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2 new revisions:

Revision: 435a50210cb6
Branch: default
Author: "Hans Petter Langtangen <h...@simula.no>"
Date: Sat Jun 29 16:04:09 2013
Log: Bugfixes. New tests run.
http://code.google.com/p/doconce/source/detail?r=435a50210cb6

Revision: de1b5fe70fc7
Branch: default
Author: "Hans Petter Langtangen <h...@simula.no>"
Date: Sat Jun 29 16:04:53 2013
Log: Added a testdoc demo file for reference.
http://code.google.com/p/doconce/source/detail?r=de1b5fe70fc7

==============================================================================
Revision: 435a50210cb6
Branch: default
Author: "Hans Petter Langtangen <h...@simula.no>"
Date: Sat Jun 29 16:04:09 2013
Log: Bugfixes. New tests run.
http://code.google.com/p/doconce/source/detail?r=435a50210cb6

Modified:
/doc/demos/quickref/html/.buildinfo
/doc/demos/quickref/html/_sources/quickref.txt
/doc/demos/quickref/html/_static/pygments.css
/doc/demos/quickref/html/_static/searchtools.js
/doc/demos/quickref/html/genindex.html
/doc/demos/quickref/html/index.html
/doc/demos/quickref/html/quickref.html
/doc/demos/quickref/html/search.html
/doc/demos/quickref/html/searchindex.js
/doc/demos/quickref/quickref.cwiki
/doc/demos/quickref/quickref.do.txt
/doc/demos/quickref/quickref.epytext
/doc/demos/quickref/quickref.gwiki
/doc/demos/quickref/quickref.html
/doc/demos/quickref/quickref.md
/doc/demos/quickref/quickref.mwiki
/doc/demos/quickref/quickref.p.tex
/doc/demos/quickref/quickref.pdf
/doc/demos/quickref/quickref.rst
/doc/demos/quickref/quickref.rst.html
/doc/demos/quickref/quickref.rst.pdf
/doc/demos/quickref/quickref.rst.tex
/doc/demos/quickref/quickref.st
/doc/demos/quickref/quickref.tex
/doc/demos/quickref/quickref.txt
/doc/demos/quickref/quickref.xml
/lib/doconce/doconce.py
/test/_testdoc.do.txt
/test/author1.do.txt
/test/make.sh
/test/refs3.bib
/test/test.r

=======================================
--- /doc/demos/quickref/html/.buildinfo Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/html/.buildinfo Sat Jun 29 16:04:09 2013
@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When
it is not found, a full rebuild will be done.
-config: 9ca91569b20bc2d4094df3d5df526c30
+config: e6de0e0cefa732423aa1a265b1f9c917
tags: fbb0d17656682115ca4d033fb2f83ba1
=======================================
--- /doc/demos/quickref/html/_sources/quickref.txt Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/html/_sources/quickref.txt Sat Jun 29 16:04:09 2013
@@ -5,7 +5,7 @@
-----------------------

:Author: Hans Petter Langtangen
-:Date: Jul 13, 2013
+:Date: Jun 29, 2013

**WARNING: This quick reference is very incomplete!**

@@ -510,6 +510,27 @@
rendered nicely anyway.

+Hyperlinks
+----------
+
+Links use either a link text or the raw URL:
+
+
+.. code-block:: text
+
+
+ Here is some "some link text": "http://some.net/address"
+ (as in "search google": "http://google.com")
+ or just the raw address: URL: "http://google.com".
+
+ Links to files typeset in verbatim mode applies backtics:
+ "`myfile.py`": "http://some.net/some/place/myfile.py".
+
+ Mail addresses works too: send problems to
+ "`h...@simula.no`": "mailto:h...@simula.no"
+ or just "send mail": "mailto:h...@simula.no".
+
+
Figures and Movies
------------------

=======================================
--- /doc/demos/quickref/html/_static/pygments.css Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/html/_static/pygments.css Sat Jun 29 16:04:09 2013
@@ -13,11 +13,11 @@
.highlight .gr { color: #FF0000 } /* Generic.Error */
.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
.highlight .gi { color: #00A000 } /* Generic.Inserted */
-.highlight .go { color: #333333 } /* Generic.Output */
+.highlight .go { color: #303030 } /* Generic.Output */
.highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */
.highlight .gs { font-weight: bold } /* Generic.Strong */
.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading
*/
-.highlight .gt { color: #0044DD } /* Generic.Traceback */
+.highlight .gt { color: #0040D0 } /* Generic.Traceback */
.highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */
.highlight .kd { color: #007020; font-weight: bold } /*
Keyword.Declaration */
.highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace
*/
=======================================
--- /doc/demos/quickref/html/_static/searchtools.js Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/html/_static/searchtools.js Sat Jun 29 16:04:09 2013
@@ -301,7 +301,7 @@
},

query : function(query) {
- var stopwords =
["and","then","into","it","as","are","in","if","for","no","there","their","was","is","be","to","that","but","they","not","such","with","by","a","on","these","of","will","this","near","the","or","at"];
+ var stopwords =
["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];

// Stem the searchterms and add them to the correct list
var stemmer = new Stemmer();
=======================================
--- /doc/demos/quickref/html/genindex.html Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/html/genindex.html Sat Jun 29 16:04:09 2013
@@ -17,7 +17,7 @@

<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '',
+ URL_ROOT: './',
VERSION: '0.7',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
@@ -98,7 +98,7 @@
</div>
<div class="footer">
© Copyright 2013, HPL.
- Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.2pre.
</div>
</body>
</html>
=======================================
--- /doc/demos/quickref/html/index.html Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/html/index.html Sat Jun 29 16:04:09 2013
@@ -15,7 +15,7 @@

<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '',
+ URL_ROOT: './',
VERSION: '0.7',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
@@ -72,6 +72,7 @@
<li class="toctree-l1"><a class="reference internal"
href="quickref.html#inline-comments">Inline comments</a></li>
<li class="toctree-l1"><a class="reference internal"
href="quickref.html#verbatim-computer-code">Verbatim/Computer Code</a></li>
<li class="toctree-l1"><a class="reference internal"
href="quickref.html#latex-mathematics">LaTeX Mathematics</a></li>
+<li class="toctree-l1"><a class="reference internal"
href="quickref.html#hyperlinks">Hyperlinks</a></li>
<li class="toctree-l1"><a class="reference internal"
href="quickref.html#figures-and-movies">Figures and Movies</a></li>
<li class="toctree-l1"><a class="reference internal"
href="quickref.html#tables">Tables</a></li>
<li class="toctree-l1"><a class="reference internal"
href="quickref.html#labels-and-references">Labels and References</a></li>
@@ -148,7 +149,7 @@
</div>
<div class="footer">
© Copyright 2013, HPL.
- Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.2pre.
</div>
</body>
</html>
=======================================
--- /doc/demos/quickref/html/quickref.html Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/html/quickref.html Sat Jun 29 16:04:09 2013
@@ -15,7 +15,7 @@

<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '',
+ URL_ROOT: './',
VERSION: '0.7',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
@@ -64,7 +64,7 @@
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Author:</th><td
class="field-body">Hans Petter Langtangen</td>
</tr>
-<tr class="field-even field"><th class="field-name">Date:</th><td
class="field-body">Jul 13, 2013</td>
+<tr class="field-even field"><th class="field-name">Date:</th><td
class="field-body">Jun 29, 2013</td>
</tr>
</tbody>
</table>
@@ -545,6 +545,22 @@
<tt class="docutils literal"><span class="pre">mwiki</span></tt>, <tt
class="docutils literal"><span class="pre">ipynb</span></tt>, and <tt
class="docutils literal"><span class="pre">pandoc</span></tt>, the
mathematics in newcommands is
rendered nicely anyway.</p>
</div>
+<div class="section" id="hyperlinks">
+<h1>Hyperlinks<a class="headerlink" href="#hyperlinks" title="Permalink to
this headline">¶</a></h1>
+<p>Links use either a link text or the raw URL:</p>
+<div class="highlight-text"><div class="highlight"><pre>Here is some
"some link text": "http://some.net/address"
+(as in "search google": "http://google.com")
+or just the raw address: URL: "http://google.com".
+
+Links to files typeset in verbatim mode applies backtics:
+"`myfile.py`": "http://some.net/some/place/myfile.py".
+
+Mail addresses works too: send problems to
+"`h...@simula.no`": "mailto:h...@simula.no"
+or just "send mail": "mailto:h...@simula.no".
+</pre></div>
+</div>
+</div>
<div class="section" id="figures-and-movies">
<h1>Figures and Movies<a class="headerlink" href="#figures-and-movies"
title="Permalink to this headline">¶</a></h1>
<p>Figures and movies have almost equal syntax:</p>
@@ -1077,6 +1093,7 @@
<li><a class="reference internal" href="#inline-comments">Inline
comments</a></li>
<li><a class="reference internal"
href="#verbatim-computer-code">Verbatim/Computer Code</a></li>
<li><a class="reference internal" href="#latex-mathematics">LaTeX
Mathematics</a></li>
+<li><a class="reference internal" href="#hyperlinks">Hyperlinks</a></li>
<li><a class="reference internal" href="#figures-and-movies">Figures and
Movies</a></li>
<li><a class="reference internal" href="#tables">Tables</a></li>
<li><a class="reference internal" href="#labels-and-references">Labels and
References</a></li>
@@ -1129,7 +1146,7 @@
</div>
<div class="footer">
© Copyright 2013, HPL.
- Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.2pre.
</div>
</body>
</html>
=======================================
--- /doc/demos/quickref/html/search.html Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/html/search.html Sat Jun 29 16:04:09 2013
@@ -15,7 +15,7 @@

<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '',
+ URL_ROOT: './',
VERSION: '0.7',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
@@ -102,7 +102,7 @@
</div>
<div class="footer">
© Copyright 2013, HPL.
- Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.2pre.
</div>
</body>
</html>
=======================================
--- /doc/demos/quickref/html/searchindex.js Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/html/searchindex.js Sat Jun 29 16:04:09 2013
@@ -1,1 +1,1 @@
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Quick
Reference","On an Ultimate Markup
Language"],objnames:{},filenames:["quickref","index"]})
=======================================
--- /doc/demos/quickref/quickref.cwiki Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/quickref.cwiki Sat Jun 29 16:04:09 2013
@@ -1,7 +1,7 @@
#summary Doconce Quick Reference
<wiki:toc max_depth="2" />
By **Hans Petter Langtangen**
-=== Jul 13, 2013 ===
+=== Jun 29, 2013 ===

<<TableOfContents>>

@@ -427,6 +427,23 @@
{{{mwiki}}}, {{{ipynb}}}, and {{{pandoc}}}, the mathematics in newcommands
is
rendered nicely anyway.

+
+== Hyperlinks ==
+
+Links use either a link text or the raw URL:
+
+{{{
+Here is some "some link text": "http://some.net/address"
+(as in "search google": "http://google.com")
+or just the raw address: URL: "http://google.com".
+
+Links to files typeset in verbatim mode applies backtics:
+"`myfile.py`": "http://some.net/some/place/myfile.py".
+
+Mail addresses works too: send problems to
+"`h...@simula.no`": "mailto:h...@simula.no"
+or just "send mail": "mailto:h...@simula.no".
+}}}

== Figures and Movies ==

=======================================
--- /doc/demos/quickref/quickref.do.txt Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/quickref.do.txt Sat Jun 29 16:04:09 2013
@@ -429,6 +429,23 @@
rendered nicely anyway.

+===== Hyperlinks =====
+
+Links use either a link text or the raw URL:
+
+!bc
+Here is some "some link text": "http://some.net/address"
+(as in "search google": "http://google.com")
+or just the raw address: URL: "http://google.com".
+
+Links to files typeset in verbatim mode applies backtics:
+"`myfile.py`": "http://some.net/some/place/myfile.py".
+
+Mail addresses works too: send problems to
+"`h...@simula.no`": "mailto:h...@simula.no"
+or just "send mail": "mailto:h...@simula.no".
+!ec
+
===== Figures and Movies =====

Figures and movies have almost equal syntax:
=======================================
--- /doc/demos/quickref/quickref.epytext Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/quickref.epytext Sat Jun 29 16:04:09 2013
@@ -1,6 +1,6 @@
TITLE: Doconce Quick Reference
BY: Hans Petter Langtangen (Center for Biomedical Computing, Simula
Research Laboratory, and Department of Informatics, University of Oslo)
-DATE: Jul 13, 2013
+DATE: Jun 29, 2013
B{WARNING: This quick reference is very incomplete!}

I{Mission.} Enable writing documentation with much mathematics and
@@ -446,6 +446,24 @@
rendered nicely anyway.

+Hyperlinks
+----------
+
+Links use either a link text or the raw URL::
+
+
+ Here is some "some link text": "http://some.net/address"
+ (as in "search google": "http://google.com")
+ or just the raw address: URL: "http://google.com".
+
+ Links to files typeset in verbatim mode applies backtics:
+ "`myfile.py`": "http://some.net/some/place/myfile.py".
+
+ Mail addresses works too: send problems to
+ "`h...@simula.no`": "mailto:h...@simula.no"
+ or just "send mail": "mailto:h...@simula.no".
+
+
Figures and Movies
------------------

=======================================
--- /doc/demos/quickref/quickref.gwiki Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/quickref.gwiki Sat Jun 29 16:04:09 2013
@@ -1,7 +1,7 @@
#summary Doconce Quick Reference

By *Hans Petter Langtangen*
-==== Jul 13, 2013 ====
+==== Jun 29, 2013 ====

<wiki: toc max_depth="2" />

@@ -425,6 +425,23 @@
`mwiki`, `ipynb`, and `pandoc`, the mathematics in newcommands is
rendered nicely anyway.

