jdrarticle.sty

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%	This is Jim Ratliff's basic preamble for LaTeX documents, which will load as a package.
%	Assumes that \documentclass[12pt]{article} is issued before this package is loaded.
%
%	Version: 2018_07_01_1449
%		Added package makecell
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\ProvidesPackage{jdrarticle}
\RequirePackage{jdrstyle}

%%%%%%%%%%%%%% INDEX (with keys to search for)
%	\PassOptionsToPackage
%	Load packages
%	Document formatting						(search: docformat )
%	Paragraph-related settings				(search: paraformat )
%	Title, header, and footer settings		(search: headfootformat )
%	Lists-related settings					(search: listsformat  )
%		Define jdr_itemize environment for bulleted lists
%		Defines jdr_enumerate environment for numbered lists
%	Sectioning-related settings				(search: secformat )
%	Table of Contents settings				(search: tocformat )
%	Footnote-related settings				(search: footnoteformat )
%	Table and Figure caption settings		(search: captionsettings )
%	showkeys-related definition				(search: showkeysdefinition )
%	Custom definitions						(search: custdefs )
%		Custom color definitions			(search:custcolors)
%		Font definitions					(search:fontDefinitions)
%		Custom column type (K)				(search: customColumns)
%		Other custom commands				(search: customCommands)
%			\jdrsum{}{}
%		Redefine \footnote
%		Define \jdrrunningtitle 			(search: definejdrrunningtitle)
%		Define \jdrcode
%		Math-related definitions			(search: mathdefs )
%			Redefine \emptyset
%			Define \lowerbar
%			Define \overbar
%			Define blackboard-bold characters
%			Define characters to enclose equation numbers
%	Loads hyperref package (should be last to load)		(search: loadhyperref)

%	\PassOptionsToPackage: To prevent option clashes when other packages load this package earlier without options.
\PassOptionsToPackage{dvipsnames,table}{xcolor} 

%%%%%%%%% Load packages %%%%%%%%%%%%%%%

%	Packages required to implement the showkeys package to display labels in drafts
\RequirePackage{seqsplit}
\RequirePackage{xstring}

%	Font-related packages
\RequirePackage{fontspec}
\RequirePackage{mathpazo} % Uses mathpazo (Palatino) as the main font.
\setmainfont
     [ BoldFont       = texgyrepagella-bold.otf ,
       ItalicFont     = texgyrepagella-italic.otf ,
       BoldItalicFont = texgyrepagella-bolditalic.otf ]
     {texgyrepagella-regular.otf}
\RequirePackage{textcomp}
\RequirePackage[scaled=0.92]{helvet} % Means to load Helvetica and its clones, scaled so it matches Times Roman
\RequirePackage{relsize}		% Package allows specifying that something should be set larger or smaller relative to the size of surrounding text

\RequirePackage{jdrunicode} % This is NOT a standard LaTeX package
						% The jdrunicode.sty must be included in the files belonging to the Overleaf project.

\RequirePackage{setspace}		% Used for tightening up vertical spacing in Table of Contents
\RequirePackage{titling}		% Preserves \thetitle, \author, and \date macros for later use after the title page is generated
\RequirePackage[small,compact]{titlesec}	% "small" is size of titles; "compact" reduces spacing above and below titles
\RequirePackage{fancyhdr}		% Package used to customize head and footlines
%\RequirePackage{tocloft}		% Package for formatting Tables of contents, figures, tables, etc.
\RequirePackage{ragged2e}		% Allows, e.g, \RaggedRight (which allows for hyphenation)

\RequirePackage{mathtools}		% Note: this loads amsmath
\RequirePackage{amsmath}		% Include the AMS Math packages
\RequirePackage{amssymb}
\RequirePackage{amsthm}

\RequirePackage{array}

\RequirePackage{xspace}

\RequirePackage{etoolbox}
%	To make the TOC "Contents" centered
%		See Gonzalo Medina's answer, https://tex.stackexchange.com/a/269712/7922, to
%		"titlesec ToC formatting — capitalization, subsection numbering for sections, title formatting", TeX Stack Exchange, September 26, 2015
%		https://tex.stackexchange.com/questions/269711/titlesec-toc-formatting-capitalization-subsection-numbering-for-sections-ti
\patchcmd{\tableofcontents}
  {\contentsname}
  {\hfill\Large{\contentsname}\hfill\null}
  {}
  {}

