From 0caac8cd280e011a333da0a15d6eef81bc812167 Mon Sep 17 00:00:00 2001
From: Aron Ahmadia <aron@ahmadia.net>
Date: Tue, 9 Oct 2012 17:51:21 +0300
Subject: [PATCH 1/4] partial refactor, can't quite get environments working

---
 .../html/notebook/static/js/mathjaxutils.js   | 230 ++++++++++++++++++
 .../html/notebook/static/js/notebookmain.js   |   2 +-
 .../html/notebook/static/js/textcell.js       |   6 +-
 .../frontend/html/notebook/static/js/utils.js | 120 ++++++++-
 .../html/notebook/templates/notebook.html     |   2 +-
 5 files changed, 356 insertions(+), 4 deletions(-)
 create mode 100644 IPython/frontend/html/notebook/static/js/mathjaxutils.js

diff --git a/IPython/frontend/html/notebook/static/js/mathjaxutils.js b/IPython/frontend/html/notebook/static/js/mathjaxutils.js
new file mode 100644
index 000000000..8eeeb7fb5
--- /dev/null
+++ b/IPython/frontend/html/notebook/static/js/mathjaxutils.js
@@ -0,0 +1,230 @@
+//----------------------------------------------------------------------------
+//  Copyright (C) 2008-2012  The IPython Development Team
+//
+//  Distributed under the terms of the BSD License.  The full license is in
+//  the file COPYING, distributed as part of this software.
+//----------------------------------------------------------------------------
+
+//============================================================================
+// MathJax utility functions
+//============================================================================
+
+IPython.namespace('IPython.mathjaxutils');
+
+IPython.mathjaxutils = (function (IPython) {
+
+    var init = function () {
+        if (window.MathJax) { 
+            // MathJax loaded
+            MathJax.Hub.Config({
+                TeX: { equationNumbers: { autoNumber: "AMS", useLabelIds: true },
+                       extensions: ["autoload-all.js"] },
+                tex2jax: {
+                    inlineMath: [ ['$','$'], ["\\(","\\)"] ],
+                    displayMath: [ ['$$','$$'], ["\\[","\\]"] ],
+                    processEnvironments: true
+                },
+                displayAlign: 'left', // Change this to 'center' to center equations.
+                "HTML-CSS": {
+                    styles: {'.MathJax_Display': {"margin": 0}}
+                }
+            });
+        } else if (window.mathjax_url != "") {
+            // Don't have MathJax, but should. Show dialog.
+            var dialog = $('<div></div>')
+                .append(
+                    $("<p></p>").addClass('dialog').html(
+                        "Math/LaTeX rendering will be disabled."
+                    )
+                ).append(
+                    $("<p></p>").addClass('dialog').html(
+                        "If you have administrative access to the notebook server and" +
+                        " a working internet connection, you can install a local copy" +
+                        " of MathJax for offline use with the following command on the server" +
+                        " at a Python or IPython prompt:"
+                    )
+                ).append(
+                    $("<pre></pre>").addClass('dialog').html(
+                        ">>> from IPython.external import mathjax; mathjax.install_mathjax()"
+                    )
+                ).append(
+                    $("<p></p>").addClass('dialog').html(
+                        "This will try to install MathJax into the IPython source directory."
+                    )
+                ).append(
+                    $("<p></p>").addClass('dialog').html(
+                        "If IPython is installed to a location that requires" +
+                        " administrative privileges to write, you will need to make this call as" +
+                        " an administrator, via 'sudo'."
+                    )
+                ).append(
+                    $("<p></p>").addClass('dialog').html(
+                        "When you start the notebook server, you can instruct it to disable MathJax support altogether:"
+                    )
+                ).append(
+                    $("<pre></pre>").addClass('dialog').html(
+                        "$ ipython notebook --no-mathjax"
+                    )
+                ).append(
+                    $("<p></p>").addClass('dialog').html(
+                        "which will prevent this dialog from appearing."
+                    )
+                ).dialog({
+                    title: "Failed to retrieve MathJax from '" + window.mathjax_url + "'",
+                    width: "70%",
+                    modal: true,
+                })
+        } else {
+            // No MathJax, but none expected. No dialog.
+        };
+    };
+
+    // Some magic for deferring mathematical expressions to MathJaX
+    // Some of the code here is adapted with permission from Stack Exchange Inc.
+
+    var inline = "$"; // the inline math delimiter
+    var blocks, start, end, last, braces; // used in searching for math
+    var math; // stores math until pagedown (Markdown parser) is done
+    var HUB = MathJax.Hub;
+
+    // MATHSPLIT contains the pattern for math delimiters and special symbols
+    // needed for searching for math in the text input.   
+    var MATHSPLIT = /(\$\$?|\\(?:begin|end)\{[a-z]*\*?\}|\\[\\{}$]|[{}]|(?:\n\s*)+|@@\d+@@)/i;
+
+    //  The math is in blocks i through j, so 
+    //    collect it into one block and clear the others.
+    //  Replace &, <, and > by named entities.
+    //  For IE, put <br> at the ends of comments since IE removes \n.
