docs(stubs): updated stubs

stubs/gridfire/_gridfire/config.pyi

@@ -3,7 +3,7 @@ GridFire configuration bindings
 """
 from __future__ import annotations
 import typing
-__all__: list[str] = ['AdaptiveEngineViewConfig', 'CVODESolverConfig', 'EngineConfig', 'EngineViewConfig', 'GridFireConfig', 'SolverConfig']
+__all__: list[str] = ['AdaptiveEngineViewConfig', 'BoundaryFluxConfig', 'EngineConfig', 'EngineViewConfig', 'GridFireConfig', 'PointSolverConfig', 'SolverConfig', 'TriggerConfig']
 class AdaptiveEngineViewConfig:
     def __init__(self) -> None:
         ...
@@ -13,20 +13,20 @@ class AdaptiveEngineViewConfig:
     @relativeCullingThreshold.setter
     def relativeCullingThreshold(self, arg0: typing.SupportsFloat) -> None:
         ...
-class CVODESolverConfig:
+class BoundaryFluxConfig:
     def __init__(self) -> None:
         ...
     @property
-    def absTol(self) -> float:
+    def absoluteThreshold(self) -> float:
         ...
-    @absTol.setter
+    @absoluteThreshold.setter
-    def absTol(self, arg0: typing.SupportsFloat) -> None:
+    def absoluteThreshold(self, arg0: typing.SupportsFloat) -> None:
         ...
     @property
-    def relTol(self) -> float:
+    def relativeThreshold(self) -> float:
         ...
-    @relTol.setter
+    @relativeThreshold.setter
-    def relTol(self, arg0: typing.SupportsFloat) -> None:
+    def relativeThreshold(self, arg0: typing.SupportsFloat) -> None:
         ...
 class EngineConfig:
     views: EngineViewConfig
@@ -41,7 +41,45 @@ class GridFireConfig:
     solver: SolverConfig
     def __init__(self) -> None:
         ...
-class SolverConfig:
+class PointSolverConfig:
-    cvode: CVODESolverConfig
+    trigger: TriggerConfig
     def __init__(self) -> None:
         ...
+    @property
+    def absTol(self) -> float:
+        ...
+    @absTol.setter
+    def absTol(self, arg0: typing.SupportsFloat) -> None:
+        ...
+    @property
+    def relTol(self) -> float:
+        ...
+    @relTol.setter
+    def relTol(self, arg0: typing.SupportsFloat) -> None:
+        ...
+class SolverConfig:
+    pointSolver: PointSolverConfig
+    def __init__(self) -> None:
+        ...
+class TriggerConfig:
+    boundaryFlux: BoundaryFluxConfig
+    def __init__(self) -> None:
+        ...
+    @property
+    def maxConvergenceFailures(self) -> float:
+        ...
+    @maxConvergenceFailures.setter
+    def maxConvergenceFailures(self, arg0: typing.SupportsFloat) -> None:
+        ...
+    @property
+    def offDiagonalThreshold(self) -> float:
+        ...
+    @offDiagonalThreshold.setter
+    def offDiagonalThreshold(self, arg0: typing.SupportsFloat) -> None:
+        ...
+    @property
+    def timestepCollapseRatio(self) -> float:
+        ...
+    @timestepCollapseRatio.setter
+    def timestepCollapseRatio(self, arg0: typing.SupportsFloat) -> None:
+        ...

