Reorganize docs and some fixes

docs/source/api.rst

@@ -10,17 +10,27 @@ API Documentation
 
 .. versionadded:: 1.0.0
 
-This module provides an updated interface for the HOLE_ suite of tools
+This toolkit provides an updated interface for the HOLE_ suite of tools
 :cite:p:`Smart1993,Smart1996` to analyse an ion channel pore or transporter
 pathway :cite:p:`Stelzl2014` as a function of time or arbitrary order
-parameters. It replaces :mod:`mdahole2.analysis.hole`.
+parameters.
 
 HOLE_ must be installed separately and can be obtained in binary form
 from http://www.holeprogram.org/ or as source from
 https://github.com/osmart/hole2. (HOLE is open source and available
 under the Apache v2.0 license.)
 
+.. _HOLE: http://www.holeprogram.org
+
 Module
 ------
 
-.. automodule:: mdahole2.analysis
+.. automodule:: mdahole2.analysis.hole
+   :members:
+
+.. automodule:: mdahole2.analysis.utils
+   :members:
+
+.. automodule:: mdahole2.analysis.templates
+   :members:
+

docs/source/conf.py

@@ -138,7 +138,7 @@
 # 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']
-html_css_files = ['custom.css']  # , 'readable.css']
+html_css_files = []  # , 'readable.css']
 
 # Custom sidebar templates, maps document names to template names.
 # alabaster sidebars

docs/source/index.rst

@@ -11,7 +11,9 @@ Welcome to mdahole2's documentation!
    :caption: Contents:
 
    getting_started
+   usage
    api
+   references
 
 Indices and tables
 ==================