biommap/documentation/template.tex

%!TEX TS-program = xelatex
\documentclass[french, 10pt]{scrartcl}

% The declaration of the document class:

% The second line here, i.e.
% \documentclass[12pt]{scrartcl}
% is a standard LaTeX document class declaration:
% we say what kind of document we are making in curly brackets,
% and specify any options in square brackets.

% (The previous line is a pseudo-comment, declaring that we will
% use the special XeTeX machinery for its more extensive font list
% and its use of unicode;
% in general, LaTeX 'comments' like this one
%  begin with % and end with a linebreak.)

% Note that there we have nothing in the nature of a template;
% it's just a standard bit of LaTeX pandoc will copy unaltered into the
% LaTeX file it is writing.  But suppose you wrote something
% more akin to the corresponding line in Pandoc's default
% latex.template file, say:

% \documentclass$if(fontsize)$[$fontsize$]$endif${scrartcl}

% then you would have invented a 'variable', fontsize,
% and could write things like

% `markdown2pdf my.txt --xetex --variable=fontsize:12pt -o my.pdf` or
% `pandoc -r markdown -w html my.txt -s --xetex --variable=fontsize:24pt -o my.tex`.

% If we specified --variable-fontsize:12, then template substitution
% would yield a LaTeX document beginning
% \documentclass[12pt]{scrarcl}
% which is just what we said anyway.
% But we could also specify a different fontsize.

% I don't use this `--variable=....`functionality myself;
% I have a couple of basic templates I call with
% `--template=whatever.template` which I can also
% easily inspect to adjust things like font size as I please.

% While we are discussing the declaration of the document class...
% here's an alternative command for two column landscape,
% not bad for some purposes. (If you strike the word 'landscape'
% you will have two narrow newspaperlike
% columns; scientists like that, because irrationality must
% show itself somewhere):
%\documentclass[12pt,twocolumn,landscape]{scrartcl}
% Columns are too close together in LaTeX so we add this
% `columnsep` command:
%\setlength{\columnsep}{.5in}


% I use the special 'komascript' article class "scrartcl"
% reasons I can't entirely remember; I'm not sure it's that great.
% One reason is the unimportant one that, like many classes,
% it allows very big fonts which are convenient for booklet printing
% in the idiotic American way by shrinking letterpaper pages.

% the standard minimal LaTeX 'article' class declaration would be something like:

% \documentclass[12pt]{article}

% or for big type:

% \documentclass[24pt]{extarticle}

% but these restrict you to old-fashioned LaTeX materials.
% Note that Kieran Healy uses the swank 'Memoir' class,
% \documentclass[11pt,article,oneside]{memoir}
% which might be worth a look.

% Enough about the document class.

% -- We are in swanky unicode, XeTeX land, and must now import these packages:
\usepackage{fontspec,xltxtra,xunicode}
% fontspec means we can specify pretty much any font.
% Because we are using XeTeX material,
% this template needs to be called with the `--xetex` flag.


% Symbols:
% Pandoc imports the extensive `amsmath` collection of symbols
% for typesetting ordinary math.
\usepackage{amsmath}
% if you use exotic symbols you need to import specific packages, eg. for
% electrical engineering diagrams, musical notation, exotic currency symbols,
% the unspeakable rites of freemasonry etc.

\usepackage{amssymb}

\usepackage{eurosym}
\usepackage{rotating}

\usepackage[%
    all,
    defaultlines=3 % nombre minimum de lignes
]{nowidow}

% `babel`:
% The `babel` package, among other things, lets you determine what
% language you are using in a given stretch of text, so that typesetting
% will go well. Here we specify that mostly, we are speaking English:
% \usepackage[francais]{babel}
%%% \usepackage[francais]{babel}
\usepackage{babel}



% Margins, etc:
% the `geometry` package makes for convenient adjusting of margins, which is what
% you asked about.  Of course it can do much more, even make coffee for you:
\usepackage{geometry}
\geometry{verbose,a4paper,tmargin=3cm,bmargin=5cm,lmargin=3cm,rmargin=5cm}
% so if you just keep a copy of this template in the directory you are working in, you
% can adjust the margins by going into this file and messing with the margins.
% the syntax is very unforgiving, but permits 3cm and 2.5in and some other things.


% Font:
% Here I set my main font, which is an Apple Corporation Exclusive, golly.

