Add draft 1 of JOSS paper

paper/Makefile

@@ -0,0 +1,11 @@
+all: paper.pdf
+
+paper.pdf: paper.md paper.bib latex.template
+	pandoc --filter pandoc-citeproc --bibliography paper.bib  paper.md \
+  --template latex.template -o paper.pdf \
+  --pdf-engine=xelatex
+
+clean:
+	rm paper.pdf
+
+.PHONY: clean

paper/latex.template

@@ -0,0 +1,377 @@
+% Taken from MIT licensed `whedon` repository, Copyright (c) 2016 Open Journals
+% https://github.com/openjournals/whedon/
+\documentclass[10pt,a4paper,onecolumn]{article}
+\usepackage{marginnote}
+\usepackage{graphicx}
+\usepackage{xcolor}
+\usepackage{authblk,etoolbox}
+\usepackage{titlesec}
+\usepackage{calc}
+\usepackage{tikz}
+\usepackage{hyperref}
+\usepackage{caption}
+\usepackage{tcolorbox}
+\usepackage{amssymb,amsmath}
+\usepackage{ifxetex,ifluatex}
+\usepackage{seqsplit}
+\usepackage{fixltx2e} % provides \textsubscript
+\usepackage[
+  backend=biber,
+%  style=alphabetic,
+%  citestyle=numeric
+]{biblatex}
+\bibliography{$bibliography$}
+
+
+% --- Page layout -------------------------------------------------------------
+\usepackage[top=3.5cm, bottom=3cm, right=1.5cm, left=1.0cm,
+            headheight=2.2cm, reversemp, includemp, marginparwidth=4.5cm]{geometry}
+
+% --- Default font ------------------------------------------------------------
+% \renewcommand\familydefault{\sfdefault}
+
+% --- Style -------------------------------------------------------------------
+\renewcommand{\bibfont}{\small \sffamily}
+\renewcommand{\captionfont}{\small\sffamily}
+\renewcommand{\captionlabelfont}{\bfseries}
+
+% --- Section/SubSection/SubSubSection ----------------------------------------
+\titleformat{\section}
+  {\normalfont\sffamily\Large\bfseries}
+  {}{0pt}{}
+\titleformat{\subsection}
+  {\normalfont\sffamily\large\bfseries}
+  {}{0pt}{}
+\titleformat{\subsubsection}
+  {\normalfont\sffamily\bfseries}
+  {}{0pt}{}
+\titleformat*{\paragraph}
+  {\sffamily\normalsize}
+
+
+% --- Header / Footer ---------------------------------------------------------
+\usepackage{fancyhdr}
+\pagestyle{fancy}
+\fancyhf{}
+%\renewcommand{\headrulewidth}{0.50pt}
+\renewcommand{\headrulewidth}{0pt}
+%\fancyhead[L]{\hspace{-0.75cm}\includegraphics[width=5.5cm]{$joss_logo_path$}}
+\fancyhead[C]{}
+\fancyhead[R]{}
+\renewcommand{\footrulewidth}{0.25pt}
+
+\fancyfoot[L]{\footnotesize{\sffamily $citation_author$, ($year$). $paper_title$. \textit{Journal of Open Source Software}, $volume$($issue$), $page$, \href{https://doi.org/$formatted_doi$}{doi:$formatted_doi$}}}
+
+
+\fancyfoot[R]{\sffamily \thepage}
+\makeatletter
+\let\ps@plain\ps@fancy
+\fancyheadoffset[L]{4.5cm}
+\fancyfootoffset[L]{4.5cm}
+
+% --- Macros ---------
+
+\definecolor{linky}{rgb}{0.0, 0.5, 1.0}
+
+\newtcolorbox{repobox}
+   {colback=red, colframe=red!75!black,
+     boxrule=0.5pt, arc=2pt, left=6pt, right=6pt, top=3pt, bottom=3pt}
+
+\newcommand{\ExternalLink}{%
+   \tikz[x=1.2ex, y=1.2ex, baseline=-0.05ex]{%
+       \begin{scope}[x=1ex, y=1ex]
+           \clip (-0.1,-0.1)
+               --++ (-0, 1.2)
+               --++ (0.6, 0)
+               --++ (0, -0.6)
+               --++ (0.6, 0)
+               --++ (0, -1);
+           \path[draw,
+               line width = 0.5,
+               rounded corners=0.5]
+               (0,0) rectangle (1,1);
+       \end{scope}
+       \path[draw, line width = 0.5] (0.5, 0.5)
+           -- (1, 1);
+       \path[draw, line width = 0.5] (0.6, 1)
+           -- (1, 1) -- (1, 0.6);
+       }
+   }
+
+% --- Title / Authors ---------------------------------------------------------
+% patch \maketitle so that it doesn't center
+\patchcmd{\@maketitle}{center}{flushleft}{}{}
