Run texhash in GH Actions

.github/workflows/publish.yml

@@ -43,6 +43,10 @@ jobs:
         - name: "Update font cache"
           run: sudo fc-cache -fv
 
+      # run texhash
+        - name: "Run texhash"
+          run: sudo texhash
+
       # Back to our regularly scheduled Quarto output
         - name: "Set up Quarto"
           uses: quarto-dev/quarto-actions/setup@v2

docs/demos/template-pdf-short-report+short+report.tex

@@ -0,0 +1,373 @@
+% original file from https://github.com/AAGI-AUS/AAGITemplates/blob/master/inst/rmarkdown/templates/AAGI_short_report/skeleton/assets/AAGI_markdown.tex
+% original author @RusselAndrewEdson
+
+\documentclass[
+]{article}
+
+\usepackage[left=12mm,right=12mm,top=22mm,bottom=22mm]{geometry}
+
+% Force placement of table
+\usepackage{float}
+\floatplacement{table}{H}
+
+% Random texts
+\usepackage{lipsum}
+
+% Colours and graphics
+\usepackage[dvipsnames,svgnames,x11names,table]{xcolor}
+\usepackage{graphicx}
+
+% AAGI palette colours
+\definecolor{aagibrightgreen}{HTML}{b6d438}
+\definecolor{aagiteal}{HTML}{00808b}
+\definecolor{aagiblue}{HTML}{648fd2}
+\definecolor{aagigreen}{HTML}{54921e}
+\definecolor{aagiyellow}{HTML}{ffbc42}
+\definecolor{aagiorange}{HTML}{ec8525}
+\definecolor{aagiblack}{HTML}{414042}
+\definecolor{aagigrey}{HTML}{f2f2f2}
+
+% Enable shading (i.e., Shaded environment) if set
+  \usepackage{color}
+  \usepackage{fancyvrb}
+  \newcommand{\VerbBar}{|}
+  \newcommand{\VERB}{\Verb[commandchars=\\\{\}]}
+  \DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}}
+  % Add ',fontsize=\small' for more characters per line
+  \usepackage{framed}
+  \definecolor{shadecolor}{RGB}{241,243,245}
+  \newenvironment{Shaded}{\begin{snugshade}}{\end{snugshade}}
+  \newcommand{\AlertTok}[1]{\textcolor[rgb]{0.68,0.00,0.00}{#1}}
+  \newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.37,0.37,0.37}{#1}}
+  \newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.40,0.45,0.13}{#1}}
+  \newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.68,0.00,0.00}{#1}}
+  \newcommand{\BuiltInTok}[1]{\textcolor[rgb]{0.00,0.23,0.31}{#1}}
+  \newcommand{\CharTok}[1]{\textcolor[rgb]{0.13,0.47,0.30}{#1}}
+  \newcommand{\CommentTok}[1]{\textcolor[rgb]{0.37,0.37,0.37}{#1}}
+  \newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.37,0.37,0.37}{\textit{#1}}}
+  \newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{#1}}
+  \newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.00,0.23,0.31}{\textbf{#1}}}
+  \newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.68,0.00,0.00}{#1}}
+  \newcommand{\DecValTok}[1]{\textcolor[rgb]{0.68,0.00,0.00}{#1}}
+  \newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.37,0.37,0.37}{\textit{#1}}}
+  \newcommand{\ErrorTok}[1]{\textcolor[rgb]{0.68,0.00,0.00}{#1}}
+  \newcommand{\ExtensionTok}[1]{\textcolor[rgb]{0.00,0.23,0.31}{#1}}
+  \newcommand{\FloatTok}[1]{\textcolor[rgb]{0.68,0.00,0.00}{#1}}
+  \newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.28,0.35,0.67}{#1}}
+  \newcommand{\ImportTok}[1]{\textcolor[rgb]{0.00,0.46,0.62}{#1}}
+  \newcommand{\InformationTok}[1]{\textcolor[rgb]{0.37,0.37,0.37}{#1}}
+  \newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.00,0.23,0.31}{\textbf{#1}}}
+  \newcommand{\NormalTok}[1]{\textcolor[rgb]{0.00,0.23,0.31}{#1}}
+  \newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.37,0.37,0.37}{#1}}
+  \newcommand{\OtherTok}[1]{\textcolor[rgb]{0.00,0.23,0.31}{#1}}
