funman.model package¶
Subpackages¶
- funman.model.generated_models package
- Submodules
- funman.model.generated_models.petrinet module
- funman.model.generated_models.regnet module
- Module contents
Submodules¶
funman.model.bilayer module¶
- pydantic model funman.model.bilayer.BilayerDynamics¶
Bases:
BilayerGraphThe BilayerDynamics class represents a state update (dynamics) model for a set of variables. The graph consists of:
state nodes (current state),
tangent nodes (next state), and
flux nodes (causal relationships).
Show JSON schema
{ "title": "BilayerDynamics", "description": "The BilayerDynamics class represents a state update (dynamics) model for a set of variables. The graph consists of:\n\n* state nodes (current state),\n\n* tangent nodes (next state), and\n\n* flux nodes (causal relationships).", "type": "object", "properties": { "json_graph": { "title": "Json Graph", "type": "object" } }, "required": [ "json_graph" ] }
- Fields:
- model_post_init(context: Any, /) None¶
We need to both initialize private attributes and call the user-defined model_post_init method.
- to_dot(values={})¶
Create a dot object for visualizing the graph.
- Returns:
The graph represented by self.
- Return type:
graphviz.Digraph
- pydantic model funman.model.bilayer.BilayerEdge¶
Bases:
BaseModelShow JSON schema
{ "title": "BilayerEdge", "type": "object", "properties": { "src": { "$ref": "#/$defs/BilayerNode" }, "tgt": { "$ref": "#/$defs/BilayerNode" } }, "$defs": { "BilayerMetadata": { "description": "Metadata for a BilayerNode", "properties": { "ref": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ref" }, "type": { "anyOf": [ { "enum": [ "float", "int" ], "type": "string" }, { "type": "null" } ], "default": null, "title": "Type" }, "initial_value": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Initial Value" }, "lb": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Lb" }, "ub": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Ub" } }, "title": "BilayerMetadata", "type": "object" }, "BilayerNode": { "description": "Node in a BilayerGraph.", "properties": { "index": { "title": "Index", "type": "integer" }, "parameter": { "title": "Parameter", "type": "string" }, "metadata": { "anyOf": [ { "$ref": "#/$defs/BilayerMetadata" }, { "type": "null" } ], "default": null } }, "required": [ "index", "parameter" ], "title": "BilayerNode", "type": "object" } }, "required": [ "src", "tgt" ] }
- field src: BilayerNode [Required]¶
- field tgt: BilayerNode [Required]¶
- to_dot(dot)¶
Create a dot object for visualizing the edge.
- Parameters:
dot (graphviz.Graph) – Graph to add the edge.
- pydantic model funman.model.bilayer.BilayerFluxNode¶
Bases:
BilayerNodeBilayerNode representing a flux.
Show JSON schema
{ "title": "BilayerFluxNode", "description": "BilayerNode representing a flux.", "type": "object", "properties": { "index": { "title": "Index", "type": "integer" }, "parameter": { "title": "Parameter", "type": "string" }, "metadata": { "anyOf": [ { "$ref": "#/$defs/BilayerMetadata" }, { "type": "null" } ], "default": null } }, "$defs": { "BilayerMetadata": { "description": "Metadata for a BilayerNode", "properties": { "ref": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ref" }, "type": { "anyOf": [ { "enum": [ "float", "int" ], "type": "string" }, { "type": "null" } ], "default": null, "title": "Type" }, "initial_value": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Initial Value" }, "lb": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Lb" }, "ub": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Ub" } }, "title": "BilayerMetadata", "type": "object" } }, "required": [ "index", "parameter" ] }
- field index: int [Required]¶
- field metadata: BilayerMetadata | None = None¶
- field parameter: str [Required]¶
- pydantic model funman.model.bilayer.BilayerGraph¶
Bases:
ABC,BaseModelAbstract representation of a Bilayer graph.
Show JSON schema
{ "title": "BilayerGraph", "description": "Abstract representation of a Bilayer graph.", "type": "object", "properties": { "json_graph": { "title": "Json Graph", "type": "object" } }, "required": [ "json_graph" ] }
- Fields:
- field json_graph: Dict [Required]¶
- model_post_init(context: Any, /) None¶
This function is meant to behave like a BaseModel method to initialise private attributes.
It takes context as an argument since that’s what pydantic-core passes when calling it.
- Parameters:
self – The BaseModel instance.
context – The context.
- pydantic model funman.model.bilayer.BilayerMeasurement¶
Bases:
BilayerGraph,BaseModelThe BilayerMeasurement class represents measurements taken on the BilayerNode state nodes of a BilayerDynamics object. The graph consists of:
state nodes (current state),
observation nodes, and
flux nodes (causal relationships).
Show JSON schema
{ "title": "BilayerMeasurement", "description": "The BilayerMeasurement class represents measurements taken on the BilayerNode state nodes of a BilayerDynamics object. The graph consists of:\n\n* state nodes (current state),\n\n* observation nodes, and\n\n* flux nodes (causal relationships).", "type": "object", "properties": { "json_graph": { "title": "Json Graph", "type": "object" }, "state": { "additionalProperties": { "$ref": "#/$defs/BilayerStateNode" }, "default": {}, "title": "State", "type": "object" }, "flux": { "additionalProperties": { "$ref": "#/$defs/BilayerFluxNode" }, "default": {}, "title": "Flux", "type": "object" }, "observable": { "additionalProperties": { "$ref": "#/$defs/BilayerStateNode" }, "default": {}, "title": "Observable", "type": "object" }, "input_edges": { "$ref": "#/$defs/BilayerEdge", "default": [] }, "output_edges": { "$ref": "#/$defs/BilayerEdge", "default": [] } }, "$defs": { "BilayerEdge": { "properties": { "src": { "$ref": "#/$defs/BilayerNode" }, "tgt": { "$ref": "#/$defs/BilayerNode" } }, "required": [ "src", "tgt" ], "title": "BilayerEdge", "type": "object" }, "BilayerFluxNode": { "description": "BilayerNode representing a flux.", "properties": { "index": { "title": "Index", "type": "integer" }, "parameter": { "title": "Parameter", "type": "string" }, "metadata": { "anyOf": [ { "$ref": "#/$defs/BilayerMetadata" }, { "type": "null" } ], "default": null } }, "required": [ "index", "parameter" ], "title": "BilayerFluxNode", "type": "object" }, "BilayerMetadata": { "description": "Metadata for a BilayerNode", "properties": { "ref": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ref" }, "type": { "anyOf": [ { "enum": [ "float", "int" ], "type": "string" }, { "type": "null" } ], "default": null, "title": "Type" }, "initial_value": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Initial Value" }, "lb": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Lb" }, "ub": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Ub" } }, "title": "BilayerMetadata", "type": "object" }, "BilayerNode": { "description": "Node in a BilayerGraph.", "properties": { "index": { "title": "Index", "type": "integer" }, "parameter": { "title": "Parameter", "type": "string" }, "metadata": { "anyOf": [ { "$ref": "#/$defs/BilayerMetadata" }, { "type": "null" } ], "default": null } }, "required": [ "index", "parameter" ], "title": "BilayerNode", "type": "object" }, "BilayerStateNode": { "description": "BilayerNode representing a state variable.", "properties": { "index": { "title": "Index", "type": "integer" }, "parameter": { "title": "Parameter", "type": "string" }, "metadata": { "anyOf": [ { "$ref": "#/$defs/BilayerMetadata" }, { "type": "null" } ], "default": null } }, "required": [ "index", "parameter" ], "title": "BilayerStateNode", "type": "object" } }, "required": [ "json_graph" ] }
- Fields:
- field flux: Dict[int, BilayerFluxNode] = {}¶
- field input_edges: BilayerEdge = []¶
- field observable: Dict[int, BilayerStateNode] = {}¶
- field output_edges: BilayerEdge = []¶
- field state: Dict[int, BilayerStateNode] = {}¶
- model_post_init(context: Any, /) None¶
We need to both initialize private attributes and call the user-defined model_post_init method.