+\patchcmd{\@maketitle}{center}{flushleft}{}{}
+% patch \maketitle so that the font size for the title is normal
+\patchcmd{\@maketitle}{\LARGE}{\LARGE\sffamily}{}{}
+% patch the patch by authblk so that the author block is flush left
+\def\maketitle{{%
+  \renewenvironment{tabular}[2][]
+    {\begin{flushleft}}
+    {\end{flushleft}}
+  \AB@maketitle}}
+\makeatletter
+\renewcommand\AB@affilsepx{ \protect\Affilfont}
+%\renewcommand\AB@affilnote[1]{{\bfseries #1}\hspace{2pt}}
+\renewcommand\AB@affilnote[1]{{\bfseries #1}\hspace{3pt}}
+\makeatother
+\renewcommand\Authfont{\sffamily\bfseries}
+\renewcommand\Affilfont{\sffamily\small\mdseries}
+\setlength{\affilsep}{1em}
+
+
+\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
+  \usepackage[$if(fontenc)$$fontenc$$else$T1$endif$]{fontenc}
+  \usepackage[utf8]{inputenc}
+
+\else % if luatex or xelatex
+  \ifxetex
+    \usepackage{mathspec}
+  \else
+    \usepackage{fontspec}
+  \fi
+  \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
+
+\fi
+% use upquote if available, for straight quotes in verbatim environments
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+% use microtype if available
+\IfFileExists{microtype.sty}{%
+\usepackage{microtype}
+\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
+}{}
+
+\usepackage{hyperref}
+$if(colorlinks)$
+\PassOptionsToPackage{usenames,dvipsnames}{color} % color is loaded by hyperref
+$endif$
+\hypersetup{unicode=true,
+$if(title-meta)$
+            pdftitle={$title-meta$},
+$endif$
+$if(author-meta)$
+            pdfauthor={$author-meta$},
+$endif$
+$if(keywords)$
+            pdfkeywords={$for(keywords)$$keywords$$sep$; $endfor$},
+$endif$
+$if(colorlinks)$
+            colorlinks=true,
+            linkcolor=$if(linkcolor)$$linkcolor$$else$Maroon$endif$,
+            citecolor=$if(citecolor)$$citecolor$$else$Blue$endif$,
+            urlcolor=$if(urlcolor)$$urlcolor$$else$Blue$endif$,
+$else$
+            pdfborder={0 0 0},
+$endif$
+            breaklinks=true}
+\urlstyle{same}  % don't use monospace font for urls
+$if(lang)$
+\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
+  \usepackage[shorthands=off,$for(babel-otherlangs)$$babel-otherlangs$,$endfor$main=$babel-lang$]{babel}
+$if(babel-newcommands)$
+  $babel-newcommands$
+$endif$
+\else
+  \usepackage{polyglossia}
+  \setmainlanguage[$polyglossia-lang.options$]{$polyglossia-lang.name$}
+$for(polyglossia-otherlangs)$
+  \setotherlanguage[$polyglossia-otherlangs.options$]{$polyglossia-otherlangs.name$}
+$endfor$
+\fi
+$endif$
+$if(natbib)$
+\usepackage{natbib}
+\bibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$}
+$endif$
+$if(biblatex)$
+\usepackage$if(biblio-style)$[style=$biblio-style$]$endif${biblatex}
+$if(biblatexoptions)$\ExecuteBibliographyOptions{$for(biblatexoptions)$$biblatexoptions$$sep$,$endfor$}$endif$
+$for(bibliography)$
+\addbibresource{$bibliography$}
+$endfor$
+$endif$
+$if(listings)$
+\usepackage{listings}
+$endif$
+$if(lhs)$
+\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
+$endif$
+$if(highlighting-macros)$
+$highlighting-macros$
+$endif$
+$if(verbatim-in-note)$
+\usepackage{fancyvrb}
+\VerbatimFootnotes % allows verbatim text in footnotes
+$endif$
+$if(tables)$
+\usepackage{longtable,booktabs}
+$endif$
+$if(graphics)$
+\usepackage{graphicx,grffile}
+\makeatletter
+\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
+\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
+\makeatother
+% Scale images if necessary, so that they will not overflow the page
+% margins by default, and it is still possible to overwrite the defaults
+% using explicit options in \includegraphics[width, height, ...]{}
