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

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==Typical templates for Python scripts, C++ programs and others==
==About programming==


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? So below are my typical templates for any Python script, C++ programs and others.
* '''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


* '''Python''': it is assumed that the code below is copied into a file named "MyClass.py".
* '''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>
#!/usr/bin/env python
help2man -o myprogram.man ./myprogram
 
man ./myprogram.man
# Author: Timothee Flutre
groff -mandoc myprogram.man > myprogram.ps
# License: GPL-3
ps2pdf myprogram.ps myprogram.pdf
# Aim: does this and that
# help2man -o MyClass.man ./MyClass.py
# groff -mandoc MyClass.man > MyClass.ps
 
import sys
import os
import getopt
import time
import datetime
import math
 
 
class MyClass(object):
   
    def __init__(self):
        self.verbose = 1
        self.input = ""
       
       
    def help(self):
        msg = "`%s' does this and that.\n" % os.path.basename(sys.argv[0])
        msg += "\n"
        msg += "Usage: %s [OPTIONS] ...\n" % os.path.basename(sys.argv[0])
        msg += "\n"
        msg += "Options:\n"
        msg += " -h, --help\tdisplay the help and exit\n"
        msg += " -V, --version\toutput version information and exit\n"
        msg += " -v, --verbose\tverbosity level (0/default=1/2/3)\n"
        msg += " -i\tinput"
        msg += "\n"
        msg += "Examples:\n"
        print msg; sys.stdout.flush()
       
       
    def version(self):
        msg = "%s 0.1\n" % os.path.basename(sys.argv[0])
        msg += "\n"
        msg += "License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>\n"
        msg += "This is free software; see the source for copying conditions.  There is NO\n"
        msg += "warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n"
        print msg; sys.stdout.flush()
       
       
    def setAttributesFromCmdLine(self):
        try:
            opts, args = getopt.getopt( sys.argv[1:], "hVv:i:",
                                        ["help", "version", "verbose="])
        except getopt.GetoptError, err:
            sys.stderr.write("%s\n" % str(err))
            self.help()
            sys.exit(2)
        for o, a in opts:
            if o == "-h" or o == "--help":
                self.help()
                sys.exit(0)
            elif o == "-V" or o == "--version":
                self.version()
                sys.exit(0)
            elif o == "-v" or o == "--verbose":
                self.verbose = int(a)
            elif o == "-i":
                self.input = a
            else:
                assert False, "unhandled option"
               
               
    def checkAttributes(self):
        if self.input == "":
            msg = "ERROR: missing required argument -i"
            sys.stderr.write("%s\n\n" % msg)
            self.help()
            sys.exit(1)
           
           
    def run(self):
        self.checkAttributes()
       
        if self.verbose > 0:
            msg = "START %s" % time.strftime("%Y-%m-%d %H:%M:%S")
            startTime = time.time()
            print msg; sys.stdout.flush()
           
        # ... specific code ...
       
        if self.verbose > 0:
            msg = "END %s" % time.strftime("%Y-%m-%d %H:%M:%S")
            endTime = time.time()
            runLength = datetime.timedelta(seconds=
                                          math.floor(endTime - startTime))
            msg += " (%s)" % str(runLength)
            print msg; sys.stdout.flush()
           
           
if __name__ == "__main__":
    i = MyClass()
    i.setAttributesFromCmdLine()
    i.run()
</nowiki>
</nowiki>


* '''C++''': it is assumed that the code below is copied into a file named "myprogram.cpp" and that the file "[https://github.com/timflutre/quantgen/blob/master/utils.cpp utils.cpp]" is present in the same directory.
* '''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]
/** \file myprogram.cpp
*
*  `myprogram' does this and that.
*  Copyright (C) 2011,2012 Timothee Flutre
*
*  This program is free software: you can redistribute it and/or modify
*  it under the terms of the GNU General Public License as published by
*  the Free Software Foundation, either version 3 of the License, or
*  (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
*  but WITHOUT ANY WARRANTY; without even the implied warranty of
*  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
*  GNU General Public License for more details.
*
*  You should have received a copy of the GNU General Public License
*  along with this program.  If not, see <http://www.gnu.org/licenses/>.
*
*  g++ -Wall -fopenmp -O3 myprogram.cpp -lgsl -lgslcblas -o myprogram
*  help2man -o .man ./myprogram
*  groff -mandoc myprogram.man > myprogram.ps
*/
 
#include <cmath>
#include <ctime>
#include <getopt.h>
 
#include <iostream>
#include <string>
using namespace std;


#include "utils.cpp"
* '''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].
 