+
+==== Hyperlinks ====
+
+Links use either a link text or the raw URL:
+
+{{{
+Here is some "some link text": "http://some.net/address"
+(as in "search google": "http://google.com")
+or just the raw address: URL: "http://google.com".
+
+Links to files typeset in verbatim mode applies backtics:
+"`myfile.py`": "http://some.net/some/place/myfile.py".
+
+Mail addresses works too: send problems to
+"`h...@simula.no`": "mailto:h...@simula.no"
+or just "send mail": "mailto:h...@simula.no".
+}}}

==== Figures and Movies ====

=======================================
--- /doc/demos/quickref/quickref.html Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/quickref.html Sat Jun 29 16:04:09 2013
@@ -12,6 +12,8 @@

<style type="text/css">
+ /* blueish style */
+
/* Color definitions: http://www.december.com/html/spec/color0.html
CSS examples: http://www.w3schools.com/css/css_examples.asp */

@@ -73,20 +75,21 @@
(' Inline comments ', 2, None, '___sec7'),
(' Verbatim/Computer Code ', 2, None, '___sec8'),
(' LaTeX Mathematics ', 2, None, '___sec9'),
- (' Figures and Movies ', 2, None, '___sec10'),
- (' Tables ', 2, None, '___sec11'),
- (' Labels and References ', 2, None, '___sec12'),
- (' Citations and Bibliography ', 2, None, '___sec13'),
- (' Generalized Citations ', 2, None, '___sec14'),
- (' Index of Keywords ', 2, None, '___sec15'),
+ (' Hyperlinks ', 2, None, '___sec10'),
+ (' Figures and Movies ', 2, None, '___sec11'),
+ (' Tables ', 2, None, '___sec12'),
+ (' Labels and References ', 2, None, '___sec13'),
+ (' Citations and Bibliography ', 2, None, '___sec14'),
+ (' Generalized Citations ', 2, None, '___sec15'),
+ (' Index of Keywords ', 2, None, '___sec16'),
(' Capabilities of The Program `doconce` ',
2,
None,
- '___sec16'),
- (' Exercises ', 2, None, '___sec17'),
- (' Environments ', 2, None, '___sec18'),
- (' Preprocessing ', 2, None, '___sec19'),
- (' Resources ', 2, None, '___sec20')]}
+ '___sec17'),
+ (' Exercises ', 2, None, '___sec18'),
+ (' Environments ', 2, None, '___sec19'),
+ (' Preprocessing ', 2, None, '___sec20'),
+ (' Resources ', 2, None, '___sec21')]}
end of tocinfo -->

<body>
@@ -132,7 +135,7 @@
<center>[1] <b>Center for Biomedical Computing, Simula Research
Laboratory</b></center>
<center>[2] <b>Department of Informatics, University of Oslo</b></center>
<p>
-<center><h4>Jul 13, 2013</h4></center> 
+<center><h4>Jun 29, 2013</h4></center> 

<h2>Table of contents</h2>

@@ -147,17 +150,18 @@
<a href="#___sec7"> Inline comments </a><br>
<a href="#___sec8"> Verbatim/Computer Code </a><br>
<a href="#___sec9"> LaTeX Mathematics </a><br>
-<a href="#___sec10"> Figures and Movies </a><br>
-<a href="#___sec11"> Tables </a><br>
-<a href="#___sec12"> Labels and References </a><br>
-<a href="#___sec13"> Citations and Bibliography </a><br>
-<a href="#___sec14"> Generalized Citations </a><br>
-<a href="#___sec15"> Index of Keywords </a><br>
-<a href="#___sec16"> Capabilities of The Program <code>doconce</code>
</a><br>
-<a href="#___sec17"> Exercises </a><br>
-<a href="#___sec18"> Environments </a><br>
-<a href="#___sec19"> Preprocessing </a><br>
-<a href="#___sec20"> Resources </a><br>
+<a href="#___sec10"> Hyperlinks </a><br>
+<a href="#___sec11"> Figures and Movies </a><br>
+<a href="#___sec12"> Tables </a><br>
+<a href="#___sec13"> Labels and References </a><br>
+<a href="#___sec14"> Citations and Bibliography </a><br>
+<a href="#___sec15"> Generalized Citations </a><br>
+<a href="#___sec16"> Index of Keywords </a><br>
+<a href="#___sec17"> Capabilities of The Program <code>doconce</code>
</a><br>
+<a href="#___sec18"> Exercises </a><br>
+<a href="#___sec19"> Environments </a><br>
+<a href="#___sec20"> Preprocessing </a><br>
+<a href="#___sec21"> Resources </a><br>

<p>
<b>WARNING: This quick reference is very incomplete!</b>
@@ -666,7 +670,27 @@
<code>mwiki</code>, <code>ipynb</code>, and <code>pandoc</code>, the
mathematics in newcommands is
rendered nicely anyway.

-<h3>Figures and Movies <a name="___sec10"></a></h3>
+<h3>Hyperlinks <a name="___sec10"></a></h3>
+
+<p>
+Links use either a link text or the raw URL:
+
+<p>
+
+<pre><code>Here is some "some link text":
"http://some.net/address"
+(as in "search google": "http://google.com")
+or just the raw address: URL: "http://google.com".
+
+Links to files typeset in verbatim mode applies backtics:
+"`myfile.py`": "http://some.net/some/place/myfile.py".
+
+Mail addresses works too: send problems to
+"`h...@simula.no`": "mailto:h...@simula.no"
+or just "send mail": "mailto:h...@simula.no".
+</code></pre>
+
+
+<h3>Figures and Movies <a name="___sec11"></a></h3>

<p>
Figures and movies have almost equal syntax:
@@ -735,7 +759,7 @@

<em>Vimeo movie.</em>

-<h3>Tables <a name="___sec11"></a></h3>
+<h3>Tables <a name="___sec12"></a></h3>

<p>
The table in the section <a href="#quick:sections">Section Types</a> was
written with this
@@ -780,7 +804,7 @@
where <code>X</code> is the table number. This feature makes it easy to
load tables into spreadsheet programs for further analysis.

-<h3>Labels and References <a name="___sec12"></a></h3>
+<h3>Labels and References <a name="___sec13"></a></h3>

<p>
The notion of labels and references (as well as bibliography and index)
@@ -810,7 +834,7 @@
by "Section" or "Chapter", or in case of an equation, surround the
reference by parenthesis.

-<h3>Citations and Bibliography <a name="___sec13"></a></h3>
+<h3>Citations and Bibliography <a name="___sec14"></a></h3>

<p>
Single citations are written as
@@ -838,7 +862,7 @@
(which Doconce needs to create bibliographies in other formats
than LaTeX).

-<h3>Generalized Citations <a name="___sec14"></a></h3>
+<h3>Generalized Citations <a name="___sec15"></a></h3>

<p>
There is a <em>generalized referencing</em> feature in Doconce that allows
@@ -870,7 +894,7 @@
documents. If none of the two situations above applies, the
<code>external</code> text will be the output.

-<h3>Index of Keywords <a name="___sec15"></a></h3>
+<h3>Index of Keywords <a name="___sec16"></a></h3>

<p>
Doconce supports creating an index of keywords. A certain keyword
@@ -887,7 +911,7 @@
forthcoming text. The index is only produced for the <code>latex</code>,
<code>pdflatex</code>, <code>rst</code>, and <code>sphinx</code> formats.

-<h3>Capabilities of The Program <code>doconce</code> <a
name="___sec16"></a></h3>
+<h3>Capabilities of The Program <code>doconce</code> <a
name="___sec17"></a></h3>

<p>
The <code>doconce</code> program can be used for a number of purposes
besides
@@ -1034,7 +1058,7 @@
</code></pre>


-<h3>Exercises <a name="___sec17"></a></h3>
+<h3>Exercises <a name="___sec18"></a></h3>

<p>
Doconce supports <em>Exercise</em>, <em>Problem</em>, <em>Project</em>,
and <em>Example</em>.
@@ -1152,7 +1176,7 @@
turn off output of answers and solutions, respectively, except for
examples.

-<h3>Environments <a name="___sec18"></a></h3>
+<h3>Environments <a name="___sec19"></a></h3>

<p>
Doconce environments start with <code>!benvirname</code> and end with
<code>!eenvirname</code>,
@@ -1175,7 +1199,7 @@
slide</li>
</ul>

-<h3>Preprocessing <a name="___sec19"></a></h3>
+<h3>Preprocessing <a name="___sec20"></a></h3>

<p>
Doconce documents may utilize a preprocessor, either
<code>preprocess</code> and/or
@@ -1229,7 +1253,7 @@
some illustrations on how to utilize <code>mako</code> (clone the GitHub
project and
examine the Doconce source and the <code>doc/src/make.sh</code> script).

-<h3>Resources <a name="___sec20"></a></h3>
+<h3>Resources <a name="___sec21"></a></h3>

<p>

=======================================
--- /doc/demos/quickref/quickref.md Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/quickref.md Sat Jun 29 16:04:09 2013
@@ -1,6 +1,6 @@
% Doconce Quick Reference
% Hans Petter Langtangen at Center for Biomedical Computing, Simula
Research Laboratory and Department of Informatics, University of Oslo
-% Jul 13, 2013
+% Jun 29, 2013



@@ -480,6 +480,24 @@
rendered nicely anyway.

+### Hyperlinks
+
+Links use either a link text or the raw URL:
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Here is some "some link text": "http://some.net/address"
+(as in "search google": "http://google.com")
+or just the raw address: URL: "http://google.com".
+
+Links to files typeset in verbatim mode applies backtics:
+"`myfile.py`": "http://some.net/some/place/myfile.py".
+
+Mail addresses works too: send problems to
+"`h...@simula.no`": "mailto:h...@simula.no"
+or just "send mail": "mailto:h...@simula.no".
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
### Figures and Movies

Figures and movies have almost equal syntax:
=======================================
--- /doc/demos/quickref/quickref.mwiki Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/quickref.mwiki Sat Jun 29 16:04:09 2013
@@ -1,7 +1,7 @@
#TITLE (actually governed by the filename): Doconce Quick Reference

By '''Hans Petter Langtangen'''
-==== Jul 13, 2013 ====
+==== Jun 29, 2013 ====

__TOC__

@@ -456,6 +456,23 @@
rendered nicely anyway.

+==== Hyperlinks ====
+
+Links use either a link text or the raw URL:
+
+<syntaxhighlight lang="text">
+Here is some "some link text": "http://some.net/address"
+(as in "search google": "http://google.com")
+or just the raw address: URL: "http://google.com".
+
+Links to files typeset in verbatim mode applies backtics:
+"`myfile.py`": "http://some.net/some/place/myfile.py".
+
+Mail addresses works too: send problems to
+"`h...@simula.no`": "mailto:h...@simula.no"
+or just "send mail": "mailto:h...@simula.no".
+</syntaxhighlight>
+
==== Figures and Movies ====

Figures and movies have almost equal syntax:
=======================================
--- /doc/demos/quickref/quickref.p.tex Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/quickref.p.tex Sat Jun 29 16:04:09 2013
@@ -310,16 +310,16 @@

% #if LATEX_HEADING == "traditional"
-\date{Jul 13, 2013}
+\date{Jun 29, 2013}
\maketitle
% #elif LATEX_HEADING == "beamer"
-\date{Jul 13, 2013
+\date{Jun 29, 2013
% <titlepage figure>
}
% #elif LATEX_HEADING == "titlepage"

\ \\ [10mm]
-{\large\textsf{Jul 13, 2013}}
+{\large\textsf{Jun 29, 2013}}

\end{center}
\vfill
@@ -327,7 +327,7 @@

% #else
\begin{center}
-Jul 13, 2013
+Jun 29, 2013
\end{center}

\vspace{1cm}
@@ -825,6 +825,23 @@
rendered nicely anyway.

+\subsection{Hyperlinks}
+
+Links use either a link text or the raw URL:
+
+\bccq
+Here is some "some link text": "http://some.net/address"
+(as in "search google": "http://google.com")
+or just the raw address: URL: "http://google.com".
+
+Links to files typeset in verbatim mode applies backtics:
+"`myfile.py`": "http://some.net/some/place/myfile.py".
+
+Mail addresses works too: send problems to
+"`h...@simula.no`": "mailto:h...@simula.no"
+or just "send mail": "mailto:h...@simula.no".
+\eccq
+
\subsection{Figures and Movies}

Figures and movies have almost equal syntax:
=======================================
--- /doc/demos/quickref/quickref.pdf Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/quickref.pdf Sat Jun 29 16:04:09 2013
Binary file, no diff available.
=======================================
--- /doc/demos/quickref/quickref.rst Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/quickref.rst Sat Jun 29 16:04:09 2013
@@ -5,7 +5,7 @@
-----------------------

:Author: Hans Petter Langtangen
-:Date: Jul 13, 2013
+:Date: Jun 29, 2013

.. contents:: Table of Contents
:depth: 2
@@ -483,6 +483,24 @@
rendered nicely anyway.

