Merge pull request #249 from PEtab-dev/release_0.2.9

Release 0.2.9

Author: dweindl

CHANGELOG.md

@@ -2,6 +2,14 @@
 
 ## 0.2 series
 
+### 0.2.9
+
+* Fixed a bug in `SbmlModel.get_free_parameter_ids_with_values` that led to
+  potentially wrong initial values in the parameter mapping for parameters that
+  are targets of `initialAssignment`s (the value from their `value` was taken
+  instead of the initial assignment)
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/248
+
 ### 0.2.8
 
 * Fixed pandas `FutureWarning` in `petab/visualize/lint.py`

petab/models/sbml_model.py

@@ -5,6 +5,7 @@
 from typing import Iterable, Optional, Tuple
 
 import libsbml
+import sympy as sp
 
 from ..sbml import (
     get_sbml_model,
@@ -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,
+            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()):
+                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]:

petab/version.py

@@ -1,2 +1,2 @@
 """PEtab library version"""
-__version__ = "0.2.8"
+__version__ = "0.2.9"

tests/test_visualization.py

@@ -107,7 +107,6 @@ def visu_file_Fujita_minimal():
     )
 
 
-@pytest.mark.filterwarnings("ignore:Visualization table is empty")
 @pytest.fixture
 def visu_file_Fujita_empty():
     return (