User:Timothee Flutre/Notebook/Postdoc/2012/05/16

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<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->
-
==Typical templates for Python scripts and C++ programs==
+
==Typical templates for Python scripts, C++ programs and others==
-
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.
+
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++ program, Beamer presentation, Bash script, etc.
 +
 
 +
* '''Easy 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>
* '''Python''': it is assumed that the code below is copied into a file named "MyClass.py".
* '''Python''': it is assumed that the code below is copied into a file named "MyClass.py".
Line 15: Line 24:
#!/usr/bin/env python
#!/usr/bin/env python
-
# Author: Timothee Flutre
 
-
# License: GPL-3
 
# Aim: does this and that
# Aim: does this and that
-
# help2man -o MyClass.man ./MyClass.py
+
# choose between:
-
# groff -mandoc MyClass.man > MyClass.ps
+
# Author: Timothee Flutre
 +
# Not copyrighted -- provided to the public domain
 +
# or:
 +
# Copyright (C) 2011-2013 Timothee Flutre
 +
# License: GPLv3+
import sys
import sys
Line 52: Line 63:
          
          
     def version(self):
     def version(self):
-
         msg = "%s 0.1\n" % os.path.basename(sys.argv[0])
+
         msg = "%s 1.0\n" % os.path.basename(sys.argv[0])
         msg += "\n"
         msg += "\n"
 +
        msg += "Written by Timothee Flutre.\n"
 +
        msg += "\n"
 +
# choose between:
 +
        msg += "Not copyrighted -- provided to the public domain\n"
 +
# or:
 +
        msg += "Copyright (C) 2011-2013 Timothee Flutre.\n"
         msg += "License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>\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 += "This is free software; see the source for copying conditions.  There is NO\n"
Line 69: Line 86:
             sys.exit(2)
             sys.exit(2)
         for o, a in opts:
         for o, a in opts:
-
             if o in ("-h", "--help"):
+
             if o == "-h" or o == "--help":
                 self.help()
                 self.help()
                 sys.exit(0)
                 sys.exit(0)
-
             elif o in ("-V", "--version"):
+
             elif o == "-V" or o == "--version":
                 self.version()
                 self.version()
                 sys.exit(0)
                 sys.exit(0)
-
             elif o in ("-v", "--verbose"):
+
             elif o == "-v" or o == "--verbose":
                 self.verbose = int(a)
                 self.verbose = int(a)
-
             elif o in ("-i"):
+
             elif o == "-i":
                 self.input = a
                 self.input = a
             else:
             else:
Line 85: Line 102:
     def checkAttributes(self):
     def checkAttributes(self):
         if self.input == "":
         if self.input == "":
-
             msg = "ERROR: missing required argument -i"
+
             msg = "ERROR: missing compulsory option -i"
 +
            sys.stderr.write("%s\n\n" % msg)
 +
            self.help()
 +
            sys.exit(1)
 +
        if not os.path.exists(self.input):
 +
            msg = "ERROR: can't find '%s'" % self.input
             sys.stderr.write("%s\n\n" % msg)
             sys.stderr.write("%s\n\n" % msg)
             self.help()
             self.help()
Line 95: Line 117:
          
          
         if self.verbose > 0:
         if self.verbose > 0:
-
            msg = "START %s" % time.strftime("%Y-%m-%d %H:%M:%S")
 
             startTime = time.time()
             startTime = time.time()
 +
            msg = "START %s %s" % (os.path.basename(sys.argv[0]),
 +
                                  time.strftime("%Y-%m-%d %H:%M:%S"))
 +
            msg += "\ncmd-line: %s" % ' '.join(sys.argv)
             print msg; sys.stdout.flush()
             print msg; sys.stdout.flush()
              
