dynlearn.sty

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% dynlearn.sty
%
% A style file for papers by the Crutchfield group
%
% This document is broken into many sections, separated by concept and
% libraries required.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Basic imports

% generic stuff
\usepackage{etex}                        %
\usepackage{ifpdf}                       % write flexible commands
\usepackage{xspace}                      % let macros play nice with spaces
\usepackage[table]{xcolor}               % colors
\usepackage{setspace}                    %

% figures
\PassOptionsToPackage{final}{graphicx}   % keep things consistant
\usepackage{graphicx}                    % \includegraphics

% formatting of particular things        %
\makeatletter                            % pagebackref doesn't work with beamer
\@ifclassloaded{beamer}{}{\PassOptionsToPackage{pagebackref}{hyperref}}
\makeatother
\usepackage{hyperref}
\usepackage{url}                         % format URLs
\usepackage[super]{nth}                  % 1st, 2nd, etc
\usepackage{contour}                     % draw an outline around text
\usepackage{verbatim}                    %
\usepackage{ragged2e}                    %
\usepackage{attrib}                      %
\usepackage{adjustbox}                   %
\usepackage[absolute,overlay]{textpos}   %
\usepackage{calc}                        %

% math formating, fonts, and symbols
\usepackage{amsmath}                     %
\usepackage{amscd}                       %
\usepackage{amsfonts}                    %
\usepackage{amssymb}                     %
\usepackage{amsthm}                      %
\usepackage{scalerel}                    %
\usepackage{bm}                          % bold
\usepackage{bbm}                         % more bold
\usepackage{braket}				               % bras and kets for quantum
\usepackage{mathtools}                   % mathclap, etc
\usepackage{etoolbox}                    %
\usepackage{textcomp}                    %
\usepackage{stmaryrd}                    % some computer science symbols
\usepackage{nicefrac}                    % pretty fractions

% generic packages for nicer fonts
\usepackage[T1]{fontenc}                 % allow copy/paste of unicode
\usepackage{lmodern}                     % nicer looking font
\usepackage[scaled=0.72]{beramono}       % more nicer fonts
\usepackage{microtype}                   % friendlier word spacing

% format algorithms in pseudocode
\usepackage{algorithm}                   %
\usepackage{algorithmicx}                % algorithmic doesn't work with revtex

% better tables
\usepackage{booktabs}                    % nicer tables
\usepackage{dcolumn}                     % align by decimal in tables
\usepackage{multirow}                    % multirow support in tables

\makeatletter
  \@ifclassloaded{revtex4-1}
  {
    \usepackage[caption=false]{subfig}   % subfigures; caption and subcaption
                                         % are incompatible with revtex4.1

     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     % foreign stuff, stolen from (and not included because of build systems)
     % \usepackage[abbreviations]{foreign}

     \DeclareRobustCommand\eg{\textit{e.g.}\xspace}
     \DeclareRobustCommand\ie{\textit{i.e.}\xspace}
     \DeclareRobustCommand\etal{\textit{et al.}\xspace}
  }
  {
    \usepackage{caption}
    \usepackage{subcaption}
    \usepackage[abbreviations]{foreign}
  }
  \@ifclassloaded{beamer}
  {
    \usepackage[backend=biber,
                autocite=superscript,
                doi=false,
                url=false,
                sorting=none,
                bibstyle=numeric,
                citestyle=numeric,
                bibencoding=utf8,
                ]{biblatex}
    \usepackage[useregional,showdow]{datetime2}
    \setbeamertemplate{bibliography item}{\insertbiblabel}
  }
  {
    % if not using beamer...
    \usepackage{enumitem}                % customizable list environments
  }
  \@ifclassloaded{beamerposter}
  {
  }
  {
    \usepackage{bm}                          % bold
    \usepackage{bbm}                         % more bold
  }
\makeatother

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% colors

% different authors
\definecolor{ryan}{RGB}{64, 0, 64}
\definecolor{nix}{RGB}{255, 0, 0}

\definecolor{ucdblue1}{cmyk}{.87,.46,0,.49} % RGB (17,70,129,255)  HTML(A) 114681(FF)
\definecolor{ucdblue2}{cmyk}{1., .56, 0., .34}
\colorlet{ucdblue}{ucdblue2}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% fixme: put todos and such in the document

\usepackage[inline,nomargin,author=]{fixme}

\makeatletter
\def\@lox@prtc{\section*{\@fxlistfixmename}\begingroup\def\@dotsep{4.5}}
\def\@lox@psttc{\endgroup}
\makeatother

