas.

https://synonym.caltech.edu/software/libsbml/5.18.0/docs/formatted/python-api/namespacelibsbml.html#a9ef0398726fb45bd1cb24c4a5ed671f0

The docstring for L3P_PARSE_LOG_AS_LOG10 looks like it actually parses log as log, not parsing log as log10, but I'm not sure I trust the docs given the docstring for L3P_PARSE_LOG_AS_ERROR. Should we instead use L3P_PARSE_LOG_AS_LN?

I think most users would expect log to be ln, and that log10 is only when explicitly specified with log(10, x) or log10(x).

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@dweindl dweindl Mar 6, 2024

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Those are the libsbml default settings. The only relevant thing here is ignoring units.

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@dilpath dilpath Mar 6, 2024

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OK, if it actually keeps log as log, not log10, then no problem

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@dweindl dweindl Mar 6, 2024 •
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Note that this is about parsing MathML, not any observableFormula or the like. In MathML log without explicit base means log10. In plain text formulae, log will be interpreted as ln.

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@dilpath dilpath Mar 6, 2024

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Oh! Good to know that log means different things in PEtab and the model 😬 Then I think we could be more careful about a math spec in the next version of PEtab, I added a comment to the draft timecourse spec.

libsbml.L3P_EXPAND_UNARY_MINUS,
libsbml.L3P_NO_UNITS,
libsbml.L3P_AVOGADRO_IS_CSYMBOL,
libsbml.L3P_COMPARE_BUILTINS_CASE_INSENSITIVE,
None,
libsbml.L3P_MODULO_IS_PIECEWISE,
)

def get_initial(p):
# return the initial assignment value if there is one, and it is a
# number; `None`, if there is a non-numeric initial assignment;
# otherwise, the parameter value
if ia := self.sbml_model.getInitialAssignmentBySymbol(p.getId()):
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@dilpath dilpath Mar 5, 2024

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Suggested change
if ia := self.sbml_model.getInitialAssignmentBySymbol(p.getId()):
if ia := self.sbml_model.getInitialAssignmentBySymbol(p.getId()) is not None:

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@dweindl dweindl Mar 6, 2024

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That's implied.

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@dilpath dilpath Mar 6, 2024

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👍 was just a PEP 8 recommendation

formula_str = libsbml.formulaToL3StringWithSettings(
ia.getMath(), parser_settings
)
try:
return float(formula_str)
except ValueError:
sym_expr = sp.sympify(formula_str)
return (
float(sym_expr.evalf())
if sym_expr.evalf().is_Number
else None
)
return p.getValue()

return (
(p.getId(), p.getValue())
(p.getId(), initial)
for p in self.sbml_model.getListOfParameters()
if p.getId() not in rule_targets
and (initial := get_initial(p)) is not None
)

def get_parameter_ids(self) -> Iterable[str]:
Expand Down