% \setmainfont{Hoefler Text}
% \setromanfont[Mapping=tex-text,Contextuals={NoWordInitial,NoWordFinal,NoLineInitial,NoLineFinal},Ligatures={NoCommon}]{Hoefler Text}

% Hoefler Text is okay, but note the long discussion of 'contextuals' which is necessary to cools off
% some of its show-offy properties. (You can make your essay look like the
% Declaration of Independence by specifying e.g. Ligatures={Rare} )
% If you have a copy you might try it; as it is
% I will comment it out and supply something more certain to be around:

\setmainfont{Open Sans}

% Properly one should specify a sanserif font and a monospace font
% see e.g. the example of Kieran Healy:
% \setromanfont[Mapping=tex-text,Numbers=OldStyle]{Minion Pro}
% \setsansfont[Mapping=tex-text]{Minion Pro}
% \setmonofont[Mapping=tex-text,Scale=0.8]{Pragmata}

% But I hate sanserif fonts, and anyway there are defaults.



% Heading styles:
% These commands keep the koma system from making stupid sans serif section headings
\setkomafont{title}{\rmfamily\mdseries\upshape\normalsize\color{clgreencolor}}
\setkomafont{sectioning}{\rmfamily\mdseries\upshape\normalsize\color{clgreencolor}}
\setkomafont{descriptionlabel}{\rmfamily\mdseries\upshape\normalsize\color{clgreencolor}}

% Add some numbering to headings and a new line until heading level 6
\usepackage{titlesec}
\setcounter{secnumdepth}{6}
\titleformat{\paragraph}{\normalfont\normalsize\color{clgreencolor}}{\theparagraph}{1em}{}
\titlespacing*{\paragraph}{0pt}{3.25ex plus 1ex minus .2ex}{1.5ex plus .2ex}
\titleformat{\subparagraph}{\normalfont\normalsize\color{clgreencolor}}{\thesubparagraph}{1em}{}
\titlespacing*{\subparagraph}{0pt}{3.25ex plus 1ex minus .2ex}{1.5ex plus .2ex}

% Hyphenation
% We played with the tolerance to increase the hyphenation
\tolerance=1000
% list of words which need hyphenation
\hyphenation{a-gen-da cha-que u-sa-ger}

% I'm puzzled why I have this foonote speciality,
% I wonder if it's part of my problem I've been having, but wont look
% into it now.
\usepackage[flushmargin]{footmisc}
% \usepackage[hang,flushmargin]{footmisc}


% So much for my personal template.


% Everything that follows is copied from the pandoc default template:
% I will interpolate a few comments, the comments that are in
% the default template will be marked % --

% Paragraph format:
% Pandoc prefers unindented paragraphs in the European style:
\setlength{\parindent}{0pt}
%  ... with paragraph breaks marked by a slight lengthening of
% the space between paragraphs:
\setlength{\parskip}{6pt plus 2pt minus 1pt}
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
% Page format:
% \pagestyle{plain}
% The default `plain` pagestyle just numbers the pages,
% whereas
\pagestyle{empty}
% would give you no numbering.
% After one-million man-years of macro-composition,
% there are also fancy pagestyles with much wilder options
% for headers and footers, of course.

\usepackage{fancyhdr}
\pagestyle{fancy}
\fancyhf{}
\rfoot{\color{clgraycolor}\thepage}
\renewcommand{\headrulewidth}{0pt}
\renewcommand{\footrulewidth}{0pt}


% Footnotes
% if you have code in your footnotes, the million macro march
% kind of bumps into itself.
% Pandoc, having just rendered your text into LaTeX,
% knows whether the 'variable' `verbatim-in-note` is True, and
% If it is, it asks for a  LaTeX package that solves the dilemma:
$if(verbatim-in-note)$
\usepackage{fancyvrb}
$endif$

% Lists formatting:
% note sure what 'fancy enums' are; something to do with lists,
% as the further comment suggests:
$if(fancy-enums)$
% -- Redefine labelwidth for lists; otherwise, the enumerate package will cause
% -- markers to extend beyond the left margin.
\makeatletter\AtBeginDocument{%
  \renewcommand{\@listi}
    {\setlength{\labelwidth}{4em}}
}\makeatother
\usepackage{enumerate}
$endif$


% Table formatting:
% What if you make a table? -- Pandoc knows, of course, and
% then declares that its  variable `table` is True and
% imports a table package suitable to its pleasantly simple tables.
% Needless to say infinitely   complicated tables are possible in
% LaTeX with suitable packages. We are spared the temptation:

$if(tables)$
\usepackage{array}

% Continuing on the topic of tables ... (we havent reached `endif`).
% The commented out line below is in the default pandoc  latex.template.
% Some unpleasantness with table formatting must be corrected.

% -- This is needed because raggedright in table elements redefines \\:
\newcommand{\PreserveBackslash}[1]{\let\temp=\\#1\let\\=\temp}
\let\PBS=\PreserveBackslash

$endif$


% Subscripts:
% Pandoc remembers whether you used subscripts, assigning True to
% its `subscript` variable
% It then needs to adopt a default with an incantation like this:
$if(subscript)$
\newcommand{\textsubscr}[1]{\ensuremath{_{\scriptsize\textrm{#1}}}}
$endif$


% Web-style links:

% markdown inclines us to use links, since our texts can be made into html.
% Why not have clickable blue links even in
% learned, scientific, religious, juridical, poetical and other suchlike texts?
% Never mind that they have been proven to destroy the nervous system!

