:orphan:

.. The content of this file was generated
.. automatically by the popy.conf.fio.rstdoc_writer module
.. at 19 Mar 2026, 01:37:09


.. _comp_spec:



.. _comp-x-method-options-x-spec:

METHOD_OPTIONS
**************

Type: :term:`dict_record <dict_record>`

method options for comp_script

Example:-

.. code-block:: pyml

    METHOD_OPTIONS:
        py_module: comp
        rand_seed: 12345
        float_format: default


.. _comp-x-method-options-x-py-module-x-spec:

py_module
=========

Type: :term:`one_of(comp) <one_of>`

Python module required to process this script file

Example:-

.. code-block:: pyml

    py_module: comp


.. _comp-x-method-options-x-rand-seed-x-spec:

rand_seed
=========

Type: :term:`int <int>` / :term:`auto <auto>`

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

Example:-

.. code-block:: pyml

    rand_seed: 12345


.. _comp-x-method-options-x-float-format-x-spec:

float_format
============

Type: :term:`str <str>`

Format string for numerical output

Example:-

.. code-block:: pyml

    float_format: default


.. _comp-x-parallel-x-spec:

PARALLEL
********

Type: :term:`one_of_record <one_of_record>`

one of many possible servers

Example:-

.. code-block:: pyml

    PARALLEL:
        SINGLE: {progress_bar_length: 0}


.. _comp-x-parallel-x-single-x-spec:

SINGLE
======

Type: :term:`dict_record <dict_record>`

single process server spec.

Example:-

.. code-block:: pyml

    SINGLE:
        progress_bar_length: 0


.. _comp-x-parallel-x-single-x-progress-bar-length-x-spec:

progress_bar_length
-------------------

Type: :term:`int <int>`

Length of progress bar on screen (default=0, off)

Example:-

.. code-block:: pyml

    progress_bar_length: 0


.. _comp-x-parallel-x-mpi-workers-x-spec:

MPI_WORKERS
===========

Type: :term:`dict_record <dict_record>`

MPI local server spec.

Example:-

.. code-block:: pyml

    MPI_WORKERS:
        n_workers: auto
        cpu_load: 1.0
        progress_bar_length: 0


.. _comp-x-parallel-x-mpi-workers-x-n-workers-x-spec:

n_workers
---------

Type: :term:`int <int>` / :term:`auto <auto>`

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

Example:-

.. code-block:: pyml

    n_workers: auto


.. _comp-x-parallel-x-mpi-workers-x-cpu-load-x-spec:

cpu_load
--------

Type: :term:`float <float>`

Desired load on CPU as a decimal greater than 0.0 (0%) and less than or equal to 1.0 (100%)

Example:-

.. code-block:: pyml

    cpu_load: 1.0


.. _comp-x-parallel-x-mpi-workers-x-progress-bar-length-x-spec:

progress_bar_length
-------------------

Type: :term:`int <int>`

Length of progress bar on screen (default=0, off)

Example:-

.. code-block:: pyml

    progress_bar_length: 0


.. _comp-x-description-x-spec:

DESCRIPTION
***********

Type: :term:`dict_record <dict_record>`

Description fields for script.

Example:-

.. code-block:: pyml

    DESCRIPTION:
        name: my_pkpd_model
        title: My PKPD model
        author: My Name
        abstract: |
            Abstract describing the model
        keywords: ['pkpd']


.. _comp-x-description-x-name-x-spec:

name
====

Type: :term:`str <str>`

Unique name used to distinguish script

Example:-

.. code-block:: pyml

    name: my_pkpd_model


.. _comp-x-description-x-title-x-spec:

title
=====

Type: :term:`str <str>`

A longer text string that could serve as a title

Example:-

.. code-block:: pyml

    title: My PKPD model


.. _comp-x-description-x-author-x-spec:

author
======

Type: :term:`str <str>`

Author of the model

Example:-

.. code-block:: pyml

    author: My Name


.. _comp-x-description-x-abstract-x-spec:

abstract
========

Type: :term:`verbatim <verbatim>`

Abstract paragraph describing model

Example:-

.. code-block:: pyml

    abstract: |
        Abstract describing the model


.. _comp-x-description-x-keywords-x-spec:

keywords
========

Type: :term:`list <list>`

Keywords list used to categorise models.

Example:-

.. code-block:: pyml

    keywords: ['pkpd']


.. _comp-x-file-paths-x-spec:

FILE_PATHS
**********

Type: :term:`dict_record <dict_record>`

File paths for comp script

Example:-

.. code-block:: pyml

    FILE_PATHS:
        output_folder: auto
        temp_folder: auto
        log_folder: auto
        output_file_ext: ['svg']
        delete_old_files_flag: False
        gen_script_path: my_pkpd_model_gen.pyml
        gen_output_folder: my_pkpd_model_gen.pyml_output
        fit_script_path: my_pkpd_model_fit.pyml
        fit_output_folder: my_pkpd_model_fit.pyml_output
        solutions:
            fit_obs: input_observations_soln.pyml
            gen_pred: my_pkpd_model_gen.pyml_output/generated_data/solution.pyml
            gen_sim_pred: my_pkpd_model_gen.pyml_output/my_pkpd_model_sim.pyml_output/gen_pred/solution.pyml
            final_fit_ipred: my_pkpd_model_fit.pyml_output/solN/solution.pyml
            final_fit_sim_ipred: my_pkpd_model_fit.pyml_output/my_pkpd_model_sim.pyml_output/final_fit_ipred/solution.pyml


