From d0e80b810ba04ced933bfe11c88f15b6ff251aa5 Mon Sep 17 00:00:00 2001 From: Nathan Baker Date: Mon, 18 May 2020 16:29:39 -0700 Subject: [PATCH] Handle multiple additions of same argument. APBS and PROPKA add the same arguments. --- propka/lib.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/propka/lib.py b/propka/lib.py index 31b2880..dff4bee 100644 --- a/propka/lib.py +++ b/propka/lib.py @@ -185,8 +185,12 @@ def build_parser(parser=None): group.add_argument("-p", "--parameters", dest="parameters", default=pkg_resources.resource_filename(__name__, "propka.cfg"), help="set the parameter file [%(default)s]") - group.add_argument("--log-level", choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"], - help="logging level verbosity", default="INFO") + try: + group.add_argument("--log-level", choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"], + help="logging level verbosity", default="INFO") + except argparse.ArgumentError: + # It is possible that --log-level has already been set by APBS + pass group.add_argument("-o", "--pH", dest="pH", type=float, default=7.0, help="setting pH-value used in e.g. stability calculations [7.0]") group.add_argument("-w", "--window", dest="window", nargs=3, type=float,