% First, what about the fact that links like http://example.com are
% technically code and thus must not be broken across lines?
% [breaklinks=true] to the rescue!

% Nowadays LaTeX can handle all of this with another half million macros:

\usepackage[dvipsnames]{xcolor}
\definecolor{linkcolor}{RGB}{0, 136, 170}
\definecolor{linkcolortoc}{RGB}{51,51,51} % same as text color
\definecolor{clgreencolor}{RGB}{136,170,0}
\definecolor{clgraycolor}{RGB}{51,51,51}
\definecolor{cctpcolor}{RGB}{0,136,170}

\usepackage[breaklinks=true]{hyperref}
\hypersetup{colorlinks,%
citecolor=linkcolor%
filecolor=linkcolor,%
linkcolor=linkcolor,
urlcolor=linkcolor}
$if(url)$
\usepackage{url}
$endif$


% Images.
% In ye olde LaTeX one could only import a limited range of image
% types, e.g. the forgotten .eps files.  Or else one simply drew the image with suitable
% commands and drawing packages.  Today we want to import .jpg files we make with
% our smart phones or whatever:

\usepackage{lscape}
\usepackage{graphicx}
\usepackage{pdfpages}

%$if(graphics)$
%\usepackage{graphicx}
% -- We will generate all images so they have a width \maxwidth. This means
% -- that they will get their normal width if they fit onto the page, but
% -- are scaled down if they would overflow the margins.
%\makeatletter
%\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth
%\else\Gin@nat@width\fi}
%\makeatother
%\let\Oldincludegraphics\includegraphics
%\renewcommand{\includegraphics}[1]{\Oldincludegraphics[width=\maxwidth]{#1}}
%$endif$


\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}

$if(csl-refs)$
\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
\newenvironment{cslreferences}%
  {$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
  \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
  {\par}
$endif$

% Section numbering.
% Here again is a variable you can specify on the commandline
% `markdown2pdf my.txt --number-sections --xetex --template=/wherever/this/is -o my.pdf`
$if(numbersections)$
$else$
\setcounter{secnumdepth}{0}
$endif$

% Footnotes:
% Wait, didn't we already discuss the crisis of code in footnotes?
% Evidently the order of unfolding of macros required that
% we import a package to deal with them earlier
% and issue a command it defines now. (Or maybe that's not the reason;
% very often the order does matter as the insane system of macro expansion
% must take place by stages.)
$if(verbatim-in-note)$
\VerbatimFootnotes % -- allows verbatim text in footnotes
$endif$

% Other stuff you specify on the command line:
% You can include stuff for the header from a file specified on the command line;
% I've never done this, but that stuff will go here:
$for(header-includes)$
$header-includes$
$endfor$

% Title, authors, date.
% If you specified title authors and date at the start of
% your pandoc-markdown file, pandoc knows the 'values' of the
% variables: title authors date and fills them in.

$if(title)$
\title{$title$}
$endif$
\author{$for(author)$$author$$sep$\\$endfor$}
$if(date)$
\date{$date$}
$endif$

% Package tcolorbox for making nice boxes around some texts
\usepackage{tcolorbox}


% Adaptations pour la SNCF

% créer un toc jusqu'au niveau 4
\setcounter{tocdepth}{3}

% Eviter l'erreur "Environment Shaded undefined"
$if(highlighting-macros)$
$highlighting-macros$
$endif$

% missing environment longtable
\usepackage{booktabs}
\usepackage{longtable}



% At last:
% The document itself!:

% After filling in all these blanks above, or erasing them
% where they are not needed, Pandoc has finished writing the
% famous LaTeX *preamble* for your document.
% Now comes the all-important command \begin{document}
% which as you can see, will be paired with an \end{document} at the end.
% Pandoc knows whether you have a title, and has already
% specified what it is; if so, it demands that the title be rendered.
% Pandoc knows whether you want a table of contents, you
% specify this on the command line.
% Then, after fiddling with alignments, there comes the real
% business: pandoc slaps its rendering of your text in the place of
% the variable `body`
% It then concludes the document it has been writing.

\color{clgraycolor}
\begin{document}


$if(title)$
\maketitle
$endif$


%\begingroup
%\hypersetup{linkcolor=linkcolortoc}

%\tableofcontents

%\listoffigures

%\listoftables

%\endgroup


$if(alignment)$
\begin{$alignment$}
$endif$

$body$

%$if(alignment)$
\end{$alignment$}
$endif$


\end{document}