+    //  Clear the current math positions and store the index of the
+    //    math, then push the math string onto the storage array.
+    //  The preProcess function is called on all blocks if it has been passed in
+    function processMath(i, j, preProcess) {
+        var block = blocks.slice(i, j + 1).join("").replace(/&/g, "&amp;") // use HTML entity for &
+        .replace(/</g, "&lt;") // use HTML entity for <
+        .replace(/>/g, "&gt;") // use HTML entity for >
+        ;
+        if (HUB.Browser.isMSIE) {
+            block = block.replace(/(%[^\n]*)\n/g, "$1<br/>\n")
+        }
+        while (j > i) {
+            blocks[j] = "";
+            j--;
+        }
+        blocks[i] = "@@" + math.length + "@@"; // replace the current block text with a unique tag to find later
+        if (preProcess)
+            block = preProcess(block);
+        math.push(block);
+        start = end = last = null;
+    }
+
+    //  Break up the text into its component parts and search
+    //    through them for math delimiters, braces, linebreaks, etc.
+    //  Math delimiters must match and braces must balance.
+    //  Don't allow math to pass through a double linebreak
+    //    (which will be a paragraph).
+    //
+    function removeMath(text) {
+        start = end = last = null; // for tracking math delimiters
+        math = []; // stores math strings for later
+        
+        // Except for extreme edge cases, this should catch precisely those pieces of the markdown
+        // source that will later be turned into code spans. While MathJax will not TeXify code spans,
+        // we still have to consider them at this point; the following issue has happened several times:
+        //
+        //     `$foo` and `$bar` are varibales.  -->  <code>$foo ` and `$bar</code> are variables.
+
+        var hasCodeSpans = /`/.test(text),
+            deTilde;
+        if (hasCodeSpans) {
+            text = text.replace(/~/g, "~T").replace(/(^|[^\\])(`+)([^\n]*?[^`\n])\2(?!`)/gm, function (wholematch) {
+                return wholematch.replace(/\$/g, "~D");
+            });
+            deTilde = function (text) { return text.replace(/~([TD])/g, function (wholematch, character) { return { T: "~", D: "$" }[character]; }) };
+        } else {
+            deTilde = function (text) { return text; };
+        }
+        
+        blocks = IPython.utils.regex_split(text.replace(/\r\n?/g, "\n"),MATHSPLIT);
+
+        for (var i = 1, m = blocks.length; i < m; i += 2) {
+            var block = blocks[i];
+            if (block.charAt(0) === "@") {
+                //
+                //  Things that look like our math markers will get
+                //  stored and then retrieved along with the math.
+                //
+                blocks[i] = "@@" + math.length + "@@";
+                math.push(block);
+            }
+            else if (start) {
+                //
+                //  If we are in math, look for the end delimiter,
+                //    but don't go past double line breaks, and
+                //    and balance braces within the math.
+                //
+                if (block === end) {
+                    if (braces) {
+                        last = i
+                    }
+                    else {
+                        processMath(start, i, deTilde)
+                    }
+                }
+                else if (block.match(/\n.*\n/)) {
+                    if (last) {
+                        i = last;
+                        processMath(start, i, deTilde)
+                    }
+                    start = end = last = null;
+                    braces = 0;
+                }
+                else if (block === "{") {
+                    braces++
+                }
+                else if (block === "}" && braces) {
+                    braces--
+                }
+            }
+            else {
+                //
+                //  Look for math start delimiters and when
+                //    found, set up the end delimiter.
+                //
+                if (block === inline || block === "$$") {
+                    start = i;
+                    end = block;
+                    braces = 0;
+                }
+                else if (block.substr(1, 5) === "begin") {
+                    start = i;
+                    end = "\\end" + block.substr(6);
+                    braces = 0;
+                }
+            }
+        }
+        if (last) {
+            processMath(start, last, deTilde)
+        }
+        return deTilde(blocks.join(""));
+    }
+
+    //
+    //  Put back the math strings that were saved,
+    //    and clear the math array (no need to keep it around).
+    //  
+    function replaceMath(text) {
+        text = text.replace(/@@(\d+)@@/g, function (match, n) {
+            return math[n]
+        });
+        math = null;
+        return text;
+    }
+
+    return {
+        init : init,
+        processMath : processMath,
+        removeMath : removeMath,
+        replaceMath : replaceMath,
+    };
+
+}(IPython));
\ No newline at end of file
diff --git a/IPython/frontend/html/notebook/static/js/notebookmain.js b/IPython/frontend/html/notebook/static/js/notebookmain.js
index a7d7d4362..13059fc0e 100644
--- a/IPython/frontend/html/notebook/static/js/notebookmain.js
+++ b/IPython/frontend/html/notebook/static/js/notebookmain.js
@@ -31,7 +31,7 @@ $(document).ready(function () {
         }
     // end monkey patching CodeMirror
 
