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

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* '''Resources''': most of the time, it's not necessary to buy a book, search online instead!
* '''Resources''': most of the time, it's not necessary to buy a book, search online instead!
** [http://software-carpentry.org/ Software Carpentry]
** [http://software-carpentry.org/ Software Carpentry] to learn about tests, versioning, Makefile, regular expressions, etc
** [http://www.cplusplus.com/doc/tutorial/ C++ tutorial]
** [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)
** Python tutorials: for [http://www.tutorialspoint.com/python/index.htm everyone] ([http://anandology.com/python-practice-book/index.html another]), [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], [https://packaging.python.org/en/latest/index.html packaging]
** [http://resrc.io/list/10/list-of-free-programming-books/ list] of free programming books


* '''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.
* '''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].
** '''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]
** '''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]
** '''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.py 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]
** '''org-mode''': download the file [http://github.com/timflutre/quantgen/blob/master/myreadme.org myreadme.org]


* '''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>
help2man -o myprogram.man ./myprogram
help2man -N -o myprogram.man ./myprogram
man ./myprogram.man
man ./myprogram.man
groff -mandoc myprogram.man > myprogram.ps
groff -mandoc myprogram.man > myprogram.ps
Line 27: Line 33:
</nowiki>
</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.
* '''Benchmarking''':
 
** via the command-line: [http://man7.org/linux/man-pages/man1/time.1.html time] (see also [https://github.com/jhclark/memusg memusg])
<nowiki>
** in R: [http://cran.r-project.org/web/packages/rbenchmark/index.html rbenchmark]
% 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>


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Revision as of 15:05, 1 July 2015

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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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