Small fixes

FCP-INDI · Jan 4, 2016 · 0f77bc8 · 0f77bc8
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diff --git a/docs/user/_sources/help.txt b/docs/user/_sources/help.txt
@@ -31,7 +31,7 @@ Common Issues and Solutions
 
 #. I'm trying to run the C-PAC GUI on a Mac with Anaconda, but I am being told that I need a "Framework build of python".  What is wrong with Anaconda?
 
-	Good news: nothing is wrong with Anaconda!  This error comes up because wx (the framework the C-PAC GUI is based upon) does not play well with Anaconda sometimes, but there is a fix.  Specifically, you must set your PYTHONPATH variable to point to your Anaconda environment.  To do this, add ``export PYTHONHOME=/home/<your_username>/anaconda`` to your .bash_profile file (in addition to the FSL and AFNI variables), open a fresh terminal, and type `cpac_gui`.
+	Good news: nothing is wrong with Anaconda!  This error comes up because wx (the framework the C-PAC GUI is based upon) does not play well with Anaconda sometimes, but there is a fix.  Specifically, you must set your PYTHONHOME variable to point to your Anaconda environment.  To do this, add ``export PYTHONHOME=/home/<your_username>/anaconda`` to your .bash_profile file (in addition to the FSL and AFNI variables), open a fresh terminal, and type `cpac_gui`.
 
 #. I'm re-running a pipeline, but I am receiving many crashes.  Most of these crashes tell me that a file that has been moved or no longer exists is being used as an input for a step in the C-PAC pipeline.  What is going on and how can I tell C-PAC to use the correct inputs?
 

diff --git a/docs/user/help.html b/docs/user/help.html
@@ -75,7 +75,7 @@ <h2>Common Issues and Solutions<a class="headerlink" href="#common-issues-and-so
 </li>
 <li><p class="first">I&#8217;m trying to run the C-PAC GUI on a Mac with Anaconda, but I am being told that I need a &#8220;Framework build of python&#8221;.  What is wrong with Anaconda?</p>
 <blockquote>
-<div><p>Good news: nothing is wrong with Anaconda!  This error comes up because wx (the framework the C-PAC GUI is based upon) does not play well with Anaconda sometimes, but there is a fix.  Specifically, you must set your PYTHONPATH variable to point to your Anaconda environment.  To do this, add <tt class="docutils literal"><span class="pre">export</span> <span class="pre">PYTHONHOME=/home/&lt;your_username&gt;/anaconda</span></tt> to your .bash_profile file (in addition to the FSL and AFNI variables), open a fresh terminal, and type <cite>cpac_gui</cite>.</p>
+<div><p>Good news: nothing is wrong with Anaconda!  This error comes up because wx (the framework the C-PAC GUI is based upon) does not play well with Anaconda sometimes, but there is a fix.  Specifically, you must set your PYTHONHOME variable to point to your Anaconda environment.  To do this, add <tt class="docutils literal"><span class="pre">export</span> <span class="pre">PYTHONHOME=/home/&lt;your_username&gt;/anaconda</span></tt> to your .bash_profile file (in addition to the FSL and AFNI variables), open a fresh terminal, and type <cite>cpac_gui</cite>.</p>
 </div></blockquote>
 </li>
 <li><p class="first">I&#8217;m re-running a pipeline, but I am receiving many crashes.  Most of these crashes tell me that a file that has been moved or no longer exists is being used as an input for a step in the C-PAC pipeline.  What is going on and how can I tell C-PAC to use the correct inputs?</p>
@@ -147,4 +147,4 @@ <h3>Navigation</h3>
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
-</html>
+</html>
diff --git a/docs/user/install.html b/docs/user/install.html
@@ -6,15 +6,15 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 
-    <title>Installing C-PAC &mdash; C-PAC 0.4.0 Alpha documentation</title>
+    <title>Installing C-PAC &mdash; C-PAC 0.3.9 Alpha documentation</title>
 
     <link rel="stylesheet" href="_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
 
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    './',
-        VERSION:     '0.4.0 Alpha',
+        VERSION:     '0.3.9 Alpha',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -24,7 +24,7 @@
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-    <link rel="top" title="C-PAC 0.4.0 Alpha documentation" href="index.html" />
+    <link rel="top" title="C-PAC 0.3.9 Alpha documentation" href="index.html" />
     <link rel="next" title="Using C-PAC" href="use.html" />
     <link rel="prev" title="Welcome to C-PAC’s Documentation!" href="index.html" /> 
   </head>
@@ -41,7 +41,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="index.html" title="Welcome to C-PAC’s Documentation!"
              accesskey="P">previous</a> |</li>
-        <li><a href="index.html">C-PAC 0.4.0 Alpha documentation</a> &raquo;</li> 
+        <li><a href="index.html">C-PAC 0.3.9 Alpha documentation</a> &raquo;</li> 
       </ul>
     </div>  
 
@@ -408,12 +408,12 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="index.html" title="Welcome to C-PAC’s Documentation!"
              >previous</a> |</li>
-        <li><a href="index.html">C-PAC 0.4.0 Alpha documentation</a> &raquo;</li> 
+        <li><a href="index.html">C-PAC 0.3.9 Alpha documentation</a> &raquo;</li> 
       </ul>
     </div>
     <div class="footer">
         &copy; Copyright 2015, C-PAC Team.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
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   </body>
-</html>
+</html>