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

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==Typical templates for Python scripts and C++ programs==
==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 and C++ programs.
* '''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]


* '''Python''': it is assumed that the code below is copied into a file named "MyClass.py".
* '''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]


    #!/usr/bin/env python
* '''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:
   
    # Author: Timothee Flutre
    # License: GPL-3
    # 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 in ("-h", "--help"):
                    self.help()
                    sys.exit(0)
                elif o in ("-V", "--version"):
                    self.version()
                    sys.exit(0)
                elif o in ("-v", "--verbose"):
                    self.verbose = int(a)
                elif o in ("-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>
help2man -o myprogram.man ./myprogram
man ./myprogram.man
groff -mandoc myprogram.man > myprogram.ps
ps2pdf myprogram.ps myprogram.pdf
</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.
* '''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>
  <nowiki>
/** \file myprogram.cpp
% Copyright (C) 2012 Timothee Flutre.
*
*  `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>
\documentclass{beamer}
#include <ctime>
\usepackage{amsmath}
#include <getopt.h>
\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}


#include <iostream>
\graphicspath{{./figures/}}
#include <string>
using namespace std;


#include "utils.cpp"
%-----------------------------------------------------------------------------


/** \brief Display the help on stdout.
\setbeamertemplate{caption}[numbered]
*/
\setbeamerfont{caption}{size=\scriptsize}
void help (char ** argv)
\setbeamertemplate{navigation symbols}{}
\setbeamercolor{alerted text}{fg=purple}
 
\setbeamertemplate{footline}
{
{
   cout << "`" << argv[0] << "'"
   \leavevmode
      << " does this and that." << endl
  \hbox{
      << endl
    \hspace*{-0.06cm}
      << "Usage: " << argv[0] << " [OPTIONS] ..." << endl
    \begin{beamercolorbox}[wd=.2\paperwidth,ht=2.25ex,dp=1ex,center]{author in head/foot}
      << endl
      \usebeamerfont{author in head/foot}\insertshortauthor \hspace*{1em} \insertshortinstitute
      << "Options:" << endl
    \end{beamercolorbox}
      << "  -h, --help\tdisplay the help and exit" << endl
    \begin{beamercolorbox}[wd=.50\paperwidth,ht=2.25ex,dp=1ex,center]{section in head/foot}
      << "  -V, --version\toutput version information and exit" << endl
      \usebeamerfont{section in head/foot}\insertshorttitle
      << "  -v, --verbose\tverbosity level (0/default=1/2/3)" << endl
    \end{beamercolorbox}
      << "  -i, --in\tinput" << endl
    \begin{beamercolorbox}[wd=.27\paperwidth,ht=2.25ex,dp=1ex,right]{section in head/foot}%
      << endl
      \usebeamerfont{section in head/foot}\insertshortdate{}\hspace*{2em}
      << "Examples:" << endl
      \insertframenumber{} / \inserttotalframenumber\hspace*{2ex}
      << "  " << argv[0] << " -i <input>" << endl
    \end{beamercolorbox}
      << endl
  }
      << "Remarks:" << endl
  \vskip0pt
      << "  This is my typical template file for C++." << endl
    ;
}
}


/** \brief Display version and license information on stdout.
\AtBeginSection[]
*/
void version (char ** argv)
{
{
   cout << argv[0] << " 0.1" << endl
   \begin{frame}
      << endl
    \frametitle{Outline}
      << "Copyright (C) 2011,2012 T. Flutre." << endl
    \addtocounter{framenumber}{-1}
      << "License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>" << endl
    \tableofcontents[currentsection]
      << "This is free software; see the source for copying conditions.  There is NO" << endl
  \end{frame}
      << "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.
 
*/
\title[Short title]{Long title}
void
\author[T. Flutre]{Timoth\'{e}e Flutre}
parse_args (
\institute[Short affiliation]{Long affiliation}
  int argc,
\date{\today}
  char ** argv,
 
  string & input,
begin{document}
  int & verbose)
 
{
\begin{frame}
  int c = 0;
\titlepage
  while (1)
\end{frame}                                                                                                                      
  {
 
    static struct option long_options[] =
\begin{frame}
      {
\frametitle{Outline}
        {"help", no_argument, 0, 'h'},
\tableofcontents
        {"version", no_argument, 0, 'V'},
\end{frame}
        {"verbose", required_argument, 0, 'v'},
 
        {"input", required_argument, 0, 'i'},
\section{First section}
        {0, 0, 0, 0}
\begin{frame}
      };
\frametitle{I.1.}
    int option_index = 0;
\begin{itemize}
    c = getopt_long (argc, argv, "hVv:i:",
\item
                    long_options, &option_index);
\end{itemize}
    if (c == -1)
\end{frame}
      break;
 
    switch (c)
\section{Second section}
    {
 
    case 0:
\begin{frame}
      if (long_options[option_index].flag != 0)
\frametitle{II.1.}
        break;
\begin{center}
    case 'h':
%\includegraphics[width=0.95\textwidth,height=0.90\textheight,keepaspectratio=true]{myplot}%
      help (argv);
\end{center}
      exit (0);
\end{frame}
    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)
end{document}
{
  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;
  }
 
  // ... specific code ...
 
  if (verbose > 0)
  {
    time (&endRawTime);
    cout << "END " << argv[0] << " (" << time2string (endRawTime)
        << ": elapsed -> " << elapsedTime(startRawTime, endRawTime)
        << ")" << endl;
  }
 
  return EXIT_SUCCESS;
}
</nowiki>
</nowiki>


Revision as of 15:13, 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}


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