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

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(Typical templates for Python scripts, C++ programs and others: improve R script)
(Typical templates for Python scripts, C++ programs and others: update C++ template)
Line 174: Line 174:
#include "utils.h"
#include "utils.h"
 +
 +
#ifndef VERSION
 +
#define VERSION "1.0"
 +
#endif
/** \brief Display the help on stdout.
/** \brief Display the help on stdout.
Line 188: Line 192:
       << "  -V, --version\toutput version information and exit" << endl
       << "  -V, --version\toutput version information and exit" << endl
       << "  -v, --verbose\tverbosity level (0/default=1/2/3)" << endl
       << "  -v, --verbose\tverbosity level (0/default=1/2/3)" << endl
-
       << " -i, --in\tinput" << endl
+
       << "     --in\tinput" << endl
       << endl
       << endl
       << "Examples:" << endl
       << "Examples:" << endl
-
       << "  " << argv[0] << " -i <input>" << endl
+
       << "  " << argv[0] << " --in <input>" << endl
       << endl
       << endl
       << "Remarks:" << endl
       << "Remarks:" << endl
Line 202: Line 206:
void version (char ** argv)
void version (char ** argv)
{
{
-
   cout << argv[0] << " 1.0" << endl
+
   cout << argv[0] << " " << VERSION << endl
       << endl
       << endl
       << "Copyright (C) 2011-2013 Timothee Flutre." << endl
       << "Copyright (C) 2011-2013 Timothee Flutre." << endl
Line 230: Line 234:
         {"version", no_argument, 0, 'V'},
         {"version", no_argument, 0, 'V'},
         {"verbose", required_argument, 0, 'v'},
         {"verbose", required_argument, 0, 'v'},
-
         {"input", required_argument, 0, 'i'},
+
         {"in", required_argument, 0, 0},
         {0, 0, 0, 0}
         {0, 0, 0, 0}
       };
       };
     int option_index = 0;
     int option_index = 0;
-
     c = getopt_long (argc, argv, "hVv:i:",
+
     c = getopt_long (argc, argv, "hVv:",
                     long_options, &option_index);
                     long_options, &option_index);
     if (c == -1)
     if (c == -1)
Line 243: Line 247:
       if (long_options[option_index].flag != 0)
       if (long_options[option_index].flag != 0)
         break;
         break;
 +
      if (strcmp(long_options[option_index].name, "in") == 0)
 +
      {
 +
        input = optarg;
 +
        break;
 +
      }
     case 'h':
     case 'h':
       help (argv);
       help (argv);
Line 265: Line 274:
   if (input.empty())
   if (input.empty())
   {
   {
-
     printCmdLine (argc, argv);
+
     getCmdLine (argc, argv);
-
     fprintf (stderr, "ERROR: missing compulsory option -i\n\n");
+
     fprintf (stderr, "ERROR: missing compulsory option --in\n\n");
     help (argv);
     help (argv);
     exit (1);
     exit (1);
Line 272: Line 281:
   if (! doesFileExist (input))
   if (! doesFileExist (input))
   {
   {
-
     printCmdLine (argc, argv);
+
     getCmdLine (argc, argv);
     fprintf (stderr, "ERROR: can't find '%s'\n\n", input.c_str());
     fprintf (stderr, "ERROR: can't find '%s'\n\n", input.c_str());
     help (argv);
     help (argv);
Line 290: Line 299:
   {
   {
     time (&startRawTime);
     time (&startRawTime);
-
     cout << "START " << argv[0] << " (" << time2string (startRawTime) << ")"
+
     cout << "START " << basename(argv[0])
-
         << endl
+
        << " " << getDateTime (startRawTime) << endl
-
        << "compiled -> " << __DATE__ << " " << __TIME__
+
         << "version " << VERSION << " compiled " << __DATE__
-
         << endl << flush;
+
        << " " << __TIME__ << endl
-
    printCmdLine (argc, argv);
+
         << "cmd-line: " << getCmdLine (argc, argv) << endl
 +
        << "cwd: " << getCurrentDirectory() << endl;
 +
    cout << flush;
   }
   }
    
    
Line 302: Line 313:
   {
   {
     time (&endRawTime);
     time (&endRawTime);
-
     cout << "END " << argv[0] << " (" << time2string (endRawTime) << ")"
+
     cout << "END " << basename(argv[0])
-
        << endl
+
        << " " << getDateTime (endRawTime) << endl
-
         << "elapsed -> " << elapsedTime(startRawTime, endRawTime)
+
         << "elapsed -> " << getElapsedTime(startRawTime, endRawTime) << endl
-
        << endl
+
         << "max.mem -> " << getMaxMemUsedByProcess2Str () << endl;
-
         << "max.mem -> " << getMaxMemUsedByProcess () << " kB"
+
-
        << endl;
+
   }
   }
    