- to_dot(values={})¶
Create a dot object for visualizing the graph.
- Returns:
The graph represented by self.
- Return type:
graphviz.Digraph
- pydantic model funman.model.bilayer.BilayerMetadata¶
Bases:
BaseModelMetadata for a BilayerNode
Show JSON schema
{ "title": "BilayerMetadata", "description": "Metadata for a BilayerNode", "type": "object", "properties": { "ref": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ref" }, "type": { "anyOf": [ { "enum": [ "float", "int" ], "type": "string" }, { "type": "null" } ], "default": null, "title": "Type" }, "initial_value": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Initial Value" }, "lb": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Lb" }, "ub": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Ub" } } }
- Fields:
- field initial_value: float | int | None = None¶
- field lb: float | int | None = None¶
- field ref: str | None = None¶
- field type: Literal['float', 'int'] | None = None¶
- field ub: float | int | None = None¶
- pydantic model funman.model.bilayer.BilayerModel¶
Bases:
FunmanModelA BilayerModel is a complete specification of a Model that uses a BilayerDynamics graph to represent dynamics. It includes the attributes:
bilayer: the BilayerDynamics graph
measurements: the BilayerMeasurement graph (used to derive additional variables from the state nodes)
init_values: a dict mapping from state variables and flux parameters to initial value
identical_parameters: a list of lists of flux parameters that have identical values
parameter_bounds: a list of lower and upper bounds on parameters
Show JSON schema
{ "title": "BilayerModel", "description": "A BilayerModel is a complete specification of a Model that uses a BilayerDynamics graph to represent dynamics. It includes the attributes:\n\n* bilayer: the BilayerDynamics graph\n\n* measurements: the BilayerMeasurement graph (used to derive additional variables from the state nodes)\n\n* init_values: a dict mapping from state variables and flux parameters to initial value\n\n* identical_parameters: a list of lists of flux parameters that have identical values\n\n* parameter_bounds: a list of lower and upper bounds on parameters", "type": "object", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" }, "bilayer": { "$ref": "#/$defs/BilayerDynamics" }, "measurements": { "$ref": "#/$defs/BilayerMeasurement", "default": null }, "identical_parameters": { "default": [], "items": { "items": { "type": "string" }, "type": "array" }, "title": "Identical Parameters", "type": "array" } }, "$defs": { "BilayerDynamics": { "description": "The BilayerDynamics class represents a state update (dynamics) model for a set of variables. The graph consists of:\n\n* state nodes (current state),\n\n* tangent nodes (next state), and\n\n* flux nodes (causal relationships).", "properties": { "json_graph": { "title": "Json Graph", "type": "object" } }, "required": [ "json_graph" ], "title": "BilayerDynamics", "type": "object" }, "BilayerEdge": { "properties": { "src": { "$ref": "#/$defs/BilayerNode" }, "tgt": { "$ref": "#/$defs/BilayerNode" } }, "required": [ "src", "tgt" ], "title": "BilayerEdge", "type": "object" }, "BilayerFluxNode": { "description": "BilayerNode representing a flux.", "properties": { "index": { "title": "Index", "type": "integer" }, "parameter": { "title": "Parameter", "type": "string" }, "metadata": { "anyOf": [ { "$ref": "#/$defs/BilayerMetadata" }, { "type": "null" } ], "default": null } }, "required": [ "index", "parameter" ], "title": "BilayerFluxNode", "type": "object" }, "BilayerMeasurement": { "description": "The BilayerMeasurement class represents measurements taken on the BilayerNode state nodes of a BilayerDynamics object. The graph consists of:\n\n* state nodes (current state),\n\n* observation nodes, and\n\n* flux nodes (causal relationships).", "properties": { "json_graph": { "title": "Json Graph", "type": "object" }, "state": { "additionalProperties": { "$ref": "#/$defs/BilayerStateNode" }, "default": {}, "title": "State", "type": "object" }, "flux": { "additionalProperties": { "$ref": "#/$defs/BilayerFluxNode" }, "default": {}, "title": "Flux", "type": "object" }, "observable": { "additionalProperties": { "$ref": "#/$defs/BilayerStateNode" }, "default": {}, "title": "Observable", "type": "object" }, "input_edges": { "$ref": "#/$defs/BilayerEdge", "default": [] }, "output_edges": { "$ref": "#/$defs/BilayerEdge", "default": [] } }, "required": [ "json_graph" ], "title": "BilayerMeasurement", "type": "object" }, "BilayerMetadata": { "description": "Metadata for a BilayerNode", "properties": { "ref": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ref" }, "type": { "anyOf": [ { "enum": [ "float", "int" ], "type": "string" }, { "type": "null" } ], "default": null, "title": "Type" }, "initial_value": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Initial Value" }, "lb": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Lb" }, "ub": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Ub" } }, "title": "BilayerMetadata", "type": "object" }, "BilayerNode": { "description": "Node in a BilayerGraph.", "properties": { "index": { "title": "Index", "type": "integer" }, "parameter": { "title": "Parameter", "type": "string" }, "metadata": { "anyOf": [ { "$ref": "#/$defs/BilayerMetadata" }, { "type": "null" } ], "default": null } }, "required": [ "index", "parameter" ], "title": "BilayerNode", "type": "object" }, "BilayerStateNode": { "description": "BilayerNode representing a state variable.", "properties": { "index": { "title": "Index", "type": "integer" }, "parameter": { "title": "Parameter", "type": "string" }, "metadata": { "anyOf": [ { "$ref": "#/$defs/BilayerMetadata" }, { "type": "null" } ], "default": null } }, "required": [ "index", "parameter" ], "title": "BilayerStateNode", "type": "object" } }, "required": [ "bilayer" ] }
- Config:
allow_inf_nan: bool = True
- Fields:
- field bilayer: BilayerDynamics [Required]¶
- field identical_parameters: List[List[str]] = []¶
- field measurements: BilayerMeasurement = None¶
- calculate_normalization_constant(scenario: AnalysisScenario, config: FUNMANConfig) float¶
- default_encoder(config: FUNMANConfig, scenario: AnalysisScenario) Encoder¶
Return the default Encoder for the model
- Returns:
SMT encoder for model
- Return type:
- model_post_init(context: Any, /) None¶
We need to both initialize private attributes and call the user-defined model_post_init method.
- pydantic model funman.model.bilayer.BilayerNegativeEdge¶
Bases:
BilayerEdgeClass representing a positive influence between a FluxNode and a StateNode.
