From 3f027035c1c0bb569393811273c00b8328bf7136 Mon Sep 17 00:00:00 2001 From: "Eric R. Scott" Date: Thu, 18 May 2023 11:24:21 -0400 Subject: [PATCH 01/12] add hikmah extension for better formatting --- .../hikmah-manuscript/_extension.yml | 69 +++++++++ .../hikmah-manuscript/include-in-header.tex | 101 +++++++++++++ .../partials/before-body.tex | 106 ++++++++++++++ .../hikmah-manuscript/partials/title.tex | 113 +++++++++++++++ .../hikmah-manuscript/styles/reference.docx | Bin 0 -> 17695 bytes .../hikmah-manuscript/styles/reference.odt | Bin 0 -> 12148 bytes .../templates/odt-manuscript.odt | 94 +++++++++++++ _extensions/andrewheiss/hikmah/_extension.yml | 46 ++++++ .../andrewheiss/hikmah/include-in-header.tex | 133 ++++++++++++++++++ .../hikmah/partials/before-body.tex | 50 +++++++ .../andrewheiss/hikmah/partials/title.tex | 78 ++++++++++ .../andrewheiss/hikmah/styles/pretty.scss | 1 + 12 files changed, 791 insertions(+) create mode 100644 _extensions/andrewheiss/hikmah-manuscript/_extension.yml create mode 100644 _extensions/andrewheiss/hikmah-manuscript/include-in-header.tex create mode 100644 _extensions/andrewheiss/hikmah-manuscript/partials/before-body.tex create mode 100644 _extensions/andrewheiss/hikmah-manuscript/partials/title.tex create mode 100644 _extensions/andrewheiss/hikmah-manuscript/styles/reference.docx create mode 100644 _extensions/andrewheiss/hikmah-manuscript/styles/reference.odt create mode 100644 _extensions/andrewheiss/hikmah-manuscript/templates/odt-manuscript.odt create mode 100644 _extensions/andrewheiss/hikmah/_extension.yml create mode 100644 _extensions/andrewheiss/hikmah/include-in-header.tex create mode 100644 _extensions/andrewheiss/hikmah/partials/before-body.tex create mode 100644 _extensions/andrewheiss/hikmah/partials/title.tex create mode 100644 _extensions/andrewheiss/hikmah/styles/pretty.scss diff --git a/_extensions/andrewheiss/hikmah-manuscript/_extension.yml b/_extensions/andrewheiss/hikmah-manuscript/_extension.yml new file mode 100644 index 0000000..df17d8e --- /dev/null +++ b/_extensions/andrewheiss/hikmah-manuscript/_extension.yml @@ -0,0 +1,69 @@ +title: Hikma Manuscript +author: Andrew Heiss +version: 0.0.1 +contributes: + formats: + common: + date-format: full + docx: + reference-doc: "styles/reference.docx" + knitr: + opts_chunk: + dev: "png" + dev-args: + - "cairo-png" + dpi: 300 + out.width: "80%" + odt: + template: "templates/odt-manuscript.odt" + reference-doc: "styles/reference.odt" + knitr: + opts_chunk: + dev: "png" + dev-args: + - "cairo-png" + dpi: 300 + out.width: "80%" + pdf: + documentclass: article + papersize: letter + fontsize: 12pt + linestretch: 2 + + # Template pieces + template-partials: + - "partials/title.tex" + - "partials/before-body.tex" + include-in-header: + - "include-in-header.tex" + + # Document styling + geometry: + - top=1in + - bottom=1in + - left=1in + - right=1in + + # Citations and links + colorlinks: true + linkcolor: DarkSlateBlue + urlcolor: DarkSlateBlue + citecolor: DarkSlateBlue + link-citations: true + + biblio-title: "References" + biblio-config: false # Don't use the default template's biblatex commands + cite-method: biblatex + biblatex-chicago: false # Custom flag for enabling biblatex-chicago + biblio-style: apa + biblatexoptions: + - backend=biber + + # The titlesec package provides its own mechanism for dealing with + # inline/block headings, so we need to disable pandoc's support for it + # (see https://stackoverflow.com/q/42916124/120898) + block-headings: false + # Indent paragraphs instead of adding space between them + indent: true + html: + theme: styles/pretty.scss diff --git a/_extensions/andrewheiss/hikmah-manuscript/include-in-header.tex b/_extensions/andrewheiss/hikmah-manuscript/include-in-header.tex new file mode 100644 index 0000000..094cdd8 --- /dev/null +++ b/_extensions/andrewheiss/hikmah-manuscript/include-in-header.tex @@ -0,0 +1,101 @@ +% ----------------------- +% CUSTOM PREAMBLE STUFF +% ----------------------- + +% ----------------- +% Typography tweaks +% ----------------- +% Indent size +\setlength{\parindent}{0.5in} +\setlength{\leftmargin}{0.5in} + +% Fix widows and orphans +\usepackage[all,defaultlines=2]{nowidow} + +% List things +\usepackage{enumitem} +% Same document-level indentation for ordered and ordered lists +\setlist[1]{labelindent=\parindent} +\setlist[itemize]{leftmargin=*} +\setlist[enumerate]{leftmargin=*} + +% Wrap definition list terms +% https://tex.stackexchange.com/a/9763/11851 +\setlist[description]{style=unboxed} + + +% For better TOCs +\usepackage{tocloft} + +% Remove left margin in lists inside longtables +% https://tex.stackexchange.com/a/378190/11851 +\AtBeginEnvironment{longtable}{\setlist[itemize]{nosep, wide=0pt, leftmargin=*, before=\vspace*{-\baselineskip}, after=\vspace*{-\baselineskip}}} + +% For fancy ORCID links +\usepackage{orcidlink} + +% Indent all first paragraphs because APA wants that +\usepackage{indentfirst} + + +% ----------------- +% Title block stuff +% ----------------- + +% Abstract +\usepackage{abstract} +\renewcommand{\abstractnamefont}{\normalfont\normalsize\bfseries} +\renewcommand{\abstracttextfont}{\normalsize} +\setlength{\absleftindent}{\parindent} +\setlength{\absrightindent}{\parindent} + + +% Keywords +\providecommand{\keywords}[1]{\textbf{\textit{Keywords---}}#1} + +% Title +\usepackage{titling} +\setlength{\droptitle}{2\baselineskip} +\pretitle{\begin{center}\normalfont\normalsize\bfseries} +\posttitle{\par\end{center}\vspace{2\baselineskip}} + + +% ------------------ +% Section headings +% ------------------ +\usepackage{titlesec} +\titleformat*{\section}{\center\normalsize\bfseries} +\titleformat*{\subsection}{\normalsize\bfseries} +\titleformat*{\subsubsection}{\normalsize\bfseries\itshape} +\titleformat{\paragraph}[runin]{\bfseries}{\theparagraph.}{3pt}{\space}[.] +\titleformat{\subparagraph}[runin]{\bfseries\itshape}{\thesubparagraph.}{3pt}{\space}[.] + +% \titlespacing{}{}{}{} +% Starred version removes indentation in following paragraph +\titlespacing*{\section}{0em}{2em}{0em} +\titlespacing*{\subsection}{0em}{1em}{0em} +\titlespacing*{\subsubsection}{0em}{0em}{0em} +\titlespacing*{\paragraph}{\parindent}{1ex}{1em} +\titlespacing*{\subparagraph}{\parindent}{1ex}{1em} + + +% ----------- +% Footnotes +% ----------- +% NB: footmisc has to come after biblatex because of conflicts +\usepackage[bottom]{footmisc} +\renewcommand*{\footnotelayout}{\footnotesize} + +\addtolength{\skip\footins}{12pt} % vertical space between rule and main text +\setlength{\footnotesep}{16pt} % vertical space between footnotes + + +% ---------- +% Captions +% ---------- +\usepackage[font=normalsize]{caption} + + +% --------------------------- +% END CUSTOM PREAMBLE STUFF +% --------------------------- diff --git a/_extensions/andrewheiss/hikmah-manuscript/partials/before-body.tex b/_extensions/andrewheiss/hikmah-manuscript/partials/before-body.tex new file mode 100644 index 0000000..480c810 --- /dev/null +++ b/_extensions/andrewheiss/hikmah-manuscript/partials/before-body.tex @@ -0,0 +1,106 @@ +% --------------- +% TITLE SECTION +% --------------- + +\begin{titlepage} +\center + +% Don't include a newpage before \maketitle +{\let\newpage\relax\maketitle} + +% Needs to come after \maketitle +\thispagestyle{title} + +\vspace{0.25in} + +$if(word-count)$ +{\center Word count: $word-count$} +$endif$ + +\vspace{0.5in} + +\begin{center} + +\textbf{Author note} + +$for(by-author)$ +\raggedright\setlength{\parindent}{0.5in}$it.name.literal$$if(it.orcid)$,~\orcidlink{$it.orcid$}~\url{https://orcid.org/$it.orcid$}$endif$$if(it.metadata.title)$, $it.metadata.title$$if(it.affiliations)$, $for(it.affiliations)$$if(it.department)$$it.department$, $endif$$it.name$$sep$; $endfor$ $endif$$endif$ + +$endfor$ + +\end{center} + +$if(correspondence-prefix)$ +\begin{center} + +\textbf{Correspondence} + +$for(by-author)$ +$if(it.attributes.corresponding)$ +\par\raggedright\setlength{\parindent}{0.5in}$correspondence-prefix$~$it.name.literal$$if(it.email)$ (\href{mailto:$it.email$}{$it.email$})$endif$$if(it.affiliations)$, $for(it.affiliations)$$if(it.department)$$it.department$, $endif$$it.name$, $if(it.address)$$it.address$, $endif$$if(it.city)$$it.city$, $endif$$if(it.region)$$it.region$ $endif$$if(it.postal-code)$$it.postal-code$$endif$$if(it.country)$, $it.country$$endif$$sep$; $endfor$ $endif$ +$endif$ +$endfor$ + +\end{center} +$endif$ + +$if(additional-info)$ +\begin{center} + +\textbf{Additional information} + +\par\raggedright\setlength{\parindent}{0.5in}$additional-info$ + +\end{center} +$endif$ + +$if(thanks)$ +\begin{center} + +\textbf{Acknowledgments} + +\par\raggedright\setlength{\parindent}{0.5in}$thanks$ + +\end{center} +$endif$ + +\vfill % Fill the rest of the page with whitespace + +\end{titlepage} + +\doublespacing + +$if(abstract)$ +\begin{abstract} +\noindent $abstract$ +\end{abstract} + +\vspace{\baselineskip} + +$if(keywords)$\indent \keywords{% +$for(keywords)$$keywords$$sep$, $endfor$% +}$endif$ + +\newpage +$endif$ + +\begin{center} +\singlespacing +\textbf{$title$$if(subtitle)$:\\$subtitle$$endif$} +\end{center} + +$if(epigraph)$ +$for(epigraph)$ +$if(epigraph.source)$ +\epigraph{$epigraph.text$}{---$epigraph.source$} +$else$ +\epigraph{$epigraph.text$} +$endif$ +$endfor$ +$endif$ + +% ------------------- +% END TITLE SECTION +% ------------------- + + diff --git a/_extensions/andrewheiss/hikmah-manuscript/partials/title.tex b/_extensions/andrewheiss/hikmah-manuscript/partials/title.tex new file mode 100644 index 0000000..4c5ab8e --- /dev/null +++ b/_extensions/andrewheiss/hikmah-manuscript/partials/title.tex @@ -0,0 +1,113 @@ +% ----------------------- +% END-OF-PREAMBLE STUFF +% ----------------------- + +% For patching commands like \subtitle +\usepackage{etoolbox} + +% ----------------- +% Running headers +% ----------------- + +\usepackage{fancyhdr} +\setlength{\headheight}{0.25in} +\renewcommand{\headrulewidth}{0pt} % Remove lines +\renewcommand{\footrulewidth}{0pt} + +% SHORT TITLE Page # +\fancypagestyle{normal}{ + \fancyhf{} + \lhead{\uppercase{$if(short-title)$ $short-title$ $else$ $title$ $endif$}} + \rhead{\thepage} +} + +% Running head: SHORT TITLE Page # +\fancypagestyle{title}{ + \fancyhf{} + \lhead{Running head: \uppercase{$if(short-title)$ $short-title$ $else$ $title$ $endif$}} + \rhead{} +} + +% Use regular heading style +\pagestyle{normal} + + +$if(epigraph)$ +% ----------- +% Epigraphs +% ----------- +\usepackage{epigraph} +\renewcommand{\epigraphsize}{\footnotesize} +\setlength{\epigraphrule}{0em} +\setlength{\beforeepigraphskip}{0em} +\setlength{\afterepigraphskip}{1em} +$endif$ + +$if(biblatex)$ +% ---------- +% BibLaTeX +% ---------- +$if(biblatex-chicago)$ +\usepackage[$if(biblio-style)$$biblio-style$,$endif$$for(biblatexoptions)$$biblatexoptions$$sep$,$endfor$]{biblatex-chicago} +$else$ +\usepackage[$if(biblio-style)$style=$biblio-style$,$endif$$for(biblatexoptions)$$biblatexoptions$$sep$,$endfor$]{biblatex} +$endif$ + +\setlength\bibitemsep{0pt} % No space between bib entries +\setlength\bibhang{\parindent} % Match document indentation + +% Fix biblatex's odd preference for using In: by default. +\renewbibmacro{in:}{% + \ifentrytype{article}{}{% + \printtext{\bibstring{}\intitlepunct}}} + +\addbibresource{$bibliography$} + +% Start bibliography on new page +\pretocmd{\printbibliography}{\clearpage}{}{} +$endif$ + +% ---------------------- +% Title block elements +% ---------------------- +\usepackage{authblk} +\renewcommand*{\Authsep}{, } +\renewcommand*{\Authand}{ and } +\renewcommand*{\Authands}{, and } +\renewcommand*{\Affilfont}{\normalsize} +\renewcommand*{\Authfont}{\normalsize} + +$if(title)$ +\title{$title$$if(subtitle)$:$endif$} +$endif$ + +$if(subtitle)$ +\makeatletter +\providecommand{\subtitle}[1]{% add subtitle to \maketitle + \apptocmd{\@title}{\par #1 \par}{}{} +} +\makeatother +\subtitle{$subtitle$} +$endif$ + +$for(by-author)$ +\author[$for(it.affiliations)$$it.number$$sep$,$endfor$]{$by-author.name.literal$} +$endfor$ + +$for(by-affiliation)$ +\affil[$it.number$]{$it.name$} +$endfor$ + +\date{} + + +% Typeset URLs in the same font as their parent environment +% +% This has to come at the end of the preamble, after any biblatex stuff because +% some biblatex styles (like APA) define their own \urlstyle{} +\usepackage{url} +\urlstyle{same} + +% --------------------------- +% END END-OF-PREAMBLE STUFF +% --------------------------- diff --git a/_extensions/andrewheiss/hikmah-manuscript/styles/reference.docx b/_extensions/andrewheiss/hikmah-manuscript/styles/reference.docx new file mode 100644 index 0000000000000000000000000000000000000000..57571aae74feffb2f52957c25d94a34c533a5fee GIT binary patch literal 17695 zcmeIa1$P`tvNqgemc`7>%*@P;7Be$5Gs|KoiCX@ zR6OiWoOJ2jZLA3jK!GXp0Kgyj|KIVycmx_#CgcVf5Jc}KUWE5)r8esYAX(1>N06u# 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a/_extensions/andrewheiss/hikmah-manuscript/templates/odt-manuscript.odt b/_extensions/andrewheiss/hikmah-manuscript/templates/odt-manuscript.odt new file mode 100644 index 0000000..15fcd15 --- /dev/null +++ b/_extensions/andrewheiss/hikmah-manuscript/templates/odt-manuscript.odt @@ -0,0 +1,94 @@ + + + + + + + + + + + $automatic-styles$ + +$for(header-includes)$ + $header-includes$ +$endfor$ + + + +$if(title)$ +$title$ +$endif$ +$if(subtitle)$ +$subtitle$ +$endif$ + +$for(author)$ +$author$ +$endfor$ + +$if(date)$ +$date$ +$endif$ + +Author note +TODO: List of authors here; there's a bug(?) in pandoc/quarto where the full author object isn't available? + +$if(correspondence-prefix)$ +Correspondence +TODO: Corresponding author details; again there's a bug that make it so we can't access other parts of the author object +$endif$ + +$if(additional-info)$ +Additional information +$additional-info$ +$endif$ + +$if(thanks)$ +Acknowledgments +$thanks$ +$endif$ + +  + +$if(abstract)$ +Abstract +$abstract$ +$endif$ + +$if(keywords)$ +Keywords: $for(keywords)$$keywords$$sep$, $endfor$ +$endif$ + +  + +$if(title)$ +$title$ +$endif$ +$if(subtitle)$ +$subtitle$ +$endif$ + +$if(epigraph)$ + $for(epigraph)$ + $if(epigraph.source)$ + $epigraph.text$ + —$epigraph.source$ + + $else$ + $epigraph.text$ + + $endif$ + $endfor$ +$endif$ + +$for(include-before)$ +$include-before$ +$endfor$ +$body$ +$for(include-after)$ +$include-after$ +$endfor$ + + + diff --git a/_extensions/andrewheiss/hikmah/_extension.yml b/_extensions/andrewheiss/hikmah/_extension.yml new file mode 100644 index 0000000..8404f9c --- /dev/null +++ b/_extensions/andrewheiss/hikmah/_extension.yml @@ -0,0 +1,46 @@ +title: Hikma +author: Andrew Heiss +version: 0.0.1 +contributes: + formats: + common: + date-format: full + pdf: + # Template pieces + template-partials: + - "partials/title.tex" + - "partials/before-body.tex" + include-in-header: + - "include-in-header.tex" + + # Document styling + geometry: + - top=10pc # 10p0 + - bottom=10pc # 10p0 + - left=11pc # 11p0 + - right=11pc # 11p0 + - heightrounded + + # Citations and links + colorlinks: true + linkcolor: DarkSlateBlue + urlcolor: DarkSlateBlue + citecolor: DarkSlateBlue + link-citations: true + + biblio-title: "References" + biblio-config: false # Don't use the default template's biblatex commands + cite-method: biblatex + biblatex-chicago: false # Custom flag for enabling biblatex-chicago + biblio-style: apa + biblatexoptions: + - backend=biber + + # The titlesec package provides its own mechanism for dealing with + # inline/block headings, so we need to disable pandoc's support for it + # (see https://stackoverflow.com/q/42916124/120898) + block-headings: false + # Indent paragraphs instead of adding space between them + indent: true + html: + theme: styles/pretty.scss diff --git a/_extensions/andrewheiss/hikmah/include-in-header.tex b/_extensions/andrewheiss/hikmah/include-in-header.tex new file mode 100644 index 0000000..af61ac6 --- /dev/null +++ b/_extensions/andrewheiss/hikmah/include-in-header.tex @@ -0,0 +1,133 @@ +% ----------------------- +% CUSTOM PREAMBLE STUFF +% ----------------------- + +% ----------------- +% Typography tweaks +% ----------------- +% Indent size +\setlength{\parindent}{1pc} % 1p0 + +% Fix widows and orphans +\usepackage[all,defaultlines=2]{nowidow} + +% List things +\usepackage{enumitem} +% Same document-level indentation for ordered and ordered lists +\setlist[1]{labelindent=\parindent} +\setlist[itemize]{leftmargin=*} +\setlist[enumerate]{leftmargin=*} + +% Wrap definition list terms +% https://tex.stackexchange.com/a/9763/11851 +\setlist[description]{style=unboxed} + + +% For better TOCs +\usepackage{tocloft} + +% Remove left margin in lists inside longtables +% https://tex.stackexchange.com/a/378190/11851 +\AtBeginEnvironment{longtable}{\setlist[itemize]{nosep, wide=0pt, leftmargin=*, before=\vspace*{-\baselineskip}, after=\vspace*{-\baselineskip}}} + + +% ----------------- +% Title block stuff +% ----------------- + +% Abstract +\usepackage[overload]{textcase} +\usepackage[runin]{abstract} +\renewcommand{\abstractnamefont}{\sffamily\footnotesize\bfseries\MakeUppercase} +\renewcommand{\abstracttextfont}{\sffamily\small} +\setlength{\absleftindent}{\parindent * 2} +\setlength{\absrightindent}{\parindent * 2} +\abslabeldelim{\quad} +\setlength{\abstitleskip}{-\parindent} + + +% Keywords +\newenvironment{keywords} +{\vskip -3em \hspace{\parindent}\small\sffamily{\sffamily\footnotesize\bfseries\MakeUppercase{Keywords}}\quad} +{\vskip 3em} + + +% Title +\usepackage{titling} +\setlength{\droptitle}{3em} +\pretitle{\par\vskip 5em \begin{flushleft}\LARGE\sffamily\bfseries} +\posttitle{\par\end{flushleft}\vskip 0.75em} + + +% Authors +% +% PHEW this is complicated for a number of reasons! +% +% When using \and with multiple authors, the article class in LaTeX wraps each +% author block in a tabluar environment with a hardcoded center alignment. It's +% possible to use \preauthor{} to start tabulars with a left alignment {l}, but +% that only applies to the first author because the others all use \and with the +% hardcoded {c}. But we can override the \and command and add our own {l} +% +% (See https://github.com/rstudio/rmarkdown/issues/1716#issuecomment-560601691 +% for an example of redefining \and to just be \\) +% +% That's all great, except tabulars have some amount of default horizontal +% padding, which makes left-aligned author blocks not actuall get fully +% left-aligned on the page. We can set the horizontal padding for the column to +% 0, but it requires some wonky syntax: {@{\hspace{0em}}l@{}} +\renewcommand{\and}{\end{tabular} \hskip 3em \begin{tabular}[t]{@{\hspace{0em}}l@{}}} +\preauthor{\begin{flushleft} + \lineskip 1.5em + \begin{tabular}[t]{@{\hspace{0em}}l@{}}} +\postauthor{\end{tabular}\par\end{flushleft}} + +% Omit