theunissenlab · Lathomas42 · Jul 14, 2015 · Dec 12, 2015 · Dec 27, 2015 · Jan 18, 2016
diff --git a/LICENSE.txt b/LICENSE.txt
diff --git a/__init__.py b/__init__.py
diff --git a/docs/README.rst b/docs/README.rst
@@ -1,6 +1,11 @@
 pyoperant
 =========
 
+
+.. image:: https://badges.gitter.im/Join%20Chat.svg
+   :alt: Join the chat at https://gitter.im/gentnerlab/pyoperant
+   :target: https://gitter.im/gentnerlab/pyoperant?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
+
 Pyoperant is a framework to easily construct and share new operant behavior paradigms.
 
 With PyOperant, you can write a single behavior script that works across different species, different computers, different hardware, different rewards, different modalities.

diff --git a/docs/conf.py b/docs/conf.py
@@ -18,6 +18,7 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
+sys.path.insert(0, os.path.abspath('.'))
 sys.path.insert(0, os.path.abspath('../'))
 
 # -- General configuration ------------------------------------------------
@@ -32,7 +33,7 @@
     'sphinx.ext.autodoc',
     'sphinx.ext.doctest',
     'sphinx.ext.viewcode',
-    # 'sphinx.ext.autosummary',
+    'sphinx.ext.autosummary',
     'sphinxcontrib.napoleon',
     # 'numpydoc',
 ]
@@ -110,7 +111,19 @@
 # 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
 # documentation.
-#html_theme_options = {}
+html_theme_options = {
+    'logo_only': False,
+    'display_version': True,
+    'prev_next_buttons_location': 'bottom',
+    'style_external_links': False,
+    'vcs_pageview_mode': '',
+    # Toc options
+    'collapse_navigation': True,
+    'sticky_navigation': True,
+    'navigation_depth': 4,
+    'includehidden': True,
+    'titles_only': False
+}
 
 # Add any paths that contain custom themes here, relative to this directory.
 #html_theme_path = []
@@ -287,7 +300,7 @@ def __getattr__(cls, name):
         else:
             return Mock()
 
-MOCK_MODULES = ['comedi','comedi_poll', 'numpy', 'ephem']
+MOCK_MODULES = ['comedi','comedi_poll', 'numpy', 'ephem', 'scipy', 'pyaudio', 'scipy.special']
 for mod_name in MOCK_MODULES:
     sys.modules[mod_name] = Mock()
 
diff --git a/docs/index.rst b/docs/index.rst
@@ -1,7 +1,7 @@
 Welcome to pyoperant's documentation!
 =====================================
 
-.. include:: ../README.rst
+.. include:: README.rst
 
 Contents
 ========

diff --git a/docs/pyoperant.behavior.base.rst b/docs/pyoperant.behavior.base.rst
@@ -1,5 +1,5 @@
 pyoperant.behavior.base module
-============================
+==============================
 
 .. automodule:: pyoperant.behavior.base
     :members:

diff --git a/docs/pyoperant.behavior.rst b/docs/pyoperant.behavior.rst
@@ -1,16 +1,16 @@
 pyoperant.behavior package
-========================
+==========================
 
 Submodules
 ----------
 
 .. toctree::
 
-   pyoperant.behavior.base
-   pyoperant.behavior.lights
-   pyoperant.behavior.shape
-   pyoperant.behavior.three_ac_matching
-   pyoperant.behavior.two_alt_choice
+   base <pyoperant.behavior.base>
+   lights <pyoperant.behavior.lights>
+   shape <pyoperant.behavior.shape>
+   three_ac_matching <pyoperant.behavior.three_ac_matching>
+   two_alt_choice <pyoperant.behavior.two_alt_choice>
 
 Module contents
 ---------------

diff --git a/docs/pyoperant.behavior.shape.rst b/docs/pyoperant.behavior.shape.rst
@@ -1,5 +1,5 @@
 pyoperant.behavior.shape module
-=============================
+===============================
 
 .. automodule:: pyoperant.behavior.shape
     :members:

diff --git a/docs/pyoperant.behavior.three_ac_matching.rst b/docs/pyoperant.behavior.three_ac_matching.rst
@@ -1,5 +1,5 @@
 pyoperant.behavior.three_ac_matching module
-=========================================
+===========================================
 
 .. automodule:: pyoperant.behavior.three_ac_matching
     :members:

diff --git a/docs/pyoperant.behavior.two_alt_choice.rst b/docs/pyoperant.behavior.two_alt_choice.rst
@@ -1,5 +1,5 @@
 pyoperant.behavior.two_alt_choice module
-======================================
+========================================
 
 .. automodule:: pyoperant.behavior.two_alt_choice
     :members:

diff --git a/docs/pyoperant.interfaces.rst b/docs/pyoperant.interfaces.rst
@@ -6,11 +6,11 @@ Submodules
 
 .. toctree::
 
-   pyoperant.interfaces.base_
-   pyoperant.interfaces.comedi_
-   pyoperant.interfaces.console_
-   pyoperant.interfaces.pyaudio_
-   pyoperant.interfaces.spike2_
+   base <pyoperant.interfaces.base_>
+   comedi <pyoperant.interfaces.comedi_>
+   console <pyoperant.interfaces.console_>
+   pyaudio <pyoperant.interfaces.pyaudio_>
+   spike2 <pyoperant.interfaces.spike2_>
 
 Module contents
 ---------------

diff --git a/docs/pyoperant.rst b/docs/pyoperant.rst
@@ -6,25 +6,24 @@ Subpackages
 
 .. toctree::
 
-    pyoperant.interfaces
-    pyoperant.behavior
+    The Interfaces Subpackage <pyoperant.interfaces>
+    The Behavior Subpackage <pyoperant.behavior>
 
-Submodules
+Modules
 ----------
 
 .. toctree::
 
-   pyoperant.behavior
-   pyoperant.components
-   pyoperant.errors
-   pyoperant.hwio
-   pyoperant.local
-   pyoperant.local_vogel
-   pyoperant.local_zog
-   pyoperant.panels
-   pyoperant.queues
-   pyoperant.reinf
-   pyoperant.utils
+   components <pyoperant.components>
+   errors <pyoperant.errors>
+   hwio <pyoperant.hwio>
+   local <pyoperant.local>
+   local_vogel <pyoperant.local_vogel>
+   local_zog <pyoperant.local_zog>
+   panels <pyoperant.panels>
+   queues <pyoperant.queues>
+   reinf <pyoperant.reinf>
+   utils <pyoperant.utils>
 
 Module contents
 ---------------