User:Timothee Flutre/Notebook/Postdoc/2012/05/16

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(About programming: add benchmark + other small changes)
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** [http://www.tldp.org/LDP/abs/html/ Advanced Bash-Scripting Guide] by Mendel Cooper  
** [http://www.tldp.org/LDP/abs/html/ Advanced Bash-Scripting Guide] by Mendel Cooper  
** my own page on [http://openwetware.org/wiki/User:Timothee_Flutre/Notebook/Postdoc/2011/11/07 R]
** my own page on [http://openwetware.org/wiki/User:Timothee_Flutre/Notebook/Postdoc/2011/11/07 R]
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** [http://www.cplusplus.com/doc/tutorial/ C++ tutorial], a must-read
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** [http://www.cplusplus.com/doc/tutorial/ C++ tutorial], a must-read (and a [http://www.mycplus.com/featured-articles/best-free-programming-courses-online/ list] of the best free C/C++ resources online)
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** [http://scipy-lectures.github.io/ Python tutorial] for scientists
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** Python tutorials: for [http://www.tutorialspoint.com/python/index.htm everyone], [http://scipy-lectures.github.io/ scientists] ([http://www.sam.math.ethz.ch/~raoulb/teaching/PythonTutorial/index.html another]), [http://www.jchr.be/python/manuel.htm in French]
** [http://resrc.io/list/10/list-of-free-programming-books/ list] of free programming books
** [http://resrc.io/list/10/list-of-free-programming-books/ list] of free programming books
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** '''R''': download the file [http://github.com/timflutre/quantgen/blob/master/myprogram.R myprogram.R]
** '''R''': download the file [http://github.com/timflutre/quantgen/blob/master/myprogram.R myprogram.R]
** '''Bash''': download the file [http://github.com/timflutre/quantgen/blob/master/myprogram.bash myprogram.bash]
** '''Bash''': download the file [http://github.com/timflutre/quantgen/blob/master/myprogram.bash myprogram.bash]
 +
** '''Latex-Beamer''': download the file [http://github.com/timflutre/quantgen/blob/master/myslides.tex myslides.tex]
* '''Language-independent user documentation''': I'm a firm believer that it is necessary to add some user documentation, even  minimal, to any program. An easy way to do this is to simply generate such documentation from the "help" message, as long as it is "properly" formatted (see [http://www.gnu.org/s/help2man/ help2man]). The following commands work for any programming language:
* '''Language-independent user documentation''': I'm a firm believer that it is necessary to add some user documentation, even  minimal, to any program. An easy way to do this is to simply generate such documentation from the "help" message, as long as it is "properly" formatted (see [http://www.gnu.org/s/help2man/ help2man]). The following commands work for any programming language:
  <nowiki>
  <nowiki>
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help2man -o myprogram.man ./myprogram
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help2man -N -o myprogram.man ./myprogram
man ./myprogram.man
man ./myprogram.man
groff -mandoc myprogram.man > myprogram.ps
groff -mandoc myprogram.man > myprogram.ps
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** via the command-line: [http://man7.org/linux/man-pages/man1/time.1.html time] (see also [https://github.com/jhclark/memusg memusg])
** via the command-line: [http://man7.org/linux/man-pages/man1/time.1.html time] (see also [https://github.com/jhclark/memusg memusg])
** in R: [http://cran.r-project.org/web/packages/rbenchmark/index.html rbenchmark]
** in R: [http://cran.r-project.org/web/packages/rbenchmark/index.html rbenchmark]
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* '''Latex-Beamer''': it is assumed that the code below is copied into a file named "mypresentation.tex" and that several packages are already installed. The current directory is also assumed to contain a sub-directory named "figures" in which are saved all picture files included in the presentation. In the future, I should have a longer look at Karl Broman's [http://kbroman.wordpress.com/2013/10/07/better-looking-latexbeamer-slides/ post], and try [http://sourceforge.net/projects/qpdfpresenter/ QPdfPresenter].
 
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<nowiki>
 
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% Copyright (C) 2012 Timothee Flutre.
 