+  \newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.68,0.00,0.00}{#1}}
+  \newcommand{\RegionMarkerTok}[1]{\textcolor[rgb]{0.00,0.23,0.31}{#1}}
+  \newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.37,0.37,0.37}{#1}}
+  \newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.13,0.47,0.30}{#1}}
+  \newcommand{\StringTok}[1]{\textcolor[rgb]{0.13,0.47,0.30}{#1}}
+  \newcommand{\VariableTok}[1]{\textcolor[rgb]{0.07,0.07,0.07}{#1}}
+  \newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.13,0.47,0.30}{#1}}
+  \newcommand{\WarningTok}[1]{\textcolor[rgb]{0.37,0.37,0.37}{\textit{#1}}}
+
+% Fonts/encoding
+\usepackage{amsmath,amssymb}
+\usepackage{iftex}
+\ifPDFTeX
+  \usepackage[T1]{fontenc}
+  \usepackage[utf8]{inputenc}
+  \usepackage{textcomp} % provide euro and other symbols
+\else % if luatex or xetex
+  \usepackage{unicode-math}
+  \defaultfontfeatures{Scale=MatchLowercase}
+  \defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
+\fi
+  \usepackage{lmodern}
+
+%Set the font
+% Check to see if this font is installed system-wide
+\IfFontExistsTF{Proxima Nova.otf}{%
+% One person has this installed system-wide
+  \setmainfont{Proxima Nova.otf}
+}{
+% If not, load it from the file
+  \setmainfont{Arial.ttf}
+}
+
+
+%TODO: more font stuff from template.latex?
+
+% use upquote if available, for straight quotes in verbatim environments
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+% use microtype if available
+\IfFileExists{microtype.sty}{%
+  \usepackage{microtype}
+  \UseMicrotypeSet[protrusion]{basicmath}}{} % disable protrusion for tt fonts
+\usepackage{bm}
+
+  \setcounter{secnumdepth}{0}
+
+% (Default) CSL referencing with citeproc
+% definitions for citeproc citations
+\NewDocumentCommand\citeproctext{}{}
+\NewDocumentCommand\citeproc{mm}{%
+  \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
+\makeatletter
+ % allow citations to break across lines
+ \let\@cite@ofmt\@firstofone
+ % avoid brackets around text for \cite:
+ \def\@biblabel#1{}
+ \def\@cite#1#2{{#1\if@tempswa , #2\fi}}
+\makeatother
+\newlength{\cslhangindent}
+\setlength{\cslhangindent}{1.5em}
+\newlength{\csllabelwidth}
+\setlength{\csllabelwidth}{3em}
+\newenvironment{CSLReferences}[2] % #1 hanging-indent, #2 entry-spacing
+ {\begin{list}{}{%
+  \setlength{\itemindent}{0pt}
+  \setlength{\leftmargin}{0pt}
+  \setlength{\parsep}{0pt}
+  % turn on hanging indent if param 1 is 1
+  \ifodd #1
+   \setlength{\leftmargin}{\cslhangindent}
+   \setlength{\itemindent}{-1\cslhangindent}
+  \fi
+  % set entry spacing
+  \setlength{\itemsep}{#2\baselineskip}}}
+ {\end{list}}
+\usepackage{calc}
+\newcommand{\CSLBlock}[1]{\hfill\break\parbox[t]{\linewidth}{\strut\ignorespaces#1\strut}}
+\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{\strut#1\strut}}
+\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{\strut#1\strut}}
+\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
+
+% Fancy header/footer, different for the first page of report
+\usepackage{fancyhdr}
+\usepackage{fancyvrb}
+\usepackage{afterpage}
+\fancypagestyle{firstpage}{%
+  \fancyhf{}
+  \fancyhead[R]{%
+    \noindent\makebox[\textwidth][r]{%
+      \includegraphics[height=2.3cm]{aagi_logo.pdf}\hspace*{-0.5cm}}}
+  \fancyfoot[C]{%
+    \rule{\textwidth}{0.4pt}\\[-10pt]
+    \noindent\makebox[\textwidth]{%
+      %TODO: In here: want a YAML option for 'project-partner' or something,
+      % in which case we swap out the footer graphic and overlay the partner
+      % logo in the right place.
