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

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 Revision as of 11:42, 16 May 2012 (view source) (Autocreate 2012/05/16 Entry for User:Timothee_Flutre/Notebook/Postdoc)← Previous diff Revision as of 11:34, 1 January 2014 (view source) (→About programming: add list free c++ courses)Next diff → (42 intermediate revisions not shown.) Line 6: Line 6: | colspan="2"| | colspan="2"| - ==Entry title== + ==About programming== - * Insert content here... + + * '''Resources''': most of the time, it's not necessary to buy a book, search online instead! + ** [http://software-carpentry.org/ Software Carpentry] to learn about tests, versioning, Makefile, regular expressions, etc + ** [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] + ** [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) + ** [http://scipy-lectures.github.io/ Python tutorial] for scientists + ** [http://resrc.io/list/10/list-of-free-programming-books/ list] of free programming books + + * '''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. + ** '''C++''': download the file [http://github.com/timflutre/quantgen/blob/master/myprogram.cpp myprogram.cpp], as well as [http://github.com/timflutre/quantgen/blob/master/utils_io.cpp utils_io.cpp] along with its header [http://github.com/timflutre/quantgen/blob/master/utils_io.hpp utils_io.hpp]. + ** '''Python''': download the file [http://github.com/timflutre/quantgen/blob/master/myprogram.py myprogram.py] + ** '''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] + + * '''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: + + + help2man -o myprogram.man ./myprogram + man ./myprogram.man + groff -mandoc myprogram.man > myprogram.ps + ps2pdf myprogram.ps myprogram.pdf + + + * '''Benchmarking''': + ** 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] + + * '''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]. + + + % Copyright (C) 2012 Timothee Flutre. + + \documentclass{beamer} + \usepackage{amsmath} + \usepackage{bm} % to have mathematical symbols in bold + \usepackage{hyperref} + \hypersetup{colorlinks, linkcolor=black, urlcolor=gray} + \usepackage{multirow} + \usepackage{tikz} + \usepackage[francais]{babel} + \usepackage[utf8]{inputenc} + + \graphicspath{{./figures/}} + + %----------------------------------------------------------------------------- + + \setbeamertemplate{caption}[numbered] + \setbeamerfont{caption}{size=\scriptsize} + \setbeamertemplate{navigation symbols}{} + \setbeamercolor{alerted text}{fg=purple} + + \setbeamertemplate{footline} + { + \leavevmode + \hbox{ + \hspace*{-0.06cm} + \begin{beamercolorbox}[wd=.2\paperwidth,ht=2.25ex,dp=1ex,center]{author in head/foot} + \usebeamerfont{author in head/foot}\insertshortauthor \hspace*{1em} \insertshortinstitute + \end{beamercolorbox} + \begin{beamercolorbox}[wd=.50\paperwidth,ht=2.25ex,dp=1ex,center]{section in head/foot} + \usebeamerfont{section in head/foot}\insertshorttitle + \end{beamercolorbox} + \begin{beamercolorbox}[wd=.27\paperwidth,ht=2.25ex,dp=1ex,right]{section in head/foot}% + \usebeamerfont{section in head/foot}\insertshortdate{}\hspace*{2em} + \insertframenumber{} / \inserttotalframenumber\hspace*{2ex} + \end{beamercolorbox} + } + \vskip0pt + } + + \AtBeginSection[] + { + \begin{frame} + \frametitle{Outline} + \addtocounter{framenumber}{-1} + \tableofcontents[currentsection] + \end{frame} + } + + %----------------------------------------------------------------------------- + + \title[Short title]{Long title} + \author[T. Flutre]{Timoth\'{e}e Flutre} + \institute[Short affiliation]{Long affiliation} + \date{\today} + + begin{document} + + \begin{frame} + \titlepage + \end{frame} + + \begin{frame} + \frametitle{Outline} + \tableofcontents + \end{frame} + + \section{First section} + \begin{frame} + \frametitle{I.1.} + \begin{itemize} + \item + \end{itemize} + \end{frame} + + \section{Second section} + + \begin{frame} + \frametitle{II.1.} + \begin{center} + %\includegraphics[width=0.95\textwidth,height=0.90\textheight,keepaspectratio=true]{myplot}% + \end{center} + \end{frame} + + end{document} +

## Revision as of 11:34, 1 January 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 -o myprogram.man ./myprogram
man ./myprogram.man
groff -mandoc myprogram.man > myprogram.ps
ps2pdf myprogram.ps myprogram.pdf


• 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 post, and try QPdfPresenter.
% Copyright (C) 2012 Timothee Flutre.

\documentclass{beamer}
\usepackage{amsmath}
\usepackage{bm} % to have mathematical symbols in bold
\usepackage{hyperref}
\hypersetup{colorlinks, linkcolor=black, urlcolor=gray}
\usepackage{multirow}
\usepackage{tikz}
\usepackage[francais]{babel}
\usepackage[utf8]{inputenc}

\graphicspath{{./figures/}}

%-----------------------------------------------------------------------------

\setbeamertemplate{caption}[numbered]
\setbeamerfont{caption}{size=\scriptsize}
\setbeamertemplate{navigation symbols}{}
\setbeamercolor{alerted text}{fg=purple}

\setbeamertemplate{footline}
{
\leavevmode
\hbox{
\hspace*{-0.06cm}
\begin{beamercolorbox}[wd=.2\paperwidth,ht=2.25ex,dp=1ex,center]{author in head/foot}
\usebeamerfont{author in head/foot}\insertshortauthor \hspace*{1em} \insertshortinstitute
\end{beamercolorbox}
\begin{beamercolorbox}[wd=.50\paperwidth,ht=2.25ex,dp=1ex,center]{section in head/foot}
\usebeamerfont{section in head/foot}\insertshorttitle
\end{beamercolorbox}
\begin{beamercolorbox}[wd=.27\paperwidth,ht=2.25ex,dp=1ex,right]{section in head/foot}%
\usebeamerfont{section in head/foot}\insertshortdate{}\hspace*{2em}
\insertframenumber{} / \inserttotalframenumber\hspace*{2ex}
\end{beamercolorbox}
}
\vskip0pt
}

\AtBeginSection[]
{
\begin{frame}
\frametitle{Outline}
\addtocounter{framenumber}{-1}
\tableofcontents[currentsection]
\end{frame}
}

%-----------------------------------------------------------------------------

\title[Short title]{Long title}
\author[T. Flutre]{Timoth\'{e}e Flutre}
\institute[Short affiliation]{Long affiliation}
\date{\today}

begin{document}

\begin{frame}
\titlepage
\end{frame}

\begin{frame}
\frametitle{Outline}
\tableofcontents
\end{frame}

\section{First section}
\begin{frame}
\frametitle{I.1.}
\begin{itemize}
\item
\end{itemize}
\end{frame}

\section{Second section}

\begin{frame}
\frametitle{II.1.}
\begin{center}
%\includegraphics[width=0.95\textwidth,height=0.90\textheight,keepaspectratio=true]{myplot}%
\end{center}
\end{frame}

end{document}