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files for building a pdf that includes all notebooks
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‎Makefile‎

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#
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# Build a PDF with all the notebooks
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#
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TEMPLATE=chapter
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NOTEBOOKS=Lecture-0-Scientific-Computing-with-Python.ipynb \
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Lecture-1-Introduction-to-Python-Programming.ipynb \
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Lecture-2-Numpy.ipynb Lecture-3-Scipy.ipynb \
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Lecture-4-Matplotlib.ipynb Lecture-5-Sympy.ipynb \
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Lecture-6A-Fortran-and-C.ipynb Lecture-6B-HPC.ipynb \
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Lecture-7-Revision-Control-Software.ipynb
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LATEXFILES=$(NOTEBOOKS:.ipynb=.tex)
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.ipynb.tex:
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ipy3-devel nbconvert --to latex --template $(TEMPLATE) $<
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#all: $(LATEXFILES) buildpdf
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all: latexfiles buildpdf
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latexfiles:
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ipy3-devel nbconvert --to latex --template $(TEMPLATE) Lecture-0-Scientific-Computing-with-Python.ipynb
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ipy3-devel nbconvert --to latex --template $(TEMPLATE) Lecture-1-Introduction-to-Python-Programming.ipynb
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ipy3-devel nbconvert --to latex --template $(TEMPLATE) Lecture-2-Numpy.ipynb Lecture-3-Scipy.ipynb
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ipy3-devel nbconvert --to latex --template $(TEMPLATE) Lecture-4-Matplotlib.ipynb
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ipy3-devel nbconvert --to latex --template $(TEMPLATE) Lecture-5-Sympy.ipynb
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ipy3-devel nbconvert --to latex --template $(TEMPLATE) Lecture-6A-Fortran-and-C.ipynb
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ipy3-devel nbconvert --to latex --template $(TEMPLATE) Lecture-6B-HPC.ipynb
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ipy3-devel nbconvert --to latex --template $(TEMPLATE) Lecture-7-Revision-Control-Software.ipynb
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buildpdf: latexfiles
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pdflatex Scientific-Computing-with-Python.tex
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‎Scientific-Computing-with-Python.pdf‎

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‎Scientific-Computing-with-Python.tex‎

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\documentclass{report}
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\usepackage{graphicx} % Used to insert images
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\usepackage{adjustbox} % Used to constrain images to a maximum size
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\usepackage{color} % Allow colors to be defined
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\usepackage{enumerate} % Needed for markdown enumerations to work
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\usepackage{geometry} % Used to adjust the document margins
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\usepackage{amsmath} % Equations
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\usepackage{amssymb} % Equations
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\usepackage[mathletters]{ucs}
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\usepackage[utf8x]{inputenc}
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\usepackage{fancyvrb}
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\usepackage{grffile}
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\usepackage{hyperref}
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\usepackage{longtable}
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\usepackage{booktabs}
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\usepackage{tikz}
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\usepackage{scrextend}
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\usepackage{needspace}
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\usepackage{framed}
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\definecolor{orange}{cmyk}{0,0.4,0.8,0.2}
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\definecolor{darkorange}{rgb}{.71,0.21,0.01}
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\definecolor{darkgreen}{rgb}{.12,.54,.11}
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\definecolor{myteal}{rgb}{.26, .44, .56}
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\definecolor{gray}{gray}{0.45}
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\definecolor{lightgray}{gray}{.95}
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\definecolor{mediumgray}{gray}{.8}
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\definecolor{inputbackground}{rgb}{.95, .95, .85}
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\definecolor{outputbackground}{rgb}{.95, .95, .95}
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\definecolor{traceback}{rgb}{1, .95, .95}
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% ansi colors
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\definecolor{red}{rgb}{.6,0,0}
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\definecolor{green}{rgb}{0,.65,0}
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\definecolor{brown}{rgb}{0.6,0.6,0}
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\definecolor{blue}{rgb}{0,.145,.698}
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\definecolor{purple}{rgb}{.698,.145,.698}
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\definecolor{cyan}{rgb}{0,.698,.698}
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\definecolor{lightgray}{gray}{0.5}
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% bright ansi colors
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\definecolor{darkgray}{gray}{0.25}
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\definecolor{lightred}{rgb}{1.0,0.39,0.28}
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\definecolor{lightgreen}{rgb}{0.48,0.99,0.0}
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\definecolor{lightblue}{rgb}{0.53,0.81,0.92}
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\definecolor{lightpurple}{rgb}{0.87,0.63,0.87}
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\definecolor{lightcyan}{rgb}{0.5,1.0,0.83}
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% commands and environments needed by pandoc snippets
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% extracted from the output of `pandoc -s`
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\DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}}
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% Add ',fontsize=\small' for more characters per line
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\newenvironment{Shaded}{}{}
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\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{\textbf{{#1}}}}
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\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.56,0.13,0.00}{{#1}}}
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\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{{#1}}}
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\newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{{#1}}}