% Packages used in tables
\RequirePackage{booktabs}
\RequirePackage{tabularx}		
\RequirePackage{booktabs}
\RequirePackage{xcolor}
\RequirePackage{makecell}
\RequirePackage{multirow}
\RequirePackage{ctable}

%\RequirePackage{footnote}% (a) for footnotes in tables; (b) MUST be loaded after xcolor

\RequirePackage{soul}			% Used in defining \jdrcode
							% Note: \jdrcode sets soul's highlighting color to light gray, probabl								% conflicting with any other highlighting use.

\RequirePackage{graphicx}		% Package for processing graphics

\RequirePackage{lastpage}		% Loads lastpage package to enable page numbers of the form "Page x of y"
                            % Note: For more-ambitious page-numbering scenarios, consider the more-robust pageslts package

\usepackage[left=1in,right=1in,top=1in,bottom=1in]{geometry}		% Uses geometry package to set margins

\RequirePackage{natbib}			%	Uses the natbib package for bibliographies

%%%%%%%%%%% DOCUMENT FORMATTING (search: docformat ) %%%%%%%%%%%%%%%%
%	Sets disincentive for widows and orphans (club lines)
\widowpenalty=1000
\clubpenalty=1000
% Prevents LaTeX from distributing a lot of vertical white space to force the text to distribute among the entire height
\raggedbottom

%%%%%%%%%%%% PARAGRAPH-RELATED SETTINGS (search: paraformat ) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Sets the inter-paragraph vertical spacing. 1 ex is the height of the letter "x".
\setlength{\parskip}{1ex}  
% Indents the first line of each paragraph by the width of the letter "M".
\setlength{\parindent}{1em}  
% Magnifies the normal distance between baselines (the line on which the letters sit. Default = 1.
\renewcommand{\baselinestretch}{1.33}   
% Suppresses extra spaces after sentence-ending periods.
\frenchspacing 

%%%%%%%%%%%%% TITLE, HEADER, AND FOOTER SETTINGS (search: headfootformat ) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%	Raise the document title to reduce the white space above the title
\setlength{\droptitle}{-1.0in}

%   Define \jdrarticleSetHeaderFooter to set elements of header and footer
%   Call this in main.tex before \maketitle
\newcommand{\jdrarticleSetElementsTitleHeaderFooter}{%
    \renewcommand{\jdrrunningtitle}{\jdrRunningHead}
    \title{\jdrTitle\thanks{\jdrVersionDateEtc}}
    \author{\jdrAuthor\thanks{\jdrAuthorAffiliation}}
    \date{}		% When empty, suppresses the date in the title; otherwise, it will supply today's date
    %\date{June 17, 2011}
    \chead{\jdrheadfootfont \jdrrunningtitle}
    \lfoot{\jdrheadfootfont \theauthor}
    \cfoot{\jdrheadfootfont \jdrConfidentialityFooter}	
    %\rfoot{\jdrheadfootfont \thepage} 		% \thepage is the number of the current page
    \rfoot{\jdrheadfootfont Page \thepage\ of \pageref{LastPage}} 	% E.g., "Page 3 of 32" 
}

% Uses the fancyhdr package to customize the head and footlines, using the "fancy" page style
% Defines font style/size for headers and footers
\newcommand{\jdrheadfootfont}{\sf \small}
\pagestyle{fancy} % Triggers use of the fancyhdr package. See https://goo.gl/ONlLj
\renewcommand{\headrulewidth}{0.4pt}
\renewcommand{\footrulewidth}{0.4pt}   % Turns on the foot rule
\setlength{\headheight}{14pt} % Overleaf complains when not changed from its default (which appears to be 12pt). See ((Overleaf complains that Fancyhdr headheight is too small)), https://goo.gl/xE2mya

%	Set the head and footline components
\lhead{}
\chead{}
\rhead{}
\lfoot{}
\cfoot{}
\rfoot{}

