%% ==============================================================================
%% NEMO_manual.sty: all customizations (packages, styles, cmds)
%% ==============================================================================


%% LaTeX packages
%% ==============================================================================

\usepackage{natbib}           %% bib
\usepackage{caption}          %% caption
\usepackage{xcolor}           %% color
\usepackage{times}            %% font
\usepackage{hyperref}         %% hyper
\usepackage{idxlayout}        %% index
\usepackage{enumitem}         %% list
\usepackage{minted}           %% listing
\usepackage{amsmath}          %% maths
\usepackage{fancyhdr}         %% page
\usepackage{minitoc}          %% toc
\usepackage{subfiles}         %% subdocs
\usepackage[utf8]{inputenc}   %% input encoding

%% Extensions in bundle package

\usepackage{amssymb, graphicx, makeidx, tabularx}


%% Configuration

\captionsetup{margin=10pt, font={small}, labelsep=colon, labelfont={bf}}
\graphicspath{{../../../figures/}}
\hypersetup{
	pdftitle={NEMO ocean engine}, pdfauthor={Gurvan Madec, and NEMO System Team},
	colorlinks
}
\idxlayout{font=footnotesize, columns=3}
\renewcommand{\bibfont}{\footnotesize}
\renewcommand{\bibsep}{3pt}


%% Styles
%% ==============================================================================

\pagestyle{fancy}
\bibliographystyle{../main/ametsoc}

%% Additionnal fonts

\DeclareMathAlphabet{\mathpzc}{OT1}{pzc}{m}{it}


%% Page layout

\fancyhf{}
\fancyhead[LE,RO]{\bfseries\thepage}
\fancyhead[LO]{\bfseries\hspace{-0em}\rightmark}
\renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}}
\fancyhead[RE]{\bfseries\leftmark}
\renewcommand{\chaptermark}[1]{\markboth{#1}{}}
\renewcommand{\headrulewidth}{0.5pt}
\renewcommand{\footrulewidth}{0pt  }
\addtolength{\headheight}{2.6pt}


%% Catcodes

\makeatletter
\def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax}
\def\LignesVerticales{\let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV}
\def\GrosCarreAvecUnChiffre#1{
	\rlap{\vrule height 0.8cm width 1cm depth 0.2cm}
	\rlap{\hbox to 1cm{\hss\mbox{\color{white} #1}\hss}}
 	\vrule height 0pt width 1cm depth 0pt
}
\def\@makechapterhead#1{
	\hbox{
		\huge\LignesVerticales\hspace{-0.5cm}
		\GrosCarreAvecUnChiffre{\thechapter}\hspace{0.2cm}
		\hbox{#1}
	}
	\par\vskip
1cm
}
\def\@makeschapterhead#1{
	\hbox{
		\huge\LignesVerticales
		\hbox{#1}
	}
	\par\vskip
2cm
}
\def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else
  \hbox{}
  \vspace*{\fill}
  \vspace{\fill}
  \thispagestyle{empty}
  \newpage
  \if@twocolumn\hbox{}\newpage\fi\fi\fi}
\def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}}
\makeatother


%% Global custom commands: \newcommand{<name>}[<args>][<first argument value>]{<code>}
%% ==============================================================================

%% NEMO and Fortran in small capitals
\newcommand{\NEMO}{\textsc{nemo}}
\newcommand{\fortran}{\textsc{Fortran}}
\newcommand{\fninety}{\textsc{Fortran 90}}

%% Common aliases
\renewcommand{\deg}[1][]{\ensuremath{^{\circ}#1}}
\newcommand{\zstar }{\ensuremath{z^\star}}
\newcommand{\sstar }{\ensuremath{s^\star}}
\newcommand{\ztilde}{\ensuremath{\tilde z}}
\newcommand{\stilde}{\ensuremath{\tilde s}}
\newcommand{\ie}{\ensuremath{i.e.}}
\newcommand{\eg}{\ensuremath{e.g.}}

%% Inline maths
\newcommand{\fractext}[2]{\textstyle \frac{#1}{#2}}
\newcommand{\rdt}{\Delta t}

%% Text env. for Gurvan
\newcommand{\gmcomment}[1]{}

%% Index (italic font for files, preformat for code)
\newcommand{\ifile}[1]{\textit{#1.nc}          \index{Input NetCDF files!#1.nc}}
\newcommand{\mdl}[1]{\textit{#1.F90}           \index{Modules!#1}}
\newcommand{\jp}[1]{\texttt{#1}                \index{Model parameters!#1}}
\newcommand{\key}[1]{\texttt{\textbf{key\_#1}} \index{CPP keys!key\_#1}}
\newcommand{\ngn}[1]{\texttt{#1}               \index{Namelist Group Name!#1}}
\newcommand{\np}[1]{\texttt{#1}                \index{Namelist variables!#1}}
\newcommand{\rou}[1]{\texttt{#1}               \index{Routines!#1}}

%% Maths
\newcommand{\lt}{\left}
\newcommand{\rt}{\right}
\newcommand{\vect}[1]{\ensuremath{\mathbf{#1}}}
\newcommand{\pd}[2][]{\ensuremath{\frac{\partial #1}{\partial #2}}}

%% Shortened DOI in bibliography
\newcommand{\doi}[1]{\href{http://dx.doi.org/#1}{doi:#1}}

%% Namelists inclusion
\newcommand{\nlst}[1]{\forfile{../../../namelists/#1}}


%% Minted package: syntax highlighting configuration
%% ==============================================================================

%% Global highlighting style
\setminted{style=emacs, fontsize=\scriptsize, breaklines, frame=leftline}
\setminted[xml]{style=borland} %% Specific per language

%% Oneliner
\newmint[forline]{fortran}{}   % \forline|...|
\newmint[xmlline]{xml}{}       % \xmlline|...|
\newmint[cmd]{console}{}       % \cmd|...|

%% Multi-lines
\newminted[forlines]{fortran}{}   % \begin{forlines}
\newminted[xmllines]{xml}{}       % \begin{xmllines}
\newminted[cmds]{console}{}       % \begin{cmds}
\newminted[clines]{c}{}           % \begin{clines}

%% File
\newmintedfile[forfile]{fortran}{}   % \forfile{../namelists/nam...}

%% Inline
\newmintinline[forcode]{fortran}{fontsize=auto, frame=lines}   % \forcode{...}
\newmintinline[xmlcode]{xml}{    fontsize=auto, frame=lines}   % \xmlcode{...}
\newmintinline[snippet]{console}{fontsize=auto, frame=lines}   % \snippet{...}