.. include:: apyt.rst


User Guide
==========

.. toctree::
   :maxdepth: 1
   :caption: User Guide
   :hidden:

   installation
   apyt_cli
   example


Installation
------------

Follow the :doc:`installation instructions<installation>` to set up the APyT
package on your system and ensure all required dependencies are installed.


Command line interface
----------------------

The recommended way to interact with the APyT package is through the provided
:doc:`command line scripts<apyt_cli>`. Each script is documented in detail,
including available options, expected input/output formats, and usage examples.


Example usage
-------------

The APyT package includes a small exemplary measurement file to allow users to
explore its functionality without requiring their own raw data. This makes it
easy to test the workflow, try out the command line scripts, and familiarize
yourself with the graphical interfaces.

For step-by-step instructions on using the example measurement, see the
:doc:`example usage instructions<example>`.


Developer Guide
===============

.. toctree::
   :maxdepth: 1
   :caption: API Documentation
   :hidden:

   The APyT analysis subpackage (apyt.analysis)<apyt.analysis>
   The APyT GUI subpackage (apyt.gui)<apyt.gui>
   The APyT file input/output subpackage (apyt.io)<apyt.io>
   The APyT reconstruction subpackage (apyt.reconstruction)<apyt.reconstruction>
   The APyT mass spectrum subpackage (apyt.spectrum)<apyt.spectrum>

While the :doc:`command line interface<apyt_cli>` provides convenient,
ready-to-use scripts for exploring the capabilities of the APyT package, its
modular design allows developers to integrate individual subpackages and modules
into custom workflows. Each subpackage is fully documented, enabling
programmatic access to core functionality such as file I/O, mass spectrum
processing, reconstruction algorithms, and data analysis.

The following list provides an overview of the main APyT subpackages:

- :doc:`The APyT analysis subpackage (apyt.analysis)<apyt.analysis>`
- :doc:`The APyT GUI subpackage (apyt.gui)<apyt.gui>`
- :doc:`The APyT file input/output subpackage (apyt.io)<apyt.io>`
- :doc:`The APyT reconstruction subpackage (apyt.reconstruction)
  <apyt.reconstruction>`
- :doc:`The APyT mass spectrum subpackage (apyt.spectrum)<apyt.spectrum>`


.. toctree::
   :maxdepth: 1
   :caption: About this Project
   :hidden:

   comparison
   release
   source


Indices and Tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`


.. sectionauthor:: Sebastian M. Eich <Sebastian.Eich@imw.uni-stuttgart.de>