+Hyperlinks
+----------
+
+Links use either a link text or the raw URL::
+
+
+ Here is some "some link text": "http://some.net/address"
+ (as in "search google": "http://google.com")
+ or just the raw address: URL: "http://google.com".
+
+ Links to files typeset in verbatim mode applies backtics:
+ "`myfile.py`": "http://some.net/some/place/myfile.py".
+
+ Mail addresses works too: send problems to
+ "`h...@simula.no`": "mailto:h...@simula.no"
+ or just "send mail": "mailto:h...@simula.no".
+
+
Figures and Movies
------------------

=======================================
--- /doc/demos/quickref/quickref.rst.html Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/quickref.rst.html Sat Jun 29 16:04:09 2013
@@ -327,7 +327,7 @@
<tbody valign="top">
<tr class="field"><th class="field-name">Author:</th><td
class="field-body">Hans Petter Langtangen</td>
</tr>
-<tr class="field"><th class="field-name">Date:</th><td
class="field-body">Jul 13, 2013</td>
+<tr class="field"><th class="field-name">Date:</th><td
class="field-body">Jun 29, 2013</td>
</tr>
</tbody>
</table>
@@ -345,17 +345,18 @@
<li><a class="reference internal" href="#inline-comments" id="id9">Inline
comments</a></li>
<li><a class="reference internal" href="#verbatim-computer-code"
id="id10">Verbatim/Computer Code</a></li>
<li><a class="reference internal" href="#latex-mathematics"
id="id11">LaTeX Mathematics</a></li>
-<li><a class="reference internal" href="#figures-and-movies"
id="id12">Figures and Movies</a></li>
-<li><a class="reference internal" href="#tables" id="id13">Tables</a></li>
-<li><a class="reference internal" href="#labels-and-references"
id="id14">Labels and References</a></li>
-<li><a class="reference internal" href="#citations-and-bibliography"
id="id15">Citations and Bibliography</a></li>
-<li><a class="reference internal" href="#generalized-citations"
id="id16">Generalized Citations</a></li>
-<li><a class="reference internal" href="#index-of-keywords"
id="id17">Index of Keywords</a></li>
-<li><a class="reference internal"
href="#capabilities-of-the-program-doconce" id="id18">Capabilities of The
Program <tt class="docutils literal">doconce</tt></a></li>
-<li><a class="reference internal" href="#exercises"
id="id19">Exercises</a></li>
-<li><a class="reference internal" href="#environments"
id="id20">Environments</a></li>
-<li><a class="reference internal" href="#preprocessing"
id="id21">Preprocessing</a></li>
-<li><a class="reference internal" href="#resources"
id="id22">Resources</a></li>
+<li><a class="reference internal" href="#hyperlinks"
id="id12">Hyperlinks</a></li>
+<li><a class="reference internal" href="#figures-and-movies"
id="id13">Figures and Movies</a></li>
+<li><a class="reference internal" href="#tables" id="id14">Tables</a></li>
+<li><a class="reference internal" href="#labels-and-references"
id="id15">Labels and References</a></li>
+<li><a class="reference internal" href="#citations-and-bibliography"
id="id16">Citations and Bibliography</a></li>
+<li><a class="reference internal" href="#generalized-citations"
id="id17">Generalized Citations</a></li>
+<li><a class="reference internal" href="#index-of-keywords"
id="id18">Index of Keywords</a></li>
+<li><a class="reference internal"
href="#capabilities-of-the-program-doconce" id="id19">Capabilities of The
Program <tt class="docutils literal">doconce</tt></a></li>
+<li><a class="reference internal" href="#exercises"
id="id20">Exercises</a></li>
+<li><a class="reference internal" href="#environments"
id="id21">Environments</a></li>
+<li><a class="reference internal" href="#preprocessing"
id="id22">Preprocessing</a></li>
+<li><a class="reference internal" href="#resources"
id="id23">Resources</a></li>
</ul>
</div>
<p><strong>WARNING: This quick reference is very incomplete!</strong></p>
@@ -841,8 +842,24 @@
<tt class="docutils literal">mwiki</tt>, <tt class="docutils
literal">ipynb</tt>, and <tt class="docutils literal">pandoc</tt>, the
mathematics in newcommands is
rendered nicely anyway.</p>
</div>
+<div class="section" id="hyperlinks">
+<h1><a class="toc-backref" href="#id12">Hyperlinks</a></h1>
+<p>Links use either a link text or the raw URL:</p>
+<pre class="literal-block">
+Here is some "some link text":
"http://some.net/address"
+(as in "search google": "http://google.com")
+or just the raw address: URL: "http://google.com".
+
+Links to files typeset in verbatim mode applies backtics:
+"`myfile.py`": "http://some.net/some/place/myfile.py".
+
+Mail addresses works too: send problems to
+"`hpl@simula.no`": "mailto:hpl@simula.no"
+or just "send mail": "mailto:hpl@simula.no".
+</pre>
+</div>
<div class="section" id="figures-and-movies">
-<h1><a class="toc-backref" href="#id12">Figures and Movies</a></h1>
+<h1><a class="toc-backref" href="#id13">Figures and Movies</a></h1>
<p>Figures and movies have almost equal syntax:</p>
<pre class="literal-block">
FIGURE: [relative/path/to/figurefile, width=500 frac=0.8] Here goes the
caption which must be on a single line. label{some:fig:label}
@@ -889,7 +906,7 @@

<em>Vimeo movie.</em></div>
<div class="section" id="tables">
-<h1><a class="toc-backref" href="#id13">Tables</a></h1>
+<h1><a class="toc-backref" href="#id14">Tables</a></h1>
<p>The table in the section <a class="reference internal"
href="#section-types">Section Types</a> was written with this
syntax:</p>
<pre class="literal-block">
@@ -928,7 +945,7 @@
load tables into spreadsheet programs for further analysis.</p>
</div>
<div class="section" id="labels-and-references">
-<h1><a class="toc-backref" href="#id14">Labels and References</a></h1>
+<h1><a class="toc-backref" href="#id15">Labels and References</a></h1>
<p>The notion of labels and references (as well as bibliography and index)
is adopted
from LaTeX with a very similar syntax. As in LaTeX, a label can be
@@ -951,7 +968,7 @@
reference by parenthesis.</p>
</div>
<div class="section" id="citations-and-bibliography">
-<h1><a class="toc-backref" href="#id15">Citations and Bibliography</a></h1>
+<h1><a class="toc-backref" href="#id16">Citations and Bibliography</a></h1>
<p>Single citations are written as:</p>
<pre class="literal-block">
cite{name}
@@ -974,7 +991,7 @@
than LaTeX).</p>
</div>
<div class="section" id="generalized-citations">
-<h1><a class="toc-backref" href="#id16">Generalized Citations</a></h1>
+<h1><a class="toc-backref" href="#id17">Generalized Citations</a></h1>
<p>There is a <em>generalized referencing</em> feature in Doconce that
allows
a reference with <tt class="docutils literal">ref</tt> to have one
formulation if the label is
in the same document and another formulation if the reference is
@@ -1004,7 +1021,7 @@
<tt class="docutils literal">external</tt> text will be the output.</p>
</div>
<div class="section" id="index-of-keywords">
-<h1><a class="toc-backref" href="#id17">Index of Keywords</a></h1>
+<h1><a class="toc-backref" href="#id18">Index of Keywords</a></h1>
<p>Doconce supports creating an index of keywords. A certain keyword
is registered for the index by a syntax like (no
backslash!):</p>
@@ -1019,7 +1036,7 @@
<tt class="docutils literal">pdflatex</tt>, <tt class="docutils
literal">rst</tt>, and <tt class="docutils literal">sphinx</tt> formats.</p>
</div>
<div class="section" id="capabilities-of-the-program-doconce">
-<h1><a class="toc-backref" href="#id18">Capabilities of The Program <tt
class="docutils literal">doconce</tt></a></h1>
+<h1><a class="toc-backref" href="#id19">Capabilities of The Program <tt
class="docutils literal">doconce</tt></a></h1>
<p>The <tt class="docutils literal">doconce</tt> program can be used for a
number of purposes besides
transforming a <tt class="docutils literal">.do.txt</tt> file to some
format. Here is the
list of capabilities:</p>
@@ -1162,7 +1179,7 @@
</pre>
</div>
<div class="section" id="exercises">
-<h1><a class="toc-backref" href="#id19">Exercises</a></h1>
+<h1><a class="toc-backref" href="#id20">Exercises</a></h1>
<p>Doconce supports <em>Exercise</em>, <em>Problem</em>, <em>Project</em>,
and <em>Example</em>.
These are typeset
as ordinary sections and referred to by their section labels.
@@ -1267,7 +1284,7 @@
examples.</p>
</div>
<div class="section" id="environments">
-<h1><a class="toc-backref" href="#id20">Environments</a></h1>
+<h1><a class="toc-backref" href="#id21">Environments</a></h1>
<p>Doconce environments start with <tt class="docutils
literal">!benvirname</tt> and end with <tt class="docutils
literal">!eenvirname</tt>,
where <tt class="docutils literal">envirname</tt> is the name of the
environment. Here is a listing of
the environments:</p>
@@ -1300,7 +1317,7 @@
</blockquote>
</div>
<div class="section" id="preprocessing">
-<h1><a class="toc-backref" href="#id21">Preprocessing</a></h1>
+<h1><a class="toc-backref" href="#id22">Preprocessing</a></h1>
<p>Doconce documents may utilize a preprocessor, either <tt
class="docutils literal">preprocess</tt> and/or
<tt class="docutils literal">mako</tt>. The former is a C-style
preprocessor that allows if-tests
and including other files (but not macros with arguments).
@@ -1346,7 +1363,7 @@
examine the Doconce source and the <tt class="docutils
literal">doc/src/make.sh</tt> script).</p>
</div>
<div class="section" id="resources">
-<h1><a class="toc-backref" href="#id22">Resources</a></h1>
+<h1><a class="toc-backref" href="#id23">Resources</a></h1>
<blockquote>
<ul class="simple">
<li>Excellent "Sphinx Tutorial" by C. Reller: "<a
class="reference external"
href="http://people.ee.ethz.ch/~creller/web/tricks/reST.html">http://people.ee.ethz.ch/~creller/web/tricks/reST.html</a>"</li>
=======================================
--- /doc/demos/quickref/quickref.rst.pdf Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/quickref.rst.pdf Sat Jun 29 16:04:09 2013
Binary file, no diff available.
=======================================
--- /doc/demos/quickref/quickref.rst.tex Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/quickref.rst.tex Sat Jun 29 16:04:09 2013
@@ -75,7 +75,7 @@
Hans Petter Langtangen

\item[{Date:}]
-Jul 13, 2013
+Jun 29, 2013

\end{DUfieldlist}

@@ -883,6 +883,31 @@
without LaTeX support. For \texttt{html}, \texttt{sphinx}, \texttt{latex},
\texttt{pdflatex},
\texttt{mwiki}, \texttt{ipynb}, and \texttt{pandoc}, the mathematics in
newcommands is
rendered nicely anyway.
+
+
+%___________________________________________________________________________
+
+\section*{\phantomsection%
+ Hyperlinks%
+ \addcontentsline{toc}{section}{Hyperlinks}%
+ \label{hyperlinks}%
+}
+
+Links use either a link text or the raw URL:
+%
+\begin{quote}{\ttfamily \raggedright \noindent
+Here~is~some~"some~link~text":~"http://some.net/address"\\
+(as~in~"search~google":~"http://google.com")\\
+or~just~the~raw~address:~URL:~"http://google.com".\\
+~\\
+Links~to~files~typeset~in~verbatim~mode~applies~backtics:\\
+"`myfile.py`":~"http://some.net/some/place/myfile.py".\\
+~\\
+Mail~addresses~works~too:~send~problems~to\\
+"`h...@simula.no`":~"mailto:h...@simula.no"\\
+or~just~"send~mail":~"mailto:h...@simula.no".
+}
+\end{quote}

%___________________________________________________________________________
=======================================
--- /doc/demos/quickref/quickref.st Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/quickref.st Sat Jun 29 16:04:09 2013
@@ -1,6 +1,6 @@
TITLE: Doconce Quick Reference
BY: Hans Petter Langtangen (Center for Biomedical Computing, Simula
Research Laboratory, and Department of Informatics, University of Oslo)
-DATE: Jul 13, 2013
+DATE: Jun 29, 2013
**WARNING: This quick reference is very incomplete!**

*Mission.* Enable writing documentation with much mathematics and
@@ -431,6 +431,23 @@
rendered nicely anyway.

+Hyperlinks
+
+Links use either a link text or the raw URL::
+
+
+ Here is some "some link text": "http://some.net/address"
+ (as in "search google": "http://google.com")
+ or just the raw address: URL: "http://google.com".
+
+ Links to files typeset in verbatim mode applies backtics:
+ "`myfile.py`": "http://some.net/some/place/myfile.py".
+
+ Mail addresses works too: send problems to
+ "`h...@simula.no`": "mailto:h...@simula.no"
+ or just "send mail": "mailto:h...@simula.no".
+
+
Figures and Movies

Figures and movies have almost equal syntax::
=======================================
--- /doc/demos/quickref/quickref.tex Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/quickref.tex Sat Jun 29 16:04:09 2013
@@ -141,7 +141,7 @@

\begin{center}
-Jul 13, 2013
+Jun 29, 2013
\end{center}

\vspace{1cm}
@@ -634,6 +634,23 @@
\Verb!mwiki!, \Verb!ipynb!, and \Verb!pandoc!, the mathematics in
newcommands is
rendered nicely anyway.

+
+\subsection{Hyperlinks}
+
+Links use either a link text or the raw URL:
+
+\begin{Verbatim}[numbers=none,fontsize=\fontsize{9pt}{9pt},baselinestretch=0.95,xleftmargin=0mm]
+Here is some "some link text": "http://some.net/address"
+(as in "search google": "http://google.com")
+or just the raw address: URL: "http://google.com".
+
+Links to files typeset in verbatim mode applies backtics:
+"`myfile.py`": "http://some.net/some/place/myfile.py".
+
+Mail addresses works too: send problems to
+"`h...@simula.no`": "mailto:h...@simula.no"
+or just "send mail": "mailto:h...@simula.no".
+\end{Verbatim}

\subsection{Figures and Movies}

=======================================
--- /doc/demos/quickref/quickref.txt Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/quickref.txt Sat Jun 29 16:04:09 2013
@@ -6,7 +6,7 @@
[1] Center for Biomedical Computing, Simula Research Laboratory
[2] Department of Informatics, University of Oslo

-Date: Jul 13, 2013
+Date: Jun 29, 2013

Table of contents:

@@ -20,6 +20,7 @@
Inline comments
Verbatim/Computer Code
LaTeX Mathematics
+ Hyperlinks
Figures and Movies
Tables
Labels and References
@@ -498,6 +499,24 @@
rendered nicely anyway.