+      \includegraphics[width=\paperwidth]{partners.pdf}}}
+  \renewcommand{\headrulewidth}{0pt}}
+\fancypagestyle{otherpages}{%
+  \fancyhf{}
+      \rhead{{\sf Project number:\;ABC1234-567XYZ}}
+        %TODO: We could make these multiple emails? for(email) email... etc.
+    \lfoot{{\sf Contact email:\;cbada@curtin.edu.au}}
+    \cfoot{\thepage}}
+
+
+\usepackage{parskip}
+\setlength{\parindent}{0cm}
+
+% Copied from the old AAGI_markdown.tex (I'm not sure we still need
+% it though)
+% Set up tightlist because Rmarkdown is crashing on it
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}
+  \setlength{\parskip}{0pt}}
+
+% A fancy coloured box for notes/warnings
+\usepackage[most]{tcolorbox}
+\newtcolorbox{note}[1][]{%
+  colback=aagiteal!7, colframe=aagiteal!7, notitle, sharp corners,
+  borderline west={2pt}{0pt}{aagiteal}, borderline east={2pt}{0pt}{aagiteal},
+  enhanced, breakable}
+
+% Any other user-defined header inclusions
+  \makeatletter
+  \@ifpackageloaded{caption}{}{\usepackage{caption}}
+  \AtBeginDocument{%
+  \ifdefined\contentsname
+    \renewcommand*\contentsname{Table of contents}
+  \else
+    \newcommand\contentsname{Table of contents}
+  \fi
+  \ifdefined\listfigurename
+    \renewcommand*\listfigurename{List of Figures}
+  \else
+    \newcommand\listfigurename{List of Figures}
+  \fi
+  \ifdefined\listtablename
+    \renewcommand*\listtablename{List of Tables}
+  \else
+    \newcommand\listtablename{List of Tables}
+  \fi
+  \ifdefined\figurename
+    \renewcommand*\figurename{Figure}
+  \else
+    \newcommand\figurename{Figure}
+  \fi
+  \ifdefined\tablename
+    \renewcommand*\tablename{Table}
+  \else
+    \newcommand\tablename{Table}
+  \fi
+  }
+  \@ifpackageloaded{float}{}{\usepackage{float}}
+  \floatstyle{ruled}
+  \@ifundefined{c@chapter}{\newfloat{codelisting}{h}{lop}}{\newfloat{codelisting}{h}{lop}[chapter]}
+  \floatname{codelisting}{Listing}
+  \newcommand*\listoflistings{\listof{codelisting}{List of Listings}}
+  \makeatother
+  \makeatletter
+  \makeatother
+  \makeatletter
+  \@ifpackageloaded{caption}{}{\usepackage{caption}}
+  \@ifpackageloaded{subcaption}{}{\usepackage{subcaption}}
+  \makeatother
+
+% Load hyperref (generally load this one last so all of the tex packages
+% play nice with each other)
+\usepackage[hyphens]{url}
+\usepackage[unicode]{hyperref}
+\hypersetup{%
+  colorlinks=true,
+  linkcolor=aagiteal,
+  urlcolor=aagiteal,
+  citecolor=aagiteal}
+
+
+
+%%% Document %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{document}
+\pagestyle{otherpages}
+\thispagestyle{firstpage}
+\newgeometry{left=12mm, right=12mm, top=20mm, bottom=24mm, includefoot}
+\afterpage{\aftergroup\restoregeometry}
+
+%%% First page top-matter
+  \setlength{\tabcolsep}{12pt}
+
+% Title
+{\Large\bf Progress report for project ABC1234-567XYZ}\\[4pt]
+  {\normalsize Subtitle here}
+
+% Authors
+{\normalsize{%
+  Your.Name\\ Author 2\\ Project Lead: Curtin University -- Prof Mark
+Gibberd, Dr Julia Easton, Prof Adam Sparks\\[-20pt]
+}}
+
+% Emails
+{\normalsize{%
+  Contact email:\;cbada@curtin.edu.au\\[-20pt]
+}}
+
+% Version
+{\normalsize{%
+  Document version:\;\texttt{1.0.0}\\[-20pt]
+}}
+
+% Last updated
+Last updated 2024-09-25
+\vspace{1mm}
+%%% End first page top-matter
+
+
+
+\section{Section 1}\label{section-1}
+
+This template is designed for smaller (``one-page'') AAGI reports. The
+AAGI logo and partners footer appear only on this first page.