-    IPython.init_mathjax();
+    IPython.mathjaxutils.init();
 
     IPython.read_only = $('body').data('readOnly') === 'True';
     $('div#main_app').addClass('border-box-sizing ui-widget');
diff --git a/IPython/frontend/html/notebook/static/js/textcell.js b/IPython/frontend/html/notebook/static/js/textcell.js
index 14704d10c..54bc5a3b9 100644
--- a/IPython/frontend/html/notebook/static/js/textcell.js
+++ b/IPython/frontend/html/notebook/static/js/textcell.js
@@ -1,5 +1,5 @@
 //----------------------------------------------------------------------------
-//  Copyright (C) 2008-2011  The IPython Development Team
+//  Copyright (C) 2008-2012  The IPython Development Team
 //
 //  Distributed under the terms of the BSD License.  The full license is in
 //  the file COPYING, distributed as part of this software.
@@ -221,7 +221,11 @@ var IPython = (function (IPython) {
         if (this.rendered === false) {
             var text = this.get_text();
             if (text === "") { text = this.placeholder; }
+
+            text = IPython.mathjaxutils.removeMath(text)
             var html = IPython.markdown_converter.makeHtml(text);
+            html = IPython.mathjaxutils.replaceMath(html)
+
             try {
                 this.set_rendered(html);
             } catch (e) {
diff --git a/IPython/frontend/html/notebook/static/js/utils.js b/IPython/frontend/html/notebook/static/js/utils.js
index 9dfa47842..d38d6da06 100644
--- a/IPython/frontend/html/notebook/static/js/utils.js
+++ b/IPython/frontend/html/notebook/static/js/utils.js
@@ -1,5 +1,5 @@
 //----------------------------------------------------------------------------
-//  Copyright (C) 2008-2011  The IPython Development Team
+//  Copyright (C) 2008-2012  The IPython Development Team
 //
 //  Distributed under the terms of the BSD License.  The full license is in
 //  the file COPYING, distributed as part of this software.
@@ -13,6 +13,123 @@ IPython.namespace('IPython.utils');
 
 IPython.utils = (function (IPython) {
 
+    //============================================================================
+    // Cross-browser RegEx Split
+    //============================================================================
+
+    // This code has been MODIFIED from the code licensed below to not replace the
+    // default browser split.  The license is reproduced here.
+
+    // see http://blog.stevenlevithan.com/archives/cross-browser-split for more info:
+    /*!
+     * Cross-Browser Split 1.1.1
+     * Copyright 2007-2012 Steven Levithan <stevenlevithan.com>
+     * Available under the MIT License
+     * ECMAScript compliant, uniform cross-browser split method
+     */
+
+    /**
+     * Splits a string into an array of strings using a regex or string
+     * separator. Matches of the separator are not included in the result array.
+     * However, if `separator` is a regex that contains capturing groups,
+     * backreferences are spliced into the result each time `separator` is
+     * matched. Fixes browser bugs compared to the native
+     * `String.prototype.split` and can be used reliably cross-browser.
+     * @param {String} str String to split.
+     * @param {RegExp|String} separator Regex or string to use for separating
+     *     the string.
+     * @param {Number} [limit] Maximum number of items to include in the result
+     *     array.
+     * @returns {Array} Array of substrings.
+     * @example
+     *
+     * // Basic use
+     * regex_split('a b c d', ' ');
+     * // -> ['a', 'b', 'c', 'd']
+     *
+     * // With limit
+     * regex_split('a b c d', ' ', 2);
+     * // -> ['a', 'b']
+     *
+     * // Backreferences in result array
+     * regex_split('..word1 word2..', /([a-z]+)(\d+)/i);
+     * // -> ['..', 'word', '1', ' ', 'word', '2', '..']
+     */
+    var regex_split = function (str, separator, limit) {
+        // If `separator` is not a regex, use `split`
+        if (Object.prototype.toString.call(separator) !== "[object RegExp]") {
+            return split.call(str, separator, limit);
+        }
+        var output = [],
+            flags = (separator.ignoreCase ? "i" : "") +
+                    (separator.multiline  ? "m" : "") +
+                    (separator.extended   ? "x" : "") + // Proposed for ES6
+                    (separator.sticky     ? "y" : ""), // Firefox 3+
+            lastLastIndex = 0,
+            // Make `global` and avoid `lastIndex` issues by working with a copy
+            separator = new RegExp(separator.source, flags + "g"),
+            separator2, match, lastIndex, lastLength;
+        str += ""; // Type-convert
+
+        compliantExecNpcg = typeof(/()??/.exec("")[1]) === "undefined"
+        if (!compliantExecNpcg) {
+            // Doesn't need flags gy, but they don't hurt
+            separator2 = new RegExp("^" + separator.source + "$(?!\\s)", flags);
+        }
+        /* Values for `limit`, per the spec:
+         * If undefined: 4294967295 // Math.pow(2, 32) - 1
+         * If 0, Infinity, or NaN: 0
+         * If positive number: limit = Math.floor(limit); if (limit > 4294967295) limit -= 4294967296;
+         * If negative number: 4294967296 - Math.floor(Math.abs(limit))
+         * If other: Type-convert, then use the above rules
+         */
+        limit = typeof(limit) === "undefined" ?
+            -1 >>> 0 : // Math.pow(2, 32) - 1
+            limit >>> 0; // ToUint32(limit)
+        while (match = separator.exec(str)) {
+            // `separator.lastIndex` is not reliable cross-browser
+            lastIndex = match.index + match[0].length;
+            if (lastIndex > lastLastIndex) {
+                output.push(str.slice(lastLastIndex, match.index));
+                // Fix browsers whose `exec` methods don't consistently return `undefined` for
+                // nonparticipating capturing groups
+                if (!compliantExecNpcg && match.length > 1) {
+                    match[0].replace(separator2, function () {
+                        for (var i = 1; i < arguments.length - 2; i++) {
+                            if (typeof(arguments[i]) === "undefined") {
+                                match[i] = undefined;
+                            }
+                        }
+                    });
+                }
+                if (match.length > 1 && match.index < str.length) {
+                    Array.prototype.push.apply(output, match.slice(1));
+                }
+                lastLength = match[0].length;
+                lastLastIndex = lastIndex;
+                if (output.length >= limit) {
+                    break;
+                }
+            }
+            if (separator.lastIndex === match.index) {
+                separator.lastIndex++; // Avoid an infinite loop
+            }
+        }
+        if (lastLastIndex === str.length) {
+            if (lastLength || !separator.test("")) {
+                output.push("");
+            }
+        } else {
+            output.push(str.slice(lastLastIndex));
+        }
+        return output.length > limit ? output.slice(0, limit) : output;
+    };
+
+    //============================================================================
+    // End contributed Cross-browser RegEx Split
+    //============================================================================
+
+
     var uuid = function () {
         // http://www.ietf.org/rfc/rfc4122.txt
         var s = [];
@@ -138,6 +255,7 @@ IPython.utils = (function (IPython) {
 