stubs/gridfire/_gridfire/engine/__init__.pyi

@@ -37,6 +37,10 @@ class AdaptiveEngineView(DynamicEngine):
         """
         Recursively collect composition from current engine and any sub engines if they exist.
         """
+    def constructStateBlob(self, blob: scratchpads.StateBlob = None) -> scratchpads.StateBlob:
+        """
+        Construct the state blob for this engine. Generally base engines (GraphEngine) can call this with no arguments whereas views should take an argument to an already constructed state blob which will be cloned and then the clone will be modified
+        """
     @typing.overload
     def generateJacobianMatrix(self: DynamicEngine, ctx: scratchpads.StateBlob, comp: fourdst._phys.composition.Composition, T9: typing.SupportsFloat, rho: typing.SupportsFloat) -> NetworkJacobian:
         """
@@ -56,6 +60,10 @@ class AdaptiveEngineView(DynamicEngine):
         """
         Get the base engine associated with this adaptive engine view.
         """
+    def getMostRecentRHSCalculation(self, ctx: scratchpads.StateBlob) -> gridfire._gridfire.engine.StepDerivatives | None:
+        """
+        Retrieve the most recent RHS calculation from the engine
+        """
     def getNetworkReactions(self, arg0: scratchpads.StateBlob) -> gridfire._gridfire.reaction.ReactionSet:
         """
         Get the set of logical reactions in the network.
@@ -115,6 +123,10 @@ class DefinedEngineView(DynamicEngine):
         """
         Recursively collect composition from current engine and any sub engines if they exist.
         """
+    def constructStateBlob(self, blob: scratchpads.StateBlob = None) -> scratchpads.StateBlob:
+        """
+        Construct the state blob for this engine. Generally base engines (GraphEngine) can call this with no arguments whereas views should take an argument to an already constructed state blob which will be cloned and then the clone will be modified
+        """
     @typing.overload
     def generateJacobianMatrix(self: DynamicEngine, ctx: scratchpads.StateBlob, comp: fourdst._phys.composition.Composition, T9: typing.SupportsFloat, rho: typing.SupportsFloat) -> NetworkJacobian:
         """
@@ -134,6 +146,10 @@ class DefinedEngineView(DynamicEngine):
         """
         Get the base engine associated with this defined engine view.
         """
+    def getMostRecentRHSCalculation(self, ctx: scratchpads.StateBlob) -> gridfire._gridfire.engine.StepDerivatives | None:
+        """
+        Retrieve the most recent RHS calculation from the engine
+        """
     def getNetworkReactions(self, arg0: scratchpads.StateBlob) -> gridfire._gridfire.reaction.ReactionSet:
         """
         Get the set of logical reactions in the network.
@@ -250,6 +266,10 @@ class FileDefinedEngineView(DefinedEngineView):
         """
         Recursively collect composition from current engine and any sub engines if they exist.
         """
+    def constructStateBlob(self, blob: scratchpads.StateBlob = None) -> scratchpads.StateBlob:
+        """
+        Construct the state blob for this engine. Generally base engines (GraphEngine) can call this with no arguments whereas views should take an argument to an already constructed state blob which will be cloned and then the clone will be modified
+        """
     @typing.overload
     def generateJacobianMatrix(self: DynamicEngine, ctx: scratchpads.StateBlob, comp: fourdst._phys.composition.Composition, T9: typing.SupportsFloat, rho: typing.SupportsFloat) -> NetworkJacobian:
         """
@@ -269,6 +289,10 @@ class FileDefinedEngineView(DefinedEngineView):
         """
         Get the base engine associated with this file defined engine view.
         """
+    def getMostRecentRHSCalculation(self, ctx: scratchpads.StateBlob) -> gridfire._gridfire.engine.StepDerivatives | None:
+        """
+        Retrieve the most recent RHS calculation from the engine
+        """
     def getNetworkFile(self) -> str:
         """
         Get the network file associated with this defined engine view.
@@ -329,6 +353,16 @@ class GraphEngine(DynamicEngine):
         """
         Initialize GraphEngine with a set of reactions.
         """
+    @typing.overload
+    def addReaction(self, reaction: ...) -> None:
+        """
+        Add a reaction to the engine's network manually.
+        """
+    @typing.overload
+    def addReaction(self, reaction_id: str) -> None:
+        """
+        Add a reaction to the engine's network manually using a reaction identifier string.
+        """
     def calculateEpsDerivatives(self, ctx: scratchpads.StateBlob, comp: ..., T9: typing.SupportsFloat, rho: typing.SupportsFloat) -> ...:
         """
         Calculate deps/dT and deps/drho
@@ -357,6 +391,10 @@ class GraphEngine(DynamicEngine):
         """
         Recursively collect composition from current engine and any sub engines if they exist.
         """
+    def constructStateBlob(self, blob: scratchpads.StateBlob = None) -> scratchpads.StateBlob:
+        """
+        Construct the state blob for this engine. Generally base engines (GraphEngine) can call this with no arguments whereas views should take an argument to an already constructed state blob which will be cloned and then the clone will be modified
+        """
     def exportToCSV(self, ctx: scratchpads.StateBlob, filename: str) -> None:
         """
         Export the network to a CSV file for analysis.
@@ -380,6 +418,10 @@ class GraphEngine(DynamicEngine):
         """
         Generate the jacobian matrix for the given sparsity pattern
         """
+    def getMostRecentRHSCalculation(self, ctx: scratchpads.StateBlob) -> gridfire._gridfire.engine.StepDerivatives | None:
+        """
+        Retrieve the most recent RHS calculation from the engine
+        """
     def getNetworkReactions(self, arg0: scratchpads.StateBlob) -> gridfire._gridfire.reaction.ReactionSet:
         """
         Get the set of logical reactions in the network.
@@ -461,6 +503,10 @@ class MultiscalePartitioningEngineView(DynamicEngine):
         """
         Recursively collect composition from current engine and any sub engines if they exist.
         """
+    def constructStateBlob(self, blob: scratchpads.StateBlob = None) -> scratchpads.StateBlob:
+        """
+        Construct the state blob for this engine. Generally base engines (GraphEngine) can call this with no arguments whereas views should take an argument to an already constructed state blob which will be cloned and then the clone will be modified
+        """
     def exportToDot(self, ctx: scratchpads.StateBlob, filename: str, comp: fourdst._phys.composition.Composition, T9: typing.SupportsFloat, rho: typing.SupportsFloat) -> None:
         """
         Export the network to a DOT file for visualization.
@@ -492,6 +538,10 @@ class MultiscalePartitioningEngineView(DynamicEngine):
         """
         Get the list of fast species in the network.
         """
+    def getMostRecentRHSCalculation(self, ctx: scratchpads.StateBlob) -> gridfire._gridfire.engine.StepDerivatives | None:
+        """
+        Retrieve the most recent RHS calculation from the engine
+        """
     def getNetworkReactions(self, arg0: scratchpads.StateBlob) -> gridfire._gridfire.reaction.ReactionSet:
         """
         Get the set of logical reactions in the network.
@@ -750,6 +800,10 @@ class NetworkPrimingEngineView(DefinedEngineView):
         """
         Recursively collect composition from current engine and any sub engines if they exist.
         """
+    def constructStateBlob(self, blob: scratchpads.StateBlob = None) -> scratchpads.StateBlob:
+        """
+        Construct the state blob for this engine. Generally base engines (GraphEngine) can call this with no arguments whereas views should take an argument to an already constructed state blob which will be cloned and then the clone will be modified
+        """
     @typing.overload
     def generateJacobianMatrix(self: DynamicEngine, ctx: scratchpads.StateBlob, comp: fourdst._phys.composition.Composition, T9: typing.SupportsFloat, rho: typing.SupportsFloat) -> NetworkJacobian:
         """
@@ -769,6 +823,10 @@ class NetworkPrimingEngineView(DefinedEngineView):
         """
         Get the base engine associated with this priming engine view.
         """
+    def getMostRecentRHSCalculation(self, ctx: scratchpads.StateBlob) -> gridfire._gridfire.engine.StepDerivatives | None:
+        """
+        Retrieve the most recent RHS calculation from the engine
+        """
     def getNetworkReactions(self, arg0: scratchpads.StateBlob) -> gridfire._gridfire.reaction.ReactionSet:
         """
         Get the set of logical reactions in the network.

