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Add ModelQuantity.get_sym, make ModelQuantity.get_id return str #3001

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Merged
dweindl merged 1 commit into from
Nov 1, 2025
Merged

Add ModelQuantity.get_sym, make ModelQuantity.get_id return str #3001

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64 changes: 33 additions & 31 deletions python/sdist/amici/de_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -648,7 +648,7 @@ def add_conservation_law(
try:
ix = next(
filter(
lambda is_s: is_s[1].get_id() == state,
lambda is_s: is_s[1].get_sym() == state,
enumerate(self._differential_states),
)
)[0]
Expand All @@ -657,7 +657,7 @@ def add_conservation_law(
f"Specified state {state} was not found in the model states."
)

state_id = self._differential_states[ix].get_id()
state_id = self._differential_states[ix].get_sym()

# \sum_{i≠j}(a_i * x_i)/a_j
target_expression = (
Expand Down Expand Up @@ -704,7 +704,7 @@ def add_spline(self, spline: AbstractSpline, spline_expr: sp.Expr) -> None:
self._splines.append(spline)
self.add_component(
Expression(
identifier=spline.sbml_id,
symbol=spline.sbml_id,
name=str(spline.sbml_id),
value=spline_expr,
)
Expand Down Expand Up @@ -1136,7 +1136,7 @@ def _generate_symbol(self, name: str) -> None:
components = sorted(
components,
key=lambda x: int(
str(strip_pysb(x.get_id())).replace(
str(strip_pysb(x.get_sym())).replace(
"observableParameter", ""
)
),
Expand All @@ -1145,13 +1145,13 @@ def _generate_symbol(self, name: str) -> None:
components = sorted(
components,
key=lambda x: int(
str(strip_pysb(x.get_id())).replace(
str(strip_pysb(x.get_sym())).replace(
"noiseParameter", ""
)
),
)
self._syms[name] = sp.Matrix(
[comp.get_id() for comp in components]
[comp.get_sym() for comp in components]
)
if name == "y":
self._syms["my"] = sp.Matrix(
Expand All @@ -1168,7 +1168,7 @@ def _generate_symbol(self, name: str) -> None:
elif name == "x":
self._syms[name] = sp.Matrix(
[
state.get_id()
state.get_sym()
for state in self.states()
if not state.has_conservation_law()
]
Expand Down Expand Up @@ -1214,8 +1214,8 @@ def _generate_symbol(self, name: str) -> None:
[
[
sp.Symbol(
f"s{strip_pysb(tcl.get_id())}__"
f"{strip_pysb(par.get_id())}",
f"s{strip_pysb(tcl.get_sym())}__"
f"{strip_pysb(par.get_sym())}",
real=True,
)
for par in self._parameters
Expand Down Expand Up @@ -1312,7 +1312,7 @@ def parse_events(self) -> None:
w_toposorted = toposort_symbols(
dict(
zip(
[expr.get_id() for expr in self._expressions],
[expr.get_sym() for expr in self._expressions],
[expr.get_val() for expr in self._expressions],
strict=True,
)
Expand Down Expand Up @@ -1393,9 +1393,11 @@ def get_appearance_counts(self, idxs: list[int]) -> list[int]:
)

return [
free_symbols_dt.count(str(self._differential_states[idx].get_id()))
free_symbols_dt.count(
str(self._differential_states[idx].get_sym())
)
+ free_symbols_expr.count(
str(self._differential_states[idx].get_id())
str(self._differential_states[idx].get_sym())
)
for idx in idxs
]
Expand Down Expand Up @@ -1528,7 +1530,7 @@ def _compute_equation(self, name: str) -> None:
elif name == "x_solver":
self._eqs[name] = sp.Matrix(
[
state.get_id()
state.get_sym()
for state in self.states()
if not state.has_conservation_law()
]
Expand Down Expand Up @@ -1704,7 +1706,7 @@ def _compute_equation(self, name: str) -> None:
event_observables = [
sp.zeros(self.num_eventobs(), 1) for _ in self._events
]
event_ids = [e.get_id() for e in self._events]
event_ids = [e.get_sym() for e in self._events]
z2event = [
event_ids.index(event_obs.get_event())
for event_obs in self._event_observables
Expand Down Expand Up @@ -2285,7 +2287,7 @@ def get_conservation_laws(self) -> list[tuple[sp.Symbol, sp.Expr]]:
list of state identifiers
"""
return [
(state.get_id(), state.get_x_rdata())
(state.get_sym(), state.get_x_rdata())
for state in self.states()
if state.has_conservation_law()
]
Expand Down Expand Up @@ -2338,7 +2340,7 @@ def state_has_fixed_parameter_initial_condition(self, ix: int) -> bool:
if not isinstance(ic, sp.Basic):
return False
return any(
fp in (c.get_id() for c in self._constants)
fp in (c.get_sym() for c in self._constants)
for fp in ic.free_symbols
)

