Python script to sort the bibitem entries according to the citation order in the text. Useful when one has for some reason to not use bibtex and .bib files. Usage is as `python bibitem-sorter.py file.tex sorted_file.tex`

bibitem-sorter.py

import argparse
import os
import sys
import re

def printBold(msg):
    HEADER = '\033[95m'
    BOLD = '\033[1m'
    print(HEADER + BOLD + msg + '\x1b[0m')


def main():
    parser = argparse.ArgumentParser()
    parser.add_argument('path', type=str)
    parser.add_argument('output_path', type=str)
    args = parser.parse_args()

    # read from file
    with open(args.path, 'r') as fp:
        text = fp.read()

    # backslashes are fucking annoying
    text = re.sub('\\\\', '\\\\\\\\', text)

    # extract text inside thebibliography environment
    matcher = re.compile(r'\\\\begin{thebibliography}.*\n'
                         r'([\s\S]*)'
                         r'\\\\end{thebibliography}')
    bibitems_text = matcher.findall(text)[0]

    matcher = re.compile(r'\\\\cite{([^}]+)}')
    cites = []
    for match in matcher.findall(text):
        if match in cites:
            continue
        if ',' in match:
            matches = [x.strip() for x in match.split(',')]
            for smatch in matches:
                if smatch not in cites:
                    cites.append(smatch)
            continue
        cites.append(match)

    bibitems = []
    matcher = re.compile(r'\\\\bibitem{([^}]+)}\s*((?:.*\n)*?)(?=\n)')
    for match in matcher.findall(bibitems_text):
        bibitems.append(match)

    # check that everything has a reference and that every reference has been
    # cited
    bibitems_refs = [item[0] for item in bibitems]
    unused_bibitems = []
    for cite in cites:
        if cite not in bibitems_refs:
            raise ValueError('Citing missing reference: {}.'.format(cite))
    for bibitem in bibitems:
        if bibitem[0] not in cites:
            # raise ValueError('Uncited reference: {}.'.format(bibitem[0]))
            printBold('WARNING: Uncited reference: {}.'.format(bibitem[0]))
            unused_bibitems.append(bibitem)
    for unused_bibitem in unused_bibitems:
        del bibitems_refs[bibitems.index(unused_bibitem)]
        del bibitems[bibitems.index(unused_bibitem)]

    # check if already sorted
    same = cites == [bibitem[0] for bibitem in bibitems]
    if same:
        printBold('References are sorted')
    else:
        printBold('References are not sorted, proceeding to sort them.')

    # sort references
    sorted_bibitems = sorted(bibitems, key=lambda x: cites.index(x[0]))
    sorted_bibitems += unused_bibitems

    output_bibitem_text = r'\n\n'
    for bibitem in sorted_bibitems:
        output_bibitem_text += r'\\\\bibitem{{{0}}}\n{1}\n'.format(
            bibitem[0], bibitem[1])
    output_bibitem_text += r'\n'
    # do the replacement
    output_text = re.sub(
        (r'(?<=\\\\begin{thebibliography})'
         r'(\S*)[\s\S]*'
         r'(?=\\\\end{thebibliography})'),
        r'\1\n' + output_bibitem_text,
        text
    )

    # convert back @ to \
    output_text = re.sub('\\\\\\\\', '\\\\', output_text)

    # save result
    printBold('Done. Saving results to {}.'.format(args.output_path))
    with open(args.output_path, 'w') as fp:
        fp.write(output_text)


if __name__ == '__main__':
    main()