stubs/gridfire/_gridfire/solver.pyi

@@ -4,6 +4,8 @@ GridFire numerical solver bindings
 from __future__ import annotations
 import collections.abc
 import fourdst._phys.atomic
+import fourdst._phys.composition
+import gridfire._gridfire.config
 import gridfire._gridfire.engine
 import gridfire._gridfire.engine.scratchpads
 import gridfire._gridfire.type
@@ -47,15 +49,25 @@ class MultiZoneDynamicNetworkSolver:
         evaluate the dynamic engine using the dynamic engine class for multiple zones (using openmp if available)
         """
 class PointSolver(SingleZoneDynamicNetworkSolver):
+    @typing.overload
     def __init__(self, engine: gridfire._gridfire.engine.DynamicEngine) -> None:
         """
         Initialize the PointSolver object.
         """
+    @typing.overload
+    def __init__(self, engine: gridfire._gridfire.engine.DynamicEngine, config: gridfire._gridfire.config.GridFireConfig) -> None:
+        """
+        Initialize the PointSolver object with a configuration set.
+        """
     def evaluate(self, solver_ctx: SolverContextBase, netIn: gridfire._gridfire.type.NetIn, display_trigger: bool = False, force_reinitialization: bool = False) -> gridfire._gridfire.type.NetOut:
         """
         evaluate the dynamic engine using the dynamic engine class
         """
-class PointSolverContext:
+    def getConfig(self) -> gridfire._gridfire.config.GridFireConfig:
+        """
+        Get a copy of the config object
+        """
+class PointSolverContext(SolverContextBase):
     callback: collections.abc.Callable[[PointSolverTimestepContext], None] | None
     detailed_logging: bool
     stdout_logging: bool
@@ -116,6 +128,9 @@ class PointSolverTimestepContext:
     def T9(self) -> float:
         ...
     @property
+    def composition(self) -> fourdst._phys.composition.Composition:
+        ...
+    @property
     def currentConvergenceFailures(self) -> int:
         ...
     @property