%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Virgil's LaTeX Environment macros
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% All of the macros and packages Virgil uses to make LaTeX experiences more pleasant
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\ProvidesPackage{virgil_env}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Packages that often need to be turned ON/OFF
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% We need amssymb for the symbol \lessgtr.  However, it likes to conflict with other stuff ):
\usepackage{amssymb}	% AMS symbols.  Disabled because it likes to conflict with other stuff.

% Decimal point alignment of numeric cells
\usepackage{dcolumn}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% End Packages that often need to be turned ON/OFF
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Figure out what to do with these later
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%Remove space to the vertical edges:
%\begin{tabular}{@{}lll@{}}

%\usepackage{calc}

%% Adds pretty caligraphy fonts
%\usepackage{mathrsfs}
%\usepackage{amsfonts}
%\usepackage{euler}
%\DeclareMathAlphabet{\mathcalligra}{T1}{calligra}{m}{n}
%\DeclareMathAlphabet{\mathpzcm}{OT1}{pzcm}{mb}{it}
%\DeclareMathAlphabet{\mathpzc}{OT1}{pzc}{m}{it}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% add ifthen powers
\usepackage{ifthen}

% add color powers
\usepackage[usenames,dvipsnames]{color}

% For debugging during document creation
%\usepackage{showkeys}	

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Fonts + text options
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{ lmodern }			% I prefer this over times
%\usepackage{ times }			% default

\usepackage{parskip}			% more skipping options

% Support non-english characters
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Enable Graphics
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{graphicx} 	% Takes the ``[draft]'' option in \document class

\DeclareGraphicsExtensions{.pdf,.eps,.png,.jpg}		% search for .pdf, then .eps, then .pngs, then .jpg

% look in these subdirectories for graphics referenced by \includegraphics
% each entry must end with a /
\graphicspath{{figs/}{figures/}{images/}{./}}



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Bibliography options
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% natbibspacing availabe at: http://dcwww.camd.dtu.dk/~schiotz/comp/LatexTips/natbibspacing.sty
%\usepackage{natbib}
%\usepackage{natbibspacing}
%\bibliographystyle{plain}
%\bibliographystyle{unsrt}
%\bibliographystyle{nature}
%\bibliographystyle{apa}
%\bibliographystyle{mslapa}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Math and Symbol packages
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{amsmath, mathtools}		% you always want this

\usepackage{amsthm}		% for theorems

% enables bold greek letters in math mode using the \bm{...} command. Supersedes package `amsbsy'.
%% Enables blackboard-bold letters
%\usepackage{bbold}	% for \textbb{}
%\usepackage{bm}
%\usepackage{bbm}		% blackboard bold with \mathbbm{}
\usepackage{bm}

%\usepackage{, wasysym}		% lots of fancy symbols
\usepackage{commath}
\usepackage{marvosym}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Better page-formatting options
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{afterpage}		% better-behaved page-formating

\usepackage{fancyhdr}		% Change header and footer on any page


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Better Math
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{array}			% replacement for eqnarray.  Must be BEFORE \usepackage{arydshln}
\usepackage{units}			% for \nicefrac{\alpha}{\beta}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Prettier tables 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{booktabs} 	% for much better looking tables
\usepackage{arydshln}		% For dashed-lines in tables




%%%%% Adds a downward line "closing" what's inside the square-root.
% New definition of square root:
% it renames \sqrt as \oldsqrt
\let\oldsqrt\sqrt
% it defines the new \sqrt in terms of the old one
\def\sqrt{\mathpalette\DHLhksqrt}
\def\DHLhksqrt#1#2{%
\setbox0=\hbox{$#1\oldsqrt{#2\,}$}\dimen0=\ht0
\advance\dimen0-0.2\ht0
\setbox2=\hbox{\vrule height\ht0 depth -\dimen0}%
{\box0\lower0.4pt\box2}}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% More customizable Figures
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{float}				% necessary for fancy positioning

\usepackage{wrapfig} 		% wrap text around your figures
\usepackage{subfig}			% supercedes subfigure

% provides the capability to rename Figure -> Fig. throughout document
% supercedes \usepackage{caption}.
%\usepackage{ccaption}		

%\usepackage{boxedminipage}		% for floating boxes.  Haven't used this much.


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% More customizable Lists
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Better symbols custom enumerative lists, define any symbol you'd like
\usepackage{enumitem}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Custom Symbols 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% \xspace at the end of custom macros never fucks up spacing.
% example of best practice: \newcommand{\apples}{\textsf{AppLeS}\xspace} 
\usepackage{xspace}



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Text formatting
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% for different styles of underlines
\usepackage{ulem} \normalem  % \normalem is to keep \emph{} italics instead of underlined.
\newcommand{\redwuline}[1]{ {\color{red}{ \uwave{\textcolor{black}{#1}} } } }
\newcommand{\orangewuline}[1]{ {\color{BurntOrange}{ \uwave{\textcolor{black}{#1}} } } }

% In-line lists.  I've never used this but here's the package for it
%\usepackage{paralist}
%\textbf{\itshape Inline lists}, which are sequential in nature, just like enumerated
%lists, but are \begin{inparaenum}[\itshape a\upshape)]
%\item formatted within their paragraph;
%\item usually labelled with letters; and 
%\item usually have the final item prefixed with `and' or `or',
%\end{inparaenum} like this example.




