diff --git a/src/ga4gh/vrs/extras/vcf_annotation.py b/src/ga4gh/vrs/extras/vcf_annotation.py index 4a21b563..98b570b8 100644 --- a/src/ga4gh/vrs/extras/vcf_annotation.py +++ b/src/ga4gh/vrs/extras/vcf_annotation.py @@ -40,7 +40,7 @@ def _cli() -> None: logging.basicConfig( filename="vrs-python-annotate.log", level=logging.INFO, - format='%(asctime)s - %(name)s - %(levelname)s - %(message)s' + format="%(asctime)s - %(name)s - %(levelname)s - %(message)s" ) @@ -62,7 +62,7 @@ def _log_level_option(func: Callable) -> Callable: :param func: incoming click command :return: same command, wrapped with log level option """ - def _set_log_level(ctx: dict, param: str, value: _LogLevel) -> None: + def _set_log_level(ctx: dict, param: str, value: _LogLevel) -> None: # pylint: disable=unused-argument level_map = { _LogLevel.DEBUG: logging.DEBUG, _LogLevel.INFO: logging.INFO, @@ -73,9 +73,9 @@ def _set_log_level(ctx: dict, param: str, value: _LogLevel) -> None: logging.getLogger(__name__).setLevel(level_map[value]) wrapped_func = click.option( - '--log_level', + "--log_level", type=click.Choice([v.value for v in _LogLevel.__members__.values()]), - default='info', + default="info", help="Set the logging level.", callback=_set_log_level, expose_value=False,