config.py

from itertools import chain, starmap
from shlex import quote as shquote
from typing import Dict, Union

flatten = chain.from_iterable


def augur_options(opts: Dict[str, Union[str, list, None]]) -> str:
    """
    Converts a dictionary of command-line config options to a string suitable
    for use in an ``augur`` invocation.

    Values are appropriately quoted/escaped:

    >>> augur_options({"--min-length": 9000, "--include-where": "state = WA"})
    "--min-length 9000 --include-where 'state = WA'"

    Flags are keys where the value is ``True``:

    >>> augur_options({"--exclude-all": True})
    '--exclude-all'

    Keys where the value is ``False`` or ``None`` are ignored:

    >>> augur_options({"--exclude-all": False})
    ''
    >>> augur_options({"--exclude-all": None})
    ''

    Multiple values for an option use a list:

    >>> augur_options({"--metadata-id-columns": ["strain", "seq name", "seq id", "$id"]})
    "--metadata-id-columns strain 'seq name' 'seq id' '$id'"
    """
    def optval(opt, val):
        if isinstance(val, list):
            return shquote(opt) + " " + " ".join(map(shquote, map(str, val)))
        elif val is True:
            return shquote(opt)
        elif val in {False, None}:
            return None
        else:
            return shquote(opt) + " " + shquote(str(val))

    return " ".join(filter(None, starmap(optval, opts.items())))