transfer from old repo

2026-08-19 09:27:27 +02:00 · 2026-08-19 09:27:27 +02:00 · 277e2b8cf3
commit 277e2b8cf3
parent cfa4a5f9cc
1111 changed files with 83736 additions and 0 deletions
--- a/_extensions/andrewheiss/hikmah-manuscript/_extension.yml
+++ 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
--- a/_extensions/andrewheiss/hikmah-manuscript/include-in-header.tex
+++ 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{<command>}{<left>}{<before-sep>}{<after-sep>}
+% 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
+% ---------------------------
--- a/_extensions/andrewheiss/hikmah-manuscript/partials/before-body.tex
+++ 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
+% -------------------
+
+
--- a/_extensions/andrewheiss/hikmah-manuscript/partials/title.tex
+++ 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
+% ---------------------------
--- a/_extensions/andrewheiss/hikmah-manuscript/styles/reference.docx
+++ b/_extensions/andrewheiss/hikmah-manuscript/styles/reference.docx
--- a/_extensions/andrewheiss/hikmah-manuscript/styles/reference.odt
+++ b/_extensions/andrewheiss/hikmah-manuscript/styles/reference.odt
--- a/_extensions/andrewheiss/hikmah-manuscript/templates/odt-manuscript.odt
+++ b/_extensions/andrewheiss/hikmah-manuscript/templates/odt-manuscript.odt
@ -0,0 +1,94 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<office:document-content xmlns:office="urn:oasis:names:tc:opendocument:xmlns:office:1.0" xmlns:style="urn:oasis:names:tc:opendocument:xmlns:style:1.0" xmlns:text="urn:oasis:names:tc:opendocument:xmlns:text:1.0" xmlns:table="urn:oasis:names:tc:opendocument:xmlns:table:1.0" xmlns:draw="urn:oasis:names:tc:opendocument:xmlns:drawing:1.0" xmlns:fo="urn:oasis:names:tc:opendocument:xmlns:xsl-fo-compatible:1.0" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:meta="urn:oasis:names:tc:opendocument:xmlns:meta:1.0" xmlns:number="urn:oasis:names:tc:opendocument:xmlns:datastyle:1.0" xmlns:svg="urn:oasis:names:tc:opendocument:xmlns:svg-compatible:1.0" xmlns:chart="urn:oasis:names:tc:opendocument:xmlns:chart:1.0" xmlns:dr3d="urn:oasis:names:tc:opendocument:xmlns:dr3d:1.0" xmlns:math="http://www.w3.org/1998/Math/MathML" xmlns:form="urn:oasis:names:tc:opendocument:xmlns:form:1.0" xmlns:script="urn:oasis:names:tc:opendocument:xmlns:script:1.0" xmlns:ooo="http://openoffice.org/2004/office" xmlns:ooow="http://openoffice.org/2004/writer" xmlns:oooc="http://openoffice.org/2004/calc" xmlns:dom="http://www.w3.org/2001/xml-events" xmlns:xforms="http://www.w3.org/2002/xforms" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" office:version="1.2">
+  <office:font-face-decls>
+    <style:font-face style:name="Courier New" style:font-family-generic="modern" style:font-pitch="fixed" svg:font-family="'Courier New'" />
+  </office:font-face-decls>
+  <office:styles>
+    <style:style style:name="Italic" style:family="text"><style:text-properties fo:font-style="italic" style:font-style-asian="italic" style:font-style-complex="italic" /></style:style>
+    <style:style style:name="Bold" style:family="text"><style:text-properties fo:font-weight="bold" style:font-weight-asian="bold" style:font-weight-complex="bold" /></style:style>
+  </office:styles>
+  <office:automatic-styles>
+    $automatic-styles$
+  </office:automatic-styles>
+$for(header-includes)$
+  $header-includes$
+$endfor$
+<office:body>
+<office:text>
+
+$if(title)$
+<text:p text:style-name="Title">$title$</text:p>
+$endif$
+$if(subtitle)$
+<text:p text:style-name="Subtitle">$subtitle$</text:p>
+$endif$
+
+$for(author)$
+<text:p text:style-name="Author">$author$</text:p>
+$endfor$
+
+$if(date)$
+<text:p text:style-name="Date">$date$</text:p>
+$endif$
+
+<text:p text:style-name="Title page heading first">Author note</text:p>
+<text:p text:style-name="Title page text">TODO: List of authors here; there's a bug(?) in pandoc/quarto where the full author object isn't available?</text:p>
+
+$if(correspondence-prefix)$
+<text:p text:style-name="Title page heading">Correspondence</text:p>
+<text:p text:style-name="Title page text">TODO: Corresponding author details; again there's a bug that make it so we can't access other parts of the author object</text:p>
+$endif$
+
+$if(additional-info)$
+<text:p text:style-name="Title page heading">Additional information</text:p>
+<text:p text:style-name="Title page text">$additional-info$</text:p>
+$endif$
+
+$if(thanks)$
+<text:p text:style-name="Title page heading">Acknowledgments</text:p>
+<text:p text:style-name="Title page text">$thanks$</text:p>
+$endif$
+
+<text:p text:style-name="Faux page break"> </text:p>
+
+$if(abstract)$
+<text:p text:style-name="Title page heading">Abstract</text:p>
+$abstract$
+$endif$
+
+$if(keywords)$
+<text:p text:style-name="Abstract"><text:span text:style-name="Italic">Keywords: </text:span>$for(keywords)$$keywords$$sep$, $endfor$</text:p>
+$endif$
+
+<text:p text:style-name="Faux page break"> </text:p>
+
+$if(title)$
+<text:p text:style-name="Title">$title$</text:p>
+$endif$
+$if(subtitle)$
+<text:p text:style-name="Subtitle">$subtitle$</text:p>
+$endif$
+
+$if(epigraph)$
+  $for(epigraph)$
+    $if(epigraph.source)$
+    <text:p text:style-name="Epigraph">$epigraph.text$</text:p>
+    <text:p text:style-name="Epigraph source">—$epigraph.source$</text:p>
+    <text:p text:style-name="Epigraph"></text:p>
+    $else$
+    <text:p text:style-name="Epigraph">$epigraph.text$</text:p>
+    <text:p text:style-name="Epigraph"></text:p>
+    $endif$
+  $endfor$
+$endif$
+
+$for(include-before)$
+$include-before$
+$endfor$
+$body$
+$for(include-after)$
+$include-after$
+$endfor$
+</office:text>
+</office:body>
+</office:document-content>