phylojunction.interface.cmdbox package

Submodules

phylojunction.interface.cmdbox.cmd_parse module

phylojunction.interface.cmdbox.cmd_parse.cmdline2dag(dag_obj: DirectedAcyclicGraph, cmd_line: str) → str

Update PGM object with user-entered .pj command.

Parameters:

  • dag_obj (DirectedAcyclicGraph) – DAG object that will hold all stochastic nodes (random variables) created by user via commands.

  • cmd_line (str) – Command line string provided by user through static script or via GUI.

Returns:

Command string if there was nothing wrong with it.

Return type:

(str)

phylojunction.interface.cmdbox.cmd_parse.parse_deterministic_function_assignment(dag_obj: DirectedAcyclicGraph, det_nd_name: str, det_node_fn_spec: str, cmd_line: str) → None

Create DeterministicNodeDAG instance from command string with ‘:=’ operator, then add it to ProbabilisticGraphiclModel instance. This node is not sampled (not a random variable) and is deterministically initialized via a deterministic function call.

Parameters:

  • dag_obj (DirectedAcyclicGraph) – DAG object that will hold all nodes created by user via commands.

  • det_nd_name (str) – Name of deterministic node being created

  • det_node_fn_spec (str) – Specification string for deterministic function that will specify the deterministic node (whatever is right of ‘:=’ operator in PJ command).

  • cmd_line (str) – Command line string provided by user through static script or via GUI.

phylojunction.interface.cmdbox.cmd_parse.parse_samp_dn_assignment(dag_obj: DirectedAcyclicGraph, stoch_node_name: str, stoch_node_dn_spec: str, cmd_line: str) → None

Create and add stochastic node to graphical model.

Called when ‘~’ operator is used. This node will be sampled from distribution and is a random variable.

Parameters:

  • dag_obj (DirectedAcyclicGraph) – Object that will hold all nodes created by user via commands.

  • stoch_node_name (str) – Name of stochastic node being created

  • stoch_node_dn_spec (str) – Specification string for distribution from which stochastic node will be sampled (whatever is right of ‘~’ operator in PJ command)

  • cmd_line (str) – Command line string provided by user through static script or via GUI

phylojunction.interface.cmdbox.cmd_parse.parse_variable_assignment(dag_obj: DirectedAcyclicGraph, stoch_node_name: str, stoch_node_spec: str, cmd_line: str) → None

Create and add constant node to DAG.

Called when ‘<-’ operator is used. This node will not be sampled and is in practice a constant node.

Parameters:

  • dag_obj (DirectedAcyclicGraph) – Object that will hold all nodes created by user via commands.

  • stoch_node_name (str) – Name of stochastic node being created.

  • stoch_node_spec (str) – Stochastic node specification string (whatever is right of ‘<-’ operator in PJ command).

  • cmd_line (str) – Command line string provided by user through static script or via GUI.

phylojunction.interface.cmdbox.cmd_parse.script2dag(script_file_path_or_model_spec: str, in_pj_file: bool = True, random_seed: int | None = None) → DirectedAcyclicGraph

Go through .pj lines and populate and return DAG.

Parameters:

  • script_file_path_or_model_spec (str) – Path to script .pj file or full string specifying model directly.

  • random_seed (int) – Random seed (integer) for simulation. Defaults to None.

Returns:

DAG object (model) built from .pj

script commands.

Return type:

(DirectedAcyclicGraph)

phylojunction.interface.cmdbox.cmd_parse_utils module

phylojunction.interface.cmdbox.cmd_parse_utils.parse_spec(dag_obj: DirectedAcyclicGraph, fn_spec_str: str, cmd_line: str) → Tuple[Dict[str, List[NodeDAG | str]], List[NodeDAG]]
phylojunction.interface.cmdbox.cmd_parse_utils.parse_val_vector(vec_str: str) → List[str]

Parse string specifying vector when a variable is assigned

Parameters:

vec_str (str) – A string specifying a vector, e.g., “[1, 2, 3]”

Raises:

ec.ScriptSyntaxError – If there are more than two squared brackets, this is thrown

Returns:

Vector of strings, each being one of the values inside

the vector being specified by ‘vec_str’.

Return type:

(str)

phylojunction.interface.cmdbox.cmd_parse_utils.tokenize_fn_spec(fn_spec_str: str, cmd_line: str) → Dict[str, str]

Tokenize string containing function specification into dictionary

Parameters:

fn_spec (str) – String containing the specification of function (i.e., what appears between ‘(’ and ‘)’.

Returns:

Dictionary containing function parameter strings as

keys, argument strings as values (e.g., {“mean”: “0.0”}).

Return type:

(dict)

phylojunction.interface.cmdbox.cmd_parse_utils.val_or_obj(dag_obj: DirectedAcyclicGraph, val: List[str]) → List[NodeDAG | str]

Return list of strings with values or node names.

Checks if provided values are directly accessible as values (e.g., 1.0, “a_string_in_quotes”)) or if they are names of nodes potentially in the graphical model. If the latter, check if they are indeed nodes in the graphical model, and if so, append to return

Parameters:

  • dag_obj (DirectedAcyclicGraph) – DAG object being interrogated.

  • val (str) – List of strings, one for each argument coming from a parsed command.

Raises:

ec.InexistentVariableError – _description_

Returns:

List of strings (representing values or quoted-enclosed

strings) and/or stochastic node objects.

Return type:

(str)

Module contents