\fxsetup{theme=color,mode=multiuser}
\fxsetface{inline}{\bfseries}

\FXRegisterAuthor{jpc}{ajpc}{JPC}
\FXRegisterAuthor{rgj}{argj}{\color{ryan}RGJ}
\FXRegisterAuthor{jrm}{ajrm}{JRM}
\FXRegisterAuthor{je}{aje}{\color{green!66!black}JE}
\FXRegisterAuthor{ca}{aca}{CA}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% siunitx setup

\usepackage[binary-units]{siunitx}       % format units including bits

\sisetup{quotient-mode=fraction, fraction-function=\nicefrac}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% cmvec setup

% \usepackage{cmvec}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% epigraph setup

\usepackage{epigraph}

\renewcommand{\epigraphflush}{center}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% TikZ related imports

\usepackage{tikz}
\usetikzlibrary{arrows}
\usetikzlibrary{automata}
\usetikzlibrary{calc}
\usetikzlibrary{decorations.markings}
\usetikzlibrary{decorations.pathreplacing}
\usetikzlibrary{external}
\usetikzlibrary{fit}
\usetikzlibrary{intersections}
\usetikzlibrary{patterns}
\usetikzlibrary{plotmarks}
\usetikzlibrary{positioning}
\usetikzlibrary{through}

\pgfkeys{/pgf/images/include external/.code=\includegraphics{#1}}

%% Externalization of TikZ images
% Uncomment to enable:

\tikzexternalize
\tikzsetexternalprefix{tikz_cache/}

%% e-Machine style and supporting code
\input{vaucanson.tikz}

%% I-Diagram stuff
\input{idiagrams.tikz}

%%% pgfplots
\usepackage{pgfplots}
\usepgfplotslibrary{colorbrewer}
\usepgfplotslibrary{fillbetween}
\usepgfplotslibrary{groupplots}
\usepgfplotslibrary{units}
\pgfplotsset{compat=newest}

%% allow visibility stuff in tikz

% \tikzset{
%   invisible/.style={opacity=0.2},
%   visible on/.style={alt={#1{}{invisible}}},
%   alt/.code args={<#1>#2#3}{%
%     \alt<#1>{\pgfkeysalso{#2}}{\pgfkeysalso{#3}}%
%   }
% }

%% Dynamically add plot labels to the legend, commented out because it is
%% incompatible with the standard legend code. Useful in Beamer talks.

% \pgfplotsset{
%     legend entry/.initial=,
%     every axis plot post/.code={%
%         \pgfkeysgetvalue{/pgfplots/legend entry}\tempValue
%         \ifx\tempValue\empty
%             \pgfkeysalso{/pgfplots/forget plot}%
%         \else
%             \expandafter\addlegendentry\expandafter{\tempValue}%
%         \fi
%     },
% }

\usepackage{pgfplotstable}

\usepackage{tcolorbox}
\tcbuselibrary{breakable}
\tcbuselibrary{skins}

\usepackage{circuitikz}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% colors

\colorlet {past_color}    {red}
\colorlet {pres_color}    {blue}
\colorlet {futu_color}    {black!30!green}

\colorlet {temp_color_1}  {red!50!blue}
\colorlet {temp_color_2}  {red!50!green}
\colorlet {temp_color_3}  {blue!50!green}

\colorlet {hmu_color}     {blue!67!green}
\colorlet {rhomu_color}   {temp_color_1!80!blue}
\colorlet {rmu_color}     {blue}
\colorlet {bmu_1_color}   {temp_color_1}
\colorlet {bmu_2_color}   {temp_color_3}
\colorlet {qmu_color}     {temp_color_1!67!green}
\colorlet {wmu_color}     {temp_color_2!57!blue}
\colorlet {sigmamu_color} {temp_color_2}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Used for code samples

%% listings

\usepackage{listings}

\lstdefinestyle{mypython}{
language=Python,                        % Code langugage
basicstyle=\small\ttfamily,             % Code font, Examples: \footnotesize, \ttfamily
keywordstyle=\color{green!50!black},    % Keywords font ('*' = uppercase)
commentstyle=\color{gray},              % Comments font
numbers=left,                           % Line nums position
numberstyle=\tiny,                      % Line-numbers fonts
stepnumber=1,                           % Step between two line-numbers
numbersep=5pt,                          % How far are line-numbers from code
backgroundcolor=\color{gray!10},        % Choose background color
frame=none,                             % A frame around the code
tabsize=2,                              % Default tab size
captionpos=b,                           % Caption-position = bottom
breaklines=true,                        % Automatic line breaking?
breakatwhitespace=false,                % Automatic breaks only at whitespace?
showspaces=false,                       % Dont make spaces visible
showtabs=false,                         % Dont make tabls visible
morekeywords={as},                      % Additional keywords
}