+Hyperlinks
+----------
+
+Links use either a link text or the raw URL::
+
+
+ Here is some "some link text": "http://some.net/address"
+ (as in "search google": "http://google.com")
+ or just the raw address: URL: "http://google.com".
+
+ Links to files typeset in verbatim mode applies backtics:
+ "`myfile.py`": "http://some.net/some/place/myfile.py".
+
+ Mail addresses works too: send problems to
+ "`h...@simula.no`": "mailto:h...@simula.no"
+ or just "send mail": "mailto:h...@simula.no".
+
+
Figures and Movies
------------------

=======================================
--- /doc/demos/quickref/quickref.xml Sat Jul 13 00:16:44 2013
+++ /doc/demos/quickref/quickref.xml Sat Jun 29 16:04:09 2013
@@ -2,7 +2,7 @@
<!DOCTYPE document PUBLIC "+//IDN docutils.sourceforge.net//DTD Docutils
Generic//EN//XML" "http://docutils.sourceforge.net/docs/ref/docutils.dtd">

<document source="quickref.rst"><comment
xml:space="preserve">Automatically generated reST file from Doconce source
-(http://code.google.com/p/doconce/)</comment><section
ids="doconce-quick-reference" names="doconce\ quick\ reference"><title
refid="id1">Doconce Quick
Reference</title><field_list><field><field_name>Author</field_name><field_body><paragraph>Hans
Petter
Langtangen</paragraph></field_body></field><field><field_name>Date</field_name><field_body><paragraph>Jul
13, 2013</paragraph></field_body></field></field_list><topic
classes="contents" ids="table-of-contents" names="table\ of\
contents"><title>Table of
Contents</title><bullet_list><list_item><paragraph><reference ids="id1"
refid="doconce-quick-reference">Doconce Quick
Reference</reference></paragraph></list_item><list_item><paragraph><reference
ids="id2" refid="supported-formats">Supported
Formats</reference></paragraph></list_item><list_item><paragraph><reference
ids="id3" refid="emacs-syntax-support">Emacs syntax
support</reference></paragraph></list_item><list_item><paragraph><reference
ids="id4" refid="title-authors-and-date">Title, Authors, and
Date</reference></paragraph></list_item><list_item><paragraph><reference
ids="id5" refid="section-types">Section
Types</reference></paragraph></list_item><list_item><paragraph><reference
ids="id6" refid="inline-formatting">Inline
Formatting</reference></paragraph></list_item><list_item><paragraph><reference
ids="id7"
refid="lists">Lists</reference></paragraph></list_item><list_item><paragraph><reference
ids="id8" refid="comment-lines">Comment
lines</reference></paragraph></list_item><list_item><paragraph><reference
ids="id9" refid="inline-comments">Inline
comments</reference></paragraph></list_item><list_item><paragraph><reference
ids="id10" refid="verbatim-computer-code">Verbatim/Computer
Code</reference></paragraph></list_item><list_item><paragraph><reference
ids="id11" refid="latex-mathematics">LaTeX
Mathematics</reference></paragraph></list_item><list_item><paragraph><reference
ids="id12" refid="figures-and-movies">Figures and
Movies</reference></paragraph></list_item><list_item><paragraph><reference
ids="id13"
refid="tables">Tables</reference></paragraph></list_item><list_item><paragraph><reference
ids="id14" refid="labels-and-references">Labels and
References</reference></paragraph></list_item><list_item><paragraph><reference
ids="id15" refid="citations-and-bibliography">Citations and
Bibliography</reference></paragraph></list_item><list_item><paragraph><reference
ids="id16" refid="generalized-citations">Generalized
Citations</reference></paragraph></list_item><list_item><paragraph><reference
ids="id17" refid="index-of-keywords">Index of
Keywords</reference></paragraph></list_item><list_item><paragraph><reference
ids="id18" refid="capabilities-of-the-program-doconce">Capabilities of The
Program
<literal>doconce</literal></reference></paragraph></list_item><list_item><paragraph><reference
ids="id19"
refid="exercises">Exercises</reference></paragraph></list_item><list_item><paragraph><reference
ids="id20"
refid="environments">Environments</reference></paragraph></list_item><list_item><paragraph><reference
ids="id21"
refid="preprocessing">Preprocessing</reference></paragraph></list_item><list_item><paragraph><reference
ids="id22"
refid="resources">Resources</reference></paragraph></list_item></bullet_list></topic><paragraph><strong>WARNING:
This quick reference is very
incomplete!</strong></paragraph><paragraph><emphasis>Mission.</emphasis>
Enable writing documentation with much mathematics and
+(http://code.google.com/p/doconce/)</comment><section
ids="doconce-quick-reference" names="doconce\ quick\ reference"><title
refid="id1">Doconce Quick
Reference</title><field_list><field><field_name>Author</field_name><field_body><paragraph>Hans
Petter
Langtangen</paragraph></field_body></field><field><field_name>Date</field_name><field_body><paragraph>Jun
29, 2013</paragraph></field_body></field></field_list><topic
classes="contents" ids="table-of-contents" names="table\ of\
contents"><title>Table of
Contents</title><bullet_list><list_item><paragraph><reference ids="id1"
refid="doconce-quick-reference">Doconce Quick
Reference</reference></paragraph></list_item><list_item><paragraph><reference
ids="id2" refid="supported-formats">Supported
Formats</reference></paragraph></list_item><list_item><paragraph><reference
ids="id3" refid="emacs-syntax-support">Emacs syntax
support</reference></paragraph></list_item><list_item><paragraph><reference
ids="id4" refid="title-authors-and-date">Title, Authors, and
Date</reference></paragraph></list_item><list_item><paragraph><reference
ids="id5" refid="section-types">Section
Types</reference></paragraph></list_item><list_item><paragraph><reference
ids="id6" refid="inline-formatting">Inline
Formatting</reference></paragraph></list_item><list_item><paragraph><reference
ids="id7"
refid="lists">Lists</reference></paragraph></list_item><list_item><paragraph><reference
ids="id8" refid="comment-lines">Comment
lines</reference></paragraph></list_item><list_item><paragraph><reference
ids="id9" refid="inline-comments">Inline
comments</reference></paragraph></list_item><list_item><paragraph><reference
ids="id10" refid="verbatim-computer-code">Verbatim/Computer
Code</reference></paragraph></list_item><list_item><paragraph><reference
ids="id11" refid="latex-mathematics">LaTeX
Mathematics</reference></paragraph></list_item><list_item><paragraph><reference
ids="id12"
refid="hyperlinks">Hyperlinks</reference></paragraph></list_item><list_item><paragraph><reference
ids="id13" refid="figures-and-movies">Figures and
Movies</reference></paragraph></list_item><list_item><paragraph><reference
ids="id14"
refid="tables">Tables</reference></paragraph></list_item><list_item><paragraph><reference
ids="id15" refid="labels-and-references">Labels and
References</reference></paragraph></list_item><list_item><paragraph><reference
ids="id16" refid="citations-and-bibliography">Citations and
Bibliography</reference></paragraph></list_item><list_item><paragraph><reference
ids="id17" refid="generalized-citations">Generalized
Citations</reference></paragraph></list_item><list_item><paragraph><reference
ids="id18" refid="index-of-keywords">Index of
Keywords</reference></paragraph></list_item><list_item><paragraph><reference
ids="id19" refid="capabilities-of-the-program-doconce">Capabilities of The
Program
<literal>doconce</literal></reference></paragraph></list_item><list_item><paragraph><reference
ids="id20"
refid="exercises">Exercises</reference></paragraph></list_item><list_item><paragraph><reference
ids="id21"
refid="environments">Environments</reference></paragraph></list_item><list_item><paragraph><reference
ids="id22"
refid="preprocessing">Preprocessing</reference></paragraph></list_item><list_item><paragraph><reference
ids="id23"
refid="resources">Resources</reference></paragraph></list_item></bullet_list></topic><paragraph><strong>WARNING:
This quick reference is very
incomplete!</strong></paragraph><paragraph><emphasis>Mission.</emphasis>
Enable writing documentation with much mathematics and
computer code <emphasis>once, in one place</emphasis> and include it in
traditional LaTeX
books, thesis, and reports, and without extra efforts also make
professionally looking web versions with Sphinx or HTML. Other outlets
@@ -181,7 +181,16 @@
LaTeX code. This conventions helps make readable documents in formats
without LaTeX support. For <literal>html</literal>,
<literal>sphinx</literal>, <literal>latex</literal>,
<literal>pdflatex</literal>,
<literal>mwiki</literal>, <literal>ipynb</literal>, and
<literal>pandoc</literal>, the mathematics in newcommands is
-rendered nicely anyway.</paragraph></section><section
ids="figures-and-movies" names="figures\ and\ movies"><title
refid="id12">Figures and Movies</title><paragraph>Figures and movies have
almost equal syntax:</paragraph><literal_block xml:space="preserve">FIGURE:
[relative/path/to/figurefile, width=500 frac=0.8] Here goes the caption
which must be on a single line. label{some:fig:label}
+rendered nicely anyway.</paragraph></section><section ids="hyperlinks"
names="hyperlinks"><title refid="id12">Hyperlinks</title><paragraph>Links
use either a link text or the raw URL:</paragraph><literal_block
xml:space="preserve">Here is some "some link text":
"http://some.net/address"
+(as in "search google": "http://google.com")
+or just the raw address: URL: "http://google.com".
+
+Links to files typeset in verbatim mode applies backtics:
+"`myfile.py`": "http://some.net/some/place/myfile.py".
+
+Mail addresses works too: send problems to
+"`h...@simula.no`": "mailto:h...@simula.no"
+or just "send mail":
"mailto:h...@simula.no".</literal_block></section><section
ids="figures-and-movies" names="figures\ and\ movies"><title
refid="id13">Figures and Movies</title><paragraph>Figures and movies have
almost equal syntax:</paragraph><literal_block xml:space="preserve">FIGURE:
[relative/path/to/figurefile, width=500 frac=0.8] Here goes the caption
which must be on a single line. label{some:fig:label}

MOVIE: [relative/path/to/moviefile, width=500] Here goes the caption which
must be on a single line.
label{some:fig:label}</literal_block><paragraph>Note three important syntax
details:</paragraph><block_quote><enumerated_list enumtype="arabic"
prefix="" suffix="."><list_item><paragraph>A mandatory comma after the
figure/movie filename,</paragraph></list_item><list_item><paragraph>no
comments between <literal>width</literal>, <literal>height</literal>, and
<literal>frac</literal> and no spaces
around the <literal>=</literal>
characters,</paragraph></list_item><list_item><paragraph>all of the command
must appear on a single
line,</paragraph></list_item><list_item><paragraph>there must be a blank
line after the
command.</paragraph></list_item></enumerated_list></block_quote><paragraph>The
figure file can be listed without extension. Doconce will then find
@@ -199,7 +208,7 @@

MOVIE: [http://vimeo.com/55562330, width=500 height=278] Vimeo
movie.</literal_block><paragraph>The latter results in</paragraph><raw
format="html" xml:space="preserve"><iframe width="500"
height="278"
src="http://player.vimeo.com/video/55562330"
frameborder="0" allowfullscreen></iframe>

-<em>Vimeo movie.</em></raw></section><section ids="tables"
names="tables"><title refid="id13">Tables</title><paragraph>The table in
the section <reference name="Section Types" refid="section-types">Section
Types</reference> was written with this
+<em>Vimeo movie.</em></raw></section><section ids="tables"
names="tables"><title refid="id14">Tables</title><paragraph>The table in
the section <reference name="Section Types" refid="section-types">Section
Types</reference> was written with this
syntax:</paragraph><literal_block xml:space="preserve">|
----------------c--------|------------------c--------------------|
| Section type | Syntax |
|----------------l--------|------------------l--------------------|
@@ -220,7 +229,7 @@
have no
effect.</paragraph></list_item></bullet_list></block_quote><paragraph>The
command-line option <literal>--tables2csv</literal> (to <literal>doconce
format</literal>)
makes Doconce dump each table to CSV format in a file
<literal>table_X.csv</literal>,
where <literal>X</literal> is the table number. This feature makes it easy
to
-load tables into spreadsheet programs for further
analysis.</paragraph></section><section ids="labels-and-references"
names="labels\ and\ references"><title refid="id14">Labels and
References</title><paragraph>The notion of labels and references (as well
as bibliography and index)
+load tables into spreadsheet programs for further
analysis.</paragraph></section><section ids="labels-and-references"
names="labels\ and\ references"><title refid="id15">Labels and
References</title><paragraph>The notion of labels and references (as well
as bibliography and index)
is adopted
from LaTeX with a very similar syntax. As in LaTeX, a label can be
inserted anywhere, using the syntax:</paragraph><literal_block
xml:space="preserve">label{name}</literal_block><paragraph>with no backslash
@@ -229,7 +238,7 @@
some abbreviations for a section and/or subsection for the topic and
<literal>c</literal> is some name for the particular unit that has a
label.</paragraph><paragraph>A reference to the label
<literal>name</literal> is written as:</paragraph><literal_block
xml:space="preserve">ref{name}</literal_block><paragraph>again with no
backslash before <literal>ref</literal>.</paragraph><paragraph>Use labels
for sections and equations only, and preceed the reference
by "Section" or "Chapter", or in case of an equation,
surround the
-reference by parenthesis.</paragraph></section><section
ids="citations-and-bibliography" names="citations\ and\
bibliography"><title refid="id15">Citations and
Bibliography</title><paragraph>Single citations are written
as:</paragraph><literal_block
xml:space="preserve">cite{name}</literal_block><paragraph>where
<literal>name</literal> is a logical name
+reference by parenthesis.</paragraph></section><section
ids="citations-and-bibliography" names="citations\ and\
bibliography"><title refid="id16">Citations and
Bibliography</title><paragraph>Single citations are written
as:</paragraph><literal_block
xml:space="preserve">cite{name}</literal_block><paragraph>where
<literal>name</literal> is a logical name
of the reference (again, LaTeX writers must not insert a backslash).
Bibliography citations often have <literal>name</literal> on the form
<literal>Author1_Author2_YYYY</literal>, <literal>Author_YYYY</literal>,
or <literal>Author1_etal_YYYY</literal>, where
@@ -240,7 +249,7 @@
<reference name="Publish"
refuri="https://bitbucket.org/logg/publish">Publish</reference><target
ids="publish" names="publish" refuri="https://bitbucket.org/logg/publish"/>
format.
BibTeX <literal>.bib</literal> files can easily be combined to a Publish
database
(which Doconce needs to create bibliographies in other formats
-than LaTeX).</paragraph></section><section ids="generalized-citations"
names="generalized\ citations"><title refid="id16">Generalized
Citations</title><paragraph>There is a <emphasis>generalized
referencing</emphasis> feature in Doconce that allows
+than LaTeX).</paragraph></section><section ids="generalized-citations"
names="generalized\ citations"><title refid="id17">Generalized
Citations</title><paragraph>There is a <emphasis>generalized
referencing</emphasis> feature in Doconce that allows
a reference with <literal>ref</literal> to have one formulation if the
label is
in the same document and another formulation if the reference is
to an item in an external document. This construction makes it easy
@@ -262,14 +271,14 @@
and date). In this case the output text is <literal>internal
cite</literal> and the
LaTeX package <literal>xr</literal> is used to handle the labels in the
external
documents. If none of the two situations above applies, the
-<literal>external</literal> text will be the
output.</paragraph></section><section ids="index-of-keywords" names="index\
of\ keywords"><title refid="id17">Index of
Keywords</title><paragraph>Doconce supports creating an index of keywords.
A certain keyword
+<literal>external</literal> text will be the
output.</paragraph></section><section ids="index-of-keywords" names="index\
of\ keywords"><title refid="id18">Index of
Keywords</title><paragraph>Doconce supports creating an index of keywords.
A certain keyword
is registered for the index by a syntax like (no
backslash!):</paragraph><literal_block
xml:space="preserve">index{name}</literal_block><paragraph>It is
recommended to place any index of this type outside
running text, i.e., after (sub)section titles and in the space between
paragraphs. Index specifications placed right before paragraphs also
gives the doconce source code an indication of the content in the
forthcoming text. The index is only produced for the
<literal>latex</literal>,
-<literal>pdflatex</literal>, <literal>rst</literal>, and
<literal>sphinx</literal> formats.</paragraph></section><section
ids="capabilities-of-the-program-doconce" names="capabilities\ of\ the\
program\ doconce"><title refid="id18">Capabilities of The Program
<literal>doconce</literal></title><paragraph>The <literal>doconce</literal>
program can be used for a number of purposes besides
+<literal>pdflatex</literal>, <literal>rst</literal>, and
<literal>sphinx</literal> formats.</paragraph></section><section
ids="capabilities-of-the-program-doconce" names="capabilities\ of\ the\
program\ doconce"><title refid="id19">Capabilities of The Program
<literal>doconce</literal></title><paragraph>The <literal>doconce</literal>
program can be used for a number of purposes besides
transforming a <literal>.do.txt</literal> file to some format. Here is the
list of capabilities:</paragraph><literal_block
xml:space="preserve">Usage: doconce command [optional arguments]
commands: format help sphinx_dir subst replace replace_from_file clean
spellcheck ptex2tex expand_commands combine_images guess_encoding
change_encoding gwiki_figsubst md2html remove_inline_comments grab remove
remove_exercise_answers split_rst split_html slides_html slides_beamer
latin2html latex_header latex_footer bbl2rst html_colorbullets list_labels
teamod sphinxfix_localURLs make_figure_code_links latex_exercise_toc
insertdocstr old2new_format latex2doconce latex_dislikes pygmentize
makefile diff gitdiff fix_bibtex4publish csv2table
@@ -405,7 +414,7 @@
doconce gitdiff file1 file2 file3 ...

