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Project configuration

The inputs.toml file is used to configure the inputs for the project. It is located in the inputs directory within the project data directory.

TOML-defined structure

Each section of the inputs.toml file defines one of the input "locations" in the project. An example of the structure is as follows:

[config]
required = true
varied = true
basename = "PhysiCell_settings.xml"

Upon initialization of the model manager, i.e., calling initializeModelManager(), the inputs.toml file is parsed and each entry (config is shown above) has four features stored:

  • required: A boolean indicating if the location is required for the model to run.
  • basename: The base name of the file to be used for the location.
  • varied: A boolean indicating if the location can vary between different model runs.
  • path_from_inputs: The path to the location relative to the inputs directory.

required

This field is necessary and must either be true or false. If true, an InputsFolder object cannot be created without this location.

basename

This field enforces the name of the file to be used for the location. A vector can be supplied of names in the order to look for the files in cases when multiple files are acceptable. This field is necessary if varied is true, but can be omitted if varied is false.

varied

This field is necessary and must either be true, false, or a vector of Booleans matching the length of the basename vector. If true, the location can be varied and the necessary databases and folders are created to support this.

path_from_inputs

This optional field sets the path to the location relative to the inputs directory. If not provided, the path is assumed to be inputs/<dict_name>s. For example, the config section above would be located at inputs/configs (note the pluralization of the section name). To provide this path, use a vector of strings, e.g., ["ics", "cells"] to define the path to the [ic_cell] location as inputs/ics/cells.