merge

Author: FFroehlich

python/sdist/amici/de_model.py

@@ -19,11 +19,12 @@
     AlgebraicEquation,
     AlgebraicState,
     ConservationLaw,
-    Constant,
     DifferentialState,
     Event,
     EventObservable,
     Expression,
+    FixedParameter,
+    FreeParameter,
     LogLikelihood,
     LogLikelihoodRZ,
     LogLikelihoodY,
@@ -32,7 +33,6 @@
     NoiseParameter,
     Observable,
     ObservableParameter,
-    Parameter,
     Sigma,
     SigmaY,
     SigmaZ,
@@ -228,8 +228,8 @@ def __init__(
         self._event_observables: list[EventObservable] = []
         self._sigma_ys: list[SigmaY] = []
         self._sigma_zs: list[SigmaZ] = []
-        self._parameters: list[Parameter] = []
-        self._constants: list[Constant] = []
+        self._parameters: list[FreeParameter] = []
+        self._constants: list[FixedParameter] = []
         self._log_likelihood_ys: list[LogLikelihoodY] = []
         self._log_likelihood_zs: list[LogLikelihoodZ] = []
         self._log_likelihood_rzs: list[LogLikelihoodRZ] = []
@@ -354,11 +354,11 @@ def observables(self) -> list[Observable]:
         """Get all observables."""
         return self._observables
 
-    def parameters(self) -> list[Parameter]:
+    def parameters(self) -> list[FreeParameter]:
         """Get all parameters."""
         return self._parameters
 
-    def constants(self) -> list[Constant]:
+    def constants(self) -> list[FixedParameter]:
         """Get all constants."""
         return self._constants
 
@@ -589,8 +589,8 @@ def add_component(
         if type(component) not in {
             Observable,
             Expression,
-            Parameter,
-            Constant,
+            FreeParameter,
+            FixedParameter,
             DifferentialState,
             AlgebraicState,
             AlgebraicEquation,
@@ -2630,7 +2630,7 @@ def _process_hybridization(self, hybridization: dict) -> None:
             for out_var, parts in outputs.items():
                 comp = parts["comp"]
                 # remove output from model components
-                if isinstance(comp, Parameter):
+                if isinstance(comp, FreeParameter):
                     self._parameters.remove(comp)
                 elif isinstance(comp, Expression):
                     self._expressions.remove(comp)

python/sdist/amici/de_model_components.py

@@ -19,7 +19,7 @@
 
 __all__ = [
     "ConservationLaw",
-    "Constant",
+    "FixedParameter",
     "Event",
     "Expression",
     "LogLikelihoodY",
@@ -29,7 +29,7 @@
     "NoiseParameter",
     "Observable",
     "ObservableParameter",
-    "Parameter",
+    "FreeParameter",
     "SigmaY",
     "SigmaZ",
     "DifferentialState",
@@ -572,10 +572,9 @@ def __init__(self, symbol: sp.Symbol, name: str, value: sp.Expr):
         super().__init__(symbol, name, value)
 
 
-class Parameter(ModelQuantity):
+class FreeParameter(ModelQuantity):
     """
-    A Parameter is a free variable in the model with respect to which
-    sensitivities may be computed, abbreviated by ``p``.
+    A Parameter is a model variable with respect to which sensitivities can be computed, abbreviated by ``p``.
     """
 
     def __init__(self, symbol: sp.Symbol, name: str, value: numbers.Number):
@@ -595,21 +594,20 @@ def __init__(self, symbol: sp.Symbol, name: str, value: numbers.Number):
         super().__init__(symbol, name, value)
 
 
-class Constant(ModelQuantity):
+class FixedParameter(ModelQuantity):
     """
-    A Constant is a fixed variable in the model with respect to which
-    sensitivities cannot be computed, abbreviated by ``k``.
+    A FixedParameter is a model variable with respect to which sensitivities cannot be computed, abbreviated by ``k``.
     """
 
     def __init__(self, symbol: sp.Symbol, name: str, value: numbers.Number):
         """
         Create a new Expression instance.
 
         :param symbol:
-            unique symbol of the Constant
+            unique symbol of the FixedParameter
 
         :param name:
-            individual name of the Constant (does not need to be unique)
+            individual name of the FixedParameter (does not need to be unique)
 
         :param value:
             numeric value
@@ -901,8 +899,8 @@ def updates_state(self) -> bool:
     SymbolId.SPECIES: DifferentialState,
     SymbolId.ALGEBRAIC_STATE: AlgebraicState,
     SymbolId.ALGEBRAIC_EQUATION: AlgebraicEquation,
-    SymbolId.PARAMETER: Parameter,
-    SymbolId.FIXED_PARAMETER: Constant,
+    SymbolId.PARAMETER: FreeParameter,
+    SymbolId.FIXED_PARAMETER: FixedParameter,
     SymbolId.OBSERVABLE: Observable,
     SymbolId.EVENT_OBSERVABLE: EventObservable,
     SymbolId.SIGMAY: SigmaY,

python/sdist/amici/importers/pysb/__init__.py

@@ -25,15 +25,15 @@
 import amici
 from amici.de_model import DEModel
 from amici.de_model_components import (
-    Constant,
     DifferentialState,
     Event,
     Expression,
+    FixedParameter,
+    FreeParameter,
     LogLikelihoodY,
     NoiseParameter,
     Observable,
     ObservableParameter,
-    Parameter,
     SigmaY,
 )
 from amici.importers.utils import (
@@ -559,14 +559,14 @@ def _process_pysb_parameters(
     for par in pysb_model.parameters:
         args = [par, f"{par.name}"]
         if par.name in constant_parameters:
-            comp = Constant
+            comp = FixedParameter
             args.append(par.value)
         elif jax and re.match(r"noiseParameter\d+", par.name):
             comp = NoiseParameter
         elif jax and re.match(r"observableParameter\d+", par.name):
             comp = ObservableParameter
         else:
-            comp = Parameter
+            comp = FreeParameter
             args.append(par.value)
 
         ode_model.add_component(comp(*args))

python/tests/test_sciml.py

@@ -379,16 +379,16 @@ def mock_de_model(self):
         from amici.de_model_components import (
             DifferentialState,
             Expression,
+            FreeParameter,
             Observable,
-            Parameter,
         )
 
         model = DEModel()
 
         # Add some parameters
         model._parameters = [
-            Parameter(sp.Symbol("p1"), "param1", sp.Float(1.0)),
-            Parameter(sp.Symbol("p2"), "param2", sp.Float(2.0)),
+            FreeParameter(sp.Symbol("p1"), "param1", sp.Float(1.0)),
+            FreeParameter(sp.Symbol("p2"), "param2", sp.Float(2.0)),
         ]
 
         # Add some expressions