 
     return {
+        regex_split : regex_split,
         uuid : uuid,
         fixConsole : fixConsole,
         keycodes : keycodes,
diff --git a/IPython/frontend/html/notebook/templates/notebook.html b/IPython/frontend/html/notebook/templates/notebook.html
index 08579a688..ef991d4d8 100644
--- a/IPython/frontend/html/notebook/templates/notebook.html
+++ b/IPython/frontend/html/notebook/templates/notebook.html
@@ -199,7 +199,7 @@ data-notebook-id={{notebook_id}}
 <script src="{{ static_url("js/events.js") }}" type="text/javascript" charset="utf-8"></script>
 <script src="{{ static_url("js/utils.js") }}" type="text/javascript" charset="utf-8"></script>
 <script src="{{ static_url("js/layoutmanager.js") }}" type="text/javascript" charset="utf-8"></script>
-<script src="{{ static_url("js/initmathjax.js") }}" type="text/javascript" charset="utf-8"></script>
+<script src="{{ static_url("js/mathjaxutils.js") }}" type="text/javascript" charset="utf-8"></script>
 <script src="{{ static_url("js/outputarea.js") }}" type="text/javascript" charset="utf-8"></script>
 <script src="{{ static_url("js/cell.js") }}" type="text/javascript" charset="utf-8"></script>
 <script src="{{ static_url("js/codecell.js") }}" type="text/javascript" charset="utf-8"></script>

From 346173bcad085192d9b5268fdf7c441d9fd38b49 Mon Sep 17 00:00:00 2001
From: Aron Ahmadia <aron@ahmadia.net>
Date: Tue, 9 Oct 2012 19:31:08 +0300
Subject: [PATCH 2/4] correct environment rendering

---
 .../html/notebook/static/js/mathjaxutils.js         | 13 +++++++++++--
 .../frontend/html/notebook/static/js/textcell.js    |  2 ++
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/IPython/frontend/html/notebook/static/js/mathjaxutils.js b/IPython/frontend/html/notebook/static/js/mathjaxutils.js
index 8eeeb7fb5..484751e99 100644
--- a/IPython/frontend/html/notebook/static/js/mathjaxutils.js
+++ b/IPython/frontend/html/notebook/static/js/mathjaxutils.js
@@ -17,8 +17,7 @@ IPython.mathjaxutils = (function (IPython) {
         if (window.MathJax) { 
             // MathJax loaded
             MathJax.Hub.Config({
-                TeX: { equationNumbers: { autoNumber: "AMS", useLabelIds: true },
-                       extensions: ["autoload-all.js"] },
+                TeX: { equationNumbers: { autoNumber: "AMS", useLabelIds: true } },
                 tex2jax: {
                     inlineMath: [ ['$','$'], ["\\(","\\)"] ],
                     displayMath: [ ['$$','$$'], ["\\[","\\]"] ],
@@ -220,11 +219,21 @@ IPython.mathjaxutils = (function (IPython) {
         return text;
     }
 
+    function queueRender() {
+        // see https://groups.google.com/forum/?fromgroups=#!topic/mathjax-users/cpwy5eCH1ZQ
+        MathJax.Hub.Queue( 
+          ["resetEquationNumbers",MathJax.InputJax.TeX], 
+          ["PreProcess",MathJax.Hub], 
+          ["Reprocess",MathJax.Hub] 
+          ); 
+    }
+
     return {
         init : init,
         processMath : processMath,
         removeMath : removeMath,
         replaceMath : replaceMath,
+        queueRender : queueRender
     };
 
 }(IPython));
\ No newline at end of file
diff --git a/IPython/frontend/html/notebook/static/js/textcell.js b/IPython/frontend/html/notebook/static/js/textcell.js
index 54bc5a3b9..94c776c1f 100644
--- a/IPython/frontend/html/notebook/static/js/textcell.js
+++ b/IPython/frontend/html/notebook/static/js/textcell.js
@@ -250,6 +250,8 @@ var IPython = (function (IPython) {
 
                 return '<code class="prettyprint">' + code + '</code>';
             });
+
+            IPython.mathjaxutils.queueRender()
             this.rendered = true;
         }
     };

From 2ec0115f7799805139868ab14a1782e9cc0bcd0e Mon Sep 17 00:00:00 2001
From: Aron Ahmadia <aron@ahmadia.net>
Date: Wed, 10 Oct 2012 13:55:33 +0300
Subject: [PATCH 3/4] added math typesetting example notebook

