Fix incorrect initialization for non-constant initial assignments

pytest.ini

@@ -30,4 +30,4 @@ filterwarnings =
     ignore:jax.* is deprecated:DeprecationWarning
 
 
-norecursedirs = .git amici_models build doc documentation matlab models ThirdParty amici sdist examples
+norecursedirs = .git amici_models build doc documentation matlab models ThirdParty amici sdist examples *build*

python/sdist/amici/de_model.py

@@ -454,14 +454,6 @@ def get_rate(symbol: sp.Symbol):
             )
             self._eqs["xdot"] = smart_subs_dict(self.eq("xdot"), subs)
 
-        # replace rateOf-instances in x0 by xdot equation
-        for i_state in range(len(self.eq("x0"))):
-            new, replacement = self._eqs["x0"][i_state].replace(
-                rate_of_func, get_rate, map=True
-            )
-            if replacement:
-                self._eqs["x0"][i_state] = new
-
         # replace rateOf-instances in w by xdot equation
         #  here we may need toposort, as xdot may depend on w
         made_substitutions = False
@@ -509,6 +501,30 @@ def get_rate(symbol: sp.Symbol):
             self._syms["w"] = sp.Matrix(topo_expr_syms)
             self._eqs["w"] = sp.Matrix(list(w_sorted.values()))
 
+        # replace rateOf-instances in x0 by xdot equation
+        # indices of state variables whose x0 was modified
+        changed_indices = []
+        for i_state in range(len(self.eq("x0"))):
+            new, replacement = self._eqs["x0"][i_state].replace(
+                rate_of_func, get_rate, map=True
+            )
+            if replacement:
+                self._eqs["x0"][i_state] = new
+                changed_indices.append(i_state)
+        if changed_indices:
+            # Replace any newly introduced state variables
+            #  by their x0 expressions.
+            # Also replace any newly introduced `w` symbols by their
+            #  expressions (after `w` was toposorted above).
+            subs = toposort_symbols(
+                dict(zip(self.sym("x_rdata"), self.eq("x0"), strict=True))
+            )
+            subs = dict(zip(self._syms["w"], self.eq("w"), strict=True)) | subs
+            for i_state in changed_indices:
+                self._eqs["x0"][i_state] = smart_subs_dict(
+                    self._eqs["x0"][i_state], subs
+                )
+
         for component in chain(
             self.observables(),
             self.events(),

python/sdist/amici/sbml_import.py

@@ -1386,13 +1386,20 @@ def _process_parameters(
         # Parameters that need to be turned into expressions or species
         #  so far, this concerns parameters with symbolic initial assignments
         #  (those have been skipped above) that are not rate rule targets
+
+        # Set of symbols in initial assignments that still allows handling them
+        #  via amici expressions
+        syms_allowed_in_expr_ia = set(self.symbols[SymbolId.PARAMETER]) | set(
+            self.symbols[SymbolId.FIXED_PARAMETER]
+        )
+
         for par in self.sbml.getListOfParameters():
             if (
                 (ia := par_id_to_ia.get(par.getId())) is not None
                 and not ia.is_Number
                 and not self.is_rate_rule_target(par)
             ):
-                if not ia.has(sbml_time_symbol):
+                if not (ia.free_symbols - syms_allowed_in_expr_ia):
                     self.symbols[SymbolId.EXPRESSION][
                         _get_identifier_symbol(par)
                     ] = {
@@ -1407,6 +1414,10 @@ def _process_parameters(
                     #  We can't represent that as expression, since the
                     #  initial simulation time is only known at the time of the
                     #  simulation, so we can't substitute it.
+                    # Also, any parameter with an initial assignment
+                    #  that expression that is implicitly time-dependent
+                    #  must be converted to a species to avoid re-evaluating
+                    #  the initial assignment at every time step.
                     self.symbols[SymbolId.SPECIES][
                         _get_identifier_symbol(par)
                     ] = {
@@ -1515,13 +1526,36 @@ def _process_rules(self) -> None:
             self.symbols[SymbolId.EXPRESSION], "value"
         )
 
