diff --git a/isoquant.py b/isoquant.py index f91b1740..0d89a940 100755 --- a/isoquant.py +++ b/isoquant.py @@ -46,7 +46,7 @@ def bool_str(s): return s == 'true' or s == '1' -def parse_args(args=None, namespace=None): +def parse_args(cmd_args=None, namespace=None): parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter) ref_args_group = parser.add_argument_group('Reference data:') input_args_group = parser.add_argument_group('Input data:') @@ -54,7 +54,7 @@ def parse_args(args=None, namespace=None): pipeline_args_group = parser.add_argument_group('Pipeline options:') other_options = parser.add_argument_group("Additional options:") - show_full_help = '--full_help' in sys.argv + show_full_help = '--full_help' in cmd_args def add_additional_option(*args, **kwargs): # show command only with --full-help if not show_full_help: @@ -222,7 +222,7 @@ def add_hidden_option(*args, **kwargs): # show command only with --full-help pass parser.add_argument('--version', '-v', action='version', version='IsoQuant ' + isoquant_version) - args = parser.parse_args(args, namespace) + args = parser.parse_args(cmd_args, namespace) if args.resume: resume_parser = argparse.ArgumentParser(add_help=False) @@ -239,7 +239,7 @@ def add_hidden_option(*args, **kwargs): # show command only with --full-help action='store_true', default=argparse.SUPPRESS) resume_parser.add_argument("--keep_tmp", help="do not remove temporary files in the end", action='store_true', default=argparse.SUPPRESS) - args, unknown_args = resume_parser.parse_known_args(sys.argv[1:]) + args, unknown_args = resume_parser.parse_known_args(cmd_args) if unknown_args: logger.error("You cannot specify options other than --output/--threads/--debug/--low_memory " "with --resume option")