Add a suffix to all labels / references in specified latex files, accounting for multiple comma-separated references in a single command as might occur with cleveref.

add_ref_suffix.py

#!/usr/bin/env python
import sys
import argparse
import re

LABEL_REGEX = r'label\{([:\w]+)\}'
REF_REGEX = r'ref\{([:\w,]+)\}'


def _append_if_unchanged(ref, suffix):
    if ref.endswith(':' + suffix):
        return ref  # unchanged
    else:
        return '{}:{}'.format(ref, suffix)


def make_ref_replace_callback(suffix):
    def _ref_replace_callback(m):
        refs = m.group(1).split(',')
        refs = ','.join(map(
            lambda ref: _append_if_unchanged(ref, suffix), refs))
        return r'ref{%s}' % refs
    return _ref_replace_callback


def main():
    label_regex = re.compile(LABEL_REGEX)
    ref_regex = re.compile(REF_REGEX)
    parser = argparse.ArgumentParser(
            description='Append suffix to all references.')
    parser.add_argument('--suffix', required=True,
                        help='Suffix to append to all labels / refs.')
    parser.add_argument('--files', nargs='+', required=True,
                        help='Files to search + replace.')
    parser.add_argument('--backup', help='File extension for backup',
                        default=None)
    args = parser.parse_args()
    ref_replace_callback = make_ref_replace_callback(args.suffix)
    for fname in args.files:
        with open(fname, 'r') as f:
            contents = f.read()
        label_repl = r'label{\1:%s}' % args.suffix
        new_contents = re.sub(label_regex, label_repl, contents)
        new_contents = re.sub(ref_regex, ref_replace_callback, new_contents)
        if args.backup is not None:
            with open(fname + '.' + args.backup, 'w') as f:
                f.write(contents)
        with open(fname, 'w') as f:
            f.write(new_contents)
    return 0


if __name__ == "__main__":
    sys.exit(main())

Example usage:
python add_ref_suffix.py --suffix chp1 --files *.tex