# convert csv file to doconce table format
-doconce csv2table somefile.csv</literal_block></section><section
ids="exercises" names="exercises"><title
refid="id19">Exercises</title><paragraph>Doconce supports
<emphasis>Exercise</emphasis>, <emphasis>Problem</emphasis>,
<emphasis>Project</emphasis>, and <emphasis>Example</emphasis>.
+doconce csv2table somefile.csv</literal_block></section><section
ids="exercises" names="exercises"><title
refid="id20">Exercises</title><paragraph>Doconce supports
<emphasis>Exercise</emphasis>, <emphasis>Problem</emphasis>,
<emphasis>Project</emphasis>, and <emphasis>Example</emphasis>.
These are typeset
as ordinary sections and referred to by their section labels.
Exercise, problem, project, or example sections contains certain
<emphasis>elements</emphasis>:</paragraph><block_quote><bullet_list
bullet="*"><list_item><paragraph>a headline at the level of a subsection
@@ -479,10 +488,10 @@
!esol</literal_block><paragraph>By default, answers, solutions, and hints
are typeset as paragraphs.
The command-line arguments <literal>--without_answers</literal> and
<literal>--without_solutions</literal>
turn off output of answers and solutions, respectively, except for
-examples.</paragraph></section><section ids="environments"
names="environments"><title
refid="id20">Environments</title><paragraph>Doconce environments start with
<literal>!benvirname</literal> and end with <literal>!eenvirname</literal>,
+examples.</paragraph></section><section ids="environments"
names="environments"><title
refid="id21">Environments</title><paragraph>Doconce environments start with
<literal>!benvirname</literal> and end with <literal>!eenvirname</literal>,
where <literal>envirname</literal> is the name of the environment. Here is
a listing of
the environments:</paragraph><block_quote><bullet_list
bullet="*"><list_item><paragraph><literal>c</literal>: computer code (or
verbatim
text)</paragraph></list_item><list_item><paragraph><literal>t</literal>:
math blocks with LaTeX
syntax</paragraph></list_item><list_item><paragraph><literal>subex</literal>:
sub-exercise</paragraph></list_item><list_item><paragraph><literal>ans</literal>:
short answer to exercise or
sub-exercise</paragraph></list_item><list_item><paragraph><literal>sol</literal>:
full solution to exercise or
sub-exercise</paragraph></list_item><list_item><paragraph><literal>quote</literal>:
indented
text</paragraph></list_item><list_item><definition_list><definition_list_item><term><literal>notice</literal>,
<literal>summary</literal>, <literal>warning</literal>,
<literal>question</literal>, <literal>hint</literal>: admonition boxes
with</term><definition><paragraph>custom title, special icon, and
(frequently) background
color</paragraph></definition></definition_list_item></definition_list></list_item><list_item><paragraph><literal>pop</literal>:
text to gradually pop up in slide
presentations</paragraph></list_item><list_item><paragraph><literal>slidecell</literal>:
indication of cells in a grid layout for elements on a
-slide</paragraph></list_item></bullet_list></block_quote></section><section
ids="preprocessing"
names="preprocessing"><title
refid="id21">Preprocessing</title><paragraph>Doconce documents may utilize
a preprocessor, either <literal>preprocess</literal> and/or
+slide</paragraph></list_item></bullet_list></block_quote></section><section
ids="preprocessing"
names="preprocessing"><title
refid="id22">Preprocessing</title><paragraph>Doconce documents may utilize
a preprocessor, either <literal>preprocess</literal> and/or
<literal>mako</literal>. The former is a C-style preprocessor that allows
if-tests
and including other files (but not macros with arguments).
The <literal>mako</literal> preprocessor is much more advanced - it is
actually a full
@@ -519,4 +528,4 @@
# #endif</literal_block><paragraph>With the <literal>mako</literal>
preprocessor the if-else tests have slightly different syntax.
An <reference name="example document"
refuri="http://hplgit.github.com/bioinf-py/">example
document</reference><target ids="example-document" names="example\
document" refuri="http://hplgit.github.com/bioinf-py/"/> contains
some illustrations on how to utilize <literal>mako</literal> (clone the
GitHub project and
-examine the Doconce source and the <literal>doc/src/make.sh</literal>
script).</paragraph></section><section ids="resources"
names="resources"><title
refid="id22">Resources</title><block_quote><bullet_list
bullet="*"><list_item><paragraph>Excellent "Sphinx Tutorial" by
C. Reller: "<reference
refuri="http://people.ee.ethz.ch/~creller/web/tricks/reST.html">http://people.ee.ethz.ch/~creller/web/tricks/reST.html</reference>"</paragraph></list_item></bullet_list></block_quote></section></document>
+examine the Doconce source and the <literal>doc/src/make.sh</literal>
script).</paragraph></section><section ids="resources"
names="resources"><title
refid="id23">Resources</title><block_quote><bullet_list
bullet="*"><list_item><paragraph>Excellent "Sphinx Tutorial" by
C. Reller: "<reference
refuri="http://people.ee.ethz.ch/~creller/web/tricks/reST.html">http://people.ee.ethz.ch/~creller/web/tricks/reST.html</reference>"</paragraph></list_item></bullet_list></block_quote></section></document>
=======================================
--- /lib/doconce/doconce.py Sun Aug 11 00:11:16 2013
+++ /lib/doconce/doconce.py Sat Jun 29 16:04:09 2013
@@ -696,6 +696,7 @@
exer_end = False
exer_counter = dict(Exercise=0, Problem=0, Project=0, Example=0)

+ # Regex: no need for re.MULTILINE since we treat one line at a time
if option('examples_as_exercises'):
exer_heading_pattern = re.compile(r'^\s*(=====)\s*\{?(Exercise|
Problem|Project|Example)\}?:\s*(?P<title>[^ =-].+?)\s*=====')
else:
@@ -875,6 +876,8 @@
exer_end = True
elif inside_exer and lines[line_no+1].startswith('====='):
exer_end = True
+ elif inside_exer and option('sections_down') and
lines[line_no+1].startswith('==='):
+ exer_end = True

if exer and exer_end:
exer['text'] = '\n'.join(exer['text']).strip()
@@ -2096,27 +2099,32 @@
('*'*80, pprint.pformat(tex_blocks)))

# Lift sections up or down?
- sections_up = option('sections_up')
- sections_down = option('sections_down')
- if sections_up or sections_down:
- s2name = {9: 'chapter', 7: 'section',
- 5: 'subsection', 3: 'subsubsection'}
- for s in 9, 7, 5, 3:
- if sections_up:
- if s == 9:
- continue
- header_old = '='*s
- header_new = '='*(s+2)
- print 'transforming %s to %s...' % (s2name[s], s2name[s+2])
- else:
- if s == 3:
- continue
- header_new = '='*(s-2)
- header_old = '='*s
- print 'transforming %s to %s...' % (s2name[s], s2name[s-2])
- pattern = r'=%s(.+?)=%s' % (header_old, header_old)
- replacement = r'=%s\g<1>%s' % (header_new, header_new)
+ s2name = {9: 'chapter', 7: 'section',
+ 5: 'subsection', 3: 'subsubsection'}
+ section_level_changed = False
+ if option('sections_up'):
+ for s in 7, 5, 3:
+ header_old = '='*s
+ header_new = '='*(s+2)
+ print 'transforming sections: %s to %s...' % (s2name[s],
s2name[s+2])
+ pattern = r'%s(.+?)%s' % (header_old, header_old)
+ replacement = r'%s\g<1>%s' % (header_new, header_new)
filestr = re.sub(pattern, replacement, filestr)
+ section_level_changed = True
+ if option('sections_down'):
+ for s in 5, 7, 9:
+ header_old = '='*s
+ header_new = '='*(s-2)
+ print 'transforming sections: %s to %s...' % (s2name[s],
s2name[s-2])
+ pattern = r'%s(.+?)%s' % (header_old, header_old)
+ replacement = r'%s\g<1>%s' % (header_new, header_new)
+ filestr = re.sub(pattern, replacement, filestr)
+ section_level_changed = True
+
+ if section_level_changed:
+ # Fix Exercise, Problem, Project, Example - they must be 5=
+ filestr = re.sub(r'^\s*=======\s*(\{?(Exercise|Problem|Project|
Example)\}?):\s*([^ =-].+?)\s*=======', '===== \g<1>: \g<3> =====',
filestr, flags=re.MULTILINE)
+ filestr = re.sub(r'^\s*===\s*(\{?(Exercise|Problem|Project|
Example)\}?):\s*([^ =-].+?)\s*===', '===== \g<1>: \g<3> =====', filestr,
flags=re.MULTILINE)

# Remove linebreaks within paragraphs
if option('oneline_paragraphs'): # (does not yet work well)
=======================================
--- /test/_testdoc.do.txt Sat Jul 13 01:32:43 2013
+++ /test/_testdoc.do.txt Sat Jun 29 16:04:09 2013
@@ -424,7 +424,7 @@
cite{Langtangen_2012,Mardal_et_al_2003a,Jeberg_et_al_2004} as well as
old work cite{Langtangen_1988d} and cite{Langtangen_1989e}, and the
talk cite{Langtangen_talk_2007a}.
-Langtangen also had two thesis cite{Langtangen:85,Langtangen:89d}.
+Langtangen also had two thesis cite{Langtangen:85,Langtangen_1989e}.
More retro citations are
the old ME-IN323 book cite{Langtangen:91} and the
cite{Langtangen:94b} OONSKI '94 paper.
=======================================
--- /test/author1.do.txt Fri Apr 12 02:28:39 2013
+++ /test/author1.do.txt Sat Jun 29 16:04:09 2013
@@ -39,18 +39,18 @@
Here is a specific example on a generalized reference:
!bc
As explained in
-ref[Section ref{subsec:ex}][in "Langtangen, 2012":
-"http://code.google.com/p/doconce/wiki/Description"
-cite{testdoc:12}][a "section": "testdoc.html#___sec2" in
-the document "A Document for Testing Doconce": "testdoc.html"
+ref[Section ref{subsec:ex}][in "Langtangen, 2013":
+"http://doconce.googlecode.com/hg/test/demo_testdoc.html"
+cite{testdoc:12}][a "section": "demo_testdoc.html#___sec2" in
+the document "A Document for Testing Doconce": "demo_testdoc.html"
cite{testdoc:12}], Doconce documents may include movies.
!ec
This is rendered to the following text:
As explained in
-ref[Section ref{subsec:ex}][in "Langtangen, 2012":
-"http://code.google.com/p/doconce/wiki/Description"
-cite{testdoc:12}][a "section": "testdoc.html#___sec2" in
-the document "A Document for Testing Doconce": "testdoc.html"
+ref[Section ref{subsec:ex}][in "Langtangen, 2013":
+"http://doconce.googlecode.com/hg/test/demo_testdoc.html"
+cite{testdoc:12}][a "section": "demo_testdoc.html#___sec2" in
+the document "A Document for Testing Doconce": "demo_testdoc.html"
cite{testdoc:12}], Doconce documents may include movies.