%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% For prettier citations and hyperlinks
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage[pdftex, colorlinks=true,
                    bookmarksnumbered=true,
                    bookmarksopen=true,
                    bookmarksopenlevel=3,
                    pdfstartview=FitV,
                    linkcolor=blue,
                    citecolor=blue,
                    urlcolor=black,
          ]{hyperref}

% if \url isn't defined yet, define it using the `url' package.  Else do nothing
\ifthenelse{ \isundefined{\url} } { \usepackage{url} }{}

\usepackage{cite}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Special customizations that I like
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Makes the tables prettier
%\renewcommand{\arraystretch}{1.05}




%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SAVETREES - space saving options
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% You'd probably want to put this right before your \documentclass{} in your .tex file
% options: normaltitle, normalmargins, normalsections, normallists, normalfloats, normalindent, , normalleading, normalbib, normalbibnotes
% use everything
%\usepackage[]{savetrees}
%\usepackage[normaltitle, normalsections, normalmargins, normalindent]{savetrees}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% For multi-line comments
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{verbatim}
\newcommand*{\bcomment}{ \begin{comment} }
\newcommand*{\ecomment}{ \end{comment} }
%\newcommand{\bCOMMENT}{ \begin{comment} }
%\newcommand{\eCOMMENT}{ \end{comment} }
%\newcommand*{\comment}[1]{}
%\newcommand{\COMMENT}[1]{}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Abbreviations you'll always want
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\newcommand*{\TODO}[1]{{\centering {\sffamily \color{red} #1} \vskip10pt }}
\newcommand*{\todo}[1]{{\sffamily [{\color{red} #1}]}}
\newcommand*{\fix}[1]{{\sffamily [{\textnormal{\color{red} #1}}]}}


%-----------------------------------------------------------------------------
%  Cross references
%-----------------------------------------------------------------------------
% The following code defines how you make references to figures, tables, etc...
% It is defined in one place only, and can be modified for all references
% in the document at the same time.
% Instead of typing each time: "see Fig. \ref{myfig}" you can create a command
% \figref which will do the job. Then in text you only type \figref{myfig} and LaTeX
% will do the rest.
\newcommand{\tblref}[1]{Table~\ref{#1}}
%\renewcommand*{\figref}[1]{Fig.~\ref{#1}}
\newcommand{\equref}[1]{(\ref{#1})}

\newcommand{\Tblref}[1]{Table~\ref{#1}}
\newcommand{\Figref}[1]{Figure~\ref{#1}}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


%-----------------------------------------------------------------------------
%  Misc symbols that I like
%-----------------------------------------------------------------------------
\newcommand*{\opname}[1]{\operatorname{#1}}
\newcommand{\opnamewl}[1]{\operatornamewithlimits{#1}}

\newcommand*{\bdot}{ {\color{Brown} \ensuremath{\newmoon} } }
\newcommand*{\rdot}{ {\color{red} \ensuremath{\newmoon} } }
\newcommand*{\gdot}{ {\color{green} \ensuremath{\newmoon} } }
%\renewcommand*{\odot}{ {\color{Orange} \ensuremath{\newmoon} } }
\renewcommand*{\:}{\ensuremath{\!:\!}}

%\newcommand*{\dequal}{\overset{\Delta}{=}}

%\newcommand{\red}{{\color{Red}\ding{108}}}
%\newcommand{\blue}{{\color{NavyBlue}\ding{108}}}
%\newcommand{\green}{{\color{Green}\ding{108}}}
\newcommand*{\highcond}{ \uparrow }
\newcommand*{\lowcond}{ \downarrow }

\newcommand*{\bphi}{ \langle \phi \rangle }
%\newcommand*{\bei}{ \ei }
\newcommand*{\red}[1]{ \color{red} #1}
\newcommand*{\RED}[1]{ \textbf{ \color{red} #1 } }

\renewcommand*{\to}{\rightarrow}

% Define over and under comment using braces
\newcommand*{\overcomment}[2]{\ensuremath{\overbrace{#1}^{\mathclap{\textnormal{#2}}} }}
\newcommand*{\undercomment}[2]{\ensuremath{\underbrace{#1}_{\mathclap{\textnormal{#2}}} }}

% Define the Kullback-Leibler divergence notation
\newcommand*{\DKL}[2]{\ensuremath{ \opname{D_{KL}} \! \left[ #1 \middle\|\, #2 \right] }}

% Define a pretty Entropy H( ... )
\newcommand*{\ent}[1]{\opnamewl{H} \! \left( #1 \right)}
% Define a pretty conditional Entropy H( ... | ... )
\newcommand*{\condent}[2]{\ent{#1\middle|#2}}

% Define a pretty Mutual Information I( ... : ... )
\newcommand*{\info}[2]{ \opnamewl{I} \! \left( #1 \!:\! #2 \right)}
\newcommand*{\infosemi}[2]{ \opnamewl{I} \! \left( #1 ; #2 \right)}
% Define a pretty Conditional Mutual Information 

% Define a pretty Probability Pr( ... )
\newcommand*{\Prob}[1]{\ensuremath{\Pr \! \left( #1 \right)}}

\renewcommand*{\flat}[1]{\ensuremath{\overline{#1}}}

% Prettier Roman Numerals
% \Roman is already defined, but I like this one better
\makeatletter % turns ON allowing @ signs inside of commands
\newcommand{\Rmn}[1]{\textbf{\expandafter\@slowromancap\romannumeral #1@}}
\makeatother % turns OFF \makeatletter

\newcommand{\argmax}{\operatornamewithlimits{argmax}}
\newcommand{\argmin}{\operatornamewithlimits{argmin}}