\section{ScholarlyMarkdown math
support}\label{scholarlymarkdown-math-support}

\subsection{Math as (fenced) code
blocks}\label{math-as-fenced-code-blocks}

This is a line of text with a \texttt{simple code block} in it.

\texttt{`this should be just a `normal` inline code block surrounded by literal backticks`}

This is another line of text. Here should be some math:
$\mathbf{F = ma}<2\mathbf{ma}$. There should be some displaymath
environment on the following line
%
\begin{equation*}
    \mathbf{F = ma} < 2\mathbf{ma}
\end{equation*}
%
 and there should be no line breaks between the displaymath block and
here. \textbf{This should be bold}. \emph{This should be italic.}

The following is a displaymath with an aligned environment in a separate
paragraph (preceded with, and followed by, two blank lines), with
identifier \texttt{matheqn1}. It should automatically be wrapped with
the \texttt{aligned} environment.

%
\begin{equation}
\label{matheqn1}
\begin{aligned}
\tag{BIGLABEL}
    \mbox{minimize}\quad & \fx = \max_{i=1,\ldots,m} (a_i^T x + b_i) \\
    & \|x\|_2 \le \sigma.
\end{aligned}
\end{equation}
%

Here is an implicit align math environment consisting of multiple lines
of equations with no newline in between, with at least one \texttt{\&}
symbol in the whole expression. It should be in the same paragraph as
this one.
%
\begin{align}
\nonumber \sum_{j_1, j_2, \ldots j_m} \sum_{k_1, k_2, \ldots, k_m} & \widetilde{A}_{j_1,k_1}^{\ast} \widetilde{A}_{j_1,k_2} \tilde{A}_{j_2,k_2}^{\ast} \widetilde{A}_{j_2,k_3}  \ldots \widetilde{A}_{j_m,k_m}^{\ast} \widetilde{A}_{j_m,k_1}\\
\label{middleAlignMathNumber} =   \sum_{j_1, j_2, \ldots j_m} \sum_{k_1, k_2, \ldots, k_m} & \left(  R_{\Lambda} T_{k_1}^{\ast} P_{\Omega} T_{j_1} R_{\Lambda}^{\ast} \right) \left(  R_{\Lambda} T_{j_1}^{\ast} P_{\Omega} T_{k_2} R_{\Lambda}^{\ast} \right)   \left(  R_{\Lambda} T_{k_2}^{\ast} P_{\Omega} T_{j_2} R_{\Lambda}^{\ast} \right)\\
\nonumber & \left(  R_{\Lambda} T_{j_2}^{\ast} P_{\Omega} T_{k_3} R_{\Lambda}^{\ast} \right) \ldots \left(  R_{\Lambda} T_{k_m}^{\ast} P_{\Omega} T_{j_m} R_{\Lambda}^{\ast} \right) \left(  R_{\Lambda} T_{j_m}^{\ast} P_{\Omega} T_{k_1} R_{\Lambda}^{\ast} \right).
\end{align}
%
 And here is an implicit gather math environment consisting of multiple
lines of equations with no newline in between, with \texttt{\&} symbol
not appearing in every statement:
%
\begin{gather}
\label{firstGatherMathNumber} \left.\begin{aligned}
    B'&=-\partial\times E\\
    E'&=\partial\times B - 4\pi j
    \end{aligned}
    \right\} \quad \textsf{Maxwell's equations}\\
\label{secondGatherMathNumber} A = B\\
\label{thirdgathernumber} AAAAAAA = BBBBBB
\end{gather}
%