.. _comp-x-file-paths-x-output-folder-x-spec:

output_folder
=============

Type: :term:`output_folder <output_folder>` / :term:`auto <auto>`

Output folder - results of computation stored here

Example:-

.. code-block:: pyml

    output_folder: auto


.. _comp-x-file-paths-x-temp-folder-x-spec:

temp_folder
===========

Type: :term:`output_folder <output_folder>` / :term:`auto <auto>`

Temp folder - temporary files stored here

Example:-

.. code-block:: pyml

    temp_folder: auto


.. _comp-x-file-paths-x-log-folder-x-spec:

log_folder
==========

Type: :term:`output_folder <output_folder>` / :term:`auto <auto>`

Log folder - log files stored here

Example:-

.. code-block:: pyml

    log_folder: auto


.. _comp-x-file-paths-x-output-file-ext-x-spec:

output_file_ext
===============

Type: :term:`list_of(pdf,png,svg) <list_of>`

Output file extension - determines graphical output file format.

Example:-

.. code-block:: pyml

    output_file_ext: ['svg']


.. _comp-x-file-paths-x-delete-old-files-flag-x-spec:

delete_old_files_flag
=====================

Type: :term:`bool <bool>`

Option to delete any existing files before running.

Example:-

.. code-block:: pyml

    delete_old_files_flag: False


.. _comp-x-file-paths-x-gen-script-path-x-spec:

gen_script_path
===============

Type: :term:`input_file <input_file>` / :term:`auto <auto>`

Path to gen_script.

Example:-

.. code-block:: pyml

    gen_script_path: my_pkpd_model_gen.pyml


.. _comp-x-file-paths-x-gen-output-folder-x-spec:

gen_output_folder
=================

Type: :term:`output_folder <output_folder>` / :term:`auto <auto>`

Gen script output folder.

Example:-

.. code-block:: pyml

    gen_output_folder: my_pkpd_model_gen.pyml_output


.. _comp-x-file-paths-x-fit-script-path-x-spec:

fit_script_path
===============

Type: :term:`input_file <input_file>` / :term:`auto <auto>`

Path to fit_script.

Example:-

.. code-block:: pyml

    fit_script_path: my_pkpd_model_fit.pyml


.. _comp-x-file-paths-x-fit-output-folder-x-spec:

fit_output_folder
=================

Type: :term:`output_folder <output_folder>` / :term:`auto <auto>`

Fit script output folder.

Example:-

.. code-block:: pyml

    fit_output_folder: my_pkpd_model_fit.pyml_output


.. _comp-x-file-paths-x-solutions-x-spec:

solutions
=========

Type: :term:`dict <dict>`

Solutions to compare

Example:-

.. code-block:: pyml

    solutions:
        fit_obs: input_observations_soln.pyml
        gen_pred: my_pkpd_model_gen.pyml_output/generated_data/solution.pyml
        gen_sim_pred: my_pkpd_model_gen.pyml_output/my_pkpd_model_sim.pyml_output/gen_pred/solution.pyml
        final_fit_ipred: my_pkpd_model_fit.pyml_output/solN/solution.pyml
        final_fit_sim_ipred: my_pkpd_model_fit.pyml_output/my_pkpd_model_sim.pyml_output/final_fit_ipred/solution.pyml


.. _comp-x-comp-options-x-spec:

COMP_OPTIONS
************

Type: :term:`dict_record <dict_record>`

Options for comp script

Example:-

.. code-block:: pyml

    COMP_OPTIONS:
        compute_gen_objective_value: True
        compute_fit_objective_value: True


.. _comp-x-comp-options-x-compute-gen-objective-value-x-spec:

compute_gen_objective_value
===========================

Type: :term:`bool <bool>`

Compute objective value of generated data given generated parameters.

Example:-

.. code-block:: pyml

    compute_gen_objective_value: True


.. _comp-x-comp-options-x-compute-fit-objective-value-x-spec:

compute_fit_objective_value
===========================

Type: :term:`bool <bool>`

Compute objective value of generated data using fitted parameters.

Example:-

.. code-block:: pyml

    compute_fit_objective_value: True


.. _comp-x-output-scripts-x-spec:

OUTPUT_SCRIPTS
**************

Type: :term:`dict_record <dict_record>`

scripts to output for further processing

Example:-

.. code-block:: pyml

    OUTPUT_SCRIPTS:
        GRPH: {output_mode: none, grph_list: ['OBS_vs_TIME']}


.. _comp-x-output-scripts-x-grph-x-spec:

GRPH
====

Type: :term:`dict_record <dict_record>`

options to pass to grph script.

Example:-

.. code-block:: pyml

    GRPH:
        output_mode: none
        grph_list: ['OBS_vs_TIME']


.. _comp-x-output-scripts-x-grph-x-output-mode-x-spec:

output_mode
-----------

Type: :term:`one_of(none,create,run) <one_of>`

Output options.

Example:-

.. code-block:: pyml

    output_mode: none


.. _comp-x-output-scripts-x-grph-x-grph-list-x-spec:

grph_list
---------

Type: :term:`list(str) <list>`

Graph types to plt

Example:-

.. code-block:: pyml

    grph_list: ['OBS_vs_TIME']