    

Revision as of 16:31, 20 March 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\n"
        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"

#ifndef VERSION
#define VERSION "1.0"
#endif

/** \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
       << "      --in\tinput" << endl
       << endl
       << "Examples:" << endl
       << "  " << argv[0] << " --in <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] << " " << VERSION << 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'},
        {"in", required_argument, 0, 0},
        {0, 0, 0, 0}
      };
    int option_index = 0;
    c = getopt_long (argc, argv, "hVv:",
                     long_options, &option_index);
    if (c == -1)
      break;
    switch (c)
    {
    case 0:
      if (long_options[option_index].flag != 0)
        break;
      if (strcmp(long_options[option_index].name, "in") == 0)
      {
        input = optarg;
        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())
  {
    getCmdLine (argc, argv);
    fprintf (stderr, "ERROR: missing compulsory option --in\n\n");
    help (argv);
    exit (1);
  }
  if (! doesFileExist (input))
  {
    getCmdLine (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 " << basename(argv[0])
         << " " << getDateTime (startRawTime) << endl
         << "version " << VERSION << " compiled " << __DATE__
         << " " << __TIME__ << endl
         << "cmd-line: " << getCmdLine (argc, argv) << endl
         << "cwd: " << getCurrentDirectory() << endl;
    cout << flush;
  }
  
  // ... specific code ...
  
  if (verbose > 0)
  {
    time (&endRawTime);
    cout << "END " << basename(argv[0])
         << " " << getDateTime (endRawTime) << endl
         << "elapsed -> " << getElapsedTime(startRawTime, endRawTime) << endl
         << "max.mem -> " << getMaxMemUsedByProcess2Str () << endl;
  }
  
  return EXIT_SUCCESS;
}

  • R:
#!/usr/bin/env Rscript

# 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+

rm(list=ls())
prog.name <- "myscript.R"

help <- function(){
  txt <- paste0("`", prog.name, "' does this and that.\n")
  txt <- paste0(txt, "\nUsage: ", prog.name, " [OPTIONS] ...\n")
  txt <- paste0(txt, "\nOptions:\n")
  txt <- paste0(txt, "  -h, --help\tdisplay the help and exit\n")
  txt <- paste0(txt, "  -V, --version\toutput version information and exit\n")
  txt <- paste0(txt, "  -v, --verbose\tverbosity level (0/default=1/2/3)\n")
  txt <- paste0(txt, "  -i\t\tinput\n")
  message(txt)
}

version <- function(){
  txt <- paste0(prog.name, " 1.0\n")
  txt <- paste0(txt, "\n")
  txt <- paste0(txt, "Written by Timothee Flutre.\n")
  txt <- paste0(txt, "\n")
# choose between:
  txt <- paste0(txt, "Not copyrighted -- provided to the public domain\n")
# or:
  txt <- paste0(txt, "Copyright (C) 2011-2013 Timothee Flutre.\n")
  txt <- paste0(txt, "License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>\n")
  txt <- paste0(txt, "This is free software; see the source for copying conditions.  There is NO\n")
  txt <- paste0(txt, "warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n")
  message(txt)
}

parseArgs <- function(params){
  args <- commandArgs(trailingOnly=TRUE)
  ## print(args)
  
  i <- 0
  while(i < length(args)){ # use "while" loop for options with no argument
    i <- i + 1
    if(args[i] == "-h" || args[i] == "--help"){
      help()
      quit("no", status=0)
    }
    else if(args[i] == "-V" || args[i] == "--version"){
      version()
      quit("no", status=0)
    }
    else if(args[i] == "-v" || args[i] == "--verbose"){
      params$verbose <- as.numeric(args[i+1])
      i <- i + 1
    }
    else if(args[i] == "-i"){
      params$in.file <- args[i+1]
      i <- i + 1
    }
    else
      stop(paste0("unknown option ", args[i]))
  }
  
  if(params$verbose > 0){
    message("parameters:")
    print(params)
  }
  
  return(params)
}

checkParams <- function(params){
  stopifnot(! is.null(params$input),
            file.exists(params$input))
}  

main <- function(){
  params <- list(verbose=1,
                 input=NULL)
  params <- parseArgs(params)
  checkParams(params)
  if(params$verbose > 0)
    message(paste0("START ", prog.name, " (", date(), ")"))
  
  ## ... specific code ...
  
  if(params$verbose > 0)
    message(paste0("END ", prog.name, " (", date(), ")"))
}

system.time(main())
print(object.size(x=lapply(ls(), get)), units="Kb")

  • 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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