===================
Configuration Guide
===================

.. currentmodule:: spk2py.autosort.spk_config

Overview
--------

This class manages configurations for the AutoSort pipeline. It reads from an INI-style configuration file and provides methods to access configurations for various sections.

.. moduleauthor:: Flynn O'Connell


Initialize a new ``SpkConfig`` object by specifying the ``cfg_path`` parameter. If no path is provided, it defaults to a predefined location.

Attributes
----------

- ``cfg_path``: Path to the configuration file, either provided by the user or a default path.
- ``config``: A ``ConfigParser`` object containing the loaded configurations.
- ``params``: A dictionary containing all the configuration parameters.

Methods
-------

get_section(section: str)
    Returns a dictionary containing key-value pairs for the given section.

set(section: str, key: str, value: Any)
    Sets a value for a configuration parameter within a specified section.

get_all()
    Returns a dictionary containing all key-value pairs from all sections.

Property Methods
----------------

run
    Returns a dictionary containing key-value pairs for the 'run' section.

path
    Returns a dictionary containing key-value pairs for the 'path' section.

cluster
    Returns a dictionary containing key-value pairs for the 'cluster' section.

breach
    Returns a dictionary containing key-value pairs for the 'breach' section.

filter
    Returns a dictionary containing key-value pairs for the 'filter' section.

spike
    Returns a dictionary containing key-value pairs for the 'spike' section.

detection
    Returns a dictionary containing key-value pairs for the 'detection' section.

pca
    Returns a dictionary containing key-value pairs for the 'pca' section.

postprocess
    Returns a dictionary containing key-value pairs for the 'postprocess' section.

INI Configuration File
----------------------

This file is the easiest entrypoint to change parameters. You can specify where this file
is created with the ``cfg_path`` attribute.

- ``run``: Contains runtime settings like ``resort-limit``, ``cores-used``.
- ``path``: Contains path settings like directories for ``run``, ``results``.
- ``cluster``: Contains clustering parameters like ``max-clusters``, ``max-iterations``.
- ``breach``: Contains breach analysis parameters like ``disconnect-voltage``, ``max-breach-rate``.
- ``filter``: Contains filter parameters like ``low-cutoff``, ``high-cutoff``.
- ``spike``: Contains spike-extraction settings like ``pre-time``, ``post-time``.

Note: All values are stored as strings due to the nature of INI files. It's up to the user to convert these to appropriate types.

Example
-------

.. code-block:: python

    cfg = SpkConfig()
    run = cfg.run
    print(type(run), run)

    cfg.set('run', 'resort-limit', 5)
    print(cfg.run['resort-limit'])

See Also
--------

- `configparser from python std library <https://docs.python.org/3/library/configparser.html>`_