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(Typical templates for Python scripts, C++ programs and others: use getopt in bash instead of getopts)
(About programming: add list free c++ courses)
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<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->
 
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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++ program, Beamer presentation, Bash script, etc.
+
* '''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].
<nowiki>
+
** '''Python''': download the file [http://github.com/timflutre/quantgen/blob/master/myprogram.py myprogram.py]
#!/usr/bin/env python
+
** '''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]
# 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
 
  
 
+
* '''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:
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()
 
</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, along with the corresponding header <nowiki>utils.h</nowiki>.
 
  
 
  <nowiki>
 
  <nowiki>
/** \file myprogram.cpp
+
help2man -o myprogram.man ./myprogram
*
+
man ./myprogram.man
*  `myprogram' does this and that.
+
groff -mandoc myprogram.man > myprogram.ps
*  Copyright (C) 2011,2012 Timothee Flutre
+
ps2pdf myprogram.ps myprogram.pdf
*
 
*  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;
 
}
 
 
</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>, 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>.
+
* '''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]
#!/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
+
* '''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].
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
 
</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>
 
  <nowiki>
% Author: Timothée Flutre
+
% Copyright (C) 2012 Timothee Flutre.
  
 
\documentclass{beamer}
 
\documentclass{beamer}
Line 479: 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}