Single math equations that have line-breaks (the
\texttt{\textbackslash{}\textbackslash{}} command) are automatically
wrapped in a \texttt{split} environment. If alignment commands (symbol
\texttt{\&}) also exist, they get wrapped in an \texttt{aligned}
environment instead. This behaviour can be disabled using the
\texttt{math\_plain} environment:
%
\begin{equation*}
\begin{split}
y = ax \\
f = kg^{-1}
\end{split}
\end{equation*}
%
%
\begin{equation*}
\begin{aligned}
y &= ax \\
f &= kg^{-1}
\end{aligned}
\end{equation*}
%
 The following has an ampersand and line breaks in comma, but is
actually a single-line equation that should be untouched:
%
\begin{equation*}
|y|\ \&\ |x| % an & and \\ that should be ignored
= 99\% z    % an & and \\ that should be ignored
\end{equation*}
%
 Below is more internal vertical alignment tests. The first is one that
uses \texttt{cases} internally:
%
\begin{equation}
\label{matheqn2}
    P_{r-j}=\begin{cases}
    0& \ensuremath\text{if $r-j$ is odd},\\
    r!\,(-1)^{(r-j)/2}& \text{if $r-j$ is even},
    \end{cases}
\end{equation}
%
 and another one that uses \texttt{aligned} internally.
%
\begin{equation}
\label{matheqn3}
    \left.\begin{aligned}
    B'&=-\partial\times E\\
    E'&=\partial\times B - 4\pi j
    \end{aligned}
    \right\}
    \qquad \text{Maxwell's equations}
\end{equation}
%

\subsection{Math and lists}\label{math-and-lists}

Here's a list with both inline and display math environments:

\begin{itemize}
\itemsep1pt\parskip0pt\parsep0pt
\item
  Item 1 is a famous item
\item
  Item 2 with a \texttt{code block} and $\mathsf{\text{inline math}}$
  with equation $\mathbf{y=Ax}$
\item
  Item 3

  \begin{itemize}
  \itemsep1pt\parskip0pt\parsep0pt
  \item
    Indented item 4
  \item
    Indented item 5, followed by display math, which cannot be indented:
    %
    \begin{equation*}
    \mathbf{F_1 = m_1a}
    \end{equation*}
    %
     with some text below
  \item
    Indented item 6, which does not recognize list-item display math
    surrounded by one additional blank line:
  \end{itemize}
\end{itemize}

%
\begin{equation*}
\mathbf{F_2 = m_2a}
\end{equation*}
%

\begin{verbatim}
  without breaking this text out of the list and into a pre block
\end{verbatim}

\begin{itemize}
\itemsep1pt\parskip0pt\parsep0pt
\item
  Item 4

  \begin{enumerate}
  \def\labelenumi{\arabic{enumi}.}
  \itemsep1pt\parskip0pt\parsep0pt
  \item
    Numerical Item 1
  \item
    Numerical item 2
  \end{enumerate}
\end{itemize}

\section{Scholarly X-refs}\label{scholarly-x-refs}

\subsection{References to figures}\label{references-to-figures}

This line refers to Figure~\ref{figure2}.

This line refers to Figure 2.

This line refers to subfigure~\eqref{reginfig3}.

\subsection{References to equations}\label{references-to-equations}

This line refers to Equation~\eqref{matheqn3}.

Referencing using the \texttt{\textbackslash{}ref} tag:
Equation~\ref{matheqn1}.

Referencing using the \texttt{\textbackslash{}eqref} tag:
Equation~\eqref{middleAlignMathNumber}.

\subsection{Automatic non-breaking
spaces}\label{automatic-non-breaking-spaces}

Any cross-references (such as Equation~\ref{middleAlignMathNumber}) will
automatically be prepended with non-breaking spaces.

Unless, they appear in a list like equations~\ref{matheqn1},
\ref{matheqn2}, \ref{matheqn3}, and~\ref{middleAlignMathNumber}.

\section{ScholarlyMarkdown Figures}\label{scholarlymarkdown-figures}

\subsection{Images with attributes}\label{images-with-attributes}

The following will be a bunch of figures with attributes:
\includegraphics[width=0.200\textwidth]{lunar_orbit.jpg}
\includegraphics[width=0.200\textwidth]{lunar_orbit.jpg} Which should
all show fine and display a picture with a baby seal.

Below is more text so that the css doesn't end abruptly! Now we'll have
an explicit Scholarly Figure environment!