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\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{{#1}}}
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\newcommand{\CharTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{{#1}}}
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\newcommand{\StringTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{{#1}}}
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\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textit{{#1}}}}
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\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{{#1}}}
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\newcommand{\AlertTok}[1]{\textcolor[rgb]{1.00,0.00,0.00}{\textbf{{#1}}}}
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\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.02,0.16,0.49}{{#1}}}
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\newcommand{\RegionMarkerTok}[1]{{#1}}
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\newcommand{\ErrorTok}[1]{\textcolor[rgb]{1.00,0.00,0.00}{\textbf{{#1}}}}
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\newcommand{\NormalTok}[1]{{#1}}
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\def\br{\hspace*{\fill} \\* }
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\def\gt{>}
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\def\lt{<}
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\makeatletter
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\def\PY@reset{\let\PY@it=\relax \let\PY@bf=\relax%
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\let\PY@ul=\relax \let\PY@tc=\relax%
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\let\PY@bc=\relax \let\PY@ff=\relax}
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\def\PY@tok#1{\csname PY@tok@#1\endcsname}
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\def\PY@toks#1+{\ifx\relax#1\empty\else%
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\PY@tok{#1}\expandafter\PY@toks\fi}
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\def\PY@do#1{\PY@bc{\PY@tc{\PY@ul{%
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\PY@it{\PY@bf{\PY@ff{#1}}}}}}}
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\def\PY#1#2{\PY@reset\PY@toks#1+\relax+\PY@do{#2}}
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\expandafter\def\csname PY@tok@bp\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PY@tok@nd\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.67,0.13,1.00}{##1}}}
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\expandafter\def\csname PY@tok@no\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.53,0.00,0.00}{##1}}}
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\expandafter\def\csname PY@tok@nv\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
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\expandafter\def\csname PY@tok@err\endcsname{\def\PY@bc##1{\setlength{\fboxsep}{0pt}\fcolorbox[rgb]{1.00,0.00,0.00}{1,1,1}{\strut ##1}}}
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\expandafter\def\csname PY@tok@gt\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.27,0.87}{##1}}}
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\expandafter\def\csname PY@tok@kp\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PY@tok@s\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
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\expandafter\def\csname PY@tok@gi\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.63,0.00}{##1}}}
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\expandafter\def\csname PY@tok@si\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.73,0.40,0.53}{##1}}}
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\expandafter\def\csname PY@tok@cs\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
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\expandafter\def\csname PY@tok@m\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
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\expandafter\def\csname PY@tok@vg\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
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\expandafter\def\csname PY@tok@nn\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}}
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\expandafter\def\csname PY@tok@sh\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
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\expandafter\def\csname PY@tok@vi\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
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\expandafter\def\csname PY@tok@ne\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.82,0.25,0.23}{##1}}}
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\expandafter\def\csname PY@tok@gu\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.50,0.00,0.50}{##1}}}
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\expandafter\def\csname PY@tok@nc\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}}
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\expandafter\def\csname PY@tok@sb\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
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\expandafter\def\csname PY@tok@k\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PY@tok@na\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.49,0.56,0.16}{##1}}}
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\expandafter\def\csname PY@tok@kc\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PY@tok@sx\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PY@tok@se\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.73,0.40,0.13}{##1}}}
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\expandafter\def\csname PY@tok@vc\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
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\expandafter\def\csname PY@tok@s1\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
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\expandafter\def\csname PY@tok@kd\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PY@tok@go\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.53,0.53,0.53}{##1}}}
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\expandafter\def\csname PY@tok@ow\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.67,0.13,1.00}{##1}}}
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\expandafter\def\csname PY@tok@nf\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}}
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\expandafter\def\csname PY@tok@gs\endcsname{\let\PY@bf=\textbf}
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\expandafter\def\csname PY@tok@cm\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
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\expandafter\def\csname PY@tok@il\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
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\expandafter\def\csname PY@tok@kt\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.69,0.00,0.25}{##1}}}
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\expandafter\def\csname PY@tok@c1\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
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\expandafter\def\csname PY@tok@mi\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
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\expandafter\def\csname PY@tok@ni\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.60,0.60,0.60}{##1}}}
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\expandafter\def\csname PY@tok@gd\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.63,0.00,0.00}{##1}}}
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\expandafter\def\csname PY@tok@ge\endcsname{\let\PY@it=\textit}
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\expandafter\def\csname PY@tok@nt\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PY@tok@s2\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