And here is another example with internal references only:
=======================================
--- /test/make.sh Sun Aug 4 11:57:04 2013
+++ /test/make.sh Sat Jun 29 16:04:09 2013
@@ -60,6 +60,8 @@
system doconce html_colorbullets testdoc.html
system doconce split_html testdoc.html

+system doconce format html testdoc.do.txt --pygments_html_linenos
--html_style=solarized --pygments_html_style=emacs $ex
--html_output=demo_testdoc
+
system doconce format latex testdoc.do.txt $ex SOMEVAR=True
--skip_inline_comments
system doconce format pdflatex testdoc.do.txt --device=paper $ex
--latex_double_hyphen
system doconce latex_exercise_toc testdoc
@@ -251,7 +253,7 @@
system doconce format mwiki admon
cp admon.mwiki admon_mwiki.mwiki

-system doconce format pandoc githu_md.do.txt --github_md
+system doconce format pandoc github_md.do.txt --github_md

#google-chrome admon_*.html
#for pdf in admon_*.pdf; do evince $pdf; done
=======================================
--- /test/refs3.bib Fri Apr 12 02:28:39 2013
+++ /test/refs3.bib Sat Jun 29 16:04:09 2013
@@ -71,14 +71,6 @@
note = {Cand.Scient. thesis},
}

-
-@PhdThesis{Langtangen:89d,
-author = {H. P. Langtangen},
-title = {Computational Methods for Two-Phase Flow in Oil Reservoirs},
-year = {1989},
-school = {Mechanics Division, Department of Mathematics, University of
Oslo},
-note = {Dr.~Scient.~thesis},
-}

@TechReport{Langtangen:91,
author = {H. P. Langtangen and A. Tveito},
@@ -97,3 +89,11 @@
year = {1994},
pdf =
{http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.22.5735&rep=rep1&type=pdf}
}
+
+@TechReport{testdoc:12,
+author = {H. P. Langtangen},
+title = {A Document for Testing Doconce},
+year = {2013},
+institution = {Simula Research Laboratory and University of Oslo},
+url = {http://doconce.googlecode.com/hg/test/demo_testdoc.html},
+}
=======================================
--- /test/test.r Sat Jun 29 07:54:16 2013
+++ /test/test.r Sat Jun 29 16:04:09 2013
File is too large to display a diff.

==============================================================================
Revision: de1b5fe70fc7
Branch: default
Author: "Hans Petter Langtangen <h...@simula.no>"
Date: Sat Jun 29 16:04:53 2013
Log: Added a testdoc demo file for reference.
http://code.google.com/p/doconce/source/detail?r=de1b5fe70fc7