%	Redefine the plain style using fancyhdr, to maintain the "page x of y" footer on the first page
%		Usage note: I typically use the plain style for the very first page only.
%	Because hyperref makes hyperlinks of the "of y" page number, I've stopped using "page x of y" except on the first page.
\fancypagestyle{plain}{%
\fancyhf{} % Clears all header and footer fields
\fancyfoot[C] {\jdrheadfootfont Page \thepage\ of \pageref{LastPage}} %Sets center footer field to "page x of y" 
\renewcommand{\headrulewidth}{0pt}
}

%%%%%%%%%%%% LIST-RELATED SETTINGS (search: listsformat ) %%%%%%%%%%%%%%%%%%%%%%%%
% Setting the bullet characters for itemize lists
\renewcommand{\labelitemi}{$\bullet$}
\renewcommand{\labelitemii}{$\diamond$}
\renewcommand{\labelitemiii}{$\circ$}
\renewcommand{\labelitemiv}{$\ast$}

%	Define custom list environments to better control the vertical spacing
%	The four parameters
%	\jdrlistparskip			Space between paragraphs outside of a list, and part of the space between a
%							non-list paragraph and a list item
%	\jdrlistparsep			Paragraph separation within a multiparagraph list item
%							(Allegedly; this isn't doing anything for me.)
%	\jdrlistitemsep			Extra inter-item spacing added to \parsep
%							can be redefined, e.g., \renewcommand{\jdrlistitemsep}{2pt}
%	\jdrlistvspacebefore	When negative, erases excessive vertical space between the paragraph preceding the list and the list itself

\newcommand{\jdrlistitemsep}{0pt}
\newcommand{\jdrlistparskip}{0pt}
\newcommand{\jdrlistparsep}{0pt}
\newcommand{\jdrlistvspacebefore}{-7pt}

\newenvironment{jdr_itemize} {
\vspace{\jdrlistvspacebefore} % When negative, erases excessive vertical space between the paragraph preceding the list and the list itself
\begin{itemize}
	\setlength{\itemsep}{\jdrlistitemsep}
	\setlength{\parskip}{\jdrlistparskip}
	\setlength{\parsep}{\jdrlistparsep}
}
{	\end{itemize}	}

\newenvironment{jdr_enumerate} {
\vspace{\jdrlistvspacebefore} % When negative, erases excessive vertical space between the paragraph preceding the list and the list itself
\begin{enumerate}
	\setlength{\itemsep}{\jdrlistitemsep}
	\setlength{\parskip}{\jdrlistparskip}
	\setlength{\parsep}{\jdrlistparsep}
}
{	\end{enumerate}	}

%%%%%%%%%%% SECTION-RELATED SETTINGS (search: secformat ) %%%%%%%%%%%%%%%%%%%%%%%%%%
%	Problem to be address: The inability to, by default, have deeper subsections than subsubsection
%	See http://goo.gl/hbWdbp , http://goo.gl/aYqExB

\RequirePackage{titlesec}
\titleformat{\section}
  {\normalfont\Large\bfseries}{\thesection}{1em}{\setstretch{1.0}}
\titleformat{\subsection}
  {\normalfont\large\bfseries}{\thesubsection}{1em}{\setstretch{1.0}}
\titleformat{\subsubsection}
  {\normalfont\normalsize\bfseries}{\thesubsubsection}{1em}{}
\titleformat{\paragraph}
  {\normalfont\normalsize\bfseries}{\theparagraph}{1em}{}
\titleformat{\subparagraph}
  {\normalfont\normalsize\bfseries}{\thesubparagraph}{1em}{}

\titlespacing*{\section}      {0pt}{3.5ex plus 1ex minus .2ex} {2.3ex plus .2ex}
\titlespacing*{\subsection}   {0pt}{3.25ex plus 1ex minus .2ex}{1.5ex plus .2ex}
\titlespacing*{\subsubsection}{0pt}{3.25ex plus 1ex minus .2ex}{1.5ex plus .2ex}
\titlespacing*{\paragraph}    {0pt}{3.25ex plus 1ex minus .2ex}{1.5ex plus .2ex}
\titlespacing*{\subparagraph} {0pt}{3.25ex plus 1ex minus .2ex}{1.5ex plus .2ex}

\RequirePackage{titletoc}
%	For the following settings, see http://goo.gl/d0ottG, http://goo.gl/xxLRFz

