Updated docstrings and documentation.

docs/source/conf.py

+#import sphinx_rtd_theme
+
+
 # Configuration file for the Sphinx documentation builder.
 #
 # This file only contains a selection of the most common options. For a full
@@ -14,7 +17,6 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 
-master_doc = 'index'    # needed for read the docs
 
 # -- Project information -----------------------------------------------------
 
@@ -24,6 +26,7 @@ author = 'Michael Blaß'
 
 # The full version, including alpha/beta/rc tags
 release = '0.1.3'
+version = '0.1.3'
 
 
 # -- General configuration ---------------------------------------------------
@@ -31,22 +34,10 @@ release = '0.1.3'
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinxcontrib.apidoc', 'sphinx.ext.napoleon']
-
-# apidoc config
-apidoc_module_dir = '../../apollon/'
-apidoc_output_dir = 'reference'
-apidoc_separate_modules = True
-apidoc_module_first = True
-apidoc_full = True
-
-# napoleaon config
-napoleon_numpy_docstring = False
-napoleon_google_docstring = True
-napoleon_use_param = True
-napoleon_use_rtype = True
-napoleon_use_keyword = True
-
+extensions = [
+            #'sphinxcontrib.apidoc',
+              'sphinx.ext.napoleon',
+              'sphinx_rtd_theme']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -68,3 +59,25 @@ html_theme = 'sphinx_rtd_theme'
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
+
+
+# -- Options for apidoc -----------------------------------------------------
+#
+apidoc_module_dir = '../../src/apollon'
+apidoc_output_dir = 'reference'
+apidoc_separate_modules = True
+apidoc_module_first = True
+apidoc_full = True
+
+
+# -- Options for Napoleon ---------------------------------------------------
+#
+napoleon_google_docstring = True
+napoleon_numpy_docstring = False
+napoleon_include_init_with_doc = True
+napoleon_include_private_with_doc = False
+napoleon_include_special_with_doc = False
+napoleon_use_ivar = True
+napoleon_use_param = True
+napoleon_use_keyword = True
+napoleon_use_rtype = True

docs/source/download.rst

+Download
+***************************************
+
+You can either download the source code from the `apollon GitHub repository`_
+or clone it directly with
+
+.. code-block:: Bash
+
+   git clone https://github.com/teagum/apollon.git 
+
+.. _apollon GitHub repository: https://github.com/teagum/apollon.git

docs/source/starters.rst → docs/source/framework.rst

-Starters
-========
+Framework
+***************************************
 
-1. Audio Feature Extraction
-----------------------------
+Audio Feature Extraction
+=======================================
 Extract some of the most common low-level audio feauters.
 
-2. Hidden Markov Model
------------------------
+
+Hidden Markov Model
+=======================================
 Estimate Poisson-distributed Hidden Markov Models.
 
-3. Self-Organizing Map
------------------------
+
+Self-Organizing Map
+=======================================
 Train some Self-organizing maps.

docs/source/index.rst

@@ -8,7 +8,7 @@ Welcome to the documentation of the apollon feature extraction framework!
 *apollon* is a feature extraction and modelling frame work for music data
 analysis. It handles low-level audio feature extraction, their aggreagation
 using Hidden Markov models, and comparison by means of the Self-Organizing Map.
-See the :doc:`starters` chapter for gentle introduction to the mentioned
+See the :doc:`framework` chapter for gentle introduction to the mentioned
 concepts.
 