---
 .../Typesetting Math Using MathJax.ipynb      | 347 ++++++++++++++++++
 1 file changed, 347 insertions(+)
 create mode 100644 docs/examples/notebooks/Typesetting Math Using MathJax.ipynb

diff --git a/docs/examples/notebooks/Typesetting Math Using MathJax.ipynb b/docs/examples/notebooks/Typesetting Math Using MathJax.ipynb
new file mode 100644
index 000000000..3595add8e
--- /dev/null
+++ b/docs/examples/notebooks/Typesetting Math Using MathJax.ipynb	
@@ -0,0 +1,347 @@
+{
+ "metadata": {
+  "name": "Typesetting Math Using MathJax"
+ },
+ "nbformat": 3,
+ "nbformat_minor": 0,
+ "worksheets": [
+  {
+   "cells": [
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "The Markdown parser included in IPython is MathJax-aware.  This means that you can freely mix in mathematical expressions using the [MathJax subset of Tex and LaTeX](http://docs.mathjax.org/en/latest/tex.html#tex-support).  [Some examples from the MathJax site](http://www.mathjax.org/demos/tex-samples/) are reproduced below, as well as the Markdown+TeX source."
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "# Motivating Examples\n",
+      "\n",
+      "---\n",
+      "\n",
+      "## The Lorenz Equations\n",
+      "### Source\n",
+      "```\\begin{aligned}\n",
+      "\\dot{x} & = \\sigma(y-x) \\\\\n",
+      "\\dot{y} & = \\rho x - y - xz \\\\\n",
+      "\\dot{z} & = -\\beta z + xy\n",
+      "\\end{aligned}\n",
+      "```\n",
+      "### Display\n",
+      "\\begin{aligned}\n",
+      "\\dot{x} & = \\sigma(y-x) \\\\\n",
+      "\\dot{y} & = \\rho x - y - xz \\\\\n",
+      "\\dot{z} & = -\\beta z + xy\n",
+      "\\end{aligned}"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "## The Cauchy-Schwarz Inequality\n",
+      "### Source\n",
+      "```\\begin{equation*}\n",
+      "\\left( \\sum_{k=1}^n a_k b_k \\right)^2 \\leq \\left( \\sum_{k=1}^n a_k^2 \\right) \\left( \\sum_{k=1}^n b_k^2 \\right)\n",
+      "\\end{equation*}\n",
+      "```\n",
+      "### Display\n",
+      "\\begin{equation*}\n",
+      "\\left( \\sum_{k=1}^n a_k b_k \\right)^2 \\leq \\left( \\sum_{k=1}^n a_k^2 \\right) \\left( \\sum_{k=1}^n b_k^2 \\right)\n",
+      "\\end{equation*}"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "## A Cross Product Formula\n",
+      "### Source\n",
+      "```\\begin{equation*}\n",
+      "\\mathbf{V}_1 \\times \\mathbf{V}_2 =  \\begin{vmatrix}\n",
+      "\\mathbf{i} & \\mathbf{j} & \\mathbf{k} \\\\\n",
+      "\\frac{\\partial X}{\\partial u} &  \\frac{\\partial Y}{\\partial u} & 0 \\\\\n",
+      "\\frac{\\partial X}{\\partial v} &  \\frac{\\partial Y}{\\partial v} & 0\n",
+      "\\end{vmatrix}  \n",
+      "\\end{equation*}\n",
+      "```\n",
+      "### Display\n",
+      "\\begin{equation*}\n",
+      "\\mathbf{V}_1 \\times \\mathbf{V}_2 =  \\begin{vmatrix}\n",
+      "\\mathbf{i} & \\mathbf{j} & \\mathbf{k} \\\\\n",
+      "\\frac{\\partial X}{\\partial u} &  \\frac{\\partial Y}{\\partial u} & 0 \\\\\n",
+      "\\frac{\\partial X}{\\partial v} &  \\frac{\\partial Y}{\\partial v} & 0\n",
+      "\\end{vmatrix}  \n",
+      "\\end{equation*}"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "## The probability of getting \\(k\\) heads when flipping \\(n\\) coins is\n",
+      "### Source\n",
+      "```\\begin{equation*}\n",
+      "P(E)   = {n \\choose k} p^k (1-p)^{ n-k} \n",
+      "\\end{equation*}\n",
+      "```\n",
+      "### Display\n",
+      "\\begin{equation*}\n",
+      "P(E)   = {n \\choose k} p^k (1-p)^{ n-k} \n",
+      "\\end{equation*}"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "## An Identity of Ramanujan\n",
+      "### Source\n",
+      "```\\begin{equation*}\n",
+      "\\frac{1}{\\Bigl(\\sqrt{\\phi \\sqrt{5}}-\\phi\\Bigr) e^{\\frac25 \\pi}} =\n",
+      "1+\\frac{e^{-2\\pi}} {1+\\frac{e^{-4\\pi}} {1+\\frac{e^{-6\\pi}}\n",
+      "{1+\\frac{e^{-8\\pi}} {1+\\ldots} } } } \n",
+      "\\end{equation*}\n",
+      "```\n",
+      "### Display\n",
+      "\\begin{equation*}\n",
+      "\\frac{1}{\\Bigl(\\sqrt{\\phi \\sqrt{5}}-\\phi\\Bigr) e^{\\frac25 \\pi}} =\n",
+      "1+\\frac{e^{-2\\pi}} {1+\\frac{e^{-4\\pi}} {1+\\frac{e^{-6\\pi}}\n",
+      "{1+\\frac{e^{-8\\pi}} {1+\\ldots} } } } \n",
+      "\\end{equation*}"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "## A Rogers-Ramanujan Identity\n",
+      "### Source\n",
+      "```\\begin{equation*}\n",
+      "1 +  \\frac{q^2}{(1-q)}+\\frac{q^6}{(1-q)(1-q^2)}+\\cdots =\n",
+      "\\prod_{j=0}^{\\infty}\\frac{1}{(1-q^{5j+2})(1-q^{5j+3})},\n",
+      "\\quad\\quad \\text{for $|q|<1$}. \n",
+      "\\end{equation*}\n",
+      "```\n",
+      "### Display\n",
+      "\\begin{equation*}\n",
+      "1 + \\frac{q^2}{(1-q)}+\\frac{q^6}{(1-q)(1-q^2)}+\\cdots =\n",
+      "\\prod_{j=0}^{\\infty}\\frac{1}{(1-q^{5j+2})(1-q^{5j+3})},\n",
+      "\\quad\\quad \\text{for $|q|<1$}. \n",
+      "\\end{equation*}"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "## Maxwell's Equations\n",
+      "### Source\n",
+      "```\\begin{aligned}\n",
+      "\\nabla \\times \\vec{\\mathbf{B}} -\\, \\frac1c\\, \\frac{\\partial\\vec{\\mathbf{E}}}{\\partial t} & = \\frac{4\\pi}{c}\\vec{\\mathbf{j}} \\\\   \\nabla \\cdot \\vec{\\mathbf{E}} & = 4 \\pi \\rho \\\\\n",
+      "\\nabla \\times \\vec{\\mathbf{E}}\\, +\\, \\frac1c\\, \\frac{\\partial\\vec{\\mathbf{B}}}{\\partial t} & = \\vec{\\mathbf{0}} \\\\\n",
+      "\\nabla \\cdot \\vec{\\mathbf{B}} & = 0 \n",
+      "\\end{aligned}\n",
+      "```\n",
+      "### Display\n",
+      "\\begin{aligned}\n",