\subsection{ScholarlyMarkdown
figure/multifigures}\label{scholarlymarkdown-figuremultifigures}

\begin{figure}
\centering
\includegraphics[width=0.500\hsize]{lunar_orbit.jpg}
\caption{Single-image figure. You can also have citations inside
captions {[}@Gill{]}.}\label{figure0}
\end{figure}

\begin{figure}
\centering
\subfloat[sub\label{reginfig1}]{\includegraphics[width=0.200\hsize]{lunar_orbit.jpg}}
\subfloat[subfig]{\includegraphics[width=0.200\hsize]{lunar_orbit.jpg}}
\subfloat[longer subcaption that
flows\label{reginfig3}]{\includegraphics[width=0.200\hsize]{lunar_orbit.jpg}}
\caption{Reference link in its own paragraph and long caption Lorem
ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy
nibh euismod tincidunt ut laoreet dolore magna aliquam erat
volutpat.}\label{figure1}
\end{figure}

\begin{figure*}
\centering
\subfloat[fdsaf\label{reginfig4}]{\includegraphics[width=0.400\hsize]{lunar_orbit.jpg}}
\subfloat[woogawooga\label{reginfig5}]{\includegraphics[width=0.300\hsize]{lunar_orbit.jpg}}
\caption{Reference link in its own paragraph and long caption Lorem
ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy
nibh euismod tincidunt ut laoreet dolore magna aliquam erat
volutpat.}\label{figure2}
\end{figure*}

\section{ScholarlyMarkdown
Algorithms}\label{scholarlymarkdown-algorithms}

Here are some algorithms using various methods. The ``most canonical
one'' is currently just using a line-block:

\begin{scholmdAlgorithm}
\texttt{ 1.}~\textbf{Inputs}:~variables~$A, b$\\\texttt{ 2.}~\textbf{Output}:~$\phi$~~~~~~~~~~~~~~~~\texttt{//this is a comment}

\texttt{ 3.}~Choose~an~initial~guess~$\phi$~to~the~solution\\\texttt{ 4.}~~\textbf{repeat}~until~convergence\\\texttt{ 5.}~~~~\textbf{for}~$i$~\textbf{from}~1~\textbf{until}~$n$~\textbf{do}\\\texttt{ 6.}~~~~~~~~$\sigma \leftarrow 0$\\\texttt{ 7.}~~~~~~~~\textbf{for}~$j$~\textbf{from}~1~\textbf{until}~$n$~\textbf{do}\\\texttt{ 8.}~~~~~~~~~~~~\textbf{if}~$j \ne i$~\textbf{then}\\\texttt{ 9.}~~~~~~~~~~~~~~~$\sigma \leftarrow \sigma + a_{ij} \phi_j$\\\texttt{10.}~~~~~~~~~~~~\textbf{end~if}\\\texttt{11.}~~~~~~~~\textbf{end}~($j$-loop)\\\texttt{12.}~~~~~~~~$\phi_i \leftarrow \frac 1 {a_{ii}} (b_i - \sigma)$\\\texttt{13.}~~~~\textbf{end}~($i$-loop)\\\texttt{14.}~~~~check~if~convergence~is~reached\\\texttt{15.}~\textbf{end}~(repeat)
\caption{caption for this algorithm}\label{alg:gs}
\end{scholmdAlgorithm}

\begin{scholmdAlgorithm}
~\textbf{Inputs}:~variables~$A, b$\\\hspace*{0.333em}\textbf{Output}:~$\phi$

~Choose~an~initial~guess~$\phi$~to~the~solution\\\hspace*{0.333em}\textbf{repeat}~until~convergence\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\textbf{for}~$i$~from~1~to~$n$~\textbf{do}\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}$\sigma \leftarrow 0$\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\textbf{for}~$j$~from~1~to~$n$~\textbf{do}\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\textbf{if}~$j \ne i$~\textbf{then}\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}$\sigma \leftarrow \sigma + a_{ij} \phi_j$\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\textbf{end~if}\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\textbf{end}~($j$-loop)\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}$\phi_i \leftarrow \frac 1 {a_{ii}} (b_i - \sigma)$\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\textbf{end}~($i$-loop)\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}check~if~convergence~is~reached\\\hspace*{0.333em}\textbf{end}~(repeat)
\label{alg:gs2}
\end{scholmdAlgorithm}

The should not be a caption

\begin{scholmdAlgorithm}
~\textbf{Inputs}:~variables~$A, b$\\\hspace*{0.333em}\textbf{Output}:~$\phi$

