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Change readme generation so it doesn't showCode, which was a little confusing in the bitbucket page.

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    <!--
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-      --><title>README</title><meta name="generator" content="MATLAB 7.10"><meta name="date" content="2010-09-01"><meta name="m-file" content="README"><style type="text/css">
+      --><title>README</title><meta name="generator" content="MATLAB 7.10"><meta name="date" content="2010-09-27"><meta name="m-file" content="README"><style type="text/css">
 
 body {
   background-color: white;
   color: gray;
 }
 
-  </style></head><body><div class="content"><h2>Contents</h2><div><ul><li><a href="#1">DOCTEST - Run examples embedded in documentation</a></li><li><a href="#2">Example output</a></li><li><a href="#3">Failure</a></li><li><a href="#4">Defining your expectations</a></li><li><a href="#5">Expecting an error</a></li><li><a href="#6">Limitations</a></li></ul></div><h2>DOCTEST - Run examples embedded in documentation<a name="1"></a></h2><p>With doctest, you can put an example of using your function, right in the m-file help.  Then, that same example can be used like a unit test, to make sure the function still does what the docs say it does.</p><p>Here's a trivial function and its documentation:</p><pre class="codeinput">type <span class="string">add3</span>
-</pre><pre class="codeoutput">
+  </style></head><body><div class="content"><h2>Contents</h2><div><ul><li><a href="#1">DOCTEST - Run examples embedded in documentation</a></li><li><a href="#2">Example output</a></li><li><a href="#3">Failure</a></li><li><a href="#4">Defining your expectations</a></li><li><a href="#5">Expecting an error</a></li><li><a href="#6">Limitations</a></li></ul></div><h2>DOCTEST - Run examples embedded in documentation<a name="1"></a></h2><p>With doctest, you can put an example of using your function, right in the m-file help.  Then, that same example can be used like a unit test, to make sure the function still does what the docs say it does.</p><p>Here's a trivial function and its documentation:</p><pre class="codeoutput">
 function sum = add3(value)
 % adds 3 to a number
 %
 end
 
