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

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</nowiki>
</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>.
* '''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>
  <nowiki>
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     msg+="\n"
     msg+="\n"
     msg+="Options:\n"
     msg+="Options:\n"
     msg+="  -h\tdisplay the help and exit\n"
     msg+="  -h, --help\t\tdisplay the help and exit\n"
     msg+="  -V\toutput version information and exit\n"
     msg+="  -V, --version\t\toutput version information and exit\n"
     msg+="  -v\tverbosity level (0/default=1/2/3)\n"
     msg+="  -v, --verbose\t\tverbosity level (0/default=1/2/3)\n"
     msg+="  -i\tinput\n"
     msg+="  -i, --in\t\tinput\n"
     msg+="\n"
     msg+="\n"
     msg+="Examples:\n"
     msg+="Examples:\n"
Line 350: Line 350:


function parseArgs () {
function parseArgs () {
     while getopts ":hVv:i:" opt; do
     TEMP=`getopt -o hVv:p:f:c:g:o:i: -l help,version,verbose: \
         case $opt in
        -n "$0" -- "$@"`
             h) help; exit 0;;
    if [ $? != 0 ] ; then echo "ERROR: getopt failed" >&2 ; exit 1 ; fi
             V) version; exit 0;;
    eval set -- "$TEMP"
             v) verbose=$OPTARG;;
    while true; do
             i) input=$OPTARG;;
         case "$1" in
             \?) echo "invalid option -$OPTARG"; exit 1;;
             -h|--help) help; exit 0; shift;;
             :) echo "option -$OPTARG requires an argument"; exit 1;;
             -V|--version) version; exit 0; shift;;
             -v|--verbose) verbose=$2; shift;;
             -i|--in) input=$2; shift 2;;
             --) shift; break;;
             *) echo "ERROR: options parsing failed"; exit 1;;
         esac
         esac
     done
     done
    shift $(($OPTIND - 1))
     if [ "x${input}" == "x" ]; then
     if [ "x${input}" == "x" ]; then
         echo "ERROR: missing compulsory option -i"; echo; help; exit 1
         echo "ERROR: missing compulsory option -i"; echo; help; exit 1

Revision as of 07:12, 27 September 2012

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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.

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

# 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 == "-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:
            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()
  • 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) 2011,2012 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 -g utils.cpp myprogram.cpp -lgsl -lgslcblas -lz -o myprogram
 *  help2man -o myprogram.man ./myprogram
 *  groff -mandoc myprogram.man > myprogram.ps
*/

#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] << " " << __DATE__ << " " << __TIME__ << 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
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

# Author: Timothee Flutre
# License: GPL-3
# Aim: does this and that

function help () {
    msg="\`$0' does this and that.\n"
    msg+="\n"
    msg+="Usage: $0 [OPTIONS] ...\n"
    msg+="\n"
    msg+="Options:\n"
    msg+="  -h, --help\t\tdisplay the help and exit\n"
    msg+="  -V, --version\t\toutput version information and exit\n"
    msg+="  -v, --verbose\t\tverbosity level (0/default=1/2/3)\n"
    msg+="  -i, --in\t\tinput\n"
    msg+="\n"
    msg+="Examples:\n"
    msg+="  $0 -i <input>\n"
    echo -e $msg
}

function version () {
    msg="$0 0.1\n"
    msg+="\n"
    msg+="Copyright (C) 2012 T. 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"
    msg+="\n"
    msg+="Written by T. Flutre.\n"
    echo -e $msg
}

# source http://www.linuxjournal.com/content/use-date-command-measure-elapsed-time
function timer () {
    if [[ $# -eq 0 ]]; then
        echo $(date '+%s')
    else
        local  stime=$1
        etime=$(date '+%s')
        if [[ -z "$stime" ]]; then stime=$etime; fi
        dt=$((etime - stime))
        ds=$((dt % 60))
        dm=$(((dt / 60) % 60))
        dh=$((dt / 3600))
        printf '%d:%02d:%02d' $dh $dm $ds
    fi
}

function parseArgs () {
    TEMP=`getopt -o hVv:p:f:c:g:o:i: -l help,version,verbose: \
        -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;;
            -i|--in) input=$2; shift 2;;
            --) shift; break;;
            *) echo "ERROR: options parsing failed"; exit 1;;
        esac
    done
    if [ "x${input}" == "x" ]; then
        echo "ERROR: missing compulsory option -i"; echo; help; exit 1
    fi
    if [ ! -f ${input} ]; then
        echo "ERROR: can't find '${input}'"; exit 1
    fi
}

verbose=1
input=""
parseArgs $@

if [ $verbose -gt "0" ]; then
    printf "START %s %s\n" $(date +"%Y-%m-%d") $(date +"%H:%M:%S")
    startTime=$(timer)
fi

# ... specific code ...
sleep 1

if [ $verbose -gt "0" ]; then
    printf "END %s %s" $(date +"%Y-%m-%d") $(date +"%H:%M:%S")
    printf " (%s)\n" $(timer startTime)
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.
% Author: Timothée 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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