the date since the \published command does that +\predate{} +\postdate{} + +% Command for a note at the top of the first page describing the publication +% status of the paper. +\newcommand{\published}[1]{% + \gdef\puB{#1}} + \newcommand{\puB}{} + \renewcommand{\maketitlehooka}{% + \par\noindent\footnotesize\sffamily \puB} + + +% ------------------ +% Section headings +% ------------------ +\usepackage{titlesec} +\titleformat*{\section}{\Large\sffamily\bfseries\raggedright} +\titleformat*{\subsection}{\large\sffamily\bfseries\raggedright} +\titleformat*{\subsubsection}{\normalsize\sffamily\bfseries\raggedright} +\titleformat*{\paragraph}{\small\sffamily\bfseries\raggedright} + +% \titlespacing{}{}{}{} +% Starred version removes indentation in following paragraph +\titlespacing*{\section}{0em}{2em}{0.1em} +\titlespacing*{\subsection}{0em}{1.25em}{0.1em} +\titlespacing*{\subsubsection}{0em}{0.75em}{0em} + + +% ----------- +% Footnotes +% ----------- +% NB: footmisc has to come after biblatex because of conflicts +\usepackage[bottom, flushmargin]{footmisc} +\renewcommand*{\footnotelayout}{\footnotesize} + +\addtolength{\skip\footins}{10pt} % vertical space between rule and main text +\setlength{\footnotesep}{5pt} % vertical space between footnotes + + +% ---------- +% Captions +% ---------- +\usepackage[font={small,sf}, labelfont={small,sf,bf}]{caption} + + +% --------------------------- +% END CUSTOM PREAMBLE STUFF +% --------------------------- diff --git a/_extensions/andrewheiss/hikmah/partials/before-body.tex b/_extensions/andrewheiss/hikmah/partials/before-body.tex new file mode 100644 index 0000000..f390a9f --- /dev/null +++ b/_extensions/andrewheiss/hikmah/partials/before-body.tex @@ -0,0 +1,50 @@ +% --------------- +% TITLE SECTION +% --------------- +$if(published)$ +$if(code-repo)$ +\published{\textbf{$date$} \qquad $published$ \\ {\scriptsize $code-repo$}} +$else$ +\published{\textbf{$date$} \qquad {\scriptsize $published$}} +$endif$ +$else$ +$if(code-repo)$ +\published{\textbf{$date$} \\ {\scriptsize $code-repo$}} +$else$ +\published{\textbf{$date$}} +$endif$ +$endif$ + +$if(title)$ +\maketitle +$endif$ + +$if(abstract)$ +\begin{abstract} +$abstract$ +\end{abstract} +\vskip 3em +$endif$ + +$if(keywords)$ +\begin{keywords} +\def\sep{;\ } +$for(keywords/allbutlast)$$keywords$\sep $endfor$ +$for(keywords/last)$$keywords$$endfor$ +\end{keywords} +$endif$ + +$if(epigraph)$ +$for(epigraph)$ +$if(epigraph.source)$ +\epigraph{$epigraph.text$}{---$epigraph.source$} +$else$ +\epigraph{$epigraph.text$} +$endif$ +$endfor$ +$endif$ +% ------------------- +% END TITLE SECTION +% ------------------- + + diff --git a/_extensions/andrewheiss/hikmah/partials/title.tex b/_extensions/andrewheiss/hikmah/partials/title.tex new file mode 100644 index 0000000..1bde112 --- /dev/null +++ b/_extensions/andrewheiss/hikmah/partials/title.tex @@ -0,0 +1,78 @@ +% ----------------------- +% END-OF-PREAMBLE STUFF +% ----------------------- + +$if(epigraph)$ +% ----------- +% Epigraphs +% ----------- +\usepackage{epigraph} +\renewcommand{\epigraphsize}{\sffamily\footnotesize} +\setlength{\epigraphrule}{0em} +\setlength{\beforeepigraphskip}{-2em} +\setlength{\afterepigraphskip}{1em} +$endif$ + +$if(biblatex)$ +% ---------- +% BibLaTeX +% ---------- +$if(biblatex-chicago)$ +\usepackage[$if(biblio-style)$$biblio-style$,$endif$$for(biblatexoptions)$$biblatexoptions$$sep$,$endfor$]{biblatex-chicago} +$else$ +\usepackage[$if(biblio-style)$style=$biblio-style$,$endif$$for(biblatexoptions)$$biblatexoptions$$sep$,$endfor$]{biblatex} +$endif$ + +\setlength\bibitemsep{0pt} % No space between bib entries +\renewcommand*{\bibfont}{\footnotesize} % Use smaller font +\setlength\bibhang{\parindent} % Match document indentation + +% Fix biblatex's odd preference for using In: by default. +\renewbibmacro{in:}{% + \ifentrytype{article}{}{% + \printtext{\bibstring{}\intitlepunct}}} + +\addbibresource{$bibliography$} +$endif$ + +% ---------------------- +% Title block elements +% ---------------------- +\usepackage{orcidlink} % Create automatic ORCID icons/links + +$if(title)$ +\title{$title$$if(thanks)$\thanks{$thanks$}$endif$} +$endif$ + +$if(subtitle)$ +\usepackage{etoolbox} +\makeatletter +\providecommand{\subtitle}[1]{% add subtitle to \maketitle + \apptocmd{\@title}{\par {\vskip 0.25em \large #1 \par}}{}{} +} +\makeatother +\subtitle{$subtitle$} +$endif$ + +\author{ +$for(by-author)$ +{\large $it.name.literal$$if(it.orcid)$~\orcidlink{$it.orcid$}$endif$}% +$if(it.attributes.corresponding)$\thanks{Corresponding author.