Expand Down Expand Up @@ -2450,20 +2452,20 @@ def _get_unique_root(

for root in roots:
if sp.simplify(root_found - root.get_val()).is_zero:
return root.get_id()
return root.get_sym()

# create an event for a new root function
root_symstr = f"Heaviside_{len(roots)}"
roots.append(
Event(
identifier=sp.Symbol(root_symstr),
symbol=sp.Symbol(root_symstr),
name=root_symstr,
value=root_found,
assignments=None,
use_values_from_trigger_time=True,
)
)
return roots[-1].get_id()
return roots[-1].get_sym()

def _collect_heaviside_roots(
self,
Expand Down Expand Up @@ -2579,22 +2581,22 @@ def _process_hybridization(self, hybridization: dict) -> None:
https://petab-sciml.readthedocs.io/latest/format.html#problem-yaml-file
"""
added_expressions = False
orig_obs = tuple([s.get_id() for s in self._observables])
orig_obs = tuple([s.get_sym() for s in self._observables])
for net_id, net in hybridization.items():
if net["static"]:
continue # do not integrate into ODEs, handle in amici.jax.petab
inputs = [
comp
for comp in self._components
if str(comp.get_id()) in net["input_vars"]
if str(comp.get_sym()) in net["input_vars"]
]
# sort inputs by order in input_vars
inputs = sorted(
inputs,
key=lambda comp: net["input_vars"].index(str(comp.get_id())),
key=lambda comp: net["input_vars"].index(str(comp.get_sym())),
)
if len(inputs) != len(net["input_vars"]):
found_vars = {str(comp.get_id()) for comp in inputs}
found_vars = {str(comp.get_sym()) for comp in inputs}
missing_vars = set(net["input_vars"]) - found_vars
raise ValueError(
f"Could not find all input variables for neural network {net_id}. "
Expand All @@ -2616,9 +2618,9 @@ def _process_hybridization(self, hybridization: dict) -> None:
outputs = {
out_var: {"comp": comp, "ind": net["output_vars"][out_var]}
for comp in self._components
if (out_var := str(comp.get_id())) in net["output_vars"]
if (out_var := str(comp.get_sym())) in net["output_vars"]
# TODO: SYNTAX NEEDS to CHANGE
or (out_var := str(comp.get_id()) + "_dot")
or (out_var := str(comp.get_sym()) + "_dot")
in net["output_vars"]
}
if len(outputs.keys()) != len(net["output_vars"]):
Expand All @@ -2645,7 +2647,7 @@ def _process_hybridization(self, hybridization: dict) -> None:

# generate dummy Function
out_val = sp.Function(net_id)(
*[input.get_id() for input in inputs], parts["ind"]
*[input.get_sym() for input in inputs], parts["ind"]
)

# add to the model
Expand All @@ -2659,7 +2661,7 @@ def _process_hybridization(self, hybridization: dict) -> None:
else:
self.add_component(
Expression(
identifier=comp.get_id(),
symbol=comp.get_sym(),
name=net_id,
value=out_val,
)
Expand All @@ -2669,7 +2671,7 @@ def _process_hybridization(self, hybridization: dict) -> None:
observables = {
ob_var: {"comp": comp, "ind": net["observable_vars"][ob_var]}
for comp in self._components
if (ob_var := str(comp.get_id())) in net["observable_vars"]
if (ob_var := str(comp.get_sym())) in net["observable_vars"]
# # TODO: SYNTAX NEEDS to CHANGE
# or (ob_var := str(comp.get_id()) + "_dot")
# in net["observable_vars"]
Expand All @@ -2691,18 +2693,18 @@ def _process_hybridization(self, hybridization: dict) -> None:
f"{comp.get_name()} ({type(comp)}) is not an observable."
)
out_val = sp.Function(net_id)(
*[input.get_id() for input in inputs], parts["ind"]
*[input.get_sym() for input in inputs], parts["ind"]
)
# add to the model
self.add_component(
Observable(
identifier=comp.get_id(),
symbol=comp.get_sym(),
name=net_id,
value=out_val,
)
)

new_order = [orig_obs.index(s.get_id()) for s in self._observables]
new_order = [orig_obs.index(s.get_sym()) for s in self._observables]
self._observables = [self._observables[i] for i in new_order]

if added_expressions:
Expand Down
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