def setupArguments():
"""Setup argument parser for commandline arguments.
and Config file. The priority is (low to high):
Default value, config file value, commandline value
"""
LOGGER_LEVELS = [
"TRACE", "VERBOSE", "DEBUG", "INFO", "NOTICE", "WARNING", "SUPPRESSED",
"ERROR", "CRITICAL", "ALERT", "EMERGENCY"
]
formatter_class = configargparse.RawDescriptionHelpFormatter
p = configargparse.ArgParser(description=DESCRIPTION,
epilog=EXAMPLE_USAGE,
default_config_files=[PROGRAM + ".cfg"],
formatter_class=formatter_class)
p.add("--version",
action="version",
version="%(prog)s {}".format(__version__))
p.add("--config",
required=False,
is_config_file=True,
help="Config file for this program")
p.add("--logger-config",
required=False,
dest="logconfig",
default="./logger.cfg",
type=str,
help="Logger config file for this program")
p.add("--log-level",
metavar="LEVEL",
dest="loglevel",
type=str,
choices=LOGGER_LEVELS,
default="INFO",
help="Sets console log level. Valid Values are " +
', '.join(LOGGER_LEVELS))
p.add('-o',
"--output",
metavar="OUTPUT FILE",
dest="outfile",
type=configargparse.FileType('w'),
default=sys.stdout,
help="Set output to a file")
p.add("-i",
"--input",
metavar="INPUT FILES",
dest="infile",
type=configargparse.FileType('r'),
nargs='+',
help="A list of input files")
return p.parse_args()
def add_yaml_arg(self):
'''
Add the yaml file argument, this is needed for scripts that
parse the model config from yaml files
'''
# yaml configuration file
self.add_argument('yaml_file',
type=configargparse.FileType('r'),
help='neon model specification file')
def _add_optional_group(parser):
parser.add_argument("--entry-class",
type=str,
help="The class to analyze",
default="")
parser.add_argument("--entry-func",
type=str,
help="The top function to analyze in `--entry-class`",
default="Top")
parser.add_argument(
"-o",
type=configargparse.FileType("w"),
help=
"output json file containing analysis result. If not specified, result will dump in stdout",
default=None,
dest="output_file",
)
parser.add_argument(
"--output-statistics",
type=configargparse.FileType("w"),
help="dump conditions statistics gathered and used to solve z3 in json",
default=None,
dest="output_statistics",
)
def add_authentication_group(parser: configargparse.ArgumentParser):
auth_group = parser.add_argument_group(
title="Authentication",
description=clr_extra(
"Authentication details are configured (and can be copied from) AppStore Connect->Users & Access->Keys."
),
)
auth_group.add_argument("--issuer-id", required=True, help="Issuer ID.")
auth_group.add_argument("--key-id", required=True, help="Key ID.")
key_group = auth_group.add_mutually_exclusive_group(required=True)
key_group.add_argument("--key", help="Private Key as a string.")
key_group.add_argument(
"--key-file",
type=configargparse.FileType(mode="r"),
help="Private Key from a filepath.",
)
def parseArguments(self):
self.parser.add('-c', '--config', is_config_file=True,
help='config file path (default is '+",".join(default_cnf_files)+').')
self.parser.add('--master','-M',default=default_master,
help='Name of the master node (default: '+default_master+')'),
self.parser.add('--node','-n',default=default_node,
help='Name of this node (default: '+default_node+')'),
self.parser.add('--machine','-a',default=default_machine,
help='Machine (default :'+default_machine+')'),
self.parser.add('-m','--mqtthost',default=default_host,
help='MQTT host (default :'+default_host+')'),
self.parser.add('--mqttprotocol',default=default_protocol,
help='MQTT protocol (default :'+str(default_protocol)+')'),
self.parser.add('--topic','-t',default=default_sub,
help='MQTT topic to subcribe to for replies from the master (default: '+default_sub+').'),
self.parser.add('--verbose', '-v', action='count', default=0,
help='Verbose on (default off)')
self.parser.add('--debug', '-d', action='count', default=0,
help='Debuging on; implies verbose (default off)')
self.parser.add('--no-mqtt-log', action='count',
help='Disable logging to MQTT log channel (default on)'),
self.parser.add('--no-syslog', action='count',
help='Disable syslogging (defautl on)'),
self.parser.add('-l','--logfile', type=configargparse.FileType('w+'),
help='Append log entries to specified file (default: none)'),
self.parser.add('--pidfile', action='store', default = self.default_pidfile,
help='File to write PID to, (Default: '+self.default_pidfile+').')
self.parser.add('--daemonize', '-b', action='count',
help='Deamonize into the background after startup (default is to stay in the foreground).')
self.cnf = self.parser.parse_args()
def get_parser():
"""Get default arguments."""
parser = configargparse.ArgumentParser(
description="Align text to audio using CTC segmentation."
"using a pre-trained speech recognition model.",
config_file_parser_class=configargparse.YAMLConfigFileParser,
formatter_class=configargparse.ArgumentDefaultsHelpFormatter,
)
# general configuration
parser.add("--config", is_config_file=True, help="Decoding config file path.")
parser.add_argument(
"--ngpu", type=int, default=0, help="Number of GPUs (max. 1 is supported)"
)
parser.add_argument(
"--dtype",
choices=("float16", "float32", "float64"),
default="float32",
help="Float precision (only available in --api v2)",
)
parser.add_argument(
"--backend",
type=str,
default="pytorch",
choices=["pytorch"],
help="Backend library",
)
parser.add_argument("--