 sum = value + 3;
-</pre><h2>Example output<a name="2"></a></h2><p>Here's the output we get from running doctest on the add3 function above:</p><pre class="codeinput">doctest <span class="string">add3</span>
-</pre><pre class="codeoutput">TAP version 13
+</pre><h2>Example output<a name="2"></a></h2><p>Now we'll run</p><p>doctest add3</p><p>Here's the output we get:</p><pre class="codeoutput">TAP version 13
 1..3
 ok 1 - "add3(7)"
 ok 2 - "add3([2 4])"
 ok 3 - "add3('hi')"
-</pre><h2>Failure<a name="3"></a></h2><p>Here's an example of what happens when something changes and your test fails.</p><p>By the way, output is in the Test Anything Protocol format, which I guess is mostly used by Perl people, but it's good enough for now.  See <a href="http://testanything.org/">http://testanything.org/</a></p><p>Normally, the failure report would include a link to somewhere near the doctest that failed, but that doesn't format properly in published m-files.</p><pre class="codeinput">type <span class="string">should_fail</span>
-disp <span class="string">-------------</span>
-doctest(<span class="string">'should_fail'</span>, <span class="string">'CreateLinks'</span>, 0) <span class="comment">% the links don't work in publish()</span>
-</pre><pre class="codeoutput">
+</pre><h2>Failure<a name="3"></a></h2><p>Here's an example of what happens when something changes and your test fails.</p><p>By the way, output is in the Test Anything Protocol format, which I guess is mostly used by Perl people, but it's good enough for now.  See <a href="http://testanything.org/">http://testanything.org/</a></p><p>Normally, the failure report would include a link to somewhere near the doctest that failed, but that doesn't format properly in published m-files.</p><pre class="codeoutput">
 % Has a doctest that should fail.
 %
 % &gt;&gt; 3 + 3
 not ok 1 - "3 + 3"
     expected: ans = 5
     got     : ans = 6
-</pre><h2>Defining your expectations<a name="4"></a></h2><p>Each time doctest runs a test, it's running a line of code and checking that the output is what you say it should be.  It knows something is an example because it's a line in help('your_function') that starts with '&gt;&gt;'.  It knows what you think the output should be by starting on the line after &gt;&gt; and looking for the next &gt;&gt;, two blank lines, or the end of the documentation.</p><p>If the output of some function will change each time you call it, for instance if it includes a random number or a stack trace, you can put '***' (three asterisks) where the changing element should be.  This acts as a wildcard, and will match anything.  See the example below.</p><p>Here are some examples of formatting, both ones that work and ones that don't.</p><pre class="codeinput">type <span class="string">formatting</span>
-disp <span class="string">-------------</span>
-doctest(<span class="string">'formatting'</span>, <span class="string">'CreateLinks'</span>, 0)
-</pre><pre class="codeoutput">
+</pre><h2>Defining your expectations<a name="4"></a></h2><p>Each time doctest runs a test, it's running a line of code and checking that the output is what you say it should be.  It knows something is an example because it's a line in help('your_function') that starts with '&gt;&gt;'.  It knows what you think the output should be by starting on the line after &gt;&gt; and looking for the next &gt;&gt;, two blank lines, or the end of the documentation.</p><p>If the output of some function will change each time you call it, for instance if it includes a random number or a stack trace, you can put '***' (three asterisks) where the changing element should be.  This acts as a wildcard, and will match anything.  See the example below.</p><p>Here are some examples of formatting, both ones that work and ones that don't.</p><pre class="codeoutput">
 % formatting examples
 %
 % &gt;&gt; 1 + 1          % should work fine
     got     : ans = 5
 not ok 7 - "dicomuid       % FAILS: no wildcard on changing output"
     expected: ans = 1.3.6.1.4.1.9590.100.1.1.944807727511025110.343357080818013
-    got     : ans = 1.3.6.1.4.1.9590.100.1.2.138027182622631308123079093120036407030
+    got     : ans = 1.3.6.1.4.1.9590.100.1.2.380240475631532521024539401934020846388
 ok 8 - "dicomuid       % passes"
-</pre><h2>Expecting an error<a name="5"></a></h2><p>doctest can deal with errors, a little bit.  You might want this to test that your function correctly detects that it is being given invalid parameters.  But if your example will emit other output BEFORE the error message, the current version can't deal with that.  For more info see Issue #4 on the bitbucket site (below).  Warnings are different from errors, and they work fine.</p><pre class="codeinput">type <span class="string">errors</span>
-disp <span class="string">-------------</span>
-doctest(<span class="string">'errors'</span>, <span class="string">'CreateLinks'</span>, 0)
-</pre><pre class="codeoutput">
+</pre><h2>Expecting an error<a name="5"></a></h2><p>doctest can deal with errors, a little bit.  You might want this to test that your function correctly detects that it is being given invalid parameters.  But if your example will emit other output BEFORE the error message, the current version can't deal with that.  For more info see Issue #4 on the bitbucket site (below).  Warnings are different from errors, and they work fine.</p><pre class="codeoutput">
 % Errors and doctest - demonstrates a current limitation of doctest
 %
 % This one works fine.
 not ok 2 - "disp('if at first you don''t succeed...'); error('nevermind')"
     expected: if at first you don't succeed... ??? nevermind
     got     : ??? nevermind
-</pre><h2>Limitations<a name="6"></a></h2><p>All adjascent white space is collapsed into a single space before comparison, so right now doctest can't detect a failure that's purely a whitespace difference.</p><p>It can't run examples that are longer than one line of code (so, for example, no loops that take more than one line).  This is difficult because I haven't found a good way to mark these subsequent lines as part-of-the-source-code rather than part-of-the-result.  However, variables that you define in one line do carry over to the next.</p><p>I haven't found a good way of isolating the variables that you define in the tests from the variables used to run the test.  So, don't run CLEAR in your doctest, and don't expect WHO/WHOS to work right, and don't mess with any variables that start with doctest_.  :-/</p><p>When you're working on writing/debugging a Matlab class, you might need to run 'clear classes' to get correct results from doctests (this is a general problem with developing classes in Matlab).</p><p>The latest version from the original author, Thomas Smith, is available at <a href="http://bitbucket.org/tgs/doctest-for-matlab/src">http://bitbucket.org/tgs/doctest-for-matlab/src</a></p><p>The bugtracker is also there, let me know if you encounter any problems!</p><p class="footer"><br>
+</pre><h2>Limitations<a name="6"></a></h2><p>All adjascent white space is collapsed into a single space before comparison, so right now doctest can't detect a failure that's purely a whitespace difference.</p><p>It can't run examples that are longer than one line of code (so, for example, no loops that take more than one line).  This is difficult because I haven't found a good way to mark these subsequent lines as part-of-the-source-code rather than part-of-the-result.  However, variables that you define in one line do carry over to the next.</p><p>I haven't found a good way of isolating the variables that you define in the tests from the variables used to run the test.  So, don't run CLEAR in your doctest, and don't expect WHO/WHOS to work right, and don't mess with any variables that start with DOCTEST__.  :-/</p><p>When you're working on writing/debugging a Matlab class, you might need to run 'clear classes' to get correct results from doctests (this is a general problem with developing classes in Matlab).</p><p>The latest version from the original author, Thomas Smith, is available at <a href="http://bitbucket.org/tgs/doctest-for-matlab/src">http://bitbucket.org/tgs/doctest-for-matlab/src</a></p><p>The bugtracker is also there, let me know if you encounter any problems!</p><p class="footer"><br>
       Published with MATLAB&reg; 7.10<br></p></div><!--
 ##### SOURCE BEGIN #####
 %% DOCTEST - Run examples embedded in documentation
 