}$endif$ \\% +$for(it.affiliations)$$it.name$ \\$endfor$% +{\footnotesize \url{$it.email$}} \and +$endfor$ +} + +\date{} + + +% Typeset URLs in the same font as their parent environment +% +% This has to come at the end of the preamble, after any biblatex stuff because +% some biblatex styles (like APA) define their own \urlstyle{} +\usepackage{url} +\urlstyle{same} + +% --------------------------- +% END END-OF-PREAMBLE STUFF +% --------------------------- diff --git a/_extensions/andrewheiss/hikmah/styles/pretty.scss b/_extensions/andrewheiss/hikmah/styles/pretty.scss new file mode 100644 index 0000000..d002b36 --- /dev/null +++ b/_extensions/andrewheiss/hikmah/styles/pretty.scss @@ -0,0 +1 @@ +/*-- scss:defaults --*/ From 9f9b1cfc3275c092bfc1de6f7240fc53c9149309 Mon Sep 17 00:00:00 2001 From: "Eric R. Scott" Date: Thu, 18 May 2023 11:24:38 -0400 Subject: [PATCH 02/12] Rmd -> Qmd --- .../{problemdefinition.Rmd => problemdefinition.Qmd} | 10 ++++++++-- proposal/{proposal.Rmd => proposal.Qmd} | 0 proposal/{requirements.Rmd => requirements.Qmd} | 0 proposal/{signatories.Rmd => signatories.Qmd} | 0 proposal/{success.Rmd => success.Qmd} | 0 proposal/{timeline.Rmd => timeline.Qmd} | 0 6 files changed, 8 insertions(+), 2 deletions(-) rename proposal/{problemdefinition.Rmd => problemdefinition.Qmd} (79%) rename proposal/{proposal.Rmd => proposal.Qmd} (100%) rename proposal/{requirements.Rmd => requirements.Qmd} (100%) rename proposal/{signatories.Rmd => signatories.Qmd} (100%) rename proposal/{success.Rmd => success.Qmd} (100%) rename proposal/{timeline.Rmd => timeline.Qmd} (100%) diff --git a/proposal/problemdefinition.Rmd b/proposal/problemdefinition.Qmd similarity index 79% rename from proposal/problemdefinition.Rmd rename to proposal/problemdefinition.Qmd index f77ec45..81e3a17 100644 --- a/proposal/problemdefinition.Rmd +++ b/proposal/problemdefinition.Qmd @@ -1,4 +1,10 @@ +--- +bibliography: references.bib +--- + # The Problem + +```{=html} - - +``` +An example in-text citation [@wickham2016]. diff --git a/proposal/proposal.Rmd b/proposal/proposal.Qmd similarity index 100% rename from proposal/proposal.Rmd rename to proposal/proposal.Qmd diff --git a/proposal/requirements.Rmd b/proposal/requirements.Qmd similarity index 100% rename from proposal/requirements.Rmd rename to proposal/requirements.Qmd diff --git a/proposal/signatories.Rmd b/proposal/signatories.Qmd similarity index 100% rename from proposal/signatories.Rmd rename to proposal/signatories.Qmd diff --git a/proposal/success.Rmd b/proposal/success.Qmd similarity index 100% rename from proposal/success.Rmd rename to proposal/success.Qmd diff --git a/proposal/timeline.Rmd b/proposal/timeline.Qmd similarity index 100% rename from proposal/timeline.Rmd rename to proposal/timeline.Qmd From 20c432fa1eb6e2f501a560117903655d81f3994a Mon Sep 17 00:00:00 2001 From: "Eric R. Scott" Date: Thu, 18 May 2023 11:24:48 -0400 Subject: [PATCH 03/12] add example references.bib --- references.bib | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 references.bib diff --git a/references.bib b/references.bib new file mode 100644 index 0000000..6a803f0 --- /dev/null +++ b/references.bib @@ -0,0 +1,9 @@ + +@book{wickham2016, + title = {ggplot2: Elegant graphics for data analysis}, + author = {Wickham, Hadley}, + year = {2016}, + date = {2016}, + publisher = {Springer-Verlag New York}, + url = {https://ggplot2.tidyverse.org} +} From 73669a4c9577a80cf174d4f03fa22da7843b02b7 Mon Sep 17 00:00:00 2001 From: "Eric R. Scott" Date: Thu, 18 May 2023 11:25:04 -0400 Subject: [PATCH 04/12] convert master doc to Qmd and add metadata --- isc-proposal.Qmd | 34 ++++++++++++++++++++++++++++++++++ isc-proposal.Rmd | 29 ----------------------------- 2 files changed, 34 insertions(+), 29 deletions(-) create mode 100644 isc-proposal.Qmd delete mode 100644 isc-proposal.Rmd diff --git a/isc-proposal.Qmd b/isc-proposal.Qmd new file mode 100644 index 0000000..7cc9d9c --- /dev/null +++ b/isc-proposal.Qmd @@ -0,0 +1,34 @@ +--- +title: "Proposal Title" +author: + - name: Annie Easley + orcid: 5555-5555-5555-5555 + affiliations: + - "Lewis Research Center, National Aeronautics and Space Administration" + +date: today +date-format: iso +format: + hikmah-pdf: + geometry: + - left=1.25in + - right=1.25in + html: + embed-resources: true +bibliography: references.bib +--- + +{{< include proposal/signatories.Qmd >}} + +{{< include proposal/problemdefinition.Qmd >}} + +{{< include proposal/proposal.Qmd >}} + +{{< include proposal/timeline.Qmd >}} + +{{< include proposal/requirements.Qmd >}} + +{{< include proposal/success.Qmd >}} + +::: refs +::: \ No newline at end of file diff --git a/isc-proposal.Rmd b/isc-proposal.Rmd deleted file mode 100644 index d60abbc..0000000 --- a/isc-proposal.Rmd +++ /dev/null @@ -1,29 +0,0 @@ ---- -title: "`r