Fix petab import: initial assignment targets as constant parameters

python/sdist/amici/petab/sbml_import.py

@@ -518,14 +518,26 @@
         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()
+    parser_settings.setModel(sbml_model)
+    parser_settings.setParseUnits(libsbml.L3P_NO_UNITS)
+
     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

@@ -187,18 +187,11 @@ 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,
-            sbml.L3P_PARSE_LOG_AS_LOG10,
-            sbml.L3P_EXPAND_UNARY_MINUS,
-            sbml.L3P_NO_UNITS,
-            sbml.L3P_AVOGADRO_IS_CSYMBOL,
-            sbml.L3P_COMPARE_BUILTINS_CASE_INSENSITIVE,
-            None,
-            sbml.L3P_MODULO_IS_PIECEWISE,
-        )
+        self.sbml_parser_settings = sbml.L3ParserSettings()
+        self.sbml_parser_settings.setModel(self.sbml)
+        self.sbml_parser_settings.setParseUnits(sbml.L3P_NO_UNITS)
 
         self._discard_annotations: bool = discard_annotations
 

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