              
Line 102: Line 126:
          
          
         if self.verbose > 0:
         if self.verbose > 0:
-
             msg = "END %s" % time.strftime("%Y-%m-%d %H:%M:%S")
+
             msg = "END %s %s" % (os.path.basename(sys.argv[0]),
 +
                                time.strftime("%Y-%m-%d %H:%M:%S"))
             endTime = time.time()
             endTime = time.time()
             runLength = datetime.timedelta(seconds=
             runLength = datetime.timedelta(seconds=
Line 116: Line 141:
</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.
+
* '''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, along with the corresponding header <nowiki>utils.h</nowiki>.
  <nowiki>
  <nowiki>
Line 122: Line 147:
  *
  *
  *  `myprogram' does this and that.
  *  `myprogram' does this and that.
-
  *  Copyright (C) 2011,2012 Timothee Flutre
+
  *  Copyright (C) 2011-2013 Timothee Flutre
  *
  *
  *  This program is free software: you can redistribute it and/or modify
  *  This program is free software: you can redistribute it and/or modify
Line 137: Line 162:
  *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
  *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
  *
  *
-
  *  g++ -Wall -fopenmp -O3 myprogram.cpp -lgsl -lgslcblas -o myprogram
+
  *  g++ -Wall -g utils.cpp myprogram.cpp -lgsl -lgslcblas -lz -o myprogram
-
*  help2man -o .man ./myprogram
+
-
*  groff -mandoc myprogram.man > myprogram.ps
+
*/
*/
Line 150: Line 173:
using namespace std;
using namespace std;
-
#include "utils.cpp"
+
#include "utils.h"
/** \brief Display the help on stdout.
/** \brief Display the help on stdout.
Line 179: Line 202:
void version (char ** argv)
void version (char ** argv)
{
{
-
   cout << argv[0] << " 0.1" << endl
+
   cout << argv[0] << " 1.0" << endl
       << endl
       << endl
-
       << "Copyright (C) 2011,2012 T. Flutre." << endl
+
       << "Copyright (C) 2011-2013 Timothee Flutre." << endl
       << "License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>" << 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
       << "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
       << "warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." << endl
       << endl
       << endl
-
       << "Written by T. Flutre." << endl;
+
       << "Written by Timothee Flutre." << endl;
}
}
Line 193: Line 216:
  */
  */
void
void
-
parse_args (
+
parseArgs (
   int argc,
   int argc,
   char ** argv,
   char ** argv,
Line 200: Line 223:
{
{
   int c = 0;
   int c = 0;
-
   while (1)
+
   while (true)
   {
   {
     static struct option long_options[] =
     static struct option long_options[] =
Line 242: Line 265:
   if (input.empty())
   if (input.empty())
   {
   {
-
     fprintf (stderr, "ERROR: missing input (-i).\n\n");
+
    printCmdLine (argc, argv);
 +
     fprintf (stderr, "ERROR: missing compulsory option -i\n\n");
     help (argv);
     help (argv);
     exit (1);
     exit (1);
Line 248: Line 272:
   if (! doesFileExist (input))
   if (! doesFileExist (input))
   {
   {
-
     fprintf (stderr, "ERROR: can't find file '%s'.\n\n", input.c_str());
+
    printCmdLine (argc, argv);
 +
     fprintf (stderr, "ERROR: can't find '%s'\n\n", input.c_str());
     help (argv);
     help (argv);
     exit (1);
     exit (1);
Line 259: Line 284:
   int verbose = 1;
   int verbose = 1;
    
    
-
   parse_args (argc, argv, input, verbose);
+
   parseArgs (argc, argv, input, verbose);
    
    
   time_t startRawTime, endRawTime;
   time_t startRawTime, endRawTime;
Line 266: Line 291:
     time (&startRawTime);
     time (&startRawTime);
     cout << "START " << argv[0] << " (" << time2string (startRawTime) << ")"
     cout << "START " << argv[0] << " (" << time2string (startRawTime) << ")"
-
         << endl;
+
         << endl
 +
        << "compiled -> " << __DATE__ << " " << __TIME__
 +
        << endl << flush;
 +
    printCmdLine (argc, argv);
   }
   }
    