 Contents
@@ -17,10 +17,10 @@ Contents
 .. toctree::
    :maxdepth: 2
 
-   installation
-   starters
-   clt 
-   contribute
+   download
+   install
+   framework
+   reference/modules
 
 * :ref:`genindex`
 * :ref:`modindex`

docs/source/install.rst

+Installation
+***************************************
+apollon can be installed on GNU/Linux, macOS, and Windows. Installation process
+is similar on each of these plaforms. Note, however, that apollon contains
+Python C extension modules, which have to be compile locally for GNU/Linux and
+Windows users. If work on any of those platforms, please make shure that there
+is a C compiler set up on your machine; otherwise the installation will fail.
+In the case of macOS, a precompiled wheel is provided for the latest version
+only.
+
+
+Install using pip
+=======================================
+The Python packager manager can automatically install download and install
+apollon from pip. Simply run the following command from your terminal:
+
+.. code-block:: Bash
+
+   python3 -m pip install apollon
+
+
+Install from source
+=======================================
+You can also install and compile apollon directly from its sources in three
+steps:
+
+* Download the apollon source code
+* Open a terminal and navigate to the apollon root directory
+* Install and compile with the following command
+
+.. code-block:: Bash
+
+   python3 -m pip install .

docs/source/installation.rst

-Before you order
-================
-
-1. Download
------------
-Download the repository from the gitlab server using
-``git clone git@gitlab.rrz.uni-hamburg.de:bla7667/apollon.git``
-
-2. Installation
-----------------
-To install apollon, navigate to its repository's source directory and install
-using pip:
-``
-cd path/to/apollon
-pip install .
-``

docs/source/modules.rst

-apollon
-=======
-
-.. toctree::
-   :maxdepth: 4
-

docs/source/reference/apollon.analyses.rst

-apollon.analyses module
-=======================
-
-.. automodule:: apollon.analyses
-    :members:
-    :undoc-members:
-    :show-inheritance:

docs/source/reference/apollon.aplot.rst

-apollon.aplot module
-====================
-
-.. automodule:: apollon.aplot
-    :members:
-    :undoc-members:
-    :show-inheritance:

docs/source/reference/apollon.audio.rst

-apollon.audio module
-====================
-
-.. automodule:: apollon.audio
-    :members:
-    :undoc-members:
-    :show-inheritance:

docs/source/reference/apollon.commands.apollon_export.rst

-apollon.commands.apollon\_export module
-=======================================
-
-.. automodule:: apollon.commands.apollon_export
-    :members:
-    :undoc-members:
-    :show-inheritance:

docs/source/reference/apollon.commands.apollon_features.rst

-apollon.commands.apollon\_features module
-=========================================
-
-.. automodule:: apollon.commands.apollon_features
-    :members:
-    :undoc-members:
-    :show-inheritance:

docs/source/reference/apollon.commands.apollon_hmm.rst

-apollon.commands.apollon\_hmm module
-====================================
-
-.. automodule:: apollon.commands.apollon_hmm
-    :members:
-    :undoc-members:
-    :show-inheritance:

docs/source/reference/apollon.commands.apollon_onsets.rst

-apollon.commands.apollon\_onsets module
-=======================================
-
-.. automodule:: apollon.commands.apollon_onsets
-    :members:
-    :undoc-members:
-    :show-inheritance:

docs/source/reference/apollon.commands.rst

-apollon.commands package
-========================
-
-.. automodule:: apollon.commands
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-Submodules
-----------
-
-.. toctree::
-
-   apollon.commands.apollon_export
-   apollon.commands.apollon_features
-   apollon.commands.apollon_hmm
-   apollon.commands.apollon_onsets
-

docs/source/reference/apollon.datasets.rst

-apollon.datasets module
-=======================
-
-.. automodule:: apollon.datasets
-    :members:
-    :undoc-members:
-    :show-inheritance:

docs/source/reference/apollon.fractal.rst

-apollon.fractal module
-======================
-
-.. automodule:: apollon.fractal
-    :members:
-    :undoc-members:
-    :show-inheritance:

docs/source/reference/apollon.hmm.graph.grapher.rst

-apollon.hmm.graph.grapher module
-================================
-
-.. automodule:: apollon.hmm.graph.grapher
-    :members:
-    :undoc-members:
-    :show-inheritance:

docs/source/reference/apollon.hmm.graph.rst

-apollon.hmm.graph package
-=========================
-
-.. automodule:: apollon.hmm.graph
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-Submodules
-----------
-
-.. toctree::
-
-   apollon.hmm.graph.grapher
-