Add global ToC, use default theme for readthedocs, add logo

docs/conf.py

@@ -117,7 +117,7 @@ todo_include_todos = True
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'alabaster'
+html_theme = 'default'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -136,7 +136,7 @@ html_theme = 'alabaster'
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+html_logo = 'ecam_logo.png'
 
 # The name of an image file (relative to this directory) to use as a favicon of
 # the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
@@ -162,7 +162,7 @@ html_static_path = ['_static']
 #html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+html_sidebars = { '**': ['globaltoc.html', 'relations.html', 'sourcelink.html', 'searchbox.html'], }
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.

docs/example_module/patch.rst

@@ -11,4 +11,5 @@ To include a patch file do something like the following:
    :emphasize-lines: 2,9-11
    :linenos:
 
-:download:`Downloadable version of patch file <simple.patch>`
\ No newline at end of file
+:download:`Downloadable version of patch file <simple.patch>`
+

docs/example_module/readme.rst

@@ -4,6 +4,8 @@
 E-CAM example module
 ####################
 
+.. contents:: :local:
+
 This is an example of what a *module* for E-CAM looks like. Please add to this template any additional items that are
 straightforward to fill out in the general case. You are free add any level of complexity you wish (within the bounds of
 what ReST_ can do).
@@ -90,9 +92,14 @@ To include a patch file do something like the following:
 
 If the patch is very long you will probably want to add it as a subpage so let's do that now
 
-:ref:`patch`
+.. toctree::
+   :glob:
+   :maxdepth: 1
+
+   patch
 
 
 .. Here are the URL references used
 
-.. _ReST: http://docutils.sourceforge.net/docs/user/rst/quickref.html
\ No newline at end of file
+.. _ReST: http://docutils.sourceforge.net/docs/user/rst/quickref.html
+

docs/index.rst

@@ -9,19 +9,23 @@
 The E-CAM Classical MD Library
 ==============================
 
+.. contents:: :local:
+
 This is a collection of the modules that have been created by E-CAM community within the area of Classical MD.
 
 ESDW Traumkirchen 2016
 ----------------------
+
 The first Classical MD ESDW in Traumkirchen in June 2016 was the starting point for the modules below.
 
 .. toctree::
+   :glob:
    :maxdepth: 1
 
    ./example_module/readme
 
 Indices and tables
-==================
+----------------------
 
 * :ref:`genindex`
 * :ref:`modindex`