 %% Example output
 %
-% Here's the output we get from running doctest on the add3 function above:
+% Now we'll run
+%
+% doctest add3
+%
+% Here's the output we get:
 %
 
 doctest add3
 % I haven't found a good way of isolating the variables that you define in
 % the tests from the variables used to run the test.  So, don't run CLEAR
 % in your doctest, and don't expect WHO/WHOS to work right, and don't mess
-% with any variables that start with doctest_.  :-/
+% with any variables that start with DOCTEST__.  :-/
 % 
 % When you're working on writing/debugging a Matlab class, you might need
 % to run 'clear classes' to get correct results from doctests (this is a
 % The bugtracker is also there, let me know if you encounter any problems!
 %
 %
+
 ##### SOURCE END #####
 --></body></html>
 
 ::
 
-    type add3
-
-::
-
     function sum = add3(value)
     % adds 3 to a number
     %
 Example output
 --------------
 
-Here's the output we get from running doctest on the add3 function
-above:
+Now we'll run
 
-::
+doctest add3
 
-    doctest add3
+Here's the output we get:
 
 ::
 
 
 ::
 
-    type should_fail
-    disp -------------
-    doctest('should_fail', 'CreateLinks', 0) % the links don't work in publish()
-
-::
-
     % Has a doctest that should fail.
     %
     % >> 3 + 3
 
 ::
 
-    type formatting
-    disp -------------
-    doctest('formatting', 'CreateLinks', 0)
-
-::
-
     % formatting examples
     %
     % >> 1 + 1          % should work fine
         got     : ans = 5
     not ok 7 - "dicomuid       % FAILS: no wildcard on changing output"
         expected: ans = 1.3.6.1.4.1.9590.100.1.1.944807727511025110.343357080818013
-        got     : ans = 1.3.6.1.4.1.9590.100.1.2.138027182622631308123079093120036407030
+        got     : ans = 1.3.6.1.4.1.9590.100.1.2.380240475631532521024539401934020846388
     ok 8 - "dicomuid       % passes"
 
 Expecting an error
 
 ::
 
-    type errors
-    disp -------------
-    doctest('errors', 'CreateLinks', 0)
-
-::
-
     % Errors and doctest - demonstrates a current limitation of doctest
     %
     % This one works fine.
 I haven't found a good way of isolating the variables that you
 define in the tests from the variables used to run the test. So,
 don't run CLEAR in your doctest, and don't expect WHO/WHOS to work
-right, and don't mess with any variables that start with doctest\_.
-:-/
+right, and don't mess with any variables that start with
+DOCTEST\_\_. :-/
 
 When you're working on writing/debugging a Matlab class, you might
 need to run 'clear classes' to get correct results from doctests
 
 %% Example output
 %
-% Here's the output we get from running doctest on the add3 function above:
+% Now we'll run
+%
+% doctest add3
+%
+% Here's the output we get:
 %
 
 doctest add3
 % I haven't found a good way of isolating the variables that you define in
 % the tests from the variables used to run the test.  So, don't run CLEAR
 % in your doctest, and don't expect WHO/WHOS to work right, and don't mess
-% with any variables that start with doctest_.  :-/
+% with any variables that start with DOCTEST__.  :-/
 % 
 % When you're working on writing/debugging a Matlab class, you might need
 % to run 'clear classes' to get correct results from doctests (this is a
 %
 % The bugtracker is also there, let me know if you encounter any problems!
 %
-%
+%
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 opts.format = 'html';
 opts.outputDir = '..';
+opts.showCode = false;
 
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