Add examples of using pandoc-secnos

output/thesis.html

@@ -335,7 +335,7 @@ <h2 data-number="1.3" id="summary-of-chapters"><span class="header-section-numbe
                                 For bold, add ** on either side of the text
                                 For bold and italic, add _** on either side of the text
                                 -->
-                                <p>This is a brief outline of what went into each chapter, and a section which shows how to reference headers (which are labelled automatically for you). <strong><a href="#introduction-with-a-citation">Chapter 1</a></strong> shows how to use citations and how to reference section headers. <strong><a href="#literature-review-with-maths">Chapter 2</a></strong> shows how use and reference equations. <strong><a href="#first-research-study-with-code">Chapter 3</a></strong> shows how to use and reference code. <strong><a href="#research-containing-a-figure">Chapter 4</a></strong> shows how to use, reference, and resize pdf and jpg figures. <strong><a href="#research-containing-a-table">Chapter 5</a></strong> shows how to use and reference tables. <strong><a href="#final-research-study">Chapter 6</a></strong> is truly revolutionary (but shows nothing functional). <strong><a href="#appendix-1-some-extra-stuff">Appendix 1</a></strong> shows how to add chapters which are not numbered, as does <strong><a href="#appendix-2-some-more-extra-stuff">Appendix 2</a></strong>. See the base <a href="https://github.com/tompollard/phd_thesis_markdown/blob/master/README.md"><code>README.md</code></a> for how References are handled - leave <code>*_references.md</code> alone, and provide it to <code>pandoc</code> last.</p>
+                                <p>This is a brief outline of what went into each chapter, and a section which shows how to reference headers (which are labelled automatically for you). This chapter, section <a href="#introduction-with-a-citation">1</a>, shows how to use citations and how to reference section headers. Section <a href="#literature-review-with-maths">2</a> shows how use and reference equations. Section <a href="#first-research-study-with-code">3</a> shows how to use and reference code. Section <a href="#research-containing-a-figure">4</a> shows how to use, reference, and resize pdf and jpg figures. Section <a href="#research-containing-a-table">5</a> shows how to use and reference tables. Section <a href="#final-research-study">6</a> is truly revolutionary (but shows nothing functional). <strong><a href="#appendix-1-some-extra-stuff">Appendix 1</a></strong> shows how to add chapters which are not numbered, and has to be referenced manually, as does <strong><a href="#appendix-2-some-more-extra-stuff">Appendix 2</a></strong>. See the base <a href="https://github.com/tompollard/phd_thesis_markdown/blob/master/README.md"><code>README.md</code></a> for how References are handled - leave <code>*_references.md</code> alone, and provide it to <code>pandoc</code> last.</p>
                                 <p>Proin faucibus nibh sit amet augue blandit varius.</p>
                                 <h1 data-number="2" id="literature-review-with-maths"><span class="header-section-number">2</span> Literature review, with maths</h1>
                                 <!--
@@ -378,7 +378,7 @@ <h3 data-number="3.2.1" id="subsection-1-with-example-code-block"><span class="h
                                 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> mood <span class="op">==</span> <span class="st">&#39;happy&#39;</span>:</span>
                                 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a>    <span class="bu">print</span>(<span class="st">&quot;I am a happy robot&quot;</span>)</span></code></pre></div>
                                 <h3 data-number="3.2.2" id="subsection-2"><span class="header-section-number">3.2.2</span> Subsection 2</h3>
-                                <p>By running the code in <a href="#subsection-1-with-example-code-block">Section Subsection 1 with example code block</a>, we solved AI completely. This is the second part of the methodology. Proin tincidunt odio non sem mollis tristique. Fusce pharetra accumsan volutpat. In nec mauris vel orci rutrum dapibus nec ac nibh. Praesent malesuada sagittis nulla, eget commodo mauris ultricies eget. Suspendisse iaculis finibus ligula.</p>
+                                <p>By running the code in section <a href="#subsection-1-with-example-code-block">3.2.1</a>, we solved AI completely. This is the second part of the methodology. Proin tincidunt odio non sem mollis tristique. Fusce pharetra accumsan volutpat. In nec mauris vel orci rutrum dapibus nec ac nibh. Praesent malesuada sagittis nulla, eget commodo mauris ultricies eget. Suspendisse iaculis finibus ligula.</p>
                                 <!-- 
                                 Comments can be added like this.
                                 -->

output/thesis.tex

@@ -292,6 +292,9 @@
 \usepackage{bbold}
 \DeclareMathOperator*{\argmin}{\arg\!\min}
 
+% For use of \cref and \Cref used by pandoc secnos
+\usepackage{cleveref}
+
 \begin{document}
 