/** \brief Display the help on stdout.
*/
void help (char ** argv)
{
  cout << "`" << argv[0] << "'"
      << " does this and that." << endl
      << endl
      << "Usage: " << argv[0] << " [OPTIONS] ..." << endl
      << endl
      << "Options:" << endl
      << "  -h, --help\tdisplay the help and exit" << endl
      << "  -V, --version\toutput version information and exit" << endl
      << "  -v, --verbose\tverbosity level (0/default=1/2/3)" << endl
      << "  -i, --in\tinput" << endl
      << endl
      << "Examples:" << endl
      << "  " << argv[0] << " -i <input>" << endl
      << endl
      << "Remarks:" << endl
      << "  This is my typical template file for C++." << endl
    ;
}
 
/** \brief Display version and license information on stdout.
*/
void version (char ** argv)
{
  cout << argv[0] << " 0.1" << endl
      << endl
      << "Copyright (C) 2011,2012 T. Flutre." << endl
      << "License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>" << endl
      << "This is free software; see the source for copying conditions.  There is NO" << endl
      << "warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." << endl
      << endl
      << "Written by T. Flutre." << endl;
}
 
/** \brief Parse the command-line arguments and check the values of the
*  compulsory ones.
*/
void
parse_args (
  int argc,
  char ** argv,
  string & input,
  int & verbose)
{
  int c = 0;
  while (1)
  {
    static struct option long_options[] =
      {
        {"help", no_argument, 0, 'h'},
        {"version", no_argument, 0, 'V'},
        {"verbose", required_argument, 0, 'v'},
        {"input", required_argument, 0, 'i'},
        {0, 0, 0, 0}
      };
    int option_index = 0;
    c = getopt_long (argc, argv, "hVv:i:",
                    long_options, &option_index);
    if (c == -1)
      break;
    switch (c)
    {
    case 0:
      if (long_options[option_index].flag != 0)
        break;
    case 'h':
      help (argv);
      exit (0);
    case 'V':
      version (argv);
      exit (0);
    case 'v':
      verbose = atoi(optarg);
      break;
    case 'i':
      input = optarg;
      break;
    case '?':
      printf ("\n"); help (argv);
      abort ();
    default:
      printf ("\n"); help (argv);
      abort ();
    }
  }
  if (input.empty())
  {
    fprintf (stderr, "ERROR: missing input (-i).\n\n");
    help (argv);
    exit (1);
  }
  if (! doesFileExist (input))
  {
    fprintf (stderr, "ERROR: can't find file '%s'.\n\n", input.c_str());
    help (argv);
    exit (1);
  }
}
 
int main (int argc, char ** argv)
{
  string input;
  int verbose = 1;
 
  parse_args (argc, argv, input, verbose);
 
  time_t startRawTime, endRawTime;
  if (verbose > 0)
  {
    time (&startRawTime);
    cout << "START " << argv[0] << " (" << time2string (startRawTime) << ")"
        << endl << flush;
  }
 
  // ... specific code ...
 
  if (verbose > 0)
  {
    time (&endRawTime);
    cout << "END " << argv[0] << " (" << time2string (endRawTime)
        << ": elapsed -> " << elapsedTime(startRawTime, endRawTime)
        << ")" << endl;
  }
 
  return EXIT_SUCCESS;
}
</nowiki>
 
* '''Latex-Beamer''': it is assumed that the code below is copied into a file named "mypresentation.tex". Several packages are assumed to be already installed. The current directory is also assumed to contain a directory named "figures" in which are saved all picture files included in the presentation.


  <nowiki>
  <nowiki>
% Author: Timothée Flutre                                                                                                                                  
% Copyright (C) 2012 Timothee Flutre.


\documentclass{beamer}
\documentclass{beamer}
\usepackage{amsmath}
\usepackage{amsmath}
\usepackage{bm} % to have mathematical symbols in bold                                                                                                      
\usepackage{bm} % to have mathematical symbols in bold
\usepackage{hyperref}
\usepackage{hyperref}
\hypersetup{colorlinks, linkcolor=black, urlcolor=gray}
\hypersetup{colorlinks, linkcolor=black, urlcolor=gray}
Line 297: Line 49:
\usepackage[francais]{babel}
\usepackage[francais]{babel}
\usepackage[utf8]{inputenc}
\usepackage[utf8]{inputenc}


\graphicspath{{./figures/}}
\graphicspath{{./figures/}}


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


\setbeamertemplate{caption}[numbered]
\setbeamertemplate{caption}[numbered]
Line 319: Line 70:
       \usebeamerfont{section in head/foot}\insertshorttitle
       \usebeamerfont{section in head/foot}\insertshorttitle
     \end{beamercolorbox}
     \end{beamercolorbox}
     \begin{beamercolorbox}[wd=.27\paperwidth,ht=2.25ex,dp=1ex,right]{section in head/foot}%                                                                
     \begin{beamercolorbox}[wd=.27\paperwidth,ht=2.25ex,dp=1ex,right]{section in head/foot}%
       \usebeamerfont{section in head/foot}\insertshortdate{}\hspace*{2em}
       \usebeamerfont{section in head/foot}\insertshortdate{}\hspace*{2em}
       \insertframenumber{} / \inserttotalframenumber\hspace*{2ex}
       \insertframenumber{} / \inserttotalframenumber\hspace*{2ex}
Line 336: Line 87:
}
}


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


\title[Short title]{Long title}
\title[Short title]{Long title}
Line 345: Line 96:
begin{document}
begin{document}


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


\section{First section}
\section{First section}
\begin{frame}
\begin{frame}
\frametitle{I.1.}
\frametitle{I.1.}
Line 368: Line 118:
\frametitle{II.1.}
\frametitle{II.1.}
\begin{center}
\begin{center}
%\includegraphics[width=0.95\textwidth,height=0.90\textheight,keepaspectratio=true]{myplot}%                                                                      
%\includegraphics[width=0.95\textwidth,height=0.90\textheight,keepaspectratio=true]{myplot}%
\end{center}
\end{center}
\end{frame}
\end{frame}
Line 374: 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

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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}


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