Added:
/test/demo_testdoc.html

=======================================
--- /dev/null
+++ /test/demo_testdoc.html Sat Jun 29 16:04:53 2013
@@ -0,0 +1,1741 @@
+<!DOCTYPE html>
+
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Doconce:
http://code.google.com/p/doconce/" />
+<meta name="description" content="A Document for Testing Doconce">
+<meta name="keywords" content="figures,movies,index with subindex,index,
with comma, and one more">
+
+
+
+<style type="text/css">
+ /* solarized style */
+ body {
+ margin:5;
+ padding:0;
+ border:0; /* Remove the border around the viewport in old versions
of IE */
+ width:100%;
+ background: #fdf6e3;
+ min-width:600px; /* Minimum width of layout - remove if not required
*/
+ font-family: Verdana, Helvetica, Arial, sans-serif;
+ font-size: 1.0em;
+ line-height: 1.3em;
+ color: #657b83;
+ }
+ a { color: #657b83; text-decoration:none; }
+ a:hover { color: #b58900; background: #eee8d5; text-decoration:none; }
+ h1, h2, h3 { margin:.8em 0 .2em 0; padding:0; line-height: 125%; }
+ h2 { font-variant: small-caps; }
+ pre {
+ background: #fdf6e3;
+ -webkit-box-shadow: inset 0 0 2px #000000;
+ -moz-box-shadow: inset 0 0 2px #000000;
+ box-shadow: inset 0 0 2px #000000;
+ color: #586e75;
+ margin-left: 0px;
+ font-family: 'Droid Sans Mono', monospace;
+ padding: 2px;
+ -webkit-border-radius: 4px;
+ -moz-border-radius: 4px;
+ border-radius: 4px;
+ -moz-background-clip: padding;
+ -webkit-background-clip: padding-box;
+ background-clip: padding-box;
+ }
+ tt { font-family: "Courier New", Courier; }
+ hr { border: 0; width: 80%; border-bottom: 1px solid #aaa}
+ p { text-indent: 0px; }
+ p.caption { width: 80%; font-style: normal; text-align: left; }
+ hr.figure { border: 0; width: 80%; border-bottom: 1px solid #aaa}
+ .alert-text-small { font-size: 80%; }
+ .alert-text-large { font-size: 130%; }
+ .alert-text-normal { font-size: 90%; }
+ .alert {
+ padding:8px 35px 8px 14px; margin-bottom:18px;
+ text-shadow:0 1px 0 rgba(255,255,255,0.5);
+ border:1px solid #FFBF00;
+ -webkit-border-radius: 4px; -moz-border-radius: 4px;
+ border-radius: 4px
+ color: #555;
+ background-color: #fbeed5;
+ background-position: 10px 5px;
+ background-repeat: no-repeat;
+ background-size: 38px;
+ padding-left: 55px;
+ width: 75%;
+ }
+ .alert-block {padding-top:14px; padding-bottom:14px}
+ .alert-block > p, .alert-block > ul {margin-bottom:0}
+ .alert li {margin-top: 1em}
+ .alert-block p+p {margin-top:5px}
+ .alert-notice { background-image:
url(https://doconce.googlecode.com/hg/bundled/html_images/small_yellow_notice.png);
}
+ .alert-summary {
background-image:url(https://doconce.googlecode.com/hg/bundled/html_images/small_yellow_summary.png);
}
+ .alert-warning { background-image:
url(https://doconce.googlecode.com/hg/bundled/html_images/small_yellow_warning.png);
}
+ .alert-question
{background-image:url(https://doconce.googlecode.com/hg/bundled/html_images/small_yellow_question.png);
}
+
+</style>
+
+</head>
+
+
+
+<body>
+
+
+
+<script type="text/x-mathjax-config">
+MathJax.Hub.Config({
+ TeX: {
+ equationNumbers: { autoNumber: "AMS" },
+ extensions: ["AMSmath.js", "AMSsymbols.js", "autobold.js"]
+ }
+});
+</script>
+<script type="text/javascript"
+
src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+
+<meta http-equiv="X-UA-Compatible" content="IE=EmulateIE7">
+
+
+
+$$
+\renewcommand{\u}{\pmb{u}}
+
+\newcommand{\xbm}{\boldsymbol{x}}
+\newcommand{\normalvecbm}{\boldsymbol{n}}
+\newcommand{\ubm}{\boldsymbol{u}}
+$$
+
+
+
+$$
+\newcommand{\x}{\pmb{x}}
+\newcommand{\normalvec}{\pmb{n}}
+\newcommand{\Ddt}[1]{\frac{D#1}{dt}}
+\newcommand{\halfi}{1/2}
+\newcommand{\half}{\frac{1}{2}}
+\newcommand{\report}{test report}
+$$
+
+
+
+
+
+
+
+
+<title>A Document for Testing Doconce</title>
+
+<center><h1>A Document for Testing Doconce</h1></center> 
+
+<p>
+
+
+<center>
+<b>Hans Petter Langtangen</b> [1, 2] (<tt>hpl at simula.no</tt>)
+</center>
+
+<center>
+<b>Kaare Dump</b> [3]
+</center>
+
+<center>
+<b>A. Dummy Author</b>
+</center>
+
+<center>
+<b>I. S. Overworked</b> [4, 5, 6, 7]
+</center>
+
+<center>
+<b>J. Doe</b> (<tt>j_doe at cyberspace.com</tt>)
+</center>
+
+
+<p>
+
+
+<center>[1] <b>Center for Biomedical Computing, Simula Research
Laboratory</b></center>
+<center>[2] <b>Department of Informatics, University of Oslo</b></center>
+<center>[3] <b>Segfault Inc, Cyberspace</b></center>
+<center>[4] <b>Inst1</b></center>
+<center>[5] <b>Inst2, Somewhere</b></center>
+<center>[6] <b>Third Inst, Elsewhere</b></center>
+<center>[7] <b>Fourth Inst</b></center>
+<p>
+<center><h4>Jun 29, 2013</h4></center> 
+
+<h2>Table of contents</h2>
+
+<p>
+<a href="#sec1"> Section 1 </a><br>
+      <a href="#___sec1"> Subsection 1 </a><br>
+      <a href="#subsec:ex"> Subsection 2: Testing figures
and movies </a><br>
+            <a href="#___sec3"> Test of
movies </a><br>
+      <a href="#decay:sec:theta"> The $ \theta $
parameter (not $ \nabla $?) </a><br>
+      <a href="#___sec5"> Custom Environments </a><br>
+      <a href="#subsec:table"> Tables </a><br>
+      <a href="#___sec7"> A test of verbatim words in
heading with subscript $ a_i $: <code>my_file_v1</code> and
<code>my_file_v2</code> </a><br>
+      <a href="#___sec8"> Bibliography test </a><br>
+      <a href="#Example"> Example 1: Examples can be
typeset as exercises </a><br>
+      <a href="#subsubsec:ex"> URLs </a><br>
+      <a href="#___sec11"> LaTeX Mathematics </a><br>
+<a href="#___sec12"> Exercises </a><br>
+      <a href="#demo:ex:1"> Problem 1: Flip a Coin </a><br>
+            <a href="#___sec14"> Remarks
</a><br>
+      <a href="#___sec15"> Not an exercise </a><br>
+      <a href="#demo:ex:2"> Project 1: Compute a
Probability </a><br>
+      <a href="#proj:circle1"> Project 2: Explore
Distributions of Random Circles </a><br>
+            <a href="#___sec18"> Remarks
</a><br>
+      <a href="#exer:dist"> Exercise 1: Determine some
Distance </a><br>
+            <a href="#___sec20"> Remarks
</a><br>
+      <a href="#___sec21"> Some exercise without
the "Exercise:" prefix </a><br>
+      <a href="#___sec22"> Example 2: Just an example
</a><br>
+<a href="#___sec23"> Here goes another section </a><br>
+<a href="#___sec24"> More Exercises </a><br>
+      <a href="#exer:some:formula"> Exercise 3: Make
references to projects and problems </a><br>
+      <a href="#exer:you"> Project 3: References in a
headings do not work well in html </a><br>
+<a href="#___sec27"> References </a><br>
+<a href="#___sec28"> Appendix: Just for testing; part I </a><br>
+      <a href="#___sec29"> A subsection within an appendix
</a><br>
+<a href="#___sec30"> Appendix: Just for testing; part II </a><br>
+      <a href="#___sec31"> Appendix: Testing identical
titles </a><br>
+      <a href="#test:title:id1"> Appendix: Testing
identical titles </a><br>
+      <a href="#test:title:id2"> Appendix: Testing
identical titles </a><br>
+      <a href="#___sec34"> Appendix: Testing identical
titles </a><br>
+      <a href="#___sec35"> Appendix: Testing inline
comments </a><br>
+      <a href="#___sec36"> Appendix: Testing headings
ending with <code>verbatim inline</code> </a><br>
+
+<p>
+
+
+<p>
+The format of this document is
+plain, homemade HTML (from Doconce).
+
+<p>
+<b>Abstract.</b> This is a document with many test constructions for
doconce syntax.
+It was used heavily for the development and kept for testing
+numerous constructions, also special and less common cases.
+
+<p>
+And exactly for test purposes we have an extra line here, which
+is part of the abstract.
+
+<p>
+
+
+
+<h2>Section 1 <a name="sec1"></a></h2>
+
+<p>
+Here is a nested list:
+
+<p>
+
+<ul>
+ <li> item1</li>
+ <li> item2</li>
+ <li> item3 which continues
+ on the next line to test that feature</li>
+ <li> and a sublist</li>
+
+<ul>
+ <li> with indented subitem1</li>
+ <li> and a subitem2</li>
+</ul>
+
+ <li> and perhaps an ordered sublist</li>
+
+<ol>
+ <li> first item</li>
+ <li> second item,
+ continuing on a new line</li>
+</ol>
+
+</ul>
+
+<blockquote>
+ Here are two lines that make up
+ a block quote.
+</blockquote>
+<p>
+
+
+<h3>Subsection 1 <a name="___sec1"></a></h3>
+
+<p>
+More text, with a reference back to the section <a href="#sec1">Section
1</a> and further
+to the section <a href="#subsubsec:ex">URLs</a>.
+
+
+<p>
+Let's do some copying from files too. First from subroutine up to the very
end,
+
+<p>
+
+
+<table class="highlighttable"><tr><td><div class="linenodiv"
style="background-color: #f0f0f0; padding-right: 10px"><pre
style="line-height: 125%"> 1
+ 2
+ 3
+ 4
+ 5
+ 6
+ 7
+ 8
+ 9
+10
+11
+12
+13</pre></div></td><td class="code"><div class="highlight"
style="background: #f8f8f8"><pre style="line-height: 125%"> <span
style="color: #AA22FF; font-weight: bold">subroutine </span><span
style="color: #B8860B">test</span>()
+ <span style="color: #00BB00; font-weight: bold">integer </span><span
style="color: #B8860B">i</span>
+ <span style="color: #00BB00; font-weight: bold">real</span><span
style="color: #666666">*8</span> <span style="color: #B8860B">r</span>
+ <span style="color: #B8860B">r</span> <span style="color:
#666666">=</span> <span style="color: #666666">0</span>
+ <span style="color: #AA22FF; font-weight: bold">do </span><span
style="color: #B8860B">i</span> <span style="color: #666666">=</span> <span
style="color: #666666">1</span>, <span style="color: #B8860B">i</span>
+ <span style="color: #B8860B">r</span> <span style="color:
#666666">=</span> <span style="color: #B8860B">r</span> <span style="color:
#666666">+</span> <span style="color: #B8860B">i</span>
+ <span style="color: #AA22FF; font-weight: bold">end do</span>
+<span style="color: #AA22FF; font-weight: bold"> return</span>
+<span style="color: #B8860B">C</span> <span style="color:
#B8860B">END1</span>
+
+ <span style="color: #AA22FF; font-weight: bold">program </span><span
style="color: #B8860B">testme</span>
+ <span style="color: #AA22FF; font-weight: bold">call </span><span
style="color: #B8860B">test</span>()
+ <span style="color: #AA22FF; font-weight: bold">return</span>
+</pre></div>
+</td></tr></table><p>
+and then just the subroutine,
+<p>
+
+
+<table class="highlighttable"><tr><td><div class="linenodiv"
style="background-color: #f0f0f0; padding-right: 10px"><pre
style="line-height: 125%">1
+2
+3
+4
+5
+6
+7
+8</pre></div></td><td class="code"><div class="highlight"
style="background: #f8f8f8"><pre style="line-height: 125%"> <span
style="color: #AA22FF; font-weight: bold">subroutine </span><span
style="color: #B8860B">test</span>()
+ <span style="color: #00BB00; font-weight: bold">integer </span><span
style="color: #B8860B">i</span>
+ <span style="color: #00BB00; font-weight: bold">real</span><span
style="color: #666666">*8</span> <span style="color: #B8860B">r</span>
+ <span style="color: #B8860B">r</span> <span style="color:
#666666">=</span> <span style="color: #666666">0</span>
+ <span style="color: #AA22FF; font-weight: bold">do </span><span
style="color: #B8860B">i</span> <span style="color: #666666">=</span> <span
style="color: #666666">1</span>, <span style="color: #B8860B">i</span>
+ <span style="color: #B8860B">r</span> <span style="color:
#666666">=</span> <span style="color: #B8860B">r</span> <span style="color:
#666666">+</span> <span style="color: #B8860B">i</span>
+ <span style="color: #AA22FF; font-weight: bold">end do</span>
+<span style="color: #AA22FF; font-weight: bold"> return</span>
+</pre></div>
+</td></tr></table><p>
+and finally the complete file:
+<p>
+
+
+<table class="highlighttable"><tr><td><div class="linenodiv"
style="background-color: #f0f0f0; padding-right: 10px"><pre
style="line-height: 125%"> 1
+ 2
+ 3
+ 4
+ 5
+ 6
+ 7
+ 8
+ 9
+10
+11
+12
+13
+14
+15</pre></div></td><td class="code"><div class="highlight"
style="background: #f8f8f8"><pre style="line-height: 125%"><span
style="color: #B8860B">C</span> <span style="color: #B8860B">a</span>
<span style="color: #B8860B">comment</span>
+
+ <span style="color: #AA22FF; font-weight: bold">subroutine
</span><span style="color: #B8860B">test</span>()
+ <span style="color: #00BB00; font-weight: bold">integer </span><span
style="color: #B8860B">i</span>
+ <span style="color: #00BB00; font-weight: bold">real</span><span
style="color: #666666">*8</span> <span style="color: #B8860B">r</span>
+ <span style="color: #B8860B">r</span> <span style="color:
#666666">=</span> <span style="color: #666666">0</span>
+ <span style="color: #AA22FF; font-weight: bold">do </span><span
style="color: #B8860B">i</span> <span style="color: #666666">=</span> <span
style="color: #666666">1</span>, <span style="color: #B8860B">i</span>
+ <span style="color: #B8860B">r</span> <span style="color:
#666666">=</span> <span style="color: #B8860B">r</span> <span style="color:
#666666">+</span> <span style="color: #B8860B">i</span>
+ <span style="color: #AA22FF; font-weight: bold">end do</span>
+<span style="color: #AA22FF; font-weight: bold"> return</span>
+<span style="color: #B8860B">C</span> <span style="color:
#B8860B">END1</span>
+
+ <span style="color: #AA22FF; font-weight: bold">program </span><span
style="color: #B8860B">testme</span>
+ <span style="color: #AA22FF; font-weight: bold">call </span><span
style="color: #B8860B">test</span>()
+ <span style="color: #AA22FF; font-weight: bold">return</span>
+</pre></div>
+</td></tr></table><p>
+Testing other code environments. First Python:
+<p>
+
+
+<table class="highlighttable"><tr><td><div class="linenodiv"
style="background-color: #f0f0f0; padding-right: 10px"><pre
style="line-height: 125%">1
+2
+3
+4</pre></div></td><td class="code"><div class="highlight"
style="background: #f8f8f8"><pre style="line-height: 125%">!bc pycod
+def f(x):
+ return x+1
+!ec
+</pre></div>
+</td></tr></table><p>
+which gets rendered as
+
+<p>
+
+
+<table class="highlighttable"><tr><td><div class="linenodiv"
style="background-color: #f0f0f0; padding-right: 10px"><pre
style="line-height: 125%">1
+2</pre></div></td><td class="code"><div class="highlight"
style="background: #f8f8f8"><pre style="line-height: 125%"><span
style="color: #AA22FF; font-weight: bold">def</span> <span style="color:
#00A000">f</span>(x):
+ <span style="color: #AA22FF; font-weight: bold">return</span> x<span
style="color: #666666">+1</span>
+</pre></div>
+</td></tr></table><p>
+Now a complete program to be shown via Python Online Tutorial:
+<p>
+
+<iframe width="950" height="500" frameborder="0"
+
src="http://pythontutor.com/iframe-embed.html#code=def+f%28x%29%3A%0A++++return+x+%2B+1%0A%0Aa+%3D+2%0Ax+%3D+a%0Aa+%3D+1%0Av+%3D+f%28x%29%0Aprint+v&curInstr=0&py=2&cumulative=false">
+</iframe>
+<p>
+Then Cython:
+<p>
+
+
+<table class="highlighttable"><tr><td><div class="linenodiv"
style="background-color: #f0f0f0; padding-right: 10px"><pre
style="line-height: 125%">1
+2</pre></div></td><td class="code"><div class="highlight"
style="background: #f8f8f8"><pre style="line-height: 125%"><span
style="color: #AA22FF; font-weight: bold">cpdef</span> <span style="color:
#00A000">f</span>(double x):
+ <span style="color: #AA22FF; font-weight: bold">return</span> x <span
style="color: #666666">+</span> <span style="color: #666666">1</span>
+</pre></div>
+</td></tr></table><p>
+
+C++:
+<p>
+
+
+<table class="highlighttable"><tr><td><div class="linenodiv"
style="background-color: #f0f0f0; padding-right: 10px"><pre
style="line-height: 125%">1
+2
+3
+4
+5
+6
+7</pre></div></td><td class="code"><div class="highlight"
style="background: #f8f8f8"><pre style="line-height: 125%"><span
style="color: #008800">#include <iostream></span>
+
+<span style="color: #00BB00; font-weight: bold">int</span> main()
+{
+ std<span style="color: #666666">::</span>cout <span style="color:
#666666"><<</span> <span style="color: #BB4444">"Sample
output"</span> <span style="color: #666666"><<</span> std<span
style="color: #666666">::</span>endl;
+ <span style="color: #AA22FF; font-weight: bold">return</span> <span
style="color: #666666">0</span>
+}
+</pre></div>
+</td></tr></table><p>
+
+And a little bit of Fortran:
+
+<p>
+
+
+<table class="highlighttable"><tr><td><div class="linenodiv"
style="background-color: #f0f0f0; padding-right: 10px"><pre
style="line-height: 125%">1
+2
+3
+4
+5
+6
+7
+8</pre></div></td><td class="code"><div class="highlight"
style="background: #f8f8f8"><pre style="line-height: 125%">!bc cod
+ subroutine midpt(x, length, a, b)
+ real*8 a, b, x
+ x = (a + b)/2
+ length = b - a
+ return
+ end
+!ec
+</pre></div>
+</td></tr></table><p>
+which then is typeset as
+
+<p>
+
+
+<table class="highlighttable"><tr><td><div class="linenodiv"
style="background-color: #f0f0f0; padding-right: 10px"><pre
style="line-height: 125%">1
+2
+3
+4
+5
+6</pre></div></td><td class="code"><div class="highlight"
style="background: #f8f8f8"><pre style="line-height: 125%"> subroutine
midpt(x, length, a, b)
+ real*8 a, b, x
+ x = (a + b)/2
+ length = b - a
+ return
+ end
+</pre></div>
