#! /usr/bin/env python
# Original author Nicholas Kim, modified by Yan Pashkovsky
# New license - GPL v3
import sys
import time
from PyPDF2 import utils, PdfFileReader, PdfFileWriter

def get_cmdline_arguments():
    """Retrieve command line arguments."""

    from optparse import OptionParser

    usage_string = "%prog [-o output_name] file1, file2 [, ...]"

    parser = OptionParser(usage_string)
    parser.add_option(
        "-o", "--output",
        dest="output_filename",
        default=time.strftime("output_%Y%m%d_%H%M%S"),
        help="specify output filename (exclude .pdf extension); default is current date/time stamp"
    )

    options, args = parser.parse_args()
    if len(args) < 2:
        parser.print_help()
        sys.exit(1)
    return options, args

def main():
    options, filenames = get_cmdline_arguments()
    output_pdf_name = options.output_filename + ".pdf"
    files_to_merge = []

    # get PDF files
    for f in filenames:
        try:
            next_pdf_file = PdfFileReader(open(f, "rb"))
        except(utils.PdfReadError):
            print >>sys.stderr, "%s is not a valid PDF file." % f
            sys.exit(1)
        except(IOError):
            print >>sys.stderr, "%s could not be found." % f
            sys.exit(1)
        else:
            files_to_merge.append(next_pdf_file)

    # merge page by page
    output_pdf_stream = PdfFileWriter()
    j=0
    k=0
    for f in files_to_merge:
        for i in range(f.numPages):
            output_pdf_stream.addPage(f.getPage(i))
            if i==0:
                output_pdf_stream.addBookmark(str(filenames[k]),j)
            j = j + 1
        k += 1

    # create output pdf file
    try:
        output_pdf_file = open(output_pdf_name, "wb")
        output_pdf_stream.write(output_pdf_file)
    finally:
        output_pdf_file.close()

    print "%s successfully created." % output_pdf_name


if __name__ == "__main__":
    main()

modifiedincludepdf{-}{doc01}{MyDoc1.pdf}

documentclass{article}
usepackage{hyperref}
usepackage{pdfpages}
usepackage[russian,english]{babel}

newcounter{includepdfpage}
newcounter{currentpagecounter}
newcommand{addlabelstoallincludedpages}[1]{
   refstepcounter{includepdfpage}
   stepcounter{currentpagecounter}
   label{#1.thecurrentpagecounter}}
newcommand{modifiedincludepdf}[3]{
    setcounter{currentpagecounter}{0}
    includepdf[pages=#1,pagecommand=addlabelstoallincludedpages{#2}]{#3}}

begin{document}

You can refer to the beginning or to a specific page: \
see page pageref{doc01.1} till pageref{doc02.3}.\

begin{itemize}
  item Here contribution from Grupmate 1 pageref{doc01.1}
  item Here contribution from Grupmate 2 pageref{doc02.1}
end{itemize}

modifiedincludepdf{-}{doc01}{MyDoc1.pdf}
modifiedincludepdf{-}{doc02}{MyDoc2.pdf}

end{document}