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sphinxcontrib-matlabdomain -- Sphinx domain for auto-documenting MATLAB

This extension provides a Sphinx <http://www.sphinx-doc.org/en/master/index.html>_ domain for automatically generating doumentation from MATLAB source files. It is modelled after the Python autodoc <http://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html>_.

The extension allows you to have your documentation and source files together and use the powerful Sphinx <http://www.sphinx-doc.org/en/master/index.html>_ documentation tool. All your MATLAB file help text can be automatically included in the your documentation and output as for instance HTML.

The extension works really well with sphinx.ext.napoleon <https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html>_.

Recent Changes <https://github.com/sphinx-contrib/matlabdomain/blob/master/CHANGES.rst>_.

Usage

The Python package must be installed with::

pip install sphinxcontrib-matlabdomain

In general, the usage is the same as for documenting Python code. The package is tested with Python >= 3.8 and Sphinx >= 4.5.0.

For a Python 2 compatible version the package must be installed with::

pip install sphinxcontrib-matlabdomain==0.11.8

Configuration

In your Sphinx conf.py file add sphinxcontrib.matlab to the list of extensions. ::

extensions = ['sphinxcontrib.matlab', 'sphinx.ext.autodoc']

For convenience the primary domain <https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-primary_domain>_ can be set to mat with.::

primary_domain = "mat"

Additional Configuration

``matlab_src_dir``
   In order for the Sphinx MATLAB domain to auto-document MATLAB source code,
   set the config value of ``matlab_src_dir`` to an absolute path or a path
   relative to the source directory. Currently only one MATLAB path can be
   specified, but that folder and all the subfolders in that tree will be
   searched.

``matlab_short_links``
   Shorten all class, package and functions to the minimum length. This assumes
   that everything is in the path as we would expect it in MATLAB. This will
   resemble a more MATLAB-like presentation. If it is ``True`` is forces
   ``matlab_keep_package_prefix = False``. Further, it allows for much shorter
   and cleaner references. Example, given a path to classes like
   ``target.subfolder.ClassFoo`` and ``[email protected]``

   * With ``False``::

      :class:`target.subfolder.ClassFoo`

      :class:`[email protected]`

   * With ``True``::

      :class:`ClassFoo`

      :class:`ClassFolder`

   Default is ``False``. *Added in Version 0.19.0*.

``matlab_auto_link``
   Automatically convert the names of known entities (e.g. classes, functions,
   properties, methods) to links. Valid values are ``"basic"``
   and ``"all"``.

   * ``"basic"`` - Auto-links (1) known classes, functions, properties, or
     methods that appear in docstring lines that begin with "See also" and any
     subsequent lines before the next blank line (unknown names are wrapped in
     double-backquotes), and (2) property and method names that appear in lists
     under "<MyClass> Properties:" and "<MyClass> Methods:" headings in class
     docstrings.

   * ``"all"`` - Auto-links everything included with ``"basic"``, plus all known
     classes and functions everywhere else they appear in any docstring, any
     fully qualified (including class name) property or method names, any
     names ending with "()" within class, property, or method docstrings that
     match a method of the corresponding class, and any property or method names
     in their own docstrings. Note that a non-breaking space before or after
     a name will prevent auto-linking.

   Default is ``None``. *Added in Version 0.20.0*.

``matlab_show_property_default_value``
   Show property default values in the rendered document. Default is ``False``,
   which is what MathWorks does in their documentation. *Added in Version
   0.16.0*.

``matlab_class_signature``
   Shows the constructor argument list in the class signature if ``True``.
   Default is ``False``. *Added in Version 0.20.0*.

``matlab_keep_package_prefix``
   Determines if the MATLAB package prefix ``+`` is displayed in the generated
   documentation.  Default is ``False``.  When ``False``, packages are still
   referred to in ReST using ``+pakage.+subpkg.func`` but the output will be
   ``pakage.subpkg.func()``. Forced to ``False`` if  ``matlab_short_links`` is
   ``True``. *Added in Version 0.11.0*.

``matlab_src_encoding``
   The encoding of the MATLAB files. By default, the files will be read as utf-8
   and parsing errors will be replaced using ? chars. *Added in Version 0.9.0*.

If you want the closest to MATLAB documentation style, use ``matlab_short_links
= True`` and ``matlab_auto_link = "basic"`` or ``matlab_auto_link = "all"`` in
your ``conf.py`` file.