~Choose~an~initial~guess~$\phi$~to~the~solution\\\hspace*{0.333em}\textbf{repeat}~until~convergence\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\textbf{for}~$i$~from~1~to~$n$~\textbf{do}\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}$\sigma \leftarrow 0$\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\textbf{for}~$j$~from~1~to~$n$~\textbf{do}\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\textbf{if}~$j \ne i$~\textbf{then}\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}$\sigma \leftarrow \sigma + a_{ij} \phi_j$\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\textbf{end~if}\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\textbf{end}~($j$-loop)\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}$\phi_i \leftarrow \frac 1 {a_{ii}} (b_i - \sigma)$\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\textbf{end}~($i$-loop)\\\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}\hspace*{0.333em}check~if~convergence~is~reached\\\hspace*{0.333em}\textbf{end}~(repeat)
\caption{This should should be a caption}\label{alg:gs3}
\end{scholmdAlgorithm}

\section{ScholarlyMarkdown Tables}\label{scholarlymarkdown-tables}

\subsection{Standard Pandoc tables}\label{standard-pandoc-tables}

The following is a normal Pandoc table

\begin{longtable}[c]{@{}rllc@{}}
\caption{Thisis a caption}\tabularnewline
\toprule
Right & Left & Default & Center\tabularnewline
\midrule
\endfirsthead
\toprule
Right & Left & Default & Center\tabularnewline
\midrule
\endhead
12 & 12 & 12 & 12\tabularnewline
123 & 123 & 123 & 123\tabularnewline
1 & 1 & 1 & 1\tabularnewline
\bottomrule
\end{longtable}

This should not be a caption

\subsection{Scholarly tables}\label{scholarly-tables}

The following is a floated ScholMD table

\begin{table}
\centering
\begin{tabular}{rllc}
\toprule\addlinespace
Right & Left & Default & Center\tabularnewline
\midrule
12 & 12 & 12 & 12\tabularnewline
123 & 123 & 123 & 123\tabularnewline
1 & 1 & 1 & 1\tabularnewline
\bottomrule
\end{tabular}
\caption{This is a really really really really really really really
really really really really really really really really really really
really really really really really really really really really really
long caption}\label{tab:exscholmd}
\end{table}

\section{ScholarlyMarkdown Code
blocks}\label{scholarlymarkdown-code-blocks}

\subsection{Standard Pandoc code
blocks}\label{standard-pandoc-code-blocks}

\subsubsection{fenced blocks}\label{fenced-blocks}

\begin{verbatim}
Value   <- [0-9.]+ / '(' Expr ')'
Product <- Expr (('*' / '/') Expr)*
Sum     <- Expr (('+' / '-') Expr)*
Expr    <- Product / Sum / Value
\end{verbatim}

\subsubsection{indented blocks}\label{indented-blocks}

\begin{verbatim}
Value   <- [0-9.]+ / '(' Expr ')'
Product <- Expr (('*' / '/') Expr)*
Sum     <- Expr (('+' / '-') Expr)*
Expr    <- Product / Sum / Value
\end{verbatim}

\subsection{Scholarly code block
floats}\label{scholarly-code-block-floats}

\begin{lstlisting}[caption={\href{http://en.wikipedia.org/wiki/Parsing_expression_grammar}{Parsing
Expression Grammar} rules for a simple calculator using
PEG.}, language=C, numbers=left, firstnumber=100, label=lst:pegcalc, float=htbp]
Value   <- [0-9.]+ / '(' Expr ')'
Product <- Expr (('*' / '/') Expr)*
Sum     <- Expr (('+' / '-') Expr)*
Expr    <- Product / Sum / Value
\end{lstlisting}

\begin{lstlisting}[caption={\href{http://en.wikipedia.org/wiki/Parsing_expression_grammar}{Parsing
Expression Grammar} rules for a simple
calculator.}, label=lst:pegcalc, float=htbp]
Value   <- [0-9.]+ / '(' Expr ')'
Product <- Expr (('*' / '/') Expr)*
Sum     <- Expr (('+' / '-') Expr)*
Expr    <- Product / Sum / Value
\end{lstlisting}

