Added Chemical Bistables section to tutorials. Rest incoming

docs/source/Extensions/hidden_code_block.py

+"""Simple, inelegant Sphinx extension which adds a directive for a
+highlighted code-block that may be toggled hidden and shown in HTML.  
+This is possibly useful for teaching courses.
+
+The directive, like the standard code-block directive, takes
+a language argument and an optional linenos parameter.  The
+hidden-code-block adds starthidden and label as optional 
+parameters.
+
+Examples:
+
+.. hidden-code-block:: python
+    :starthidden: False
+
+    a = 10
+    b = a + 5
+
+.. hidden-code-block:: python
+    :label: --- SHOW/HIDE ---
+
+    x = 10
+    y = x + 5
+
+Thanks to http://www.javascriptkit.com/javatutors/dom3.shtml for 
+inspiration on the javascript.  
+
+Thanks to Milad 'animal' Fatenejad for suggesting this extension 
+in the first place.
+
+Written by Anthony 'el Scopz' Scopatz, January 2012.
+
+Released under the WTFPL (http://sam.zoy.org/wtfpl/).
+"""
+
+from docutils import nodes
+from docutils.parsers.rst import directives
+from sphinx.directives.code import CodeBlock
+from sphinx.util.compat import make_admonition
+
+HCB_COUNTER = 0
+
+js_showhide = """\
+<script type="text/javascript">
+    function showhide(element){
+        if (!document.getElementById)
+            return
+
+        if (element.style.display == "block")
+            element.style.display = "none"
+        else
+            element.style.display = "block"
+    };
+</script>
+"""
+
+def nice_bool(arg):
+    tvalues = ('true',  't', 'yes', 'y')
+    fvalues = ('false', 'f', 'no',  'n')
+    arg = directives.choice(arg, tvalues + fvalues)
+    return arg in tvalues
+
+
+class hidden_code_block(nodes.General, nodes.FixedTextElement):
+    pass
+
+
+class HiddenCodeBlock(CodeBlock):
+    """Hidden code block is Hidden"""
+
+    option_spec = dict(starthidden=nice_bool, 
+                       label=str,
+                       **CodeBlock.option_spec)
+
+    def run(self):
+        # Body of the method is more or less copied from CodeBlock
+        code = u'\n'.join(self.content)
+        hcb = hidden_code_block(code, code)
+        hcb['language'] = self.arguments[0]
+        hcb['linenos'] = 'linenos' in self.options
+        hcb['starthidden'] = self.options.get('starthidden', True)
+        hcb['label'] = self.options.get('label', '+ show/hide code')
+        hcb.line = self.lineno
+        return [hcb]
+
+
+def visit_hcb_html(self, node):
+    """Visit hidden code block"""
+    global HCB_COUNTER
+    HCB_COUNTER += 1
+
+    # We want to use the original highlighter so that we don't
+    # have to reimplement it.  However it raises a SkipNode 
+    # error at the end of the function call.  Thus we intercept
+    # it and raise it again later.
+    try: 
+        self.visit_literal_block(node)
+    except nodes.SkipNode:
+        pass
+
+    # The last element of the body should be the literal code 
+    # block that was just made.
+    code_block = self.body[-1]
+
+    fill_header = {'divname': 'hiddencodeblock{0}'.format(HCB_COUNTER), 
+                   'startdisplay': 'none' if node['starthidden'] else 'block', 
+                   'label': node.get('label'), 
+                   }
+
+    divheader = ("""<a href="javascript:showhide(document.getElementById('{divname}'))">"""
+                 """{label}</a><br />"""
+                 '''<div id="{divname}" style="display: {startdisplay}">'''
+                 ).format(**fill_header)
+
+    code_block = js_showhide + divheader + code_block + "</div>"
+
+    # reassign and exit
+    self.body[-1] = code_block
+    raise nodes.SkipNode
+
+
+def depart_hcb_html(self, node):
+    """Depart hidden code block"""
+    # Stub because of SkipNode in visit
+
+
+def setup(app):
+    app.add_directive('hidden-code-block', HiddenCodeBlock)
+    app.add_node(hidden_code_block, html=(visit_hcb_html, depart_hcb_html))
+

docs/source/conf.py

@@ -11,6 +11,11 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
+#Workaround to fix bug where extensions werent added
+from docutils.parsers.rst.directives.admonitions import BaseAdmonition
+from sphinx.util import compat
+compat.make_admonition = BaseAdmonition
+
 import subprocess
 import os
 import sys
@@ -21,13 +26,13 @@ import mock
 # 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('../python'))
+sys.path.insert(0, os.path.abspath('./Extensions'))
 sys.path.append(os.path.abspath('../../moose-examples/snippets'))
 sys.path.append(os.path.abspath('../../moose-examples/tutorials/ChemicalOscillators'))
 sys.path.append(os.path.abspath('../../moose-examples/tutorials/ChemicalBistables'))
 sys.path.append(os.path.abspath('../../moose-examples/tutorials/ExcInhNet'))
 sys.path.append(os.path.abspath('../../moose-examples/neuroml/lobster_pyloric'))
 sys.path.append(os.path.abspath('../../moose-examples/tutorials/ExcInhNetCaPlasticity'))
-sys.path.append('../../docproj/ext/breathe/')
 
 # -- General configuration -----------------------------------------------------
 
@@ -42,6 +47,7 @@ extensions = ['sphinx.ext.autodoc',
               'sphinx.ext.autosummary',
               'sphinx.ext.todo',
               'sphinx.ext.viewcode',
+              'hidden_code_block'
 		]
 
 todo_include_todos = True