 
@@ -478,21 +481,18 @@ \section{Summary of chapters}\label{summary-of-chapters}}
 
 This is a brief outline of what went into each chapter, and a section
 which shows how to reference headers (which are labelled automatically
-for you).
-\textbf{\protect\hyperlink{introduction-with-a-citation}{Chapter 1}}
-shows how to use citations and how to reference section headers.
-\textbf{\protect\hyperlink{literature-review-with-maths}{Chapter 2}}
-shows how use and reference equations.
-\textbf{\protect\hyperlink{first-research-study-with-code}{Chapter 3}}
-shows how to use and reference code.
-\textbf{\protect\hyperlink{research-containing-a-figure}{Chapter 4}}
-shows how to use, reference, and resize pdf and jpg figures.
-\textbf{\protect\hyperlink{research-containing-a-table}{Chapter 5}}
-shows how to use and reference tables.
-\textbf{\protect\hyperlink{final-research-study}{Chapter 6}} is truly
-revolutionary (but shows nothing functional).
+for you). This chapter, \cref{introduction-with-a-citation}, shows how
+to use citations and how to reference section headers.
+\Cref{literature-review-with-maths} shows how use and reference
+equations. \Cref{first-research-study-with-code} shows how to use and
+reference code. \Cref{research-containing-a-figure} shows how to use,
+reference, and resize pdf and jpg figures.
+\Cref{research-containing-a-table} shows how to use and reference
+tables. \Cref{final-research-study} is truly revolutionary (but shows
+nothing functional).
 \textbf{\protect\hyperlink{appendix-1-some-extra-stuff}{Appendix 1}}
-shows how to add chapters which are not numbered, as does
+shows how to add chapters which are not numbered, and has to be
+referenced manually, as does
 \textbf{\protect\hyperlink{appendix-2-some-more-extra-stuff}{Appendix
 2}}. See the base
 \href{https://github.com/tompollard/phd_thesis_markdown/blob/master/README.md}{\texttt{README.md}}
@@ -613,13 +613,12 @@ \subsection{Subsection 1 with example code
 \hypertarget{subsection-2}{%
 \subsection{Subsection 2}\label{subsection-2}}
 
-By running the code in
-\protect\hyperlink{subsection-1-with-example-code-block}{Section
-Subsection 1 with example code block}, we solved AI completely. This is
-the second part of the methodology. Proin tincidunt odio non sem mollis
-tristique. Fusce pharetra accumsan volutpat. In nec mauris vel orci
-rutrum dapibus nec ac nibh. Praesent malesuada sagittis nulla, eget
-commodo mauris ultricies eget. Suspendisse iaculis finibus ligula.
+By running the code in \cref{subsection-1-with-example-code-block}, we
+solved AI completely. This is the second part of the methodology. Proin
+tincidunt odio non sem mollis tristique. Fusce pharetra accumsan
+volutpat. In nec mauris vel orci rutrum dapibus nec ac nibh. Praesent
+malesuada sagittis nulla, eget commodo mauris ultricies eget.
+Suspendisse iaculis finibus ligula.
 
 \hypertarget{results}{%
 \section{Results}\label{results}}

source/09_chapter_1.md

@@ -37,7 +37,7 @@ For bold, add ** on either side of the text
 For bold and italic, add _** on either side of the text
 -->
 
-This is a brief outline of what went into each chapter, and a section which shows how to reference headers (which are labelled automatically for you). **[Chapter 1](#introduction-with-a-citation)** shows how to use citations and how to reference section headers. **[Chapter 2](#literature-review-with-maths)** shows how use and reference equations.  **[Chapter 3](#first-research-study-with-code)** shows how to use and reference code.  **[Chapter 4](#research-containing-a-figure)** shows how to use, reference, and resize pdf and jpg figures. **[Chapter 5](#research-containing-a-table)** shows how to use and reference tables. **[Chapter 6](#final-research-study)** is truly revolutionary (but shows nothing functional). **[Appendix 1](#appendix-1-some-extra-stuff)** shows how to add chapters which are not numbered, as does **[Appendix 2](#appendix-2-some-more-extra-stuff)**. See the base [`README.md`](https://github.com/tompollard/phd_thesis_markdown/blob/master/README.md) for how References are handled - leave `*_references.md` alone, and provide it to `pandoc` last.
+This is a brief outline of what went into each chapter, and a section which shows how to reference headers (which are labelled automatically for you). This chapter, +@sec:introduction-with-a-citation, shows how to use citations and how to reference section headers. \*@sec:literature-review-with-maths shows how use and reference equations. \*@sec:first-research-study-with-code shows how to use and reference code. \*@sec:research-containing-a-figure shows how to use, reference, and resize pdf and jpg figures. \*@sec:research-containing-a-table shows how to use and reference tables. \*@sec:final-research-study is truly revolutionary (but shows nothing functional). **[Appendix 1](#appendix-1-some-extra-stuff)** shows how to add chapters which are not numbered, and has to be referenced manually, as does **[Appendix 2](#appendix-2-some-more-extra-stuff)**. See the base [`README.md`](https://github.com/tompollard/phd_thesis_markdown/blob/master/README.md) for how References are handled - leave `*_references.md` alone, and provide it to `pandoc` last.
 
 Proin faucibus nibh sit amet augue blandit varius.
 

source/11_chapter_3.md

@@ -22,7 +22,7 @@ if mood == 'happy':
 
 ### Subsection 2
 
-By running the code in [Section Subsection 1 with example code block](#subsection-1-with-example-code-block), we solved AI completely. This is the second part of the methodology. Proin tincidunt odio non sem mollis tristique. Fusce pharetra accumsan volutpat. In nec mauris vel orci rutrum dapibus nec ac nibh. Praesent malesuada sagittis nulla, eget commodo mauris ultricies eget. Suspendisse iaculis finibus ligula.
+By running the code in +@sec:subsection-1-with-example-code-block, we solved AI completely. This is the second part of the methodology. Proin tincidunt odio non sem mollis tristique. Fusce pharetra accumsan volutpat. In nec mauris vel orci rutrum dapibus nec ac nibh. Praesent malesuada sagittis nulla, eget commodo mauris ultricies eget. Suspendisse iaculis finibus ligula.
 
 <!-- 
 Comments can be added like this.

style/preamble.tex

@@ -141,4 +141,7 @@
 
 % Custom math
 \usepackage{bbold}
-\DeclareMathOperator*{\argmin}{\arg\!\min}
+\DeclareMathOperator*{\argmin}{\arg\!\min}
+
+% For use of \cref and \Cref used by pandoc secnos
+\usepackage{cleveref}