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\expandafter\def\csname PY@tok@w\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.73,0.73}{##1}}}
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\expandafter\def\csname PY@tok@cp\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.74,0.48,0.00}{##1}}}
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\expandafter\def\csname PY@tok@nl\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.63,0.63,0.00}{##1}}}
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\expandafter\def\csname PY@tok@ss\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
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\expandafter\def\csname PY@tok@o\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
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\expandafter\def\csname PY@tok@mf\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
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\expandafter\def\csname PY@tok@gp\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.00,0.50}{##1}}}
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\expandafter\def\csname PY@tok@kn\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PY@tok@sc\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
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\expandafter\def\csname PY@tok@mo\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
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\expandafter\def\csname PY@tok@sd\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
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\expandafter\def\csname PY@tok@nb\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PY@tok@gr\endcsname{\def\PY@tc##1{\textcolor[rgb]{1.00,0.00,0.00}{##1}}}
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\expandafter\def\csname PY@tok@kr\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PY@tok@gh\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.00,0.50}{##1}}}
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\expandafter\def\csname PY@tok@c\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
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\expandafter\def\csname PY@tok@mh\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
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\expandafter\def\csname PY@tok@sr\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.40,0.53}{##1}}}
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\def\PYZbs{\char`\\}
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\def\PYZus{\char`\_}
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\def\PYZob{\char`\{}
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\def\PYZcb{\char`\}}
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\def\PYZca{\char`\^}
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\def\PYZam{\char`\&}
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\def\PYZlt{\char`\<}
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\def\PYZgt{\char`\>}
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\def\PYZsh{\char`\#}
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\def\PYZpc{\char`\%}
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\def\PYZdl{\char`\$}
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\def\PYZhy{\char`\-}
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\def\PYZsq{\char`\'}
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\def\PYZdq{\char`\"}
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\def\PYZti{\char`\~}
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\def\PYZat{@}
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\def\PYZlb{[}
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\def\PYZrb{]}
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\makeatother
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% NB prompt colors
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\definecolor{nbframe-border}{rgb}{0.867,0.867,0.867}
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\definecolor{nbframe-bg}{rgb}{0.969,0.969,0.969}
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\definecolor{nbframe-in-prompt}{rgb}{0.0,0.0,0.502}
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\definecolor{nbframe-out-prompt}{rgb}{0.545,0.0,0.0}
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% NB prompt lengths
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\newlength{\inputpadding}
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\setlength{\inputpadding}{0.5em}
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\newlength{\cellleftmargin}
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\setlength{\cellleftmargin}{0.15\linewidth}
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\newlength{\borderthickness}
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\setlength{\borderthickness}{0.4pt}
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\newlength{\smallerfontscale}
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\setlength{\smallerfontscale}{9.5pt}
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% NB prompt font size
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\def\smaller{\fontsize{\smallerfontscale}{\smallerfontscale}\selectfont}
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% Define a background layer, in which the nb prompt shape is drawn
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\pgfdeclarelayer{background}
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\pgfsetlayers{background,main}
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\usetikzlibrary{calc}
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% define styles for the normal border and the torn border
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\tikzset{
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normal border/.style={draw=nbframe-border, fill=nbframe-bg,
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rectangle, rounded corners=2.5pt, line width=\borderthickness},
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torn border/.style={draw=white, fill=white, line width=\borderthickness}}
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% Macro to draw the shape behind the text, when it fits completly in the
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% page
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\def\notebookcellframe#1{%
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\tikz{%
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\node[inner sep=\inputpadding] (A) {#1};% Draw the text of the node
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\begin{pgfonlayer}{background}% Draw the shape behind
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\fill[normal border]%
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(A.south east) -- ($(A.south west)+(\cellleftmargin,0)$) --
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($(A.north west)+(\cellleftmargin,0)$) -- (A.north east) -- cycle;
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\end{pgfonlayer}}}%
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% Macro to draw the shape, when the text will continue in next page
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\def\notebookcellframetop#1{%
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\tikz{%
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\node[inner sep=\inputpadding] (A) {#1}; % Draw the text of the node
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\begin{pgfonlayer}{background}
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\fill[normal border] % Draw the ``complete shape'' behind
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(A.south east) -- ($(A.south west)+(\cellleftmargin,0)$) --
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($(A.north west)+(\cellleftmargin,0)$) -- (A.north east) -- cycle;
