:orphan:

.. The content of this file was generated
.. automatically by the popy.conf.fio.rstdoc_writer module


.. _comp_spec:



.. _comp-method_options_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-method_options-py_module_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-method_options-rand_seed_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-method_options-float_format_spec:

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

Type: :term:`str <str>`

Format string for numerical output

Example:-

.. code-block:: pyml

    float_format: default


.. _comp-parallel_spec:

PARALLEL
********

Type: :term:`one_of_record <one_of_record>`

one of many possible servers

Example:-

.. code-block:: pyml

    PARALLEL:
        SINGLE: {}


.. _comp-parallel-single_spec:

SINGLE
======

Type: :term:`dict_record <dict_record>`

single process server spec.

Example:-

.. code-block:: pyml

    SINGLE: {}


.. _comp-parallel-mpi_workers_spec:

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

Type: :term:`dict_record <dict_record>`

MPI local server spec.

Example:-

.. code-block:: pyml

    MPI_WORKERS:
        n_workers: auto


.. _comp-parallel-mpi_workers-n_workers_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-description_spec:

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

Type: :term:`dict_record <dict_record>`

Description fields for script.

Example:-

.. code-block:: pyml

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


.. _comp-description-name_spec:

name
====

Type: :term:`str <str>`

Unique name used to distinguish script

Example:-

.. code-block:: pyml

    name: example


.. _comp-description-title_spec:

title
=====

Type: :term:`str <str>`

A longer text string that could serve as a title

Example:-

.. code-block:: pyml

    title: A PKPD model


.. _comp-description-author_spec:

author
======

Type: :term:`str <str>`

Author of the model

Example:-

.. code-block:: pyml

    author: A.N. Other


.. _comp-description-abstract_spec:

abstract
========

Type: :term:`verbatim <verbatim>`

Abstract paragraph describing model

Example:-

.. code-block:: pyml

    abstract: |


.. _comp-description-keywords_spec:

keywords
========

Type: :term:`list <list>`

Keywords list used to categorise models.

Example:-

.. code-block:: pyml

    keywords: []


.. _comp-file_paths_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: auto
        gen_output_folder: auto
        fit_script_path: auto
        fit_output_folder: auto


.. _comp-file_paths-output_folder_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-file_paths-temp_folder_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-file_paths-log_folder_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-file_paths-output_file_ext_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-file_paths-delete_old_files_flag_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-file_paths-gen_script_path_spec:

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

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

Path to gen_script.

Example:-

.. code-block:: pyml

    gen_script_path: auto


.. _comp-file_paths-gen_output_folder_spec:

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

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

Gen script output folder.

Example:-

.. code-block:: pyml

    gen_output_folder: auto


.. _comp-file_paths-fit_script_path_spec:

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

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

Path to fit_script.

Example:-

.. code-block:: pyml

    fit_script_path: auto


.. _comp-file_paths-fit_output_folder_spec:

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

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

Fit script output folder.

Example:-

.. code-block:: pyml

    fit_output_folder: auto


.. _comp-comp_options_spec:

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

Type: :term:`dict_record <dict_record>`

Options for comp script

Example:-

.. code-block:: pyml

    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


.. _comp-comp_options-create_gen_vs_fit_raw_graph_spec:

create_gen_vs_fit_raw_graph
===========================

Type: :term:`bool <bool>`

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

Example:-

.. code-block:: pyml

    create_gen_vs_fit_raw_graph: True


.. _comp-comp_options-create_gen_vs_fit_dense_graph_spec:

create_gen_vs_fit_dense_graph
=============================

Type: :term:`bool <bool>`

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

Example:-

.. code-block:: pyml

    create_gen_vs_fit_dense_graph: True


.. _comp-comp_options-compute_gen_objective_value_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-comp_options-compute_fit_objective_value_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-comp_options-share_axes_spec:

share_axes
==========

Type: :term:`bool <bool>`

Option to share axes between individuals when plotting
graphical data

Example:-

.. code-block:: pyml

    share_axes: False


.. _comp-comp_options-y_scale_spec:

y_scale
=======

Type: :term:`one_of(linear,log) <one_of>`

y axis scale - can be either 'linear' or 'log'.

Example:-

.. code-block:: pyml

    y_scale: linear



