Which is the best way to allow configuration options be overridden at the command line in Python?

I just discovered you can do this with argparse.ArgumentParser.parse_known_args(). Start by using parse_known_args() to parse a configuration file from the commandline, then read it with ConfigParser and set the defaults, and then parse the rest of the options with parse_args(). This will allow you to have a default value, override that with a configuration file and then override that with a commandline option. E.g.:

Default with no user input:

$ ./argparse-partial.py
Option is "default"

Default from configuration file:

$ cat argparse-partial.config 
[Defaults]
option=Hello world!
$ ./argparse-partial.py -c argparse-partial.config 
Option is "Hello world!"

Default from configuration file, overridden by commandline:

$ ./argparse-partial.py -c argparse-partial.config --option override
Option is "override"

argprase-partial.py follows. It is slightly complicated to handle -h for help properly.

import argparse
import ConfigParser
import sys

def main(argv=None):
    # Do argv default this way, as doing it in the functional
    # declaration sets it at compile time.
    if argv is None:
        argv = sys.argv

    # Parse any conf_file specification
    # We make this parser with add_help=False so that
    # it doesn't parse -h and print help.
    conf_parser = argparse.ArgumentParser(
        description=__doc__, # printed with -h/--help
        # Don't mess with format of description
        formatter_class=argparse.RawDescriptionHelpFormatter,
        # Turn off help, so we print all options in response to -h
        add_help=False
        )
    conf_parser.add_argument("-c", "--conf_file",
                        help="Specify config file", metavar="FILE")
    args, remaining_argv = conf_parser.parse_known_args()

    defaults = { "option":"default" }

    if args.conf_file:
        config = ConfigParser.SafeConfigParser()
        config.read([args.conf_file])
        defaults.update(dict(config.items("Defaults")))

    # Parse rest of arguments
    # Don't suppress add_help here so it will handle -h
    parser = argparse.ArgumentParser(
        # Inherit options from config_parser
        parents=[conf_parser]
        )
    parser.set_defaults(**defaults)
    parser.add_argument("--option")
    args = parser.parse_args(remaining_argv)
    print "Option is \"{}\"".format(args.option)
    return(0)

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