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\fill[torn border] % Add the torn lower border
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($(A.south east)-(0,.1)$) -- ($(A.south west)+(\cellleftmargin,-.1)$) --
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($(A.south west)+(\cellleftmargin,.1)$) -- ($(A.south east)+(0,.1)$) -- cycle;
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\end{pgfonlayer}}}
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% Macro to draw the shape, when the text continues from previous page
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\def\notebookcellframebottom#1{%
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\tikz{%
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\node[inner sep=\inputpadding] (A) {#1}; % Draw the text of the node
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\begin{pgfonlayer}{background}
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\fill[normal border] % Draw the ``complete shape'' behind
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(A.south east) -- ($(A.south west)+(\cellleftmargin,0)$) --
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($(A.north west)+(\cellleftmargin,0)$) -- (A.north east) -- cycle;
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\fill[torn border] % Add the torn upper border
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($(A.north east)-(0,.1)$) -- ($(A.north west)+(\cellleftmargin,-.1)$) --
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($(A.north west)+(\cellleftmargin,.1)$) -- ($(A.north east)+(0,.1)$) -- cycle;
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\end{pgfonlayer}}}
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% Macro to draw the shape, when both the text continues from previous page
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% and it will continue in next page
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\def\notebookcellframemiddle#1{%
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\tikz{%
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\node[inner sep=\inputpadding] (A) {#1}; % Draw the text of the node
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\begin{pgfonlayer}{background}
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\fill[normal border] % Draw the ``complete shape'' behind
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(A.south east) -- ($(A.south west)+(\cellleftmargin,0)$) --
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($(A.north west)+(\cellleftmargin,0)$) -- (A.north east) -- cycle;
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\fill[torn border] % Add the torn lower border
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($(A.south east)-(0,.1)$) -- ($(A.south west)+(\cellleftmargin,-.1)$) --
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($(A.south west)+(\cellleftmargin,.1)$) -- ($(A.south east)+(0,.1)$) -- cycle;
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\fill[torn border] % Add the torn upper border
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($(A.north east)-(0,.1)$) -- ($(A.north west)+(\cellleftmargin,-.1)$) --
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($(A.north west)+(\cellleftmargin,.1)$) -- ($(A.north east)+(0,.1)$) -- cycle;
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\end{pgfonlayer}}}
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% Define the environment which puts the frame
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% In this case, the environment also accepts an argument with an optional
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% title (which defaults to ``Example'', which is typeset in a box overlaid
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% on the top border
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\newenvironment{notebookcell}[1][0]{%
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\def\FrameCommand{\notebookcellframe}%
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\def\FirstFrameCommand{\notebookcellframetop}%
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\def\LastFrameCommand{\notebookcellframebottom}%
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\def\MidFrameCommand{\notebookcellframemiddle}%
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\par\vspace{1\baselineskip}%
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\MakeFramed {\FrameRestore}%
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\noindent\tikz\node[inner sep=0em] at ($(A.north west)-(0,0)$) {%
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\begin{minipage}{\cellleftmargin}%
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\hfill%
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{\smaller%
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\tt%
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\color{nbframe-in-prompt}%
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In[#1]:}%
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\hspace{\inputpadding}%
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\hspace{2pt}%
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\hspace{3pt}%
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\end{minipage}%%
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}; \par}%
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{\endMakeFramed}
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\sloppy
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\hypersetup{
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breaklinks=true, % so long urls are correctly broken across lines
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colorlinks=true,
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urlcolor=blue,
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linkcolor=darkorange,
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citecolor=darkgreen,
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}
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\geometry{verbose,tmargin=1in,bmargin=1in,lmargin=1in,rmargin=1in}
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\title{Introduction to Scientific Computing in Python}
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\author{Robert Johansson}
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\begin{document}
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\maketitle
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\tableofcontents
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\newpage
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\input{Lecture-0-Scientific-Computing-with-Python}
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\newpage
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\input{Lecture-1-Introduction-to-Python-Programming}
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\newpage
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\input{Lecture-2-Numpy}
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\newpage
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\input{Lecture-3-Scipy}
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\newpage
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\input{Lecture-4-Matplotlib}
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\newpage
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\input{Lecture-5-Sympy}
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\newpage
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\input{Lecture-6A-Fortran-and-C}
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\newpage
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\input{Lecture-6B-HPC}
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\newpage
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\input{Lecture-7-Revision-Control-Software}
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\end{document}

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