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Fix verbosity/logging in PROPKA.

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This commit is contained in:
Nathan Baker
2020-05-14 19:02:11 -07:00
parent 387d0a5664
commit cddda2f515
1 changed files with 4 additions and 13 deletions
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17
propka/lib.py
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@@ -159,7 +159,6 @@ def build_parser(parser=None):
group = parser group = parser
group.add_argument("input_pdb", help="read data from <filename>") group.add_argument("input_pdb", help="read data from <filename>")
group.add_argument("-f", "--file", action="append", dest="filenames", default=[], group.add_argument("-f", "--file", action="append", dest="filenames", default=[],
help="read data from <filename>, i.e. <filename> is added to arguments") help="read data from <filename>, i.e. <filename> is added to arguments")
group.add_argument("-r", "--reference", dest="reference", default="neutral", group.add_argument("-r", "--reference", dest="reference", default="neutral",
@@ -186,10 +185,8 @@ def build_parser(parser=None):
group.add_argument("-p", "--parameters", dest="parameters", group.add_argument("-p", "--parameters", dest="parameters",
default=pkg_resources.resource_filename(__name__, "propka.cfg"), default=pkg_resources.resource_filename(__name__, "propka.cfg"),
help="set the parameter file [%(default)s]") help="set the parameter file [%(default)s]")
group.add_argument("-z", "--verbose", dest="verbosity", action="store_const", group.add_argument("--log-level", choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
const=2, help="output debugging information") help="logging level verbosity", default="INFO")
group.add_argument("-q", "--quiet", dest="verbosity", action="store_const",
const=0, default=1, help="inhibit printing to stdout")
group.add_argument("-o", "--pH", dest="pH", type=float, default=7.0, group.add_argument("-o", "--pH", dest="pH", type=float, default=7.0,
help="setting pH-value used in e.g. stability calculations [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, group.add_argument("-w", "--window", dest="window", nargs=3, type=float,
@@ -262,14 +259,8 @@ def loadOptions(*args):
# Set the no-print variable # Set the no-print variable
if options.verbosity == 0: level = getattr(logging, options.log_level)
logger.setLevel(logging.CRITICAL) logger.setLevel(level)
elif options.verbosity == 1:
logger.setLevel(logging.INFO)
elif options.verbosity == 2:
logger.setLevel(logging.DEBUG)
else:
logger.warning("Invalid verbosity level, using default")
# done! # done!
return options return options