assignments_to_experiments: fix lost switches, dropped changes and late evaluation of condition changes

CHANGELOG.md

@@ -59,6 +59,15 @@
   that PEtab condition changes are applied before its assignments.
   Previously, their order was undefined
   (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/562)
+* Several fixes to `assignments_to_experiments`: keep a switch at the start
+  of a later period, keep the condition changes of symbols that the model
+  still uses elsewhere, evaluate a condition change once at the start of its
+  period, leave time-dependent initial assignments in the model, reject
+  assignments to species or compartments, leave problems without
+  time-dependent assignments unchanged, give a ramp's slope parameter an
+  unused ID, and accept switching times that conditions set from parameters
+  fixed by the parameter table
+  (by @FFroehlich in https://github.com/PEtab-dev/libpetab-python/pull/574)
 
 **Features**
 * `petab1to2` and `petab_files_1to2` can skip validation via `validate=False`

doc/modules.rst

@@ -32,6 +32,7 @@ API Reference
    petab.v1.yaml
    petab.v2
    petab.v2.C
+   petab.v2.assignments_to_experiments
    petab.v2.converters
    petab.v2.core
    petab.v2.experiments

petab/v1/models/sbml_model.py

@@ -262,6 +262,37 @@ def get_valid_ids_for_condition_table(self) -> Iterable[str]:
     def symbol_allowed_in_observable_formula(self, id_: str) -> bool:
         return self.sbml_model.getElementBySId(id_) or id_ == "time"
 
+    def get_referenced_ids(self) -> set[str]:
+        """Get the IDs that the model refers to.
+
+        These are the IDs in the math of any model element (e.g., kinetic
+        laws, rules, initial assignments, events), and those referred to as
+        conversion factors. IDs that are only defined, but not referred to,
+        are not included.
+        """
+        ids = set()
+        for element in self.sbml_model.getListOfAllElements():
+            if not (hasattr(element, "isSetMath") and element.isSetMath()):
+                continue
+            nodes = [element.getMath()]
+            while nodes:
+                node = nodes.pop()
+                if node.getType() == libsbml.AST_NAME:
+                    ids.add(node.getName())
+                nodes += [
+                    node.getChild(i) for i in range(node.getNumChildren())
+                ]
+        # conversion factors refer to parameters by attribute, not in math
+        ids |= {
+            element.getConversionFactor()
+            for element in [
+                self.sbml_model,
+                *self.sbml_model.getListOfSpecies(),
+            ]
+            if element.isSetConversionFactor()
+        }
+        return ids
+
     def is_valid(self) -> bool:
         return is_sbml_consistent(self.sbml_model.getSBMLDocument())