+      "\\nabla \\times \\vec{\\mathbf{B}} -\\, \\frac1c\\, \\frac{\\partial\\vec{\\mathbf{E}}}{\\partial t} & = \\frac{4\\pi}{c}\\vec{\\mathbf{j}} \\\\   \\nabla \\cdot \\vec{\\mathbf{E}} & = 4 \\pi \\rho \\\\\n",
+      "\\nabla \\times \\vec{\\mathbf{E}}\\, +\\, \\frac1c\\, \\frac{\\partial\\vec{\\mathbf{B}}}{\\partial t} & = \\vec{\\mathbf{0}} \\\\\n",
+      "\\nabla \\cdot \\vec{\\mathbf{B}} & = 0 \n",
+      "\\end{aligned}"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "# Equation Numbering and References\n",
+      "\n",
+      "---\n",
+      "\n",
+      "These equation reference examples are adapted from an [example page in the MathJax documentation](http://cdn.mathjax.org/mathjax/latest/test/sample-eqrefs.html).  Note that it's okay to reference equations across cells.  Click inside this cell to see the source.\n",
+      "\n",
+      "## Labeled equations and references\n",
+      "\n",
+      "Here is a labeled equation:\n",
+      "\\begin{equation}\n",
+      "x+1\\over\\sqrt{1-x^2}\\label{ref1}\n",
+      "\\end{equation}\n",
+      "\n",
+      "with a reference to ref1: \\ref{ref1},\n",
+      "and another numbered one with no label:\n",
+      "\\begin{equation}\n",
+      "x+1\\over\\sqrt{1-x^2}\n",
+      "\\end{equation}"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "## \\nonumber and equation*\n",
+      "\n",
+      "This one uses \\nonumber:\n",
+      "\\begin{equation}\n",
+      "x+1\\over\\sqrt{1-x^2}\\nonumber\n",
+      "\\end{equation}\n",
+      "\n",
+      "Here's one with the equation* environment:\n",
+      "\\begin{equation*}\n",
+      "x+1\\over\\sqrt{1-x^2}\n",
+      "\\end{equation*}"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "## Forward references\n",
+      "\n",
+      "This is a forward reference [\\ref{ref2}] and another \\eqref{ref2} for the \n",
+      "following equation:\n",
+      "\n",
+      "\\begin{equation}\n",
+      "x+1\\over\\sqrt{1-x^2}\\label{ref2}\n",
+      "\\end{equation}\n",
+      "\n",
+      "More math:\n",
+      "\\begin{equation}\n",
+      "x+1\\over\\sqrt{1-x^2}\n",
+      "\\end{equation}"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "### References inline and in environments\n",
+      "\n",
+      "Here is a ref inside math: $\\ref{ref2}+1$ and text after it.\n",
+      "\n",
+      "\\begin{align} \n",
+      "x& = y_1-y_2+y_3-y_5+y_8-\\dots \n",
+      "&& \\text{by \\eqref{ref1}}\\\\ \n",
+      "& = y'\\circ y^* && \\text{(by \\eqref{ref3})}\\\\ \n",
+      "& = y(0) y' && \\text {by Axiom 1.} \n",
+      "\\end{align} \n",
+      "\n",
+      "### Missing references\n",
+      "Here's a bad ref [\\ref{ref4}] to a nonexistent label.\n",
+      "\n",
+      "### Numbering align environments\n",
+      "An alignment:\n",
+      "\\begin{align}\n",
+      "a&=b\\label{ref3}\\cr\n",
+      "&=c+d\n",
+      "\\end{align}\n",
+      "and a starred one:\n",
+      "\\begin{align*}\n",
+      "a&=b\\cr\n",
+      "&=c+d\n",
+      "\\end{align*}"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "# Inline Typesetting (Mixing Markdown and TeX)\n",
+      "\n",
+      "---\n",
+      "\n",
+      "While display equations look good for a page of samples, the ability to mix math and *formatted* **text** in a paragraph is also important.\n",
+      "\n",
+      "## Source\n",
+      "``` This expression $\\sqrt{3x-1}+(1+x)^2$ is an example of a TeX inline equation in a **[Markdown-formatted](http://daringfireball.net/projects/markdown/)** sentence.  \n",
+      "```\n",
+      "## Display\n",
+      "This expression $\\sqrt{3x-1}+(1+x)^2$ is an example of a TeX inline equation in a **[Markdown-formatted](http://daringfireball.net/projects/markdown/)** sentence.  "
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "# Other Syntax\n",
+      "\n",
+      "---\n",
+      "\n",
+      "You will notice in other places on the web that `$$` are needed explicitly to begin and end MathJax typesetting.  This is **not** required if you will be using TeX environments, but the IPython notebook will accept this syntax on legacy notebooks.  \n",
+      "\n",
+      "### Source\n",
+      "```$$\n",
+      "\\begin{array}{c}\n",
+      "y_1 \\\\\\\n",
+      "y_2 \\mathtt{t}_i \\\\\\\n",
+      "z_{3,4}\n",
+      "\\end{array}\n",
+      "$$\n",
+      "```\n",
+      "\n",
+      "```\n",
+      "$$\n",
+      "\\begin{array}{c}\n",
+      "y_1 \\cr\n",
+      "y_2 \\mathtt{t}_i \\cr\n",
+      "y_{3}\n",
+      "\\end{array}\n",
+      "$$\n",
+      "```\n",
+      "\n",
+      "```\n",
+      "$$\\begin{eqnarray} \n",
+      "x' &=& &x \\sin\\phi &+& z \\cos\\phi \\\\\n",
+      "z' &=& - &x \\cos\\phi &+& z \\sin\\phi \\\\\n",
+      "\\end{eqnarray}$$\n",
+      "```\n",
+      "\n",
+      "```\n",
+      "$$\n",
+      "x=4\n",
+      "$$\n",
+      "```\n",
+      "\n",
+      "### Display\n",
+      "$$\n",
+      "\\begin{array}{c}\n",
+      "y_1 \\\\\\\n",
+      "y_2 \\mathtt{t}_i \\\\\\\n",
+      "z_{3,4}\n",
+      "\\end{array}\n",
+      "$$\n",
+      "\n",
+      "$$\n",
+      "\\begin{array}{c}\n",
+      "y_1 \\cr\n",
+      "y_2 \\mathtt{t}_i \\cr\n",
+      "y_{3}\n",
+      "\\end{array}\n",
+      "$$\n",
+      "\n",
+      "$$\\begin{eqnarray} \n",
+      "x' &=& &x \\sin\\phi &+& z \\cos\\phi \\\\\n",
+      "z' &=& - &x \\cos\\phi &+& z \\sin\\phi \\\\\n",
+      "\\end{eqnarray}$$\n",
+      "\n",
+      "$$\n",
+      "x=4\n",
+      "$$"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    }
+   ],
+   "metadata": {}
+  }
+ ]
+}
\ No newline at end of file