proposal`" -author: "`r author`" -date: "`r Sys.Date()`" -output: html_document ---- - -```{r setup, eval=TRUE, results='hide', echo=FALSE} -knitr::opts_knit$set(warning = FALSE, message= FALSE) -``` - - -```{r autodoc, child='proposal/signatories.Rmd', eval=TRUE} -``` - -```{r autodoc, child='proposal/problemdefinition.Rmd', eval=TRUE} -``` - -```{r autodoc, child='proposal/proposal.Rmd', eval=TRUE} -``` - -```{r autodoc, child='proposal/timeline.Rmd', eval=TRUE} -``` - -```{r autodoc, child='proposal/requirements.Rmd', eval=TRUE} -``` - -```{r autodoc, child='proposal/success.Rmd', eval=TRUE} -``` From 142914e55d6b9d16950e754152626e205439cf6f Mon Sep 17 00:00:00 2001 From: "Eric R. Scott" Date: Thu, 18 May 2023 11:25:12 -0400 Subject: [PATCH 05/12] remove unused files --- .travis.yml | 8 -------- ghgenerate.R | 8 -------- 2 files changed, 16 deletions(-) delete mode 100644 .travis.yml delete mode 100644 ghgenerate.R diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 59d2506..0000000 --- a/.travis.yml +++ /dev/null @@ -1,8 +0,0 @@ -language: r -cache: packages -install: - - Rscript -e 'install.packages("rmarkdown")' - - chmod 755 .push_gh_pages.sh - - chmod 755 ghgenerate.R -script: - - ./.push_gh_pages.sh diff --git a/ghgenerate.R b/ghgenerate.R deleted file mode 100644 index 3c3d4fd..0000000 --- a/ghgenerate.R +++ /dev/null @@ -1,8 +0,0 @@ -proposal<-"Boilerplate ISC Proposal" -proposal.file<-"isc-proposal.Rmd" -author<-"Steph Locke" - -rmarkdown::render(proposal.file, output_format="html_document", - output_dir="out", quiet=TRUE) -rmarkdown::render(proposal.file, output_format="pdf_document", - output_dir="out", quiet=TRUE) \ No newline at end of file From 243a24b7a19efc566e8d7ab7b107883db718e4e6 Mon Sep 17 00:00:00 2001 From: "Eric R. Scott" Date: Thu, 18 May 2023 11:28:15 -0400 Subject: [PATCH 06/12] add github action --- .github/workflows/publish-proposal.yaml | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 .github/workflows/publish-proposal.yaml diff --git a/.github/workflows/publish-proposal.yaml b/.github/workflows/publish-proposal.yaml new file mode 100644 index 0000000..10f041c --- /dev/null +++ b/.github/workflows/publish-proposal.yaml @@ -0,0 +1,22 @@ +on: + push: + branches: [main, master] + +name: publish-proposal + +jobs: + render-proposal: + runs-on: ubuntu-latest + steps: + - name: Check out repository + uses: actions/checkout@v3 + - name: Setup Quarto + uses: quarto-dev/quarto-actions/setup@v2 + with: + tinytex: true + + - name: Render and publish to GitHub Pages + uses: quarto-dev/quarto-actions/publish@v2 + with: + target: gh-pages + path: "isc-proposal.Qmd" \ No newline at end of file From 75ecd8244465fc4ce22ff735b261ebe7e32f3421 Mon Sep 17 00:00:00 2001 From: "Eric R. Scott" Date: Thu, 18 May 2023 11:42:22 -0400 Subject: [PATCH 07/12] move html up --- isc-proposal.Qmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/isc-proposal.Qmd b/isc-proposal.Qmd index 7cc9d9c..da2aa86 100644 --- a/isc-proposal.Qmd +++ b/isc-proposal.Qmd @@ -9,12 +9,12 @@ author: date: today date-format: iso format: + html: + embed-resources: true hikmah-pdf: geometry: - left=1.25in - right=1.25in - html: - embed-resources: true bibliography: references.bib --- From 3a73b2d74d0dfc9fa6570eb8f321c579dbc996d9 Mon Sep 17 00:00:00 2001 From: "Eric R. Scott" Date: Thu, 18 May 2023 11:52:06 -0400 Subject: [PATCH 08/12] add toc to show other format download --- isc-proposal.Qmd | 1 + 1 file changed, 1 insertion(+) diff --git a/isc-proposal.Qmd b/isc-proposal.Qmd index da2aa86..be84597 100644 --- a/isc-proposal.Qmd +++ b/isc-proposal.Qmd @@ -8,6 +8,7 @@ author: date: today date-format: iso +toc: true format: html: embed-resources: true From 1640dfceb8eb89c5063f3a892bcaddb62300e64b Mon Sep 17 00:00:00 2001 From: "Eric R. Scott" Date: Thu, 18 May 2023 12:09:19 -0400 Subject: [PATCH 09/12] remove unneeded file --- .push_gh_pages.sh | 20 -------------------- 1 file changed, 20 deletions(-) delete mode 100644 .push_gh_pages.sh diff --git a/.push_gh_pages.sh b/.push_gh_pages.sh deleted file mode 100644 index 5921f50..0000000 --- a/.push_gh_pages.sh +++ /dev/null @@ -1,20 +0,0 @@ -#!