Lots of book formatting changes.

Changed default sizes of plots, changed the book template for
pdf creation, and lots of minor edits, most changing bold to
italic, and removing italic for emphasis.

code/book_plots.py

@@ -101,17 +101,6 @@ def plot_measurements(xs, ys=None, color='k', lw=2, label='Measurements',
     """
 
     plt.autoscale(tight=True)
-    '''if ys is not None:
-        plt.scatter(xs, ys, marker=marker, c=c, s=s,
-                    label=label, alpha=alpha)
-        if connect:
-           plt.plot(xs, ys, c=c, lw=1, alpha=alpha)
-    else:
-        plt.scatter(range(len(xs)), xs, marker=marker, c=c, s=s,
-                    label=label, alpha=alpha)
-        if connect:
-           plt.plot(range(len(xs)), xs, lw=1, c=c, alpha=alpha)'''
-
     if lines:
         if ys is not None:
             plt.plot(xs, ys, color=color, lw=lw, ls='--', label=label, **kwargs)

code/custom.css

@@ -4,6 +4,9 @@
 @import url('http://fonts.googleapis.com/css?family=Arimo');
 @import url('http://fonts.googleapis.com/css?family=Fira_sans');
 
+.CodeMirror pre {
+    font-family: 'Source Code Pro', Consolas, monocco, monospace;
+}
     div.cell{
         width: 900px;
         margin-left: 0% !important;
@@ -23,7 +26,7 @@
 	
     div.input_area {
         background: #F6F6F9;
-        border: 1px solid #586e75;
+        border: 1px solid #586e75;      
     }
 
     .text_cell_render h1 {
@@ -82,6 +85,7 @@
     h5 {
         font-family: 'Open sans',verdana,arial,sans-serif;
     }
+
     .text_cell_render h5 {
         font-weight: 200;
         font-style: normal;
@@ -116,7 +120,8 @@
 }
 
     code{
-      font-size: 70%;
+        font-size: 6pt;
+
     }
     .rendered_html code{
     background-color: transparent;
@@ -209,7 +214,8 @@
 <script>
     MathJax.Hub.Config({
                         TeX: {
-                           extensions: ["AMSmath.js", "autobold.js"]
+                           extensions: ["AMSmath.js"],
+                           equationNumbers: { autoNumber: "AMS", useLabelIds: true}
                            },
                 tex2jax: {
                     inlineMath: [ ['$','$'], ["\\(","\\)"] ],
@@ -217,7 +223,7 @@
                 },
                 displayAlign: 'center', // Change this to 'center' to center equations.
                 "HTML-CSS": {
-                    scale:100,
+                    scale:95,
                         availableFonts: [],
                         preferredFont:null,
                         webFont: "TeX",