Difference between revisions of "User:Timothee Flutre/Notebook/Postdoc/2012/05/16"

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(Autocreate 2012/05/16 Entry for User:Timothee_Flutre/Notebook/Postdoc)
 
(Typical templates for Python scripts, C++ programs and others: upload code on github + refactor)
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<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->
 
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==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]
 +
** [http://www.cplusplus.com/doc/tutorial/ C++ tutorial]
 +
 +
* '''Program templates''': it is always rewarding on the long term to start any piece of computer software with a minimum amount of generic code (verbose, command-line options, help message, license, 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.py myprogram.R]
 +
** '''Bash''': download the file [http://github.com/timflutre/quantgen/blob/master/myprogram.py 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:
 +
 +
<nowiki>
 +
help2man -o myprogram.man ./myprogram
 +
man ./myprogram.man
 +
groff -mandoc myprogram.man > myprogram.ps
 +
ps2pdf myprogram.ps myprogram.pdf
 +
</nowiki>
 +
 +
* '''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.
 +
 +
<nowiki>
 +
% 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}
 +
</nowiki>
  
 
<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->
 
<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->

Revision as of 14:13, 11 October 2013

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About programming

  • Program templates: it is always rewarding on the long term to start any piece of computer software with a minimum amount of generic code (verbose, command-line options, help message, license, 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.
% 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}