    
Line 274: Line 302:
   {
   {
     time (&endRawTime);
     time (&endRawTime);
-
     cout << "END " << argv[0] << " (" << time2string (endRawTime)
+
     cout << "END " << argv[0] << " (" << time2string (endRawTime) << ")"
-
         << ": elapsed -> " << elapsedTime(startRawTime, endRawTime)
+
        << endl
-
         << ")" << endl;
+
         << "elapsed -> " << elapsedTime(startRawTime, endRawTime)
 +
        << endl
 +
         << "max.mem -> " << getMaxMemUsedByProcess () << " kB"
 +
        << endl;
   }
   }
    
    
   return EXIT_SUCCESS;
   return EXIT_SUCCESS;
}
}
 +
</nowiki>
 +
 +
* '''Bash''': sometimes it's easier to write a script in bash rather than in python. This is especially the case when one wants to use pipes, eg. <nowiki>zcat data.txt.gz | awk '{print $1}'</nowiki>, or when one wants to use a [http://en.wikipedia.org/wiki/Glob_%28programming%29 glob] to pass multiple files to the script, eg. <nowiki>./myscript.bash -i "input*.txt"</nowiki>.
 +
 +
<nowiki>
 +
#!/usr/bin/env bash
 +
 +
# Aim: does this and that
 +
# choose between:
 +
# Author: Timothee Flutre
 +
# Not copyrighted -- provided to the public domain
 +
# or:
 +
# Copyright (C) 2011-2013 Timothee Flutre
 +
# License: GPLv3+
 +
 +
function help () {
 +
    msg="\`${0##*/}' does this and that.\n"
 +
    msg+="\n"
 +
    msg+="Usage: ${0##*/} [OPTIONS] ...\n"
 +
    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, --in\tinput\n"
 +
    msg+="\n"
 +
    msg+="Examples:\n"
 +
    msg+="  ${0##*/} -i <input>\n"
 +
    echo -e "$msg"
 +
}
 +
 +
function version () {
 +
    msg="${0##*/} 1.0\n"
 +
    msg+="\n"
 +
    msg+="Written by Timothee Flutre.\n"
 +
    msg+="\n"
 +
# choose between:
 +
    msg += "Not copyrighted -- provided to the public domain\n"
 +
# or:
 +
    msg+="Copyright (C) 2011-2013 Timothee Flutre.\n"
 +
    msg+="License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>\n"
 +
    msg+="This is free software; see the source for copying conditions.  There is NO\n"
 +
    msg+="warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n"
 +
    echo -e "$msg"
 +
}
 +
 +
# http://www.linuxjournal.com/content/use-date-command-measure-elapsed-time
 +
function timer () {
 +
    if [[ $# -eq 0 ]]; then
 +
        echo $(date '+%s')
 +
    else
 +
        local startRawTime=$1
 +
        endRawTime=$(date '+%s')
 +
        if [[ -z "$startRawTime" ]]; then startRawTime=$endRawTime; fi
 +
        elapsed=$((endRawTime - startRawTime)) # in sec
 +
        nbDays=$((elapsed / 86400))
 +
        nbHours=$(((elapsed / 3600) % 24))
 +
        nbMins=$(((elapsed / 60) % 60))
 +
        nbSecs=$((elapsed % 60))
 +
        printf "%01dd %01dh %01dm %01ds" $nbDays $nbHours $nbMins $nbSecs
 +
    fi
 +
}
 +
 +
function parseArgs () {
 +
    TEMP=`getopt -o hVv:i: -l help,version,verbose:,in: \
 +
        -n "$0" -- "$@"`
 +
    if [ $? != 0 ] ; then echo "ERROR: getopt failed" >&2 ; exit 1 ; fi
 +
    eval set -- "$TEMP"
 +
    while true; do
 +
        case "$1" in
 +
            -h|--help) help; exit 0; shift;;
 +
            -V|--version) version; exit 0; shift;;
 +
            -v|--verbose) verbose=$2; shift 2;;
 +
            -i|--in) input=$2; shift 2;;
 +
            --) shift; break;;
 +
            *) echo "ERROR: options parsing failed"; exit 1;;
 +
        esac
 +
    done
 +
    if [ -z "${input}" ]; then
 +
        echo -e "ERROR: missing compulsory option -i\n"
 +
        help
 +
        exit 1
 +
    fi
 +
    if [ ! -f "${input}" ]; then
 +
        echo -e "ERROR: can't find '${input}'\n"
 +
        help
 +
        exit 1
 +
    fi
 +
}
 +
 +
verbose=1
 +
input=""
 +
parseArgs "$@"
 +
 +
if [ $verbose -gt "0" ]; then
 +
    startTime=$(timer)
 +
    msg="START ${0##*/} $(date +"%Y-%m-%d") $(date +"%H:%M:%S")"
 +
    msg+="\ncmd-line: $0 "$@ # comment if an option takes a glob as argument
 +
    echo -e $msg
 +
fi
 +
 +
# ... specific code ...
 +
 +
if [ $verbose -gt "0" ]; then
 +
    msg="END ${0##*/} $(date +"%Y-%m-%d") $(date +"%H:%M:%S")"
 +
    msg+=" ($(timer startTime))"
 +
    echo $msg
 +
fi
 +
</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>
</nowiki>