%% minted

\makeatletter
  \@ifclassloaded{beamer}
  {
    \usepackage{minted}

    % automatic line breaks:
    \ExplSyntaxOn
    \box_new:N \l_fvrb_box
    \tl_new:N \l_fvrb_tl

    \RenewDocumentCommand \FancyVerbFormatLine { m }
     {
       \hbox_set:Nn \l_fvrb_box { #1 }
        \dim_compare:nNnTF { \box_wd:N \l_fvrb_box }>{ \linewidth }
          {%box to big
           \tl_set:Nn \l_fvrb_tl { #1 }
           \fvrb_use_tl:N \l_fvrb_tl
          }
          {%box fits
           \box_use:N \l_fvrb_box
          }
     }

    \cs_new:Npn \fvrb_use_tl:N  #1
     {
      \group_begin:
       \null\hfill\vbox_set:Nn \l_fvrb_box
         {\hsize=\linewidth
          \renewcommand\thelinenumber{
            \ifnum\value{linenumber}=1\relax\else\fi
          }
          \begin{internallinenumbers}
            \advance\hsize by -2em
            \hspace*{-2em}\tl_use:N #1
          \end{internallinenumbers}
         }
       \box_use:N \l_fvrb_box
      \group_end:
    }

    \ExplSyntaxOff
  }
  {
  }
\makeatother

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Various theorem styles

\theoremstyle{plain}    \newtheorem{Lem}{Lemma}
\theoremstyle{plain}    \newtheorem*{ProLem}{Proof}
\theoremstyle{plain}    \newtheorem{Cor}{Corollary}
\theoremstyle{plain}    \newtheorem*{ProCor}{Proof}
\theoremstyle{plain}    \newtheorem{The}{Theorem}
\theoremstyle{plain}    \newtheorem*{ProThe}{Proof}
\theoremstyle{plain}    \newtheorem{Prop}{Proposition}
\theoremstyle{plain}    \newtheorem*{ProProp}{Proof}
\theoremstyle{plain}    \newtheorem*{Conj}{Conjecture}
\theoremstyle{plain}    \newtheorem*{Rem}{Remark}
\theoremstyle{plain}    \newtheorem{Def}{Definition}
\theoremstyle{plain}    \newtheorem*{Not}{Notation}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Configure cleveref

\usepackage[capitalise]{cleveref}        % Automatically label references
\crefname{Lem}{Lemma}{Lemmas}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Logos

\newcommand{\csclogo}{
  \centering
  \tikzsetnextfilename{csclogo}
  \begin{tikzpicture}
    \draw (0, 0) node {\includegraphics[height=1.0cm]{images/expanded_logo_cmyk_blue}};
    \draw (0, 0.7) node [color=ucdblue, scale=0.9] {\small Complexity Sciences Center};
  \end{tikzpicture}
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Finally, computational mechanics and information theory macros

\DeclareMathOperator*{\argmax}{arg\,max}
\DeclareMathOperator*{\argmin}{arg\,min}

\input{cmechabbrev}
\input{infotheory}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Uncomment to list package versions:

% \listfiles

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Document configuration

\setlength{\parindent}{0pt}
\setlength{\parskip}{3pt plus 2pt minus 2pt}

\def \justify {\justifying \leftskip 0.0cm \rightskip 0.5cm}
\newcommand{\vtiny}{\fontsize{5.5pt}{1pt}\selectfont}

\makeatletter
  \@ifclassloaded{beamer}
  {
    \hypersetup{
      linkcolor={blue!50!black},
      citecolor={blue!50!black},
      urlcolor={blue!80!black},
    }
  }
  {
    \hypersetup{
      colorlinks,
      linkcolor={blue!50!black},
      citecolor={blue!50!black},
      urlcolor={blue!80!black},
    }
  }
\makeatother

% working paper commands
\newcommand{\arxiv}[1]{\href{http://arxiv.org/abs/#1}{\texttt{arXiv}:#1}}
% SFI working papers do not have friendly URLs:
\newcommand{\sfiwp}[1]{Santa Fe Institute Working Paper #1}