\dottedcontents{section}%
  [0em]% left indent
  {\addvspace{0pt}}% stuff before
  {2.0em}% spacing of \contentslabel
  {0.75em}% space between the dots
  [\addvspace{0pt}]% stuff after

\dottedcontents{subsection}%
  [2.75em]% left indent
  {\addvspace{0pt}}% stuff before
  {2.75em}% spacing of \contentslabel
  {0.75em}% space between the dots
  [\addvspace{0pt}]% stuff after

\dottedcontents{subsubsection}%
  [6.25em]% left indent
  {\addvspace{0pt}}% stuff before
  {3.5em}% spacing of \contentslabel
  {0.75em}% space between the dots
  [\addvspace{0pt}]% stuff after

\dottedcontents{paragraph}%
  [10.75em]% left indent
  {\addvspace{0pt}}% stuff before
  {4.25em}% spacing of \contentslabel
  {0.75em}% space between the dots
  [\addvspace{0pt}]% stuff after

\dottedcontents{subparagraph}%
  [13.0em]% left indent
  {\addvspace{0pt}}% stuff before
  {5.0em}% spacing of \contentslabel
  {0.75em}% space between the dots
  [\addvspace{0pt}]% stuff after

%	Change section headings to II.B.3 format
%\renewcommand\cftsecaftersnum{.}
\def\thesection{\Roman{section}} 
\def\thesubsection{\thesection.\Alph{subsection}}
\def\thesubsubsection{\thesubsection.\arabic{subsubsection}}

% Sets the depth of section numbering
\setcounter{secnumdepth}{5}
% Sets the depth to which the section hierarchy is represented in the table of contents.
\setcounter{tocdepth}{5}
%	Uses titlesec package to tighten up vertical space between section headings and the following text
\titlespacing*{\section} {0pt}{*0}{*-1}
\titlespacing*{\subsection}  {0pt}{*0}{*-1}
\titlespacing*{\subsubsection} {0pt}{*0}{*-1}

%%%%%%%%%%% TABLE OF CONTENTS-RELATED SETTINGS (search: tocformat ) %%%%%%%%%%%%%%%%%%%%%%%%%%
%	Changes title of Table of Contents to be Large, bold, and centered
%	Relies on the tocloft package. See https://goo.gl/yGjf2v at page 7
%\renewcommand{\cfttoctitlefont}{\hspace*{\fill}\Large\bfseries} 
%\renewcommand{\cftaftertoctitle}{\hspace*{\fill}} 

%	Sets \@tocrmarg (the TOC right margin; defaults to 2.55em) to be large enough that the content (name of the section)
%		doesn't overrun the page number on the right margin.
%		Note that \@tocrmarg must be greater than \@pnumwidth, which defaults to 1.55em
%		Note: since the default values imply that \@tocrmarg > \@pnumwidth, it's a mystery why empirically
%			I've encountered the content spilling so far to the right that it knocked the page number (which 
%			should be right justified) into the middle of the page, and without leading dots.
\makeatletter % changes the catcode of @ to 11. See https://goo.gl/m2t83t
\renewcommand{\@tocrmarg}{3em}
\makeatother % changes the catcode of @ back to 12. See https://goo.gl/m2t83t

%%%%%%%%%%% FOOTNOTE-RELATED SETTINGS (search: footnoteformat ) %%%%%%%%%%%%%%%%%%%%%%%%%%
%	Discourage splitting footnotes across different pages
\interfootnotelinepenalty=10000
%	Adds additional vertical space beneath the footnote rule (above the first footnote)
\renewcommand\footnoterule{\vspace*{-9pt}%
	\hrule height 0.4pt width 0.4\columnwidth
	\vspace*{8.6pt}}
%	Defines the vertical spacing between the bottom of the main text and the top of the first footnote
\addtolength{\skip\footins}{1em}
%	Adds spacing between footnotes
\setlength{\footnotesep}{1em}
% Use the footmisc portmanteau package of footnote-customizing commands to make footnotes hang with the footmark just inside the left margin.
\usepackage[hang,multiple,bottom]{footmisc}
\newlength{\jdrstyleFootnoteMargin}
\setlength{\jdrstyleFootnoteMargin}{1.8em}
\renewcommand{\footnotemargin}{\jdrstyleFootnoteMargin}