From 8d3fbe5901f783cdebc9781c3530fa9a154d5093 Mon Sep 17 00:00:00 2001
From: Aron Ahmadia <aron@ahmadia.net>
Date: Sat, 13 Oct 2012 14:29:17 +0300
Subject: [PATCH 4/4] Refactored to JS standards.  Fixed Attribution.

thisStyle      --> this_style.
function foo() --> var foo = function()

StackExchange improperly attributed for Davide Cervone's
Markdown+MathJax handling.  This has been fixed.

Ref:
http://stackoverflow.com/a/11231030/122022
http://www.math.union.edu/~dpvc/transfer/mathjax/mathjax-editing.js
---
 .../html/notebook/static/js/mathjaxutils.js   | 42 ++++++++++---------
 .../html/notebook/static/js/textcell.js       |  6 +--
 2 files changed, 26 insertions(+), 22 deletions(-)

diff --git a/IPython/frontend/html/notebook/static/js/mathjaxutils.js b/IPython/frontend/html/notebook/static/js/mathjaxutils.js
index 484751e99..2dea85e65 100644
--- a/IPython/frontend/html/notebook/static/js/mathjaxutils.js
+++ b/IPython/frontend/html/notebook/static/js/mathjaxutils.js
@@ -78,8 +78,12 @@ IPython.mathjaxutils = (function (IPython) {
         };
     };
 
-    // Some magic for deferring mathematical expressions to MathJaX
-    // Some of the code here is adapted with permission from Stack Exchange Inc.
+    // Some magic for deferring mathematical expressions to MathJax
+    // by hiding them from the Markdown parser.
+    // Some of the code here is adapted with permission from Davide Cervone
+    // under the terms of the Apache2 license governing the MathJax project.
+    // Other minor modifications are also due to StackExchange and are used with
+    // permission.
 
