User:Timothee Flutre/Notebook/Postdoc/2012/05/16: Difference between revisions
From OpenWetWare
m (fix beamer display) |
(→About programming: add list free c++ courses) |
||
(27 intermediate revisions by the same user not shown) | |||
Line 6: | Line 6: | ||
| colspan="2"| | | colspan="2"| | ||
<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### --> | <!-- ##### DO NOT edit above this line unless you know what you are doing. ##### --> | ||
== | ==About programming== | ||
* '''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: | |||
<nowiki> | <nowiki> | ||
help2man -o myprogram.man ./myprogram | |||
man ./myprogram.man | |||
groff -mandoc myprogram.man > myprogram.ps | |||
ps2pdf myprogram.ps myprogram.pdf | |||
</nowiki> | </nowiki> | ||
* ''' | * '''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]. | |||
* '''Latex-Beamer''': it is assumed that the code below is copied into a file named "mypresentation.tex" | |||
<nowiki> | <nowiki> | ||
% | % Copyright (C) 2012 Timothee Flutre. | ||
\documentclass{beamer} | \documentclass{beamer} | ||
Line 385: | Line 124: | ||
end{document} | end{document} | ||
</nowiki> | </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 08:34, 1 January 2014
Project name | <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page <html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html> </html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html> |
About programming
help2man -o myprogram.man ./myprogram man ./myprogram.man groff -mandoc myprogram.man > myprogram.ps ps2pdf myprogram.ps myprogram.pdf
% 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} |