+\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
+$endif$
+$if(links-as-notes)$
+% Make links footnotes instead of hotlinks:
+\renewcommand{\href}[2]{#2\footnote{\url{#1}}}
+$endif$
+$if(strikeout)$
+\usepackage[normalem]{ulem}
+% avoid problems with \sout in headers with hyperref:
+\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
+$endif$
+$if(indent)$
+$else$
+\IfFileExists{parskip.sty}{%
+\usepackage{parskip}
+}{% else
+\setlength{\parindent}{0pt}
+\setlength{\parskip}{6pt plus 2pt minus 1pt}
+}
+$endif$
+\setlength{\emergencystretch}{3em}  % prevent overfull lines
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+$if(numbersections)$
+\setcounter{secnumdepth}{5}
+$else$
+\setcounter{secnumdepth}{0}
+$endif$
+$if(subparagraph)$
+$else$
+% Redefines (sub)paragraphs to behave more like sections
+\ifx\paragraph\undefined\else
+\let\oldparagraph\paragraph
+\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
+\fi
+\ifx\subparagraph\undefined\else
+\let\oldsubparagraph\subparagraph
+\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
+\fi
+$endif$
+$if(dir)$
+\ifxetex
+  % load bidi as late as possible as it modifies e.g. graphicx
+  $if(latex-dir-rtl)$
+  \usepackage[RTLdocument]{bidi}
+  $else$
+  \usepackage{bidi}
+  $endif$
+\fi
+\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
+  \TeXXeTstate=1
+  \newcommand{\RL}[1]{\beginR #1\endR}
+  \newcommand{\LR}[1]{\beginL #1\endL}
+  \newenvironment{RTL}{\beginR}{\endR}
+  \newenvironment{LTR}{\beginL}{\endL}
+\fi
+$endif$
+$for(header-includes)$
+$header-includes$
+$endfor$
+
+$if(title)$
+\title{$title$$if(thanks)$\thanks{$thanks$}$endif$}
+$endif$
+$if(subtitle)$
+\providecommand{\subtitle}[1]{}
+\subtitle{$subtitle$}
+$endif$
+
+$if(authors)$
+  $for(authors)$
+  $if(authors.affiliation)$
+    \author[$authors.affiliation$]{$authors.name$}
+  $else$
+    \author{$authors.name$}
+  $endif$
+  $endfor$
+$endif$
+
+$if(affiliations)$
+  $for(affiliations)$
+    \affil[$affiliations.index$]{$affiliations.name$}
+  $endfor$
+$endif$
+\date{\vspace{-5ex}}
+
+\begin{document}
+$if(title)$
+\maketitle
+$endif$
+$if(abstract)$
+\begin{abstract}
+$abstract$
+\end{abstract}
+$endif$
+
+\marginpar{
+  %\hrule
+  \sffamily\small
+
+  {\bfseries DOI:} \href{https://doi.org/$formatted_doi$}{\color{linky}{$formatted_doi$}}
+
+  \vspace{2mm}
+
+  {\bfseries Software}
+  \begin{itemize}
+    \setlength\itemsep{0em}
+    \item \href{$review_issue_url$}{\color{linky}{Review}} \ExternalLink
+    \item \href{$repository$}{\color{linky}{Repository}} \ExternalLink
+    \item \href{$archive_doi$}{\color{linky}{Archive}} \ExternalLink
+  \end{itemize}
+
+  \vspace{2mm}
+  {\bfseries Licence}\\
+  Authors of JOSS papers retain copyright and release the work under a Creative Commons Attribution 4.0 International License (\href{http://creativecommons.org/licenses/by/4.0/}{\color{linky}{CC-BY}}).
+}
+
+$for(include-before)$
+$include-before$
+
+$endfor$
+$if(toc)$
+{
+$if(colorlinks)$
+\hypersetup{linkcolor=$if(toccolor)$$toccolor$$else$black$endif$}
+$endif$
+\setcounter{tocdepth}{$toc-depth$}
+\tableofcontents
+}
+$endif$
+$if(lot)$
+\listoftables
+$endif$
+$if(lof)$
+\listoffigures
+$endif$
+$body$
+
+$if(natbib)$
+$if(bibliography)$
+$if(biblio-title)$
+$if(book-class)$
+\renewcommand\bibname{$biblio-title$}
+$else$
+\renewcommand\refname{$biblio-title$}
+$endif$
+$endif$
+\bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
+
+$endif$
+$endif$
+$if(biblatex)$
+\printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$
+
+$endif$
+$for(include-after)$
+$include-after$
+
+$endfor$
+\end{document}