Roles and Directives
--------------------

Please see `Sphinx Domains <https://www.sphinx-doc.org/en/master/usage/restructuredtext/domains.html>`_ and
`sphinx.ext.autodoc
<http://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html>`_ for
documentation on the use of roles and directives. MATLAB code can be documented
using the following roles and directives:

====================================  ===========================================
Directive                             MATLAB object
====================================  ===========================================
``.. module:: foldername``            **folders, packages and namespaces**
``.. currentmodule:: foldername``     * set folder but do not link
``.. automodule:: foldername``        * auto-document
``:mod:`foldername```                 * reference
``.. function:: funcname``            **function definition and signature**
``.. autofunction:: funcname()``      * auto-document
``:func:`funcname```                  * reference
``.. script:: scriptname``            **script definition**
``.. autoscript:: scriptname``        * auto-document
``:scpt:`scriptname```                * reference
``.. class:: classname()``            **class definition and optional signature**
``.. autoclass:: classname``          * auto-document
``:class:`classname```                * reference
``.. method:: methname()``            **method definition and signature**
``.. automethod:: methname``          * auto-document
``:meth:`methname```                  * reference
``.. staticmethod:: statmethname()``  **static method definition and signature**
``.. automethod:: statmethname``      * auto-document
``:meth:`methname```                  * reference
``.. attribute:: attrname``           **property definition**
``.. autoattribute:: attrname``       * auto-document
``:attr:`attrname```                  * reference
``.. application:: appname``          **application definition**
``.. autoapplication:: appname``      * auto-document
``:app:`appname```                    * reference
====================================  ===========================================

Several options are available for auto-directives.

* ``:members:`` auto-document public members
* ``:show-inheritance:`` list bases
* ``:undoc-members:`` document members without docstrings
* ``:annotation:`` specifies attribute annotation instead of default

There are also several config values that can be set in ``conf.py`` that will
affect auto-docementation.

* ``autoclass_content`` can be set to ``class``, ``both`` or ``init``, which
  determines which docstring is used for classes. The constructor docstring
  is used when this is set to ``init``.
* ``autodoc_member_order`` can be set to ``alphabetical``, ``groupwise`` or
  ``bysource``.
* ``autodoc_default_flags`` can be set to a list of options to apply. Use
  the ``no-flag`` directive option to disable this config value once.

.. note::

    The module roles and directives create a psuedo namespace for MATLAB
    objects, similar to a package. They represent the path to the folder
    containing the MATLAB object. If no module is specified then Sphinx will
    assume that the object is a built-in.

Example: given the following MATLAB source in folder ``test_data``::

    classdef MyHandleClass < handle & my.super.Class
        % a handle class
        %
        % :param x: a variable

        %% some comments
        properties
            x % a property

            % Multiple lines before a
            % property can also be used
            y
        end
        methods
            function h = MyHandleClass(x)
                h.x = x
            end
            function x = get.x(obj)
            % how is this displayed?
                x = obj.x
            end
        end
        methods (Static)
            function w = my_static_function(z)
            % A static function in :class:`MyHandleClass`.
            %
            % :param z: input z
            % :returns: w

                w = z
            end
        end
    end

Use the following to document::

    Test Data
    =========
    This is the test data module.

    .. automodule:: test_data

    :mod:`test_data` is a really cool module.

    My Handle Class
    ---------------
    This is the handle class definition.

    .. autoclass:: MyHandleClass
        :show-inheritance:
        :members:

In version 0.19.0 the ``.. automodule::`` directive can also take a ``.`` as
argument, which allows you to document classes or functions in the root of
``matlab_src_dir``.


Module Index
------------

Since version 0.10.0 the *MATLAB Module Index* should be linked to with::

   `MATLAB Module Index <mat-modindex.html>`_

Older versions, used the *Python Module Index*, which was linked to with::

   :ref:`modindex`


Documenting Python and MATLAB sources together
==============================================

Since version 0.10.0 MATLAB and Python sources can be (auto-)documented in the same
Sphinx documentation. For this to work, do not set the `primary domain <https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-primary_domain>`_.

Instead use the ``mat:`` prefix before the desired directives::

   .. automodule:: func
   .. autofunction:: func.main

   .. mat:automodule:: matsrc
   .. mat:autofunction:: matsrc.func


Online Demo
===========

.. warning::

   The online demo is highly outdated!

The test docs in the repository are online here:
http://bwanamarko.alwaysdata.net/matlabdomain/

.. note::

    Sphinx style markup are used to document parameters, types, returns and
    exceptions. There must be a blank comment line before and after the
    parameter descriptions.


Users
=====

* `Cantera <http://cantera.github.io/docs/sphinx/html/compiling/dependencies.html?highlight=matlabdomain>`_
* `CoSMo MVPA <http://cosmomvpa.org/download.html?highlight=matlabdomain#developers>`_
* `The Cobra Toolbox <https://opencobra.github.io/cobratoolbox/stable/index.html#>`_
* `The RepLAB Toolbox <https://replab.github.io/replab>`_


Citation
========
.. image:: https://zenodo.org/badge/105161090.svg
   :target: https://zenodo.org/badge/latestdoi/105161090