     var inline = "$"; // the inline math delimiter
     var blocks, start, end, last, braces; // used in searching for math
@@ -97,7 +101,7 @@ IPython.mathjaxutils = (function (IPython) {
     //  Clear the current math positions and store the index of the
     //    math, then push the math string onto the storage array.
     //  The preProcess function is called on all blocks if it has been passed in
-    function processMath(i, j, preProcess) {
+    var process_math = function (i, j, pre_process) {
         var block = blocks.slice(i, j + 1).join("").replace(/&/g, "&amp;") // use HTML entity for &
         .replace(/</g, "&lt;") // use HTML entity for <
         .replace(/>/g, "&gt;") // use HTML entity for >
@@ -110,8 +114,8 @@ IPython.mathjaxutils = (function (IPython) {
             j--;
         }
         blocks[i] = "@@" + math.length + "@@"; // replace the current block text with a unique tag to find later
-        if (preProcess)
-            block = preProcess(block);
+        if (pre_process)
+            block = pre_process(block);
         math.push(block);
         start = end = last = null;
     }
@@ -122,7 +126,7 @@ IPython.mathjaxutils = (function (IPython) {
     //  Don't allow math to pass through a double linebreak
     //    (which will be a paragraph).
     //
-    function removeMath(text) {
+    var remove_math = function (text) {
         start = end = last = null; // for tracking math delimiters
         math = []; // stores math strings for later
         
@@ -133,14 +137,14 @@ IPython.mathjaxutils = (function (IPython) {
         //     `$foo` and `$bar` are varibales.  -->  <code>$foo ` and `$bar</code> are variables.
 
         var hasCodeSpans = /`/.test(text),
-            deTilde;
+            de_tilde;
         if (hasCodeSpans) {
             text = text.replace(/~/g, "~T").replace(/(^|[^\\])(`+)([^\n]*?[^`\n])\2(?!`)/gm, function (wholematch) {
                 return wholematch.replace(/\$/g, "~D");
             });
-            deTilde = function (text) { return text.replace(/~([TD])/g, function (wholematch, character) { return { T: "~", D: "$" }[character]; }) };
+            de_tilde = function (text) { return text.replace(/~([TD])/g, function (wholematch, character) { return { T: "~", D: "$" }[character]; }) };
         } else {
-            deTilde = function (text) { return text; };
+            de_tilde = function (text) { return text; };
         }
         
         blocks = IPython.utils.regex_split(text.replace(/\r\n?/g, "\n"),MATHSPLIT);
@@ -166,13 +170,13 @@ IPython.mathjaxutils = (function (IPython) {
                         last = i
                     }
                     else {
-                        processMath(start, i, deTilde)
+                        process_math(start, i, de_tilde)
                     }
                 }
                 else if (block.match(/\n.*\n/)) {
                     if (last) {
                         i = last;
-                        processMath(start, i, deTilde)
+                        process_math(start, i, de_tilde)
                     }
                     start = end = last = null;
                     braces = 0;
@@ -202,16 +206,16 @@ IPython.mathjaxutils = (function (IPython) {
             }
         }
         if (last) {
-            processMath(start, last, deTilde)
+            process_math(start, last, de_tilde)
         }
-        return deTilde(blocks.join(""));
+        return de_tilde(blocks.join(""));
     }
 
     //
     //  Put back the math strings that were saved,
     //    and clear the math array (no need to keep it around).
     //  
-    function replaceMath(text) {
+    var replace_math = function (text) {
         text = text.replace(/@@(\d+)@@/g, function (match, n) {
             return math[n]
         });
@@ -219,7 +223,7 @@ IPython.mathjaxutils = (function (IPython) {
         return text;
     }
 
-    function queueRender() {
+    var queue_render = function () {
         // see https://groups.google.com/forum/?fromgroups=#!topic/mathjax-users/cpwy5eCH1ZQ
         MathJax.Hub.Queue( 
           ["resetEquationNumbers",MathJax.InputJax.TeX], 
@@ -230,10 +234,10 @@ IPython.mathjaxutils = (function (IPython) {
 
     return {
         init : init,
-        processMath : processMath,
-        removeMath : removeMath,
-        replaceMath : replaceMath,
-        queueRender : queueRender
+        process_math : process_math,
+        remove_math : remove_math,
+        replace_math : replace_math,
+        queue_render : queue_render
     };
 
 }(IPython));
\ No newline at end of file
diff --git a/IPython/frontend/html/notebook/static/js/textcell.js b/IPython/frontend/html/notebook/static/js/textcell.js
index 94c776c1f..8b46bbef0 100644
--- a/IPython/frontend/html/notebook/static/js/textcell.js
+++ b/IPython/frontend/html/notebook/static/js/textcell.js
@@ -222,9 +222,9 @@ var IPython = (function (IPython) {
             var text = this.get_text();
             if (text === "") { text = this.placeholder; }
 
-            text = IPython.mathjaxutils.removeMath(text)
+            text = IPython.mathjaxutils.remove_math(text)
             var html = IPython.markdown_converter.makeHtml(text);
-            html = IPython.mathjaxutils.replaceMath(html)
+            html = IPython.mathjaxutils.replace_math(html)
 
             try {
                 this.set_rendered(html);
@@ -251,7 +251,7 @@ var IPython = (function (IPython) {
                 return '<code class="prettyprint">' + code + '</code>';
             });
 
-            IPython.mathjaxutils.queueRender()
+            IPython.mathjaxutils.queue_render()
             this.rendered = true;
         }
     };