-        # expressions must not occur in definition of x0
+        # expressions must not occur in the definition of x0
+        allowed_syms = (
+            set(self.symbols[SymbolId.PARAMETER])
+            | set(self.symbols[SymbolId.FIXED_PARAMETER])
+            | {sbml_time_symbol}
+        )
         for species in self.symbols[SymbolId.SPECIES].values():
-            species["init"] = self._make_initial(
-                smart_subs_dict(
-                    species["init"], self.symbols[SymbolId.EXPRESSION], "value"
+            # only parameters are allowed as free symbols
+            while True:
+                species["init"] = species["init"].subs(self.compartments)
+                sym_math, rateof_to_dummy = _rateof_to_dummy(species["init"])
+                old_init = species["init"]
+                if (
+                    sym_math.free_symbols
+                    - allowed_syms
+                    - set(rateof_to_dummy.values())
+                    == set()
+                ):
+                    break
+                species["init"] = self._make_initial(
+                    smart_subs_dict(
+                        species["init"],
+                        self.symbols[SymbolId.EXPRESSION],
+                        "value",
+                    )
                 )
-            )
+                if species["init"] == old_init:
+                    raise AssertionError(
+                        f"Infinite loop detected in _process_rules {species}."
+                    )
 
     def _process_rule_algebraic(self, rule: libsbml.AlgebraicRule):
         formula = self._sympify(rule)
@@ -2359,6 +2393,10 @@ def _make_initial(
                 sym_math = sym_math.subs(
                     var, self.symbols[SymbolId.SPECIES][var]["init"]
                 )
+            elif var in self.symbols[SymbolId.ALGEBRAIC_STATE]:
+                sym_math = sym_math.subs(
+                    var, self.symbols[SymbolId.ALGEBRAIC_STATE][var]["init"]
+                )
             elif (
                 element := self.sbml.getElementBySId(element_id)
             ) and self.is_rate_rule_target(element):

python/tests/test_sbml_import.py

@@ -5,16 +5,16 @@
 import sys
 from numbers import Number
 from pathlib import Path
-
 import amici
 import libsbml
 import numpy as np
 import pytest
 from amici.gradient_check import check_derivatives
-from amici.sbml_import import SbmlImporter
-from amici.testing import skip_on_valgrind
+from amici.sbml_import import SbmlImporter, SymbolId
+from amici.import_utils import symbol_with_assumptions
 from numpy.testing import assert_allclose, assert_array_equal
 from amici import import_model_module
+from amici.testing import skip_on_valgrind
 from amici.testing import TemporaryDirectoryWinSafe as TemporaryDirectory
 from conftest import MODEL_STEADYSTATE_SCALED_XML
 import sympy as sp
@@ -1142,3 +1142,42 @@ def test_contains_periodic_subexpression():
     assert cps(sp.sin(t), t) is True
     assert cps(sp.cos(t), t) is True
     assert cps(t + sp.sin(t), t) is True
+
+
+@skip_on_valgrind
+@pytest.mark.parametrize("compute_conservation_laws", [True, False])
+def test_time_dependent_initial_assignment(compute_conservation_laws: bool):
+    """Check that dynamic expressions for initial assignments are only
+    evaluated at t=t0."""
+    from amici.antimony_import import antimony2sbml
+
+    ant_model = """
+    x1' = 1
+    x1 = p0
+    p0 = 1
+    p1 = x1
+    x2 := x1
+    p2 = x2
+    """
+
+    sbml_model = antimony2sbml(ant_model)
+    print(sbml_model)
+    si = SbmlImporter(sbml_model, from_file=False)
+    de_model = si._build_ode_model(
+        observables={"obs_p1": {"formula": "p1"}, "obs_p2": {"formula": "p2"}},
+        compute_conservation_laws=compute_conservation_laws,
+    )
+    # "species", because the initial assignment expression is time-dependent
+    assert symbol_with_assumptions("p2") in si.symbols[SymbolId.SPECIES].keys()
+    # "species", because differential state
+    assert symbol_with_assumptions("x1") in si.symbols[SymbolId.SPECIES].keys()
+
+    assert "p0" in [str(p.get_id()) for p in de_model.parameters()]
+    assert "p1" not in [str(p.get_id()) for p in de_model.parameters()]
+    assert "p2" not in [str(p.get_id()) for p in de_model.parameters()]
+
+    assert list(de_model.sym("x_rdata")) == [
+        symbol_with_assumptions("p2"),
+        symbol_with_assumptions("x1"),
+    ]
+    assert list(de_model.eq("x0")) == [symbol_with_assumptions("p0")] * 2