+</td></tr></table><p>
+HTML:
+
+<p>
+
+
+<table class="highlighttable"><tr><td><div class="linenodiv"
style="background-color: #f0f0f0; padding-right: 10px"><pre
style="line-height: 125%">1
+2
+3
+4
+5</pre></div></td><td class="code"><div class="highlight"
style="background: #f8f8f8"><pre style="line-height: 125%"><span
style="color: #008000; font-weight: bold"><table></span>
+<span style="color: #008000; font-weight:
bold"><tr><td></span>Column 1<span style="color: #008000;
font-weight: bold"></td><td></span>Column 2<span style="color:
#008000; font-weight: bold"></td></tr></span>
+<span style="color: #008000; font-weight:
bold"><tr><td></span>0.67526 <span style="color: #008000;
font-weight: bold"></td><td></span>0.92871 <span style="color:
#008000; font-weight: bold"></td></tr></span>
+<span style="color: #008800; font-style: italic"></span>
+<span style="color: #008000; font-weight: bold"></table></span>
+</pre></div>
+</td></tr></table><p>
+System call:
+<p>
+
+
+<table class="highlighttable"><tr><td><div class="linenodiv"
style="background-color: #f0f0f0; padding-right: 10px"><pre
style="line-height: 125%">1
+2
+3
+4
+5</pre></div></td><td class="code"><div class="highlight"
style="background: #f8f8f8"><pre style="line-height: 125%">Terminal>
mkdir <span style="color: #AA22FF">test</span>
+Terminal> <span style="color: #AA22FF">cd test</span>
+Terminal> myprog -f
+output1
+output2
+</pre></div>
+</td></tr></table><p>
+It is time to test <code>verbatim inline font</code> especially with
<code>a newline
+inside the text</code> and an exclamation mark at the end:
<code>BEGIN</code>! The
+exclamation mark inside the verbatim text is not smart for latex as
+we use ! in the <code>verb</code> typesetting... Also test backslashes
+like <code>\begin</code> and <code>\end</code> in inline verbatim text.
+
+<p>
+Here is some <font color="red">red</font> color and an attempt to write
<font color="green">with
+green color containing a linebreak.
+And one more.</font> Some formats will only display this correctly when
+HTML is the output format.
+
+<h3>Subsection 2: Testing figures and movies <a name="subsec:ex"></a></h3>
+
+<p>
+Test of figures. In particular we refer to Figure <a
href="#fig:impact">1</a> in which
+there is a flow.
+
+<p>
+<center> 
+<hr class="figure">
+<center><p class="caption">Figure 1: Visualization of flow by
streamtubes. <a name="fig:impact"></a> </p></center>
+<p><img src="../doc/manual/figs/streamtubes.png" align="bottom"
width=200></p>
+</center>
+
+<p>
+Figures without captions are allowed and will be inlined.
+
+<p>
+<center><p><img src="../doc/manual/figs/streamtubes.png" align="bottom"
width=200></p></center>
+
+<h4>Test of movies <a name="___sec3"></a></h4>
+
+<p>
+Movie <a href="#mov:tsunami">mov:tsunami</a> shows a tsunami.
+
+<p>
+
+<embed src="../doc/manual/figs/mjolnir.mpeg" width=700 height=400
autoplay="false" loop="true"></embed>
+<p><em>Mjolnir tsunami (by Sylfest Glimsdal) <a
name="mov:tsunami"></a>.</em></p>
+
+
+<p>
+Test empty caption (for inline movie):
+
+<p>
+
+<embed src="../doc/manual/figs/wavepacket.mpeg" width=700 height=400
autoplay="false" loop="true"></embed>
+<p><em></em></p>
+
+
+<p>
+
+
+<p><a href="wavepacket_0001.html">Movie of files
<tt>../doc/manual/figs/wavepacket_*.png</tt></a>
+<em>Movie based on collection of frames (here just a few frames compared
with the full wavepacket.mpeg movie). <a name="mymov"></a></em></p>
+
+<p>
+
+
+
+<p>
+
+<iframe width="420" height="315"
src="http://www.youtube.com/embed/_O7iUiftbKU" frameborder="0"
allowfullscreen></iframe>
+
+<em>Movies can be uploaded to YouTube and embedded as HTML or as a
link.</em>
+
+
+
+<p>
+
+<iframe width="500" height="278"
src="http://player.vimeo.com/video/55562330" frameborder="0"
allowfullscreen></iframe>
+
+<em>Computational fluid dynamics movie.</em>
+
+
+
+<p>
+
+
+<p>
+Here is figure <a href="#myfig">2</a> with a long multi-line caption
+and an extra space before the FIGURE keyword.
+
+<p>
+<center> 
+<hr class="figure">
+<center><p class="caption">Figure 2: A long caption spanning several
lines and containing verbatim words like <code>my_file_v1</code> and
<code>my_file_v2</code> as well as math with subscript as in $ t_{i+1} $.
<a name="myfig"></a> </p></center>
+<p><img src="../doc/manual/figs/wavepacket_0001.png" align="bottom"
width=500></p>
+</center>
+
+<p>
+
+
+<p>
+
+
+<p>
+<center><p><img
src="https://doconce.googlecode.com/hg/doc/blog/f_plot.png" align="bottom"
width=500,></p></center>
+
+<p>
+
+
+<p>
+
+
+<h3>The $ \theta $ parameter (not $ \nabla $?) <a
name="decay:sec:theta"></a></h3>
+
+<p>
+Functions do not always need to be advanced, here is one
+involving $ \theta $:
+<p>
+
+
+<table class="highlighttable"><tr><td><div class="linenodiv"
style="background-color: #f0f0f0; padding-right: 10px"><pre
style="line-height: 125%">1
+2</pre></div></td><td class="code"><div class="highlight"
style="background: #f8f8f8"><pre style="line-height: 125%">def f(theta):
+ return theta**2
+</pre></div>
+</td></tr></table><p>
+<b>More on $ \theta $.</b>
+Here is more text following headline with math.
+
+<p>
+Newcommands must also be tested in this test report:
+$ \frac{1}{2} $, $ {1/2} $, $ \pmb{x} $, $ \frac{Du}{dt} $,
+both inline and in block:
+
+<p>
+$$
+\begin{align*}
+\frac{Du}{dt} &= 0
+\\
+\frac{1}{2} &= {1/2}\\
+\frac{1}{2}\pmb{x} &= \pmb{n}
+\end{align*}
+$$
+
+
+<p>
+Or with align with label and numbers:
+
+<p>
+$$
+\begin{align}
+\frac{Du}{dt} &= 0
+\label{aligneq1}\\
+\frac{1}{2} &= {1/2}\\
+\frac{1}{2}\pmb{x} &= \pmb{n}
+\label{aligneq2}
+\end{align}
+$$
+
+<h3>Custom Environments <a name="___sec5"></a></h3>
+
+<p>
+Here is an attempt to create a theorem environment via Mako
+(for counting theorems) and comment lines to help replacing lines in
+the <code>.tex</code> by proper begin-end LaTeX environments for theorems.
+Should look nice in most formats!
+
+<p>
+
+<a name="theorem:fundamental1"></a>
+
+<p>
+<b>Theorem 5.</b>
+Let $ a=1 $ and $ b=2 $. Then $ c=3 $.
+
+
+<p>
+
+<b>Proof.</b>
+Since $ c=a+b $, the result follows from straightforward addition.
+$ \Diamond $
+
+
+<p>
+As we see, the proof of Theorem 5 is a modest
+achievement.
+
+<h3>Tables <a name="subsec:table"></a></h3>
+
+<p>
+
+
+<p>
+Let us take this table from the manual:
+
+<p>
+<table border="1">
+<tr><td align="center"><b> time </b></td> <td align="center"><b>
velocity </b></td> <td align="center"><b> acceleration </b></td> </tr>
+<tr><td align="left"> 0.0 </td> <td align="right">
1.4186 </td> <td align="right"> -5.01 </td> </tr>
+<tr><td align="left"> 2.0 </td> <td align="right">
1.376512 </td> <td align="right"> 11.919 </td> </tr>
+<tr><td align="left"> 4.0 </td> <td align="right">
1.1E+1 </td> <td align="right"> 14.717624 </td> </tr>
+</table>
+<p>
+The Doconce source code reads
+<p>
+
+
+<table class="highlighttable"><tr><td><div class="linenodiv"
style="background-color: #f0f0f0; padding-right: 10px"><pre
style="line-height: 125%">1
+2
+3
+4
+5
+6
+7</pre></div></td><td class="code"><div class="highlight"
style="background: #f8f8f8"><pre style="line-height: 125%"> |
--------------------------------|
+ |time | velocity | acceleration |
+ |--l--------r-----------r--------|
+ | 0.0 | 1.4186 | -5.01 |
+ | 2.0 | 1.376512 | 11.919 |
+ | 4.0 | 1.1E+1 | 14.717624 |
+ |--------------------------------|
+</pre></div>
+</td></tr></table><p>
+Here is yet another table to test that we can handle more than
+one table:
+
+<p>
+<table border="1">
+<tr><td align="center"><b> time </b></td> <td align="center"><b>
velocity </b></td> <td align="center"><b> acceleration </b></td> </tr>
+<tr><td align="left"> 0.0 </td> <td align="left">
1.4186 </td> <td align="left"> -5.01 </td> </tr>
+<tr><td align="left"> 1.0 </td> <td align="left">
1.376512 </td> <td align="left"> 11.919 </td> </tr>
+<tr><td align="left"> 3.0 </td> <td align="left">
1.1E+1 </td> <td align="left"> 14.717624 </td> </tr>
+</table>
+<p>
+And one with math headings (that are expanded and must be treated
+accordingly) and verbatim heading and entry:
+
+<p>
+<table border="1">
+<tr><td align="center"><b> $ i $ </b></td> <td
align="center"><b> $ h_i $ </b></td> <td align="center"><b> $
\bar T_i $ </b></td> <td align="center"><b> <code>L_i</code> </b></td>
</tr>
+<tr><td align="left"> 0 </td> <td align="right">
0 </td> <td align="right"> 288 </td>
<td align="right"> -0.0065 </td> </tr>
+<tr><td align="left"> 1 </td> <td align="right">
11,000 </td> <td align="right"> 216 </td>
<td align="right"> 0.0 </td> </tr>
+<tr><td align="left"> 2 </td> <td align="right">
20,000 </td> <td align="right"> 216 </td>
<td align="right"> 0.001 </td> </tr>
+<tr><td align="left"> 3 </td> <td align="right">
32,000 </td> <td align="right"> 228 </td>
<td align="right"> 0.0028 </td> </tr>
+<tr><td align="left"> 4 </td> <td align="right">
47,000 </td> <td align="right"> 270 </td>
<td align="right"> 0.0 </td> </tr>
+<tr><td align="left"> 5 </td> <td align="right">
51,000 </td> <td align="right"> 270 </td>
<td align="right"> -0.0028 </td> </tr>
+<tr><td align="left"> 6 </td> <td align="right">
71,000 </td> <td align="right"> 214 </td>
<td align="right"> <code>NaN</code> </td> </tr>
+</table>
+<p>
+And add one with verbatim headings (with underscores),
+and rows starting with <code>|-</code> because of a negative number,
+and <code>|</code> right after verbatim word (with no space):
+
+<p>
+<table border="1">
+<tr><td align="center"><b> exact </b></td> <td
align="center"><b> <code>v_1</code> </b></td> <td
align="center"><b> $ a_i $ + <code>v_2</code> </b></td> <td
align="center"><b> <code>verb_3_</code> </b></td> </tr>
+<tr><td align="right"> 9 </td> <td
align="right"> 9.62 </td> <td align="right">
5.57 </td> <td align="right">
8.98 </td> </tr>
+<tr><td align="right"> -20 </td> <td
align="right"> -23.39 </td> <td align="right">
-7.65 </td> <td align="right">
-19.93 </td> </tr>
+<tr><td align="right"> 10 </td> <td
align="right"> 17.74 </td> <td align="right">
-4.50 </td> <td align="right">
9.96 </td> </tr>
+<tr><td align="right"> 0 </td> <td
align="right"> -9.19 </td> <td align="right">
4.13 </td> <td align="right">
-0.26 </td> </tr>
+</table>
+
+<h3>A test of verbatim words in heading with subscript $ a_i $:
<code>my_file_v1</code> and <code>my_file_v2</code> <a
name="___sec7"></a></h3>
+
+<p>
+<b>Files <code>my_file_v1.py</code> and <code>my_file_v2.py</code> define
some math $ a_{i-1} $.</b>
+Here is
+some text.
+
+<h3>Bibliography test <a name="___sec8"></a></h3>
+
+<p>
+Here is an example: <a href="#Langtangen_Pedersen_2002">[1]</a> discussed
propagation of
+large destructive water waves, <a href="#Langtangen_et_al_2002">[2]</a>
gave
+an overview of numerical methods for solving the Navier-Stokes equations,
+while the use of Backward Kolmogorov equations for analyzing
+random vibrations was investigated in <a href="#Langtangen_1994a">[3]</a>.
+The book chapter <a href="#Mardal_et_al_2003a">[4]</a> contains
information on
+C++ software tools for programming multigrid methods. A real retro
+reference is <a href="#Langtangen_1988d">[5]</a> about a big FORTRAN
package.
+Multiple references are also possible, e.g., see
+<a href="#Langtangen_Pedersen_2002">[1]</a> <a
href="#Mardal_et_al_2003a">[4]</a>.
+
+<p>
+We need to cite more than 10 papers to reproduce an old formatting
+problem with blanks in the keys in reST format:
+<a href="#Langtangen_1992c">[6]</a> <a href="#Langtangen_1994a">[3]</a> <a
href="#Mortensen_et_al_2011">[7]</a> <a
href="#Langtangen_Pedersen_2002">[1]</a>
+and
+<a href="#Langtangen_et_al_2002">[2]</a> <a
href="#Glimsdal_et_al_20006">[8]</a> <a href="#Rahman_et_al_2006b">[9]</a>
<a href="#Haga_et_al_2011a">[10]</a> <a href="#Langtangen_2003a">[11]</a>
<a href="#Langtangen_2008a">[12]</a> <a href="#Langtangen:95">[13]</a>
+and all the work of
+<a href="#Langtangen_2012">[14]</a> <a href="#Mardal_et_al_2003a">[4]</a>
<a href="#Jeberg_et_al_2004">[15]</a> as well as
+old work <a href="#Langtangen_1988d">[5]</a> and <a
href="#Langtangen_1989e">[16]</a>, and the
+talk <a href="#Langtangen_talk_2007a">[17]</a>.
+Langtangen also had two thesis <a href="#Langtangen:85">[18]</a> <a
href="#Langtangen_1989e">[16]</a>.
+More retro citations are
+the old ME-IN323 book <a href="#Langtangen:91">[19]</a> and the
+<a href="#Langtangen:94b">[20]</a> OONSKI '94 paper.
+
+<p>
+
+
+<h3>Example 1: Examples can be typeset as exercises <a
name="Example"></a></h3>
+
+<p>
+Examples can start with a subsection heading starting with
<code>Example:</code>
+and then, with the command-line option
<code>--examples_as_exercises</code> be
+typeset as exercises. This is useful if one has solution
+environments as part of the example.
+
+<p>
+<b>a)</b>
+State some problem.
+
+<p>
+<b>Solution.</b>
+The answer to this subproblem can be written here.
+
+<p>
+<b>b)</b>
+State some other problem.
+
+<p>
+<b>Hint 1.</b>
+A hint can be given.
+
+<p>
+<b>Hint 2.</b>
+Maybe even another hint?
+
+<p>
+<b>Solution.</b>
+The answer to this other subproblem goes here,
+maybe over multiple doconce input lines.
+
+<p>
+
+
+<h3>URLs <a name="subsubsec:ex"></a></h3>
+
+<p>
+Testing of URLs: hpl's home page <a href="http://folk.uio.no/hpl">hpl</a>,
or
+the entire URL if desired, <a
href="http://folk.uio.no/hpl"><tt>http://folk.uio.no/hpl</tt></a>. Here is
a
+plain file link <a href="testdoc.do.txt"><tt>testdoc.do.txt</tt></a>, or
<a href="testdoc.do.txt"><tt>testdoc.do.txt</tt></a>, or
+<a href="testdoc.do.txt"><tt>testdoc.do.txt</tt></a> or <a
href="testdoc.do.txt"><tt>testdoc.do.txt</tt></a> or <a
href="testdoc.do.txt">a link with
+newline</a>. Can test spaces with the link with word
+too: <a href="http://folk.uio.no/hpl">hpl</a> or <a
href="http://folk.uio.no/hpl">hpl</a>. Also <code>file:///</code> works: <a
href="file:///home/hpl/vc/doconce/doc/demos/manual/manual.html">link to a
+file</a> is
+fine to have. Moreover, "loose" URLs work, i.e., no quotes, just
+the plain URL as in <a
href="http://folk.uio.no/hpl"><tt>http://folk.uio.no/hpl</tt></a>, if
followed by space, comma,
+colon, semi-colon, question mark, exclamation mark, but not a period
+(which gets confused with the periods inside the URL).
+
+<p>
+Mail addresses can also be used: <a
href="mailto:h...@simula.no"><tt>h...@simula.no</tt></a>, or just a <a
href="mailto:h...@simula.no">mail link</a>, or a raw <a
href="mailto:h...@simula.no"><tt>mailto:h...@simula.no</tt></a>.
+
+<p>
+Here are some tough tests of URLs, especially for the <code>latex</code>
format:
+<a
href="http://en.wikipedia.org/wiki/Newton%E2%80%93Cotes_formulas">Newton-Cotes</a>
formulas
+and a <a
href="http://www.springer.com/mathematics/computational+science+%26+engineering/book/978-3-642-23098-1">good
book</a>. Need to test
+Newton-Cotes with percentage in URL too:
+<a
href="http://en.wikipedia.org/wiki/Newton%E2%80%93Cotes_formulas"><tt>http://en.wikipedia.org/wiki/Newton%E2%80%93Cotes_formulas</tt></a>
+and <a
href="http://en.wikipedia.org/wiki/Newton-Cotes#Open_Newton.E2.80.93Cotes_formulae"><tt>http://en.wikipedia.org/wiki/Newton-Cotes#Open_Newton.E2.80.93Cotes_formulae</tt></a>
which has a shebang.
+
+<p>
+For the <code>--device=paper</code> option it is important to test that
URLs with
+monofont link text get a footnote, as in this reference to
+<a
href="https://github.com/hplgit/INF5620/tree/gh-pages/src/decay/experiments/decay_mod.py"><tt>decay_mod</tt></a>.
+
+<p>
+
+
+
+<p>
+
+
+
+
+<p>
+More tough tests: repeated URLs whose footnotes when using the
+<code>--device=paper</code> option must be correct. We have
+<a href="http://google.com">google</a>, <a
href="http://google.com">google</a>, and
+<a href="http://google.com">google</a>, which should result in exactly
three
+footnotes.
+
+<h3>LaTeX Mathematics <a name="___sec11"></a></h3>
+
+<p>
+Here is an equation without label using backslash-bracket environment:
+$$ a = b + c $$
+
+or with number and label, as in \eqref{my:eq1}, using the equation
environment:
+$$
+\begin{equation}
+{\partial u\over\partial t} = \nabla^2 u \label{my:eq1}
+\end{equation}
+$$
+
+We can refer to this equation by \eqref{my:eq1}.
+
+<p>
+Here is a system without equation numbers, using the align-astrisk
environment:
+$$
+\begin{align*}
+\pmb{a} &= \pmb{q}\times\pmb{n} \\
+b &= \nabla^2 u + \nabla^4 v
+\end{align*}
+$$
+
+
+<p>
+And here is a system of equations with labels in an align environment:
+$$
+\begin{align}
+a &= q + 4 + 5+ 6 \label{eq1} \\
+b &= \nabla^2 u + \nabla^4 x \label{eq2}
+\end{align}
+$$
+
+We can refer to \eqref{eq1}-\eqref{eq2}. They are a bit simpler than
+the Navier-Stokes equations. And test LaTeX hyphen in <code>CG-2</code>.
+Also test $ a_{i-j} $ as well as $ kx-wt $.
+
+<p>
+Many of the next environments will fail in non-latex formats.
+Testing multiline:
+$$
+\begin{multline}
+a = b = q + \\
+ f + \nabla\cdot\nabla u
+\label{multiline:eq1}
+\end{multline}
+$$
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