Show JSON schema
{ "title": "BilayerNegativeEdge", "description": "Class representing a positive influence between a FluxNode and a StateNode.", "type": "object", "properties": { "src": { "$ref": "#/$defs/BilayerNode" }, "tgt": { "$ref": "#/$defs/BilayerNode" } }, "$defs": { "BilayerMetadata": { "description": "Metadata for a BilayerNode", "properties": { "ref": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ref" }, "type": { "anyOf": [ { "enum": [ "float", "int" ], "type": "string" }, { "type": "null" } ], "default": null, "title": "Type" }, "initial_value": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Initial Value" }, "lb": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Lb" }, "ub": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Ub" } }, "title": "BilayerMetadata", "type": "object" }, "BilayerNode": { "description": "Node in a BilayerGraph.", "properties": { "index": { "title": "Index", "type": "integer" }, "parameter": { "title": "Parameter", "type": "string" }, "metadata": { "anyOf": [ { "$ref": "#/$defs/BilayerMetadata" }, { "type": "null" } ], "default": null } }, "required": [ "index", "parameter" ], "title": "BilayerNode", "type": "object" } }, "required": [ "src", "tgt" ] }
- field src: BilayerNode [Required]¶
- field tgt: BilayerNode [Required]¶
- to_dot(dot)¶
Create a dot object for visualizing the edge.
- Parameters:
dot (graphviz.Graph) – Graph to add the edge.
- pydantic model funman.model.bilayer.BilayerNode¶
Bases:
BaseModelNode in a BilayerGraph.
Show JSON schema
{ "title": "BilayerNode", "description": "Node in a BilayerGraph.", "type": "object", "properties": { "index": { "title": "Index", "type": "integer" }, "parameter": { "title": "Parameter", "type": "string" }, "metadata": { "anyOf": [ { "$ref": "#/$defs/BilayerMetadata" }, { "type": "null" } ], "default": null } }, "$defs": { "BilayerMetadata": { "description": "Metadata for a BilayerNode", "properties": { "ref": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ref" }, "type": { "anyOf": [ { "enum": [ "float", "int" ], "type": "string" }, { "type": "null" } ], "default": null, "title": "Type" }, "initial_value": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Initial Value" }, "lb": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Lb" }, "ub": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Ub" } }, "title": "BilayerMetadata", "type": "object" } }, "required": [ "index", "parameter" ] }
- field index: int [Required]¶
- field metadata: BilayerMetadata | None = None¶
- field parameter: str [Required]¶
- to_dot(dot, values={})¶
- pydantic model funman.model.bilayer.BilayerPositiveEdge¶
Bases:
BilayerEdgeClass representing a positive influence between a FluxNode and a StateNode.
Show JSON schema
{ "title": "BilayerPositiveEdge", "description": "Class representing a positive influence between a FluxNode and a StateNode.", "type": "object", "properties": { "src": { "$ref": "#/$defs/BilayerNode" }, "tgt": { "$ref": "#/$defs/BilayerNode" } }, "$defs": { "BilayerMetadata": { "description": "Metadata for a BilayerNode", "properties": { "ref": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ref" }, "type": { "anyOf": [ { "enum": [ "float", "int" ], "type": "string" }, { "type": "null" } ], "default": null, "title": "Type" }, "initial_value": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Initial Value" }, "lb": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Lb" }, "ub": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Ub" } }, "title": "BilayerMetadata", "type": "object" }, "BilayerNode": { "description": "Node in a BilayerGraph.", "properties": { "index": { "title": "Index", "type": "integer" }, "parameter": { "title": "Parameter", "type": "string" }, "metadata": { "anyOf": [ { "$ref": "#/$defs/BilayerMetadata" }, { "type": "null" } ], "default": null } }, "required": [ "index", "parameter" ], "title": "BilayerNode", "type": "object" } }, "required": [ "src", "tgt" ] }
- field src: BilayerNode [Required]¶
- field tgt: BilayerNode [Required]¶
- pydantic model funman.model.bilayer.BilayerStateNode¶
Bases:
BilayerNodeBilayerNode representing a state variable.
Show JSON schema
{ "title": "BilayerStateNode", "description": "BilayerNode representing a state variable.", "type": "object", "properties": { "index": { "title": "Index", "type": "integer" }, "parameter": { "title": "Parameter", "type": "string" }, "metadata": { "anyOf": [ { "$ref": "#/$defs/BilayerMetadata" }, { "type": "null" } ], "default": null } }, "$defs": { "BilayerMetadata": { "description": "Metadata for a BilayerNode", "properties": { "ref": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ref" }, "type": { "anyOf": [ { "enum": [ "float", "int" ], "type": "string" }, { "type": "null" } ], "default": null, "title": "Type" }, "initial_value": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Initial Value" }, "lb": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Lb" }, "ub": { "anyOf": [ { "type": "number" }, { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Ub" } }, "title": "BilayerMetadata", "type": "object" } }, "required": [ "index", "parameter" ] }
- field index: int [Required]¶
- field metadata: BilayerMetadata | None = None¶
- field parameter: str [Required]¶
funman.model.decapode module¶
- pydantic model funman.model.decapode.DecapodeDynamics¶
Bases:
BaseModelShow JSON schema
{ "title": "DecapodeDynamics", "type": "object", "properties": { "json_graph": { "additionalProperties": { "items": { "additionalProperties": { "anyOf": [ { "type": "integer" }, { "type": "string" } ] }, "type": "object" }, "type": "array" }, "title": "Json Graph", "type": "object" } }, "required": [ "json_graph" ] }
- field json_graph: Dict[str, List[Dict[str, int | str]]] [Required]¶
- pydantic model funman.model.decapode.DecapodeModel¶
Bases:
FunmanModelShow JSON schema
{ "title": "DecapodeModel", "type": "object", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" }, "decapode": { "$ref": "#/$defs/DecapodeDynamics" } }, "$defs": { "DecapodeDynamics": { "properties": { "json_graph": { "additionalProperties": { "items": { "additionalProperties": { "anyOf": [ { "type": "integer" }, { "type": "string" } ] }, "type": "object" }, "type": "array" }, "title": "Json Graph", "type": "object" } }, "required": [ "json_graph" ], "title": "DecapodeDynamics", "type": "object" } }, "required": [ "decapode" ] }
- Config:
allow_inf_nan: bool = True
- Fields:
- field decapode: DecapodeDynamics [Required]¶
- default_encoder(config: FUNMANConfig, scenario: AnalysisScenario) Encoder¶
Return the default Encoder for the model
- Returns:
SMT encoder for model
- Return type:
- model_post_init(context: Any, /) None¶
We need to both initialize private attributes and call the user-defined model_post_init method.
funman.model.encoded module¶
- pydantic model funman.model.encoded.EncodedModel¶
Bases:
FunmanModelModel that holds an SMT formula encoding a model. This class is meant to wrap hand-coded SMT formulas.