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\documentclass{beamer}
 
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\usepackage{amsmath}
 
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\usepackage{bm} % to have mathematical symbols in bold
 
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\usepackage{hyperref}
 
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\hypersetup{colorlinks, linkcolor=black, urlcolor=gray}
 
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\usepackage{multirow}
 
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\usepackage{tikz}
 
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\usepackage[francais]{babel}
 
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\usepackage[utf8]{inputenc}
 
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\graphicspath{{./figures/}}
 
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%-----------------------------------------------------------------------------
 
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\setbeamertemplate{caption}[numbered]
 
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\setbeamerfont{caption}{size=\scriptsize}
 
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\setbeamertemplate{navigation symbols}{}
 
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\setbeamercolor{alerted text}{fg=purple}
 
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\setbeamertemplate{footline}
 
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{
 
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  \leavevmode
 
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  \hbox{
 
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    \hspace*{-0.06cm}
 
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    \begin{beamercolorbox}[wd=.2\paperwidth,ht=2.25ex,dp=1ex,center]{author in head/foot}
 
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      \usebeamerfont{author in head/foot}\insertshortauthor \hspace*{1em} \insertshortinstitute
 
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    \end{beamercolorbox}
 
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    \begin{beamercolorbox}[wd=.50\paperwidth,ht=2.25ex,dp=1ex,center]{section in head/foot}
 
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      \usebeamerfont{section in head/foot}\insertshorttitle
 
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    \end{beamercolorbox}
 
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    \begin{beamercolorbox}[wd=.27\paperwidth,ht=2.25ex,dp=1ex,right]{section in head/foot}%
 
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      \usebeamerfont{section in head/foot}\insertshortdate{}\hspace*{2em}
 
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      \insertframenumber{} / \inserttotalframenumber\hspace*{2ex}
 
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    \end{beamercolorbox}
 
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  }
 
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  \vskip0pt
 
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}
 
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\AtBeginSection[]
 
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{
 
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  \begin{frame}
 
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    \frametitle{Outline}
 
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    \addtocounter{framenumber}{-1}
 
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    \tableofcontents[currentsection]
 
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  \end{frame}
 
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}
 
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%-----------------------------------------------------------------------------
 
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\title[Short title]{Long title}
 
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\author[T. Flutre]{Timoth\'{e}e Flutre}
 
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\institute[Short affiliation]{Long affiliation}
 
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\date{\today}
 
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begin{document}
 
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\begin{frame}
 
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\titlepage
 
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\end{frame}                                                                                                                     
 
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\begin{frame}
 
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\frametitle{Outline}
 
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\tableofcontents
 
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\end{frame}
 
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\section{First section}
 
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\begin{frame}
 
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\frametitle{I.1.}
 
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\begin{itemize}
 
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\item
 
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\end{itemize}
 
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\end{frame}
 
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\section{Second section}
 
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\begin{frame}
 
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\frametitle{II.1.}
 
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\begin{center}
 
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%\includegraphics[width=0.95\textwidth,height=0.90\textheight,keepaspectratio=true]{myplot}%
 
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\end{center}
 
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\end{frame}
 
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end{document}
 
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</nowiki>
 
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Revision as of 08:52, 19 February 2014

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About programming

  • Templates: it is always rewarding on the long term to start any piece of computer software with a minimum amount of generic code (command-line options, help message, license, usage of gzipped files, running time, etc). But it's a pain to write all this every time, right? And often we know how to do something in one language but not in another. So below are my typical templates for any C++/Python/R/Bash program, as well as Beamer presentation.
  • Language-independent user documentation: I'm a firm believer that it is necessary to add some user documentation, even minimal, to any program. An easy way to do this is to simply generate such documentation from the "help" message, as long as it is "properly" formatted (see help2man). The following commands work for any programming language:
help2man -N -o myprogram.man ./myprogram
man ./myprogram.man
groff -mandoc myprogram.man > myprogram.ps
ps2pdf myprogram.ps myprogram.pdf


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