assignments_to_experiments: model change only makes a ramp's target differential

The slope parameter is a placeholder at 0; every ramp's start value and
slope, including at time 0, are set through the condition table. Constant
model parameters in changes at an experiment's start take their model
values, since those changes may only refer to parameter table symbols.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01MNJePorYs9zmPYMam6g4EP

Author: Fabian Fröhlich

petab/v2/converters.py

@@ -779,8 +779,9 @@ def assignments_to_experiments(problem: Problem) -> Problem:
         target = sbml_model.getParameter(target_id)
         # A value that changes with time within a period (a ramp) cannot be a
         #  condition change on a constant target, which is applied once at
-        #  the start of its period. The target becomes a differential entity
-        #  instead, `d target/dt = <target>_slope`, and each period sets both.
+        #  the start of its period. The model only makes the target a
+        #  differential entity, `d target/dt = <target>_slope`; the slope's
+        #  value, like the target's, is set by every period that starts one.
         ramps = expr.xreplace({c: sp.Dummy() for c in switches}).has(time)
         slope_id = None
         if ramps:
@@ -790,7 +791,7 @@ def assignments_to_experiments(problem: Problem) -> Problem:
             slope = sbml_model.createParameter()
             slope.setId(slope_id)
             slope.setConstant(False)
-            slope.setValue(float(sp.diff(default, time).subs(model_values)))
+            slope.setValue(0.0)
             rate_rule = sbml_model.createRateRule()
             rate_rule.setVariable(target_id)
             rate_rule.setMath(libsbml.parseL3Formula(slope_id))
@@ -852,9 +853,11 @@ def assignments_to_experiments(problem: Problem) -> Problem:
                     previous = value
                 # The model already has the pre-switch value at the start of
                 #  the first period, and the switches can become the first
-                #  periods if they only refer to parameter table symbols.
+                #  periods if they only refer to parameter table symbols. A
+                #  ramp's start and slope are always set by the tables.
                 redundant = (
-                    i == 0
+                    not ramps
+                    and i == 0
                     and (start_value - default).is_zero
                     and all(
                         {str(s) for s in value.free_symbols} <= parameter_ids
@@ -870,6 +873,17 @@ def assignments_to_experiments(problem: Problem) -> Problem:
                     # preequilibration held the slope at zero
                     or (ramps and after_preequilibration)
                 ):
+                    if i == 0:
+                        # at the start of an experiment, a change may only
+                        #  refer to parameter table symbols; other symbols
+                        #  are constant model parameters, at their values
+                        start_value = start_value.subs(
+                            {
+                                s: sbml_model.getParameter(str(s)).getValue()
+                                for s in start_value.free_symbols - {time}
+                                if str(s) not in parameter_ids
+                            }
+                        )
                     additions += _changes(
                         experiment,
                         period.time,

tests/v2/test_conversion.py

@@ -1082,13 +1082,15 @@ def test_assignments_to_experiments_ramp():
     converted = assignments_to_experiments(problem)
 
     sbml = converted.model.sbml_model
-    # the ramp's start and slope are the model's own initial values
+    # the model only makes the target differential; the slope is a
+    #  placeholder until the tables set it
     assert _rate_rule(converted, "k1") == "k1_slope"
-    assert sbml.getParameter("k1").getValue() == 1.0
-    assert sbml.getParameter("k1_slope").getValue() == 0.5
-    # at the switch, the target and its slope drop to zero
+    assert sbml.getParameter("k1_slope").getValue() == 0.0
+    # the ramp starts at time 0, and at the switch, the target and its slope
+    #  drop to zero
     assert _changes_by_period(converted) == {
-        (DEFAULT_EXPERIMENT_ID, 10.0): {"k1": 0.0, "k1_slope": 0.0}
+        (DEFAULT_EXPERIMENT_ID, 0.0): {"k1": 1.0, "k1_slope": 0.5},
+        (DEFAULT_EXPERIMENT_ID, 10.0): {"k1": 0.0, "k1_slope": 0.0},
     }