/bin/bash - -rm -rf out || exit 0; -mkdir out; - -GH_REPO="@github.com/$TRAVIS_REPO_SLUG.git" - -FULL_REPO="https://$GH_TOKEN$GH_REPO" - -git config --global user.name "stephs-travis" -git config --global user.email "steph@travis.ci" - -R CMD BATCH 'ghgenerate.R' -cp ghgenerate.Rout out - -cd out -git init -git add . -git commit -m "deployed to github pages" -git push --force --quiet $FULL_REPO master:gh-pages From 7cc84e4a29f151b2b6cb6e9a4763b3458e661955 Mon Sep 17 00:00:00 2001 From: "Eric R. Scott" Date: Thu, 18 May 2023 12:09:50 -0400 Subject: [PATCH 10/12] remove toc --- isc-proposal.Qmd | 1 - 1 file changed, 1 deletion(-) diff --git a/isc-proposal.Qmd b/isc-proposal.Qmd index be84597..da2aa86 100644 --- a/isc-proposal.Qmd +++ b/isc-proposal.Qmd @@ -8,7 +8,6 @@ author: date: today date-format: iso -toc: true format: html: embed-resources: true From fe1f019e5196aa52f4fe40c1bfbebb50edb03938 Mon Sep 17 00:00:00 2001 From: "Eric R. Scott" Date: Thu, 18 May 2023 12:11:45 -0400 Subject: [PATCH 11/12] update README --- README.md | 26 ++++++++++++-------------- 1 file changed, 12 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index e118027..1c95028 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ # isc-proposal -[![Build Status](https://travis-ci.org/stephlocke/isc-proposal.svg?branch=master)](https://travis-ci.org/stephlocke/isc-proposal) +[![build-status](https://github.com/your-user-name/your-repo-name/actions/workflows/publish-proposal.yaml/badge.svg)](https://github.com/your-user-name/your-repo-name/actions/workflows/publish-proposal.yaml) This repository is a boilerplate repository that helps you prepare your proposal for the [R Consortium](https://www.r-consortium.org). @@ -35,25 +35,23 @@ Here we detail useful guidance notes on making proposals to the ISC but you shou - Proposals should be submitted through this Google form: https://forms.gle/Cuk7pKHabXg9viXWA ## Making your proposal + This is a boilerplate repository that you will need to fork, title appropriately and start filling in. -- Use the github [fork command](https://github.com/stephlocke/isc-proposal#fork-destination-box) -- Go to the repository settings and change the name to reflect your proposal -- Create a new Rstudio project from version control and use the git URL for the repo -- Write an overview of the proposal instead of this boilerplate for the README -- Start completing the relevant Rmd pages of the proposal -- Use `ghgenerate.R` to build the document -- Regularly commit and push the changes to github -- Solicit feedback and contributions from others +- Use the "Use this template" button on GitHub +- Create a new repository with a name to reflect your proposal +- Create a new Rstudio project from version control and use the git URL for the repo +- Write an overview of the proposal instead of this boilerplate for the README +- Start completing the relevant Rmd pages of the proposal +- Render `isc-proposal.Qmd` to build the document locally +- Regularly commit and push the changes to github +- Solicit feedback and contributions from others ### Automatically generate your proposal -You can configure this to produce the needed documents and publish them to the github.io for browsing and posterity. This assumes a reasonable amount of comfort with using Travis-CI but if you're not, please check out my [post on auto-deploying documents](http://itsalocke.com/automated-documentation-hosting-on-github-via-travis-ci/) for background. -- Turn on [Travis-CI](https://travis-ci.org) for the repository -- Add an environment variable called GH_TOKEN to the travis environment, set the value to an OAuth key generated by github to allow "public repo" privileges only -- Amend the `.push_gh_pages.sh` and `ghgenerate.R` with the details of your repository and preferred commit details -- Use the gh-pages branch to host your proposal online and to retrieve the HTML or PDF variants for emailing +This repository comes with a GitHub actions setup to automatically render your proposal to HTML and PDF formats. To take advantage of it, you must publish the proposal to GitHub pages interactively the first time. +From the command line, run `quarto publish gh-pages isc-proposal.Qmd`. After this, the GitHub action should run every time you push a commit to the main branch. Your rendered proposal can then be viewed at https://your-user-name.github.io/your-repo-name/ ## License Creative Commons Licence
ISC Boilerplate by Stephanie Locke is licensed under a Creative Commons Attribution 4.0 International License.
Based on a work at https://github.com/RConsortium/isc-proposal. From 5f9c6da13c104238524a392ce3ca3ef244679cd2 Mon Sep 17 00:00:00 2001 From: "Eric R. Scott" Date: Tue, 12 Mar 2024 11:29:02 -0700 Subject: [PATCH 12/12] Update checkout to v4 --- .github/workflows/publish-proposal.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/publish-proposal.yaml b/.github/workflows/publish-proposal.yaml index 10f041c..e07bc70 100644 --- a/.github/workflows/publish-proposal.yaml +++ b/.github/workflows/publish-proposal.yaml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out repository - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Setup Quarto uses: quarto-dev/quarto-actions/setup@v2 with: