pyRBM.Core package

Submodules

pyRBM.Core.Cache module

class ModelPaths(matched_rules_filename: str | None = None, compartments_filename: str | None = None, model_folder_path_to: str | None = None, model_name: str | None = '', classes_filename: str | None = None, metarules_filename: str | None = None)

Bases: object

Provides paths for created and loaded model files.

All paths follow the format (model_folder_path_to)(model_name)(filename).

Filenames should NOT include the file ending.

A new ModelPaths object should overwrite the old object when a new model is saved/loaded.

compartment_path

the path to the compartments .json file saved or loaded or created at this object’s creation, if it was saved/loaded, otherwise None.

Type:

str|None

classes_path

the path to the classes .json file saved or loaded or created at this object’s creation, if it was saved/loaded, otherwise None.

Type:

str|None

matched_rules_path

the path to the matched_rules .json file saved or loaded or created at this object’s creation, if it was saved/loaded, otherwise None.

Type:

str|None

metarule_path

the path to the metarule .json file saved or loaded at this object’s creation, if it was saved/loaded, otherwise None.

Type:

str|None

save_model_folder

the model folder that the

Type:

str|None

property classes_path: str | None

The path to the classes .json file saved or loaded or created at this object’s creation, if it was saved/loaded, otherwise None

property compartments_path: str | None

The path to the compartments .json file saved or loaded or created at this object’s creation, if it was saved/loaded, otherwise None.

property matched_rules_path: str | None

The path to the matched_rules .json file saved or loaded or created at this object’s creation, if it was saved/loaded, otherwise None.

property metarules_path: str | None

The path to the metarule .json file saved or loaded at this object’s creation, if it was saved/loaded, otherwise None.

loadClasses(model_prefix: str = 'model_', classes_filename: str | None = None, classes_dict: dict | None = None) → tuple[dict, dict]

Loads classes from either a model class json file (see ModelCreation for details) or from a pyRBM.Build.Classes dictionary, and returns pyRBM.Simulation’s requirements of a class_dict (a dict of all non-model classes) and a built_in_class_dict (a dict of all model classes).

Requires either classes_filename or classes_dict to be passed as an argument.

If both arguments are provided, the function will load from the json at the classes_filename path.

Parameters:

  • model_prefix (str, optional) – the prefix used to denote a model class in the model

  • classes_filename (str) – ts

  • classes_dict (dict) – a

Returns:

class_dict dict: built_in_class_dict

Return type:

dict

loadCompartments(compartments_filename: str | None = None, build_compartments_dict: dict[str, dict[str, Any]] | None = None) → list[pyRBM.Simulation.Compartment.Compartment]

Loads compartments from either a model compartment json file (see ModelCreation for details) or from a pyRBM.Build.Compartments dictionary.

Requires either compartments_filename or build_compartments_dict to be passed as an argument.

If both arguments are provided, the function will load from the json at the compartments_filename path.

Parameters:

  • compartments_filename (str, optional) – the string of the file compartment containing the compartment definitions.

  • build_compartments_dict (dict, optional) – a dictionary of pyRBM.Build.Compartments (e.g. from calling Compartments.returnCompartmentsDict())

Returns:

pyRBM.Simulation compatible Compartments for each compartment in either compartment_file or build_compartments_dict.

Return type:

list

loadMatchedRules(compartments, num_builtin_classes: int, random_state, matched_rules_filename: str | None = None, matched_rule_dict: dict | None = None) → tuple[list[pyRBM.Simulation.Rule.Rule], list[list[int]]]

Loads all rules from a model matched rules json (see ModelCreation for details).

Parameters:

  • () (compartments) –

  • num_builtin_classes –

  • matched_rules_filename – the string of the file compartment containing the rule definitions.

  • matched_rule_dict –

Returns: [a list of rules remapped to all possible compartment sets,

a 2d list of lists of satisfying indices for the corresponding rule]

processFilenameOrDict(filename: str | None, provided_dict: dict[str, Any] | None) → dict[str, Any] | None
readDictFromJSON(filename: str) → dict

Read a JSON file found at the filename path and return the dictionary representation of it. :param filename: the string representation of the path to the json file to be loaded (excluding the .json file ending). :type filename: str

Returns:

dictionary representation of the JSON file found at the path, filename.

Return type:

dict

writeDictToJSON(dict_to_write: dict, filename: str, dict_name: str = '') → None

Writes dict_to_write to a json file at the filename path. Orders the json keys alphabetically and uses utf-8 encoding.

Creates all folders and then the file if they don’t already exist.

Parameters:

  • dict_to_write (dict) – a dictionary to be written to a .json file.

  • filename (str) – the string representation of the path and filename of the json file that is being written to (excluding the .json file ending).

  • dict_name (str, optional) – a string to include to provide user friendly output as to which file is being written.

pyRBM.Core.Interfaces module

class ICompartment(name: str, comp_type: str, compartment_constants: Iterable[str] | None, comp_prefix: str = 'comp_')

Bases: object

checkConditionDict(inital_conditions_dict: dict[str, Any]) → None
setConstants(constants_dict: dict[str, Any]) → None
setInitialConditions(inital_conditions_dict: dict[str, Any]) → None

pyRBM.Core.Model module

pyRBM.Core.Plotting module

class FrequencyBarChart(fig, plot, title: str, x_label_str: str, solver_data, x_labels: list, data_key: str, rerender_all: bool = True)

Bases: object

animate(i)
class SolverDataPlotting(model)

Bases: object

pyRBM.Core.StringUtilities module

parseVarName(class_name: str)
replaceVarName(propensity_str, var_name, replacement, ignore_underscore=True)

Module contents