Show JSON schema
{ "title": "EncodedModel", "description": "Model that holds an SMT formula encoding a model. This class is meant to wrap hand-coded SMT formulas.", "type": "object", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" }, "parameters": { "anyOf": [ { "items": { "$ref": "#/$defs/ModelParameter" }, "type": "array" }, { "type": "null" } ], "default": null, "title": "Parameters" } }, "$defs": { "Interval": { "description": "An interval is a pair [lb, ub) that is open (i.e., an interval specifies all points x where lb <= x and ub < x).", "properties": { "lb": { "anyOf": [ { "type": "number" }, { "type": "string" }, { "type": "null" } ], "default": -1.7976931348623157e+308, "title": "Lb" }, "ub": { "anyOf": [ { "type": "number" }, { "type": "string" }, { "type": "null" } ], "default": 1.7976931348623157e+308, "title": "Ub" }, "closed_upper_bound": { "default": false, "title": "Closed Upper Bound", "type": "boolean" }, "original_width": { "anyOf": [ { "type": "number" }, { "type": "string" }, { "type": "null" } ], "default": null, "title": "Original Width" }, "normalized": { "default": false, "title": "Normalized", "type": "boolean" }, "unnormalized_lb": { "anyOf": [ { "type": "number" }, { "type": "string" }, { "type": "null" } ], "default": null, "title": "Unnormalized Lb" }, "unnormalized_ub": { "anyOf": [ { "type": "number" }, { "type": "string" }, { "type": "null" } ], "default": null, "title": "Unnormalized Ub" } }, "title": "Interval", "type": "object" }, "ModelParameter": { "additionalProperties": false, "description": "A parameter is a free variable for a Model. It has the following attributes:\n\n* lb: lower bound\n\n* ub: upper bound\n\n* symbol: a pysmt FNode corresponding to the parameter variable", "properties": { "name": { "anyOf": [ { "type": "string" }, { "$ref": "#/$defs/ModelSymbol" } ], "title": "Name" }, "interval": { "$ref": "#/$defs/Interval", "default": { "lb": -1.7976931348623157e+308, "ub": 1.7976931348623157e+308, "closed_upper_bound": false, "original_width": Infinity, "normalized": false, "unnormalized_lb": null, "unnormalized_ub": null } }, "label": { "default": "any", "enum": [ "any", "all" ], "title": "Label", "type": "string" } }, "required": [ "name" ], "title": "ModelParameter", "type": "object" }, "ModelSymbol": { "properties": { "name": { "title": "Name", "type": "string" }, "model": { "title": "Model", "type": "string" } }, "required": [ "name", "model" ], "title": "ModelSymbol", "type": "object" } } }- Config:
allow_inf_nan: bool = True
arbitrary_types_allowed: bool = True
- Fields:
- field parameters: List[ModelParameter] | None = None¶
- default_encoder(config: FUNMANConfig, scenario: AnalysisScenario) Encoder¶
EncodedModel uses EncodedEncoder as the default.
- Returns:
the EncodedEncoder
- Return type:
- model_post_init(context: Any, /) None¶
We need to both initialize private attributes and call the user-defined model_post_init method.
funman.model.ensemble module¶
- pydantic model funman.model.ensemble.EnsembleModel¶
Bases:
FunmanModelShow JSON schema
{ "title": "EnsembleModel", "type": "object", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" }, "models": { "items": { "$ref": "#/$defs/FunmanModel" }, "title": "Models", "type": "array" } }, "$defs": { "FunmanModel": { "description": "The abstract base class for Models.", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" } }, "title": "FunmanModel", "type": "object" } }, "required": [ "models" ] }
- Config:
allow_inf_nan: bool = True
- Fields:
- field models: List[FunmanModel] [Required]¶
- calculate_normalization_constant(scenario: AnalysisScenario, config: FUNMANConfig) float¶
- default_encoder(config: FUNMANConfig, scenario: AnalysisScenario) Encoder¶
Return the default Encoder for the model
- Returns:
SMT encoder for model
- Return type:
- gradient(y, t, *p)¶
- model_post_init(context: Any, /) None¶
We need to both initialize private attributes and call the user-defined model_post_init method.
- to_dot(values={})¶
Create a dot object for visualizing the graph.
- Returns:
The graph represented by self.
- Return type:
graphviz.Digraph
funman.model.gromet module¶
funman.model.model module¶
This module represents the abstract base classes for models.
- pydantic model funman.model.model.FunmanModel¶
Bases:
ABC,BaseModelThe abstract base class for Models.
Show JSON schema
{ "title": "FunmanModel", "description": "The abstract base class for Models.", "type": "object", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" } } }
- Config:
allow_inf_nan: bool = True
- Fields:
- field init_values: Dict[str, float] = {}¶
- field name: str = 'model_a6f04917-34c0-45e0-a42c-128947736090'¶
- field parameter_bounds: Dict[str, List[float]] = {}¶
- calculate_normalization_constant(scenario: AnalysisScenario, config: FUNMANConfig) float¶
- compartmental_constraints(populuation: int, noise: float)¶
- model_post_init(context: Any, /) None¶
This function is meant to behave like a BaseModel method to initialise private attributes.
It takes context as an argument since that’s what pydantic-core passes when calling it.
- Parameters:
self – The BaseModel instance.
context – The context.
- observables()¶
- variables(include_next_state=False)¶
Get all initial values and parameters.
- funman.model.model.is_observable(var_string, model: FunmanModel, time_pattern: str = '[\\d]+$') bool¶
- funman.model.model.is_state_variable(var_string, model: FunmanModel, time_pattern: str = '[\\d]+$') bool¶
funman.model.petrinet module¶
- pydantic model funman.model.petrinet.AbstractPetriNetModel¶
Bases:
FunmanModelShow JSON schema
{ "title": "AbstractPetriNetModel", "type": "object", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" } } }
- Config:
allow_inf_nan: bool = True
- Fields:
- calculate_normalization_constant(scenario: AnalysisScenario, config: FUNMANConfig) float¶
- compartmental_constraints(population: float | int, noise: float) List[Constraint]¶
- derivative(var_name, t, values, params, var_to_value, param_to_value, get_lambda=False)¶
- gradient(t, y, *p)¶
- model_post_init(context: Any, /) None¶
We need to both initialize private attributes and call the user-defined model_post_init method.
- to_dot(values={})¶
Create a dot object for visualizing the graph.
- Returns:
The graph represented by self.
