Fix petab import: initial assignment targets as constant parameters

During PEtab import, parameters that are targets of initial assignments
have so far not been turned into constant parameters, because they didn't
exist in the amici model (see #2304).
Now that those parameters remain in the model, they should be turned into
constant parameters, unless specified otherwise.

python/sdist/amici/petab/sbml_import.py

@@ -518,14 +518,33 @@ def _get_fixed_parameters_sbml(
         petab_problem, non_estimated_parameters_as_constants
     )
 
-    # exclude targets of rules or initial assignments
+    # exclude targets of rules or initial assignments that are not numbers
     sbml_model = petab_problem.model.sbml_model
+    parser_settings = libsbml.L3ParserSettings(
+        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,
+    )
+
     for fixed_parameter in fixed_parameters.copy():
         # check global parameters
-        if sbml_model.getInitialAssignmentBySymbol(
-            fixed_parameter
-        ) or sbml_model.getRuleByVariable(fixed_parameter):
+        if sbml_model.getRuleByVariable(fixed_parameter):
             fixed_parameters.remove(fixed_parameter)
+            continue
+        if ia := sbml_model.getInitialAssignmentBySymbol(fixed_parameter):
+            sym_math = sp.sympify(
+                libsbml.formulaToL3StringWithSettings(
+                    ia.getMath(), parser_settings
+                )
+            )
+            if not sym_math.is_Number:
+                fixed_parameters.remove(fixed_parameter)
+                continue
 
     return list(sorted(fixed_parameters))
 

python/sdist/amici/sbml_import.py

@@ -187,7 +187,7 @@ def __init__(
 
         self._reset_symbols()
 
-        # http://sbml.org/Software/libSBML/5.18.0/docs/python-api/classlibsbml_1_1_l3_parser_settings.html#abcfedd34efd3cae2081ba8f42ea43f52
+        # https://sbml.org/software/libsbml/5.18.0/docs/formatted/python-api/classlibsbml_1_1_l3_parser_settings.html#ab30d7ed52ca24cbb842d0a7fed7f4bfd
         # all defaults except disable unit parsing
         self.sbml_parser_settings = sbml.L3ParserSettings(
             self.sbml,

python/sdist/setup.cfg

@@ -47,7 +47,7 @@ zip_safe = False
 # Don't include any URLs here - they are not supported by PyPI:
 #  HTTPError: 400 Bad Request from https://upload.pypi.org/legacy/
 #  Invalid value for requires_dist. Error: Can't have direct dependency: ...
-petab = petab>=0.2.1
+petab = petab>=0.2.9
 pysb = pysb>=1.13.1
 test =
     benchmark_models_petab @ git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python

python/tests/test_petab_import.py

@@ -36,22 +36,49 @@ def simple_sbml_model():
     return document, model
 
 
+@pytest.fixture()
+def get_fixed_parameters_model():
+    """Create test SBML model for test_get_fixed_parameters"""
+    ant_model = """
+    p1 = 1
+    p2 = 2
+    p3 = 3
+    p4 = 4
+    p5 = 5
+    p6 = 3^2
+    p7 = p6
+    p8 = 8
+    p8' = 1
+    p9 := p8
+    """
+    from amici.antimony_import import antimony2sbml
+
+    sbml_str = antimony2sbml(ant_model)
+    sbml_doc = libsbml.SBMLReader().readSBMLFromString(sbml_str)
+    return sbml_doc, sbml_doc.getModel()
+
+
 @skip_on_valgrind
-def test_get_fixed_parameters(simple_sbml_model):
+def test_get_fixed_parameters(get_fixed_parameters_model):
     """Check for correct identification of fixed parameters:
 
     p1: fixed (via condition table)
     p2: (so far) not fixed (parametric override in condition table)
     p3: fixed (via parameter table `estimate=0`)
     p4: not fixed (via parameter table `estimate=1`)
     p5: fixed (implicitly, because not listed as estimated)
+    p6: fixed (implicitly, because not listed as estimated
+        initial assignment is a number)
+    p7: not fixed (initial assignment is not a number)
+    p8: not fixed (rate rule target)
+    p9: not fixed (assignment rule target)
     """
     from amici.petab.sbml_import import (
         _get_fixed_parameters_sbml as get_fixed_parameters,
     )
     from petab.models.sbml_model import SbmlModel
 
-    sbml_doc, sbml_model = simple_sbml_model
+    sbml_doc, sbml_model = get_fixed_parameters_model
     condition_df = petab.get_condition_df(
         pd.DataFrame(
             {
@@ -77,13 +104,14 @@ def test_get_fixed_parameters(simple_sbml_model):
         "p1",
         "p3",
         "p5",
+        "p6",
     }
 
     assert set(
         get_fixed_parameters(
             petab_problem, non_estimated_parameters_as_constants=False
         )
-    ) == {"p1", "p5"}
+    ) == {"p1", "p5", "p6"}
 
 
 @skip_on_valgrind