%	Styles the \thanks to align with the footnotes
%		See Alan Munn's answer to "Thanks?," comp.text.tex, May 22, 2009.
%		https://groups.google.com/d/embed/msg/comp.text.tex/pGeZMVEGIF4/T-99cNaDiKYJ
\renewcommand{\thanksscript}[1]{#1}
\renewcommand{\thanksmargin}{-\thanksmarkwidth}
\renewcommand{\thanksmarkwidth}{\jdrstyleFootnoteMargin}
\thanksfootextra{}{\hfill}

%%%%%%%%%%% CAPTION AND FIGURE CAPTION SETTINGS (search: captionsettings ) %%%%%%%%%%%%%%%%%%%%%%%%%%
%	Defines format for table and figure captions
%	margin=2em, established 2em margin on both left and right side
%	labelfont={bf,sc} makes caption label (e.g., "Table 1") both bold (bf) and small-caps (sc)
%	format=hang, indention=-0em causes the second and later lines of the caption to hang to the
%		right of the label, but 0em (can be changed) futher to the left than the end of the label
%		This will be ignored if the caption text is only a single line, in which case the caption
%			will be center justified.
%	tableposition=top and figureposition=bottom do not by themselves position the captions
%		above/below tables/figures, respectively
\usepackage[margin=2em, labelfont={bf,sc}, format=hang, indention=-0em, tableposition=top, figureposition=bottom]{caption}
%	The below gives more space after the colon in "Table 1:  This is the caption text."
\DeclareCaptionLabelSeparator{colonquad}{:\quad}
\captionsetup{labelsep=colonquad}

%%%%%%%%%%% SHOWKEYS INITIALIZING DEFINITION (search: showkeysdefinition )
%	Usage: In main.tex:
%		For final version, add "final" to \documentclass options
\usepackage[notref,notcite,color]{showkeys}
\newcommand{\jdrShowKeysInitialize}[1]{%
\noexpandarg%
	\StrSubstitute{\(\{\)#1\(\}\)}{ }{~}[\TEMP]%
	\parbox[t]{\marginparwidth}%
    {\raggedright\normalfont\footnotesize\ttfamily\expandafter\seqsplit\expandafter{\TEMP}}
}
\renewcommand*\showkeyslabelformat[1]{\jdrShowKeysInitialize{#1}}

%%%%%%%%%%% CUSTOM DEFINITIONS (search: custdefs ) %%%%%%%%%%%%%%%%%%%%%%%%%%
%	Custom color definitions				(search:custcolors)
%	Defining a color ("tableShade") for shading alternate rows of a table
%\definecolor{tableShade}{gray}{0.9}
%	Define a color for package showkeys to optionally print labels in margins during document development 
\definecolor{labelkey}{rgb}{1, 0.6, 0.6}
%	Define a color ("hyperrefcommandcolor") for the links produced by package hyperref
\definecolor{hyperrefcommandcolor}{rgb}{0.1,0.1,0.6}


%	Font definitions					(search:fontDefinitions)
%	Defines some standard fonts/colors for particular elements
%	\jdrheadingfont describes the font/color for (currently, Definition)
%	\bfseries\itshape = bold, italic
%	\textsf = sans serif
%	WARNING: I don't think this is used anywhere. Do I have Definition anywhere?
\newcommand{\jdrheadingfont}[1]{\textsf{\bfseries\itshape\color{RoyalBlue}#1}}

%	Define custom column types					(search: customColumns)
%	K is my custom-specified column type for tables. See
%		https://tex.stackexchange.com/questions/238018/tables-with-centered-columns-of-specific-width
%		A "K" column is both centered horizontally and of the specified width
%		To change to paragraph (full justification), change "K" to "m", which retains middle vertical alignment.
\newcolumntype{K}[1]{>{\centering\arraybackslash}m{#1}}
%	R is custom column type for raggedleft column
\newcolumntype{R}[1]{>{\RaggedLeft\arraybackslash}m{#1}}
%	R is custom column type for raggedright column
\newcolumntype{L}[1]{>{\RaggedRight\arraybackslash}m{#1}}






%	Define \jdrrunningtitle the running head that appears in the header of each page
%	(search: definejdrrunningtitle)
%	User should uncomment one of the two commands below.
\newcommand{\jdrrunningtitle}{ }



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