Revision as of 14:30, 31 January 2013

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Typical templates for Python scripts, C++ programs and others

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++ program, Beamer presentation, Bash script, etc.

  • Easy 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

  • Python: it is assumed that the code below is copied into a file named "MyClass.py".
#!/usr/bin/env python

# Aim: does this and that
# choose between:
# Author: Timothee Flutre
# Not copyrighted -- provided to the public domain
# or:
# Copyright (C) 2011-2013 Timothee Flutre
# License: GPLv3+

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 1.0\n" % os.path.basename(sys.argv[0])
        msg += "\n"
        msg += "Written by Timothee Flutre.\n"
        msg += "\n"
# choose between:
        msg += "Not copyrighted -- provided to the public domain\n"
# or:
        msg += "Copyright (C) 2011-2013 Timothee Flutre.\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 compulsory option -i"
            sys.stderr.write("%s\n\n" % msg)
            self.help()
            sys.exit(1)
        if not os.path.exists(self.input):
            msg = "ERROR: can't find '%s'" % self.input
            sys.stderr.write("%s\n\n" % msg)
            self.help()
            sys.exit(1)
            
            
    def run(self):
        self.checkAttributes()
        
        if self.verbose > 0:
            startTime = time.time()
            msg = "START %s %s" % (os.path.basename(sys.argv[0]),
                                   time.strftime("%Y-%m-%d %H:%M:%S"))
            msg += "\ncmd-line: %s" % ' '.join(sys.argv)
            print msg; sys.stdout.flush()
            
        # ... specific code ...
        
        if self.verbose > 0:
            msg = "END %s %s" % (os.path.basename(sys.argv[0]),
                                 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()

  • C++: it is assumed that the code below is copied into a file named "myprogram.cpp" and that the file "utils.cpp" is present in the same directory, along with the corresponding header utils.h.
/** \file myprogram.cpp
 *
 *  `myprogram' does this and that.
 *  Copyright (C) 2011-2013 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 -g utils.cpp myprogram.cpp -lgsl -lgslcblas -lz -o myprogram
*/

#include <cmath>
#include <ctime>
#include <getopt.h>

#include <iostream>
#include <string>
using namespace std;

#include "utils.h"

/** \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] << " 1.0" << endl
       << endl
       << "Copyright (C) 2011-2013 Timothee 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 Timothee Flutre." << endl;
}

/** \brief Parse the command-line arguments and check the values of the 
 *  compulsory ones.
 */
void
parseArgs (
  int argc,
  char ** argv,
  string & input,
  int & verbose)
{
  int c = 0;
  while (true)
  {
    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())
  {
    printCmdLine (argc, argv);
    fprintf (stderr, "ERROR: missing compulsory option -i\n\n");
    help (argv);
    exit (1);
  }
  if (! doesFileExist (input))
  {
    printCmdLine (argc, argv);
    fprintf (stderr, "ERROR: can't find '%s'\n\n", input.c_str());
    help (argv);
    exit (1);
  }
}

int main (int argc, char ** argv)
{
  string input;
  int verbose = 1;
  
  parseArgs (argc, argv, input, verbose);
  
  time_t startRawTime, endRawTime;
  if (verbose > 0)
  {
    time (&startRawTime);
    cout << "START " << argv[0] << " (" << time2string (startRawTime) << ")"
         << endl
         << "compiled -> " << __DATE__ << " " << __TIME__
         << endl << flush;
    printCmdLine (argc, argv);
  }
  