- Return type:
graphviz.Digraph
- pydantic model funman.model.petrinet.GeneratedPetriNetModel¶
Bases:
AbstractPetriNetModelShow JSON schema
{ "title": "GeneratedPetriNetModel", "type": "object", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" }, "petrinet": { "$ref": "#/$defs/Model" } }, "$defs": { "Distribution": { "additionalProperties": true, "properties": { "type": { "title": "Type", "type": "string" }, "parameters": { "title": "Parameters", "type": "object" } }, "required": [ "type", "parameters" ], "title": "Distribution", "type": "object" }, "Grounding": { "additionalProperties": false, "properties": { "identifiers": { "title": "Identifiers", "type": "object" }, "modifiers": { "anyOf": [ { "type": "object" }, { "type": "null" } ], "default": null, "title": "Modifiers" } }, "required": [ "identifiers" ], "title": "Grounding", "type": "object" }, "Header": { "properties": { "name": { "title": "Name", "type": "string" }, "schema": { "format": "uri", "minLength": 1, "title": "Schema", "type": "string" }, "schema_name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Schema Name" }, "description": { "title": "Description", "type": "string" }, "model_version": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Model Version" } }, "required": [ "name", "schema", "description" ], "title": "Header", "type": "object" }, "Initial": { "properties": { "target": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Target" }, "expression": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Expression" }, "expression_mathml": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Expression Mathml" } }, "title": "Initial", "type": "object" }, "Model": { "additionalProperties": true, "properties": { "header": { "$ref": "#/$defs/Header" }, "properties": { "anyOf": [ { "type": "object" }, { "type": "null" } ], "default": null, "title": "Properties" }, "model": { "$ref": "#/$defs/Model1" }, "semantics": { "anyOf": [ { "$ref": "#/$defs/Semantics" }, { "type": "null" } ], "default": null, "description": "Information specific to a given semantics (e.g., ODEs) associated with a model." }, "metadata": { "anyOf": [ { "type": "object" }, { "type": "null" } ], "default": null, "description": "(Optional) Information not useful for execution of the model, but that may be useful to some consumer in the future. E.g. creation timestamp or source paper's author.", "title": "Metadata" } }, "required": [ "header", "model" ], "title": "Model", "type": "object" }, "Model1": { "additionalProperties": false, "properties": { "states": { "$ref": "#/$defs/States" }, "transitions": { "$ref": "#/$defs/Transitions" } }, "required": [ "states", "transitions" ], "title": "Model1", "type": "object" }, "Observable": { "properties": { "id": { "title": "Id", "type": "string" }, "name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Name" }, "expression": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Expression" }, "expression_mathml": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Expression Mathml" } }, "required": [ "id" ], "title": "Observable", "type": "object" }, "OdeSemantics": { "properties": { "rates": { "anyOf": [ { "items": { "$ref": "#/$defs/Rate" }, "type": "array" }, { "type": "null" } ], "default": null, "title": "Rates" }, "initials": { "anyOf": [ { "items": { "$ref": "#/$defs/Initial" }, "type": "array" }, { "type": "null" } ], "default": null, "title": "Initials" }, "parameters": { "anyOf": [ { "items": { "$ref": "#/$defs/Parameter" }, "type": "array" }, { "type": "null" } ], "default": null, "title": "Parameters" }, "observables": { "anyOf": [ { "items": { "$ref": "#/$defs/Observable" }, "type": "array" }, { "type": "null" } ], "default": null, "title": "Observables" }, "time": { "anyOf": [ { "$ref": "#/$defs/Time" }, { "type": "null" } ], "default": null } }, "title": "OdeSemantics", "type": "object" }, "Parameter": { "properties": { "id": { "title": "Id", "type": "string" }, "name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Name" }, "description": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Description" }, "value": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "title": "Value" }, "grounding": { "anyOf": [ { "$ref": "#/$defs/Grounding" }, { "type": "null" } ], "default": null }, "distribution": { "anyOf": [ { "$ref": "#/$defs/Distribution" }, { "type": "null" } ], "default": null }, "units": { "anyOf": [ { "$ref": "#/$defs/Unit" }, { "type": "null" } ], "default": null } }, "required": [ "id" ], "title": "Parameter", "type": "object" }, "Properties": { "additionalProperties": true, "properties": { "name": { "title": "Name", "type": "string" }, "description": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Description" }, "grounding": { "anyOf": [ { "$ref": "#/$defs/Grounding" }, { "type": "null" } ], "default": null } }, "required": [ "name" ], "title": "Properties", "type": "object" }, "Rate": { "properties": { "target": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Target" }, "expression": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Expression" }, "expression_mathml": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Expression Mathml" } }, "title": "Rate", "type": "object" }, "Semantics": { "properties": { "ode": { "anyOf": [ { "$ref": "#/$defs/OdeSemantics" }, { "type": "null" } ], "default": null }, "typing": { "anyOf": [ { "$ref": "#/$defs/TypingSemantics" }, { "type": "null" } ], "default": null, "description": "(Optional) Information for aligning models for stratification" }, "span": { "anyOf": [ { "items": { "$ref": "#/$defs/TypingSemantics" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "(Optional) Legs of a span, each of which are a full ASKEM Petri Net", "title": "Span" } }, "title": "Semantics", "type": "object" }, "State": { "properties": { "id": { "title": "Id", "type": "string" }, "name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Name" }, "description": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Description" }, "grounding": { "anyOf": [ { "$ref": "#/$defs/Grounding" }, { "type": "null" } ], "default": null }, "units": { "anyOf": [ { "$ref": "#/$defs/Unit" }, { "type": "null" } ], "default": null } }, "required": [ "id" ], "title": "State", "type": "object" }, "States": { "items": { "$ref": "#/$defs/State" }, "title": "States", "type": "array" }, "Time": { "properties": { "id": { "title": "Id", "type": "string" }, "units": { "anyOf": [ { "$ref": "#/$defs/Unit" }, { "type": "null" } ], "default": null } }, "required": [ "id" ], "title": "Time", "type": "object" }, "Transition": { "properties": { "id": { "title": "Id", "type": "string" }, "input": { "items": { "type": "string" }, "title": "Input", "type": "array" }, "output": { "items": { "type": "string" }, "title": "Output", "type": "array" }, "grounding": { "anyOf": [ { "$ref": "#/$defs/Grounding" }, { "type": "null" } ], "default": null }, "properties": { "anyOf": [ { "$ref": "#/$defs/Properties" }, { "type": "null" } ], "default": null } }, "required": [ "id", "input", "output" ], "title": "Transition", "type": "object" }, "Transitions": { "items": { "$ref": "#/$defs/Transition" }, "title": "Transitions", "type": "array" }, "TypingSemantics": { "properties": { "system": { "$ref": "#/$defs/Model", "description": "A Petri net representing the 'type system' that is necessary to align states and transitions across different models during stratification." }, "map": { "description": "A map between the (state and transition) nodes of the model and the (state and transition) nodes of the type system", "items": { "items": { "type": "string" }, "type": "array" }, "title": "Map", "type": "array" } }, "required": [ "system", "map" ], "title": "TypingSemantics", "type": "object" }, "Unit": { "additionalProperties": true, "properties": { "expression": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Expression" }, "expression_mathml": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Expression Mathml" } }, "title": "Unit", "type": "object" } }, "required": [ "petrinet" ] }
- Config:
allow_inf_nan: bool = True
arbitrary_types_allowed: bool = True
- Fields:
- abstract(state_abstraction: Dict[str, str])¶
- default_encoder(config: FUNMANConfig, scenario: AnalysisScenario) Encoder¶
Return the default Encoder for the model
- Returns:
SMT encoder for model
- Return type:
- formulate_bounds()¶
- is_timed_observable(observation_id)¶
- model_post_init(context: Any, /) None¶
We need to both initialize private attributes and call the user-defined model_post_init method.
- observable_expression(observation_id)¶
- observables()¶
- stratified_parameter_id(parameter, index, strata)¶
- stratified_state_id(state_var, index, strata)¶
- stratified_trans_id(transition, index, strata)¶
- stratify(state_var: str, strata: List[str], strata_parameters: List[str] | None = None, strata_transitions=[], self_strata_transition=False)¶
Generate a new model that stratifies self. The ‘state_var’ will be replaced by one copy per entry in the ‘strata’ list. The ‘strata_parameters’, if specified, will be replaced by a fresh copy that corresponds to each element of the strata list in each transition involving the ‘state_var’. The ‘strata_transitions’ list includes all transitions involving ‘state_var’ to allow transitioning between the elements of ‘strata’, if possible (e.g., if ‘state_var’ is both and input and an output of the transition). The ‘self_strata_transition’ flag adds transitions between all pairs of entries in ‘strata’. When either ‘strata_transitions’ or ‘self_strata_transition’ are specified, the rates will incorporate a new parameter that defines the probability of transitioning between elements of the strata list. The transition probability parameters are assigned a value of 1/len(‘strata’), treating the transitions as a uniform probability distribution.