+
+You can colour text/tables/etc using the various AAGI palette colours.
+Use \texttt{\textbackslash{}textcolor\{aagiteal\}\{...\}} for
+\texttt{\textbackslash{}textcolor\{aagiteal\}\{AAGI\ Teal\}}, or
+\texttt{\textbackslash{}textcolor\{aagibrightgreen\}\{...\}} for
+\texttt{\textbackslash{}textcolor\{aagibrightgreen\}\{AAGI\ Bright\ Green\}},
+for instance. Table~\ref{tbl-aagipalette} shows the standard palette
+colours available for use.
+
+\begin{table}
+
+\caption{\label{tbl-aagipalette}The AAGI palette colours.}
+
+\centering{
+
+  \centering
+  \begin{tabular}{|c | c | c | c |}
+    \hline
+    \cellcolor{aagibrightgreen}\texttt{aagibrightgreen} & %
+    \cellcolor{aagiteal}\color{white}\texttt{aagiteal} & %
+    \cellcolor{aagiblue}\texttt{aagiblue} & %
+    \cellcolor{aagigreen}\texttt{aagigreen} \\
+    \hline
+    \cellcolor{aagiyellow}\texttt{aagiyellow} & %
+    \cellcolor{aagiorange}\texttt{aagiorange} & %
+    \cellcolor{aagiblack}\color{white}\texttt{aagiblack} & %
+    \cellcolor{aagigrey}\texttt{aagigrey} \\
+    \hline
+  \end{tabular} 
+
+}
+
+\end{table}%
+
+\subsection{This is a subsection
+heading}\label{this-is-a-subsection-heading}
+
+This is an example of a reference (\citeproc{ref-blah}{Person, 2024}).
+References appear at the end of the report by default, after the last
+heading \texttt{\#\ References} on the last line of this .Rmd file (but
+feel free to change the title to whatever you like).
+
+\begin{note}
+  {\bf\color{aagiteal!75!black} Example Note}\quad
+  Use \verb|\begin{note}...\end{note}| to create coloured notes like this
+  that stand out on the page.
+\end{note}
+
+Example R code, using the
+\href{https://aagi-aus.github.io/AAGIThemes/}{\{AAGIThemes\}} package to
+produce Figure Figure~\ref{fig-example1}.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\FunctionTok{plot\_aagi}\NormalTok{(pressure)}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{figure}[H]
+
+\centering{
+
+\includegraphics{template-pdf-short-report_files/figure-pdf/fig-example1-1.pdf}
+
+}
+
+\caption{\label{fig-example1}Here is a plot.}
+
+\end{figure}%
+
+\subsubsection{This is a subsubsection
+heading}\label{this-is-a-subsubsection-heading}
+
+\lipsum[1-3]
+
+And so on.
+
+\section{Next Section}\label{next-section}
+
+Add as many sections as needed.
+
+\section*{References}\label{references}
+\addcontentsline{toc}{section}{References}
+
+\phantomsection\label{refs}
+\begin{CSLReferences}{1}{1}
+\bibitem[\citeproctext]{ref-blah}
+\textsc{Person, M.} (2024) \href{https://doi.org/10.1000/182}{My article
+title goes here}. \emph{My Journal}, \textbf{13}, pp.~12--34.
+
+\end{CSLReferences}
+\end{document}