  // ... specific code ...
  
  if (verbose > 0)
  {
    time (&endRawTime);
    cout << "END " << argv[0] << " (" << time2string (endRawTime) << ")"
         << endl
         << "elapsed -> " << elapsedTime(startRawTime, endRawTime)
         << endl
         << "max.mem -> " << getMaxMemUsedByProcess () << " kB"
         << endl;
  }
  
  return EXIT_SUCCESS;
}

  • Bash: sometimes it's easier to write a script in bash rather than in python. This is especially the case when one wants to use pipes, eg. zcat data.txt.gz | awk '{print $1}', or when one wants to use a glob to pass multiple files to the script, eg. ./myscript.bash -i "input*.txt".
#!/usr/bin/env bash

# Aim: does this and that
# choose between:
# Author: Timothee Flutre
# Not copyrighted -- provided to the public domain
# or:
# Copyright (C) 2011-2013 Timothee Flutre
# License: GPLv3+

function help () {
    msg="\`${0##*/}' does this and that.\n"
    msg+="\n"
    msg+="Usage: ${0##*/} [OPTIONS] ...\n"
    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, --in\tinput\n"
    msg+="\n"
    msg+="Examples:\n"
    msg+="  ${0##*/} -i <input>\n"
    echo -e "$msg"
}

function version () {
    msg="${0##*/} 1.0\n"
    msg+="\n"
    msg+="Written by Timothee Flutre.\n"
    msg+="\n"
# choose between:
    msg += "Not copyrighted -- provided to the public domain\n"
# or:
    msg+="Copyright (C) 2011-2013 Timothee Flutre.\n"
    msg+="License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>\n"
    msg+="This is free software; see the source for copying conditions.  There is NO\n"
    msg+="warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n"
    echo -e "$msg"
}

# http://www.linuxjournal.com/content/use-date-command-measure-elapsed-time
function timer () {
    if [[ $# -eq 0 ]]; then
        echo $(date '+%s')
    else
        local startRawTime=$1
        endRawTime=$(date '+%s')
        if [[ -z "$startRawTime" ]]; then startRawTime=$endRawTime; fi
        elapsed=$((endRawTime - startRawTime)) # in sec
        nbDays=$((elapsed / 86400))
        nbHours=$(((elapsed / 3600) % 24))
        nbMins=$(((elapsed / 60) % 60))
        nbSecs=$((elapsed % 60))
        printf "%01dd %01dh %01dm %01ds" $nbDays $nbHours $nbMins $nbSecs
    fi
}

function parseArgs () {
    TEMP=`getopt -o hVv:i: -l help,version,verbose:,in: \
        -n "$0" -- "$@"`
    if [ $? != 0 ] ; then echo "ERROR: getopt failed" >&2 ; exit 1 ; fi
    eval set -- "$TEMP"
    while true; do
        case "$1" in
            -h|--help) help; exit 0; shift;;
            -V|--version) version; exit 0; shift;;
            -v|--verbose) verbose=$2; shift 2;;
            -i|--in) input=$2; shift 2;;
            --) shift; break;;
            *) echo "ERROR: options parsing failed"; exit 1;;
        esac
    done
    if [ -z "${input}" ]; then
        echo -e "ERROR: missing compulsory option -i\n"
        help
        exit 1
    fi
    if [ ! -f "${input}" ]; then
        echo -e "ERROR: can't find '${input}'\n"
        help
        exit 1
    fi
}

verbose=1
input=""
parseArgs "$@"

if [ $verbose -gt "0" ]; then
    startTime=$(timer)
    msg="START ${0##*/} $(date +"%Y-%m-%d") $(date +"%H:%M:%S")"
    msg+="\ncmd-line: $0 "$@ # comment if an option takes a glob as argument
    echo -e $msg
fi

# ... specific code ...

if [ $verbose -gt "0" ]; then
    msg="END ${0##*/} $(date +"%Y-%m-%d") $(date +"%H:%M:%S")"
    msg+=" ($(timer startTime))"
    echo $msg
fi

  • 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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