# METHOD_OPTIONS

Type: dict_record

method options for comp_script

Example:-

    METHOD_OPTIONS:
        py_module: comp
        rand_seed: 12345
        float_format: default

## py_module

Type: one_of(comp)

Python module required to process this script file

Example:-

    py_module: comp

## rand_seed

Type: int / auto

Option to set seed to make run result reproducible -e.g. when debugging.

Example:-

    rand_seed: 12345

## float_format

Type: str

Format string for numerical output

Example:-

    float_format: default

# PARALLEL

Type: one_of_record

one of many possible servers

Example:-

    PARALLEL:
        SINGLE: {}

## SINGLE

Type: dict_record

single process server spec.

Example:-

    SINGLE: {}

## MPI_WORKERS

Type: dict_record

MPI local server spec.

Example:-

    MPI_WORKERS:
        n_workers: auto

### n_workers

Type: int / auto

Number of workers to use on this machine, defaults to number of processors, but could be more or fewer.

Example:-

    n_workers: auto

# DESCRIPTION

Type: dict_record

Description fields for script.

Example:-

    DESCRIPTION:
        name: example
        title: A PKPD model
        author: A.N. Other
        abstract: |
        keywords: []

## name

Type: str

Unique name used to distinguish script

Example:-

    name: example

## title

Type: str

A longer text string that could serve as a title

Example:-

    title: A PKPD model

## author

Type: str

Author of the model

Example:-

    author: A.N. Other

## abstract

Type: verbatim

Abstract paragraph describing model

Example:-

    abstract: |

## keywords

Type: list

Keywords list used to categorise models.

Example:-

    keywords: []

# FILE_PATHS

Type: dict_record

File paths for comp script

Example:-

    FILE_PATHS:
        output_folder: auto
        temp_folder: auto
        log_folder: auto
        output_file_ext: ['svg']
        delete_old_files_flag: False
        gen_script_path: auto
        gen_output_folder: auto
        fit_script_path: auto
        fit_output_folder: auto

## output_folder

Type: output_folder / auto

Output folder - results of computation stored here

Example:-

    output_folder: auto

## temp_folder

Type: output_folder / auto

Temp folder - temporary files stored here

Example:-

    temp_folder: auto

## log_folder

Type: output_folder / auto

Log folder - log files stored here

Example:-

    log_folder: auto

## output_file_ext

Type: list_of(pdf,png,svg)

Output file extension - determines graphical output file format.

Example:-

    output_file_ext: ['svg']

## delete_old_files_flag

Type: bool

Option to delete any existing files before running.

Example:-

    delete_old_files_flag: False

## gen_script_path

Type: input_file / auto

Path to gen_script.

Example:-

    gen_script_path: auto

## gen_output_folder

Type: output_folder / auto

Gen script output folder.

Example:-

    gen_output_folder: auto

## fit_script_path

Type: input_file / auto

Path to fit_script.

Example:-

    fit_script_path: auto

## fit_output_folder

Type: output_folder / auto

Fit script output folder.

Example:-

    fit_output_folder: auto

# COMP_OPTIONS

Type: dict_record

Options for comp script

Example:-

    COMP_OPTIONS:
        create_gen_vs_fit_raw_graph: True
        create_gen_vs_fit_dense_graph: True
        compute_gen_objective_value: True
        compute_fit_objective_value: True
        share_axes: False
        y_scale: linear

## create_gen_vs_fit_raw_graph

Type: bool

Create raw graph to compare final fit result vs gen data.

Example:-

    create_gen_vs_fit_raw_graph: True

## create_gen_vs_fit_dense_graph

Type: bool

Create dense graph to compare final fit result vs gen data.

Example:-

    create_gen_vs_fit_dense_graph: True

## compute_gen_objective_value

Type: bool

Compute objective value of generated data given generated parameters.

Example:-

    compute_gen_objective_value: True

## compute_fit_objective_value

Type: bool

Compute objective value of generated data using fitted parameters.

Example:-

    compute_fit_objective_value: True

## share_axes

Type: bool

Option to share axes between individuals when plotting graphical data

Example:-

    share_axes: False

## y_scale

Type: one_of(linear,log)

y axis scale - can be either ‘linear’ or ‘log’.

Example:-

    y_scale: linear