sortncx.py (py3 + lxml)

#! /usr/bin/env python3

from lxml import etree as ET
import zipfile as ZIP
import sys
import os

namespaces = {  "opf":"http://www.idpf.org/2007/opf",
        "dc":"http://purl.org/dc/elements/1.1/",
        "ncx":"http://www.daisy.org/z3986/2005/ncx/"
        }

info = {}

def sortncx(file):
    ncx = parseNCX(file)
    navpoints = ncx.xpath(".//ncx:navPoint",namespaces=namespaces)

    counter = 1
    for item in navpoints:
        item.set("playOrder",str(counter))
        counter += 1
    else:
        counter = 1

    ncx = ET.ElementTree(ncx)

    return ET.tostring(ncx)

def parseInfo(file):
    global info
    try:
        f = ZIP.ZipFile(file).read("META-INF/container.xml")
    except KeyError:
        print("The %s file is not a valid OCF." % str(file))
    try:
        m = ET.fromstring(f)
        info["path_to_opf"] = m[0][0].get("full-path")
        root_folder = os.path.dirname(info["path_to_opf"])
    except:
        pass
    opf = ET.fromstring(ZIP.ZipFile(file).read(info["path_to_opf"]))

    id = opf.xpath("//opf:spine",namespaces=namespaces)[0].get("toc")
    expr = "//*[@id='%s']" % id
    info["ncx_name"] = opf.xpath(expr)[0].get("href")
    info["path_to_ncx"] = root_folder + "/" + info["ncx_name"]
    info.pop("ncx_name")

    return info

def parseNCX(file):

    ncx = {}
    ncx = ET.fromstring(ZIP.ZipFile(file).read(parseInfo(file)["path_to_ncx"]))

    return ncx

if __name__ == '__main__':

    info = parseInfo(sys.argv[1])
    sorted_ncx = sortncx(sys.argv[1])
    epub = ZIP.ZipFile(sys.argv[1],"a")
    epub.writestr(info["path_to_ncx"],sorted_ncx)
    epub.close()