- Parameters:
self (PetrinetModel) – _description_
state_var (str) – _description_
strata (List[str]) – _description_
strata_parameters (Optional[List[str]], optional) – _description_, by default None
strata_transitions (list, optional) – _description_, by default []
self_strata_transition (bool, optional) – _description_, by default False
- Returns:
_description_
- Return type:
_type_
- stratify_transition(transition: Transition, state_var: str, strata: List[str], strata_parameters: List[str] | None = None, strata_transition=False)¶
- pydantic model funman.model.petrinet.PetrinetDynamics¶
Bases:
BaseModelShow JSON schema
{ "title": "PetrinetDynamics", "type": "object", "properties": { "json_graph": { "additionalProperties": { "items": { "additionalProperties": { "anyOf": [ { "additionalProperties": { "anyOf": [ { "type": "string" }, { "type": "boolean" }, { "type": "number" }, { "type": "null" } ] }, "type": "object" }, { "type": "integer" }, { "type": "string" }, { "type": "number" }, { "type": "null" } ] }, "type": "object" }, "type": "array" }, "title": "Json Graph", "type": "object" } }, "required": [ "json_graph" ] }
- field json_graph: Dict[str, List[Dict[str, Dict[str, str | bool | float | None] | int | str | float | None]]] [Required]¶
- pydantic model funman.model.petrinet.PetrinetModel¶
Bases:
AbstractPetriNetModelShow JSON schema
{ "title": "PetrinetModel", "type": "object", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" }, "petrinet": { "$ref": "#/$defs/PetrinetDynamics" } }, "$defs": { "PetrinetDynamics": { "properties": { "json_graph": { "additionalProperties": { "items": { "additionalProperties": { "anyOf": [ { "additionalProperties": { "anyOf": [ { "type": "string" }, { "type": "boolean" }, { "type": "number" }, { "type": "null" } ] }, "type": "object" }, { "type": "integer" }, { "type": "string" }, { "type": "number" }, { "type": "null" } ] }, "type": "object" }, "type": "array" }, "title": "Json Graph", "type": "object" } }, "required": [ "json_graph" ], "title": "PetrinetDynamics", "type": "object" } }, "required": [ "petrinet" ] }
- Config:
allow_inf_nan: bool = True
- Fields:
- field petrinet: PetrinetDynamics [Required]¶
- default_encoder(config: FUNMANConfig) Encoder¶
Return the default Encoder for the model
- Returns:
SMT encoder for model
- Return type:
- model_post_init(context: Any, /) None¶
We need to both initialize private attributes and call the user-defined model_post_init method.
funman.model.query module¶
This module defines all Query classes. Queries are combined with Model objects in Scenarios to determine whether the model satisfies the query.
- pydantic model funman.model.query.Query¶
Bases:
BaseModelAbstract base class for queries.
Show JSON schema
{ "title": "Query", "description": "Abstract base class for queries.", "type": "object", "properties": { "model": { "anyOf": [ { "$ref": "#/$defs/FunmanModel" }, { "type": "null" } ], "default": null } }, "$defs": { "FunmanModel": { "description": "The abstract base class for Models.", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" } }, "title": "FunmanModel", "type": "object" } } }
- field model: FunmanModel | None = None¶
- pydantic model funman.model.query.QueryAnd¶
Bases:
QueryConjunction of queries.
- Parameters:
queries (List[Query]) – queries to conjoin.
Show JSON schema
{ "title": "QueryAnd", "description": "Conjunction of queries.\n\nParameters\n----------\nqueries : List[Query]\n queries to conjoin.", "type": "object", "properties": { "model": { "anyOf": [ { "$ref": "#/$defs/FunmanModel" }, { "type": "null" } ], "default": null }, "queries": { "items": { "anyOf": [ { "$ref": "#/$defs/QueryLE" }, { "$ref": "#/$defs/QueryGE" }, { "$ref": "#/$defs/QueryEquals" }, { "$ref": "#/$defs/Query" } ] }, "title": "Queries", "type": "array" } }, "$defs": { "FunmanModel": { "description": "The abstract base class for Models.", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" } }, "title": "FunmanModel", "type": "object" }, "ModelSymbol": { "properties": { "name": { "title": "Name", "type": "string" }, "model": { "title": "Model", "type": "string" } }, "required": [ "name", "model" ], "title": "ModelSymbol", "type": "object" }, "Query": { "description": "Abstract base class for queries.", "properties": { "model": { "anyOf": [ { "$ref": "#/$defs/FunmanModel" }, { "type": "null" } ], "default": null } }, "title": "Query", "type": "object" }, "QueryEquals": { "description": "Class to represent a query of the form: var == value, where var is a variable, and value is a constant.\n\nParameters\n----------\nvariable : str\n model variable name\nvalue : float\n value\nat_end : bool, optional\n apply the constraint to the last timepoint of a scenario only, by default False", "properties": { "model": { "anyOf": [ { "$ref": "#/$defs/FunmanModel" }, { "type": "null" } ], "default": null }, "variable": { "anyOf": [ { "type": "string" }, { "$ref": "#/$defs/ModelSymbol" } ], "title": "Variable" }, "value": { "title": "Value", "type": "number" }, "at_end": { "default": false, "title": "At End", "type": "boolean" } }, "required": [ "variable", "value" ], "title": "QueryEquals", "type": "object" }, "QueryGE": { "description": "Class to represent a query of the form: var >= lb, where var is a variable, and lb is a constant lower bound.\n\nParameters\n----------\nvariable : str\n model variable name\nlb : float\n lower bound constant\nat_end : bool, optional\n apply the constraint to the last timepoint of a scenario only, by default False", "properties": { "model": { "anyOf": [ { "$ref": "#/$defs/FunmanModel" }, { "type": "null" } ], "default": null }, "variable": { "anyOf": [ { "type": "string" }, { "$ref": "#/$defs/ModelSymbol" } ], "title": "Variable" }, "lb": { "title": "Lb", "type": "number" }, "at_end": { "default": false, "title": "At End", "type": "boolean" } }, "required": [ "variable", "lb" ], "title": "QueryGE", "type": "object" }, "QueryLE": { "description": "Class to represent a query of the form: var <= ub, where var is a variable, and ub is a constant upper bound.\n\nParameters\n----------\nvariable : str\n model variable name\nub : float\n upper bound constant\nat_end : bool, optional\n apply the constraint to the last timepoint of a scenario only, by default False", "properties": { "model": { "anyOf": [ { "$ref": "#/$defs/FunmanModel" }, { "type": "null" } ], "default": null }, "variable": { "anyOf": [ { "type": "string" }, { "$ref": "#/$defs/ModelSymbol" } ], "title": "Variable" }, "ub": { "title": "Ub", "type": "number" }, "at_end": { "default": false, "title": "At End", "type": "boolean" } }, "required": [ "variable", "ub" ], "title": "QueryLE", "type": "object" } }, "required": [ "queries" ] }
- field queries: List[QueryLE | QueryGE | QueryEquals | Query] [Required]¶
- pydantic model funman.model.query.QueryEncoded¶
Bases:
QueryClass to contain a formula that is already encoded by a pysmt FNode.
Show JSON schema
{ "title": "QueryEncoded", "description": "Class to contain a formula that is already encoded by a pysmt FNode.", "type": "object", "properties": { "model": { "anyOf": [ { "$ref": "#/$defs/FunmanModel" }, { "type": "null" } ], "default": null } }, "$defs": { "FunmanModel": { "description": "The abstract base class for Models.", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" } }, "title": "FunmanModel", "type": "object" } } }
- Config:
arbitrary_types_allowed: bool = True
- Fields:
- model_post_init(context: Any, /) None¶
This function is meant to behave like a BaseModel method to initialise private attributes.
It takes context as an argument since that’s what pydantic-core passes when calling it.
- Parameters:
self – The BaseModel instance.
context – The context.
- pydantic model funman.model.query.QueryEquals¶
Bases:
QueryClass to represent a query of the form: var == value, where var is a variable, and value is a constant.
- Parameters:
variable (str) – model variable name
value (float) – value
at_end (bool, optional) – apply the constraint to the last timepoint of a scenario only, by default False
Show JSON schema
{ "title": "QueryEquals", "description": "Class to represent a query of the form: var == value, where var is a variable, and value is a constant.\n\nParameters\n----------\nvariable : str\n model variable name\nvalue : float\n value\nat_end : bool, optional\n apply the constraint to the last timepoint of a scenario only, by default False", "type": "object", "properties": { "model": { "anyOf": [ { "$ref": "#/$defs/FunmanModel" }, { "type": "null" } ], "default": null }, "variable": { "anyOf": [ { "type": "string" }, { "$ref": "#/$defs/ModelSymbol" } ], "title": "Variable" }, "value": { "title": "Value", "type": "number" }, "at_end": { "default": false, "title": "At End", "type": "boolean" } }, "$defs": { "FunmanModel": { "description": "The abstract base class for Models.", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" } }, "title": "FunmanModel", "type": "object" }, "ModelSymbol": { "properties": { "name": { "title": "Name", "type": "string" }, "model": { "title": "Model", "type": "string" } }, "required": [ "name", "model" ], "title": "ModelSymbol", "type": "object" } }, "required": [ "variable", "value" ] }
- field at_end: bool = False¶
- field value: float [Required]¶
- field variable: str | ModelSymbol [Required]¶
- pydantic model funman.model.query.QueryFunction¶
Bases:
QueryThis query uses a Python function passed to the constructor to evaluate a query on the results of a scenario.
Show JSON schema
{ "title": "QueryFunction", "description": "This query uses a Python function passed to the constructor to evaluate a query on the results of a scenario.", "type": "object", "properties": { "model": { "anyOf": [ { "$ref": "#/$defs/FunmanModel" }, { "type": "null" } ], "default": null }, "function": { "title": "Function", "type": "string" } }, "$defs": { "FunmanModel": { "description": "The abstract base class for Models.", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" } }, "title": "FunmanModel", "type": "object" } }, "required": [ "function" ] }
- Fields:
- field function: str [Required]¶
- pydantic model funman.model.query.QueryGE¶
Bases:
QueryClass to represent a query of the form: var >= lb, where var is a variable, and lb is a constant lower bound.
- Parameters:
variable (str) – model variable name
lb (float) – lower bound constant
at_end (bool, optional) – apply the constraint to the last timepoint of a scenario only, by default False
Show JSON schema
{ "title": "QueryGE", "description": "Class to represent a query of the form: var >= lb, where var is a variable, and lb is a constant lower bound.\n\nParameters\n----------\nvariable : str\n model variable name\nlb : float\n lower bound constant\nat_end : bool, optional\n apply the constraint to the last timepoint of a scenario only, by default False", "type": "object", "properties": { "model": { "anyOf": [ { "$ref": "#/$defs/FunmanModel" }, { "type": "null" } ], "default": null }, "variable": { "anyOf": [ { "type": "string" }, { "$ref": "#/$defs/ModelSymbol" } ], "title": "Variable" }, "lb": { "title": "Lb", "type": "number" }, "at_end": { "default": false, "title": "At End", "type": "boolean" } }, "$defs": { "FunmanModel": { "description": "The abstract base class for Models.", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" } }, "title": "FunmanModel", "type": "object" }, "ModelSymbol": { "properties": { "name": { "title": "Name", "type": "string" }, "model": { "title": "Model", "type": "string" } }, "required": [ "name", "model" ], "title": "ModelSymbol", "type": "object" } }, "required": [ "variable", "lb" ] }
- field at_end: bool = False¶
- field lb: float [Required]¶
- field variable: str | ModelSymbol [Required]¶
- pydantic model funman.model.query.QueryLE¶
Bases:
QueryClass to represent a query of the form: var <= ub, where var is a variable, and ub is a constant upper bound.
- Parameters:
variable (str) – model variable name
ub (float) – upper bound constant
at_end (bool, optional) – apply the constraint to the last timepoint of a scenario only, by default False
Show JSON schema
{ "title": "QueryLE", "description": "Class to represent a query of the form: var <= ub, where var is a variable, and ub is a constant upper bound.\n\nParameters\n----------\nvariable : str\n model variable name\nub : float\n upper bound constant\nat_end : bool, optional\n apply the constraint to the last timepoint of a scenario only, by default False", "type": "object", "properties": { "model": { "anyOf": [ { "$ref": "#/$defs/FunmanModel" }, { "type": "null" } ], "default": null }, "variable": { "anyOf": [ { "type": "string" }, { "$ref": "#/$defs/ModelSymbol" } ], "title": "Variable" }, "ub": { "title": "Ub", "type": "number" }, "at_end": { "default": false, "title": "At End", "type": "boolean" } }, "$defs": { "FunmanModel": { "description": "The abstract base class for Models.", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" } }, "title": "FunmanModel", "type": "object" }, "ModelSymbol": { "properties": { "name": { "title": "Name", "type": "string" }, "model": { "title": "Model", "type": "string" } }, "required": [ "name", "model" ], "title": "ModelSymbol", "type": "object" } }, "required": [ "variable", "ub" ] }
- field at_end: bool = False¶
- field ub: float [Required]¶
- field variable: str | ModelSymbol [Required]¶
- pydantic model funman.model.query.QueryTrue¶
Bases:
QueryQuery that represents logical true. I.e., this query does not place any additional constraints upon a model.
Show JSON schema
{ "title": "QueryTrue", "description": "Query that represents logical true. I.e., this query does not place any additional constraints upon a model.", "type": "object", "properties": { "model": { "anyOf": [ { "$ref": "#/$defs/FunmanModel" }, { "type": "null" } ], "default": null } }, "$defs": { "FunmanModel": { "description": "The abstract base class for Models.", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" } }, "title": "FunmanModel", "type": "object" } }, "additionalProperties": false }
- Config:
extra: str = forbid
- Fields:
- field model: FunmanModel | None = None¶
funman.model.regnet module¶
- pydantic model funman.model.regnet.AbstractRegnetModel¶
Bases:
FunmanModelShow JSON schema
{ "title": "AbstractRegnetModel", "type": "object", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" } } }
- Config:
allow_inf_nan: bool = True
- Fields:
- field init_values: Dict[str, float] = {}¶
- field name: str = 'model_a6f04917-34c0-45e0-a42c-128947736090'¶
- field parameter_bounds: Dict[str, List[float]] = {}¶
- default_encoder(config: FUNMANConfig, scenario: AnalysisScenario) Encoder¶
Return the default Encoder for the model
- Returns:
SMT encoder for model
- Return type:
- model_post_init(context: Any, /) None¶
We need to both initialize private attributes and call the user-defined model_post_init method.
- pydantic model funman.model.regnet.GeneratedRegnetModel¶
Bases:
AbstractRegnetModelShow JSON schema
{ "title": "GeneratedRegnetModel", "type": "object", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" }, "regnet": { "$ref": "#/$defs/Model" } }, "$defs": { "BaseProperties": { "properties": { "name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Name" }, "grounding": { "anyOf": [ { "$ref": "#/$defs/Grounding" }, { "type": "null" } ], "default": null }, "rate_constant": { "anyOf": [ { "$ref": "#/$defs/ParamOrNumber" }, { "type": "null" } ], "default": null } }, "title": "BaseProperties", "type": "object" }, "Distribution": { "properties": { "type": { "title": "Type", "type": "string" }, "parameters": { "title": "Parameters", "type": "object" } }, "required": [ "type", "parameters" ], "title": "Distribution", "type": "object" }, "Edge": { "properties": { "id": { "title": "Id", "type": "string" }, "sign": { "title": "Sign", "type": "boolean" }, "source": { "title": "Source", "type": "string" }, "target": { "title": "Target", "type": "string" }, "properties": { "anyOf": [ { "$ref": "#/$defs/BaseProperties" }, { "type": "null" } ], "default": null } }, "required": [ "id", "sign", "source", "target" ], "title": "Edge", "type": "object" }, "Grounding": { "additionalProperties": false, "properties": { "identifiers": { "anyOf": [ { "type": "object" }, { "type": "null" } ], "default": null, "title": "Identifiers" }, "modifiers": { "anyOf": [ { "type": "object" }, { "type": "null" } ], "default": null, "title": "Modifiers" } }, "title": "Grounding", "type": "object" }, "Header": { "properties": { "name": { "title": "Name", "type": "string" }, "schema": { "format": "uri", "minLength": 1, "title": "Schema", "type": "string" }, "schema_name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Schema Name" }, "description": { "title": "Description", "type": "string" }, "model_version": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Model Version" } }, "required": [ "name", "schema", "description" ], "title": "Header", "type": "object" }, "Model": { "properties": { "header": { "$ref": "#/$defs/Header" }, "properties": { "anyOf": [ { "type": "object" }, { "type": "null" } ], "default": null, "title": "Properties" }, "model": { "$ref": "#/$defs/Model1" }, "metadata": { "anyOf": [ { "type": "object" }, { "type": "null" } ], "default": null, "description": "(Optional) Information not useful for execution of the model, but that may be useful to some consumer in the future. E.g. creation timestamp or source paper's author.", "title": "Metadata" } }, "required": [ "header", "model" ], "title": "Model", "type": "object" }, "Model1": { "additionalProperties": false, "properties": { "vertices": { "items": { "$ref": "#/$defs/Vertice" }, "title": "Vertices", "type": "array" }, "edges": { "items": { "$ref": "#/$defs/Edge" }, "title": "Edges", "type": "array" }, "parameters": { "anyOf": [ { "items": { "$ref": "#/$defs/Parameter" }, "type": "array" }, { "type": "null" } ], "default": null, "title": "Parameters" } }, "required": [ "vertices", "edges" ], "title": "Model1", "type": "object" }, "ParamOrNumber": { "anyOf": [ { "type": "number" }, { "type": "string" } ], "title": "ParamOrNumber" }, "Parameter": { "properties": { "id": { "title": "Id", "type": "string" }, "description": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Description" }, "value": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "title": "Value" }, "grounding": { "anyOf": [ { "$ref": "#/$defs/Grounding" }, { "type": "null" } ], "default": null }, "distribution": { "anyOf": [ { "$ref": "#/$defs/Distribution" }, { "type": "null" } ], "default": null } }, "required": [ "id" ], "title": "Parameter", "type": "object" }, "Vertice": { "properties": { "name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Name" }, "grounding": { "anyOf": [ { "$ref": "#/$defs/Grounding" }, { "type": "null" } ], "default": null }, "rate_constant": { "anyOf": [ { "$ref": "#/$defs/ParamOrNumber" }, { "type": "null" } ], "default": null }, "id": { "title": "Id", "type": "string" }, "sign": { "title": "Sign", "type": "boolean" }, "initial": { "anyOf": [ { "$ref": "#/$defs/ParamOrNumber" }, { "type": "null" } ], "default": null } }, "required": [ "id", "sign" ], "title": "Vertice", "type": "object" } }, "required": [ "regnet" ] }
- Config:
allow_inf_nan: bool = True
- Fields:
- model_post_init(context: Any, /) None¶
We need to both initialize private attributes and call the user-defined model_post_init method.
- pydantic model funman.model.regnet.RegnetDynamics¶
Bases:
BaseModelShow JSON schema
{ "title": "RegnetDynamics", "type": "object", "properties": { "json_graph": { "additionalProperties": { "anyOf": [ { "type": "string" }, { "additionalProperties": { "items": { "type": "object" }, "type": "array" }, "type": "object" } ] }, "title": "Json Graph", "type": "object" } }, "required": [ "json_graph" ] }
- field json_graph: Dict[str, str | Dict[str, List[Dict[str, Any]]]] [Required]¶
- pydantic model funman.model.regnet.RegnetModel¶
Bases:
AbstractRegnetModelShow JSON schema
{ "title": "RegnetModel", "type": "object", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" }, "regnet": { "$ref": "#/$defs/RegnetDynamics" } }, "$defs": { "RegnetDynamics": { "properties": { "json_graph": { "additionalProperties": { "anyOf": [ { "type": "string" }, { "additionalProperties": { "items": { "type": "object" }, "type": "array" }, "type": "object" } ] }, "title": "Json Graph", "type": "object" } }, "required": [ "json_graph" ], "title": "RegnetDynamics", "type": "object" } }, "required": [ "regnet" ] }
- Config:
allow_inf_nan: bool = True
- Fields:
- field regnet: RegnetDynamics [Required]¶
- model_post_init(context: Any, /) None¶
We need to both initialize private attributes and call the user-defined model_post_init method.
- to_dot(values={})¶
Create a dot object for visualizing the graph.
- Returns:
The graph represented by self.
- Return type:
graphviz.Digraph
funman.model.simulator module¶
This module defines classes that wrap a simulator to function as a Model.
- pydantic model funman.model.simulator.SimulatorModel¶
Bases:
FunmanModelShow JSON schema
{ "title": "SimulatorModel", "type": "object", "properties": { "name": { "default": "model_a6f04917-34c0-45e0-a42c-128947736090", "title": "Name", "type": "string" }, "init_values": { "additionalProperties": { "type": "number" }, "default": {}, "title": "Init Values", "type": "object" }, "parameter_bounds": { "additionalProperties": { "items": { "type": "number" }, "type": "array" }, "default": {}, "title": "Parameter Bounds", "type": "object" }, "main_fn": { "default": "", "title": "Main Fn", "type": "string" } } }
- Config:
allow_inf_nan: bool = True
- Fields:
- field main_fn: str = ''¶
- default_encoder() Encoder¶
Simulators do not rely on encodings, so return a generic encoder.
- Returns:
_description_
- Return type:
- model_post_init(context: Any, /) None¶
We need to both initialize private attributes and call the user-defined model_post_init method.
Module contents¶
This module contains class definitions used to represent and interact with models in FUNMAN. The submodules include:
model: abstract classes for representing models
query: classes for representing model queries
bilayer: classes for bilayer models
gromet: classes for GroMet models
encoded: classes for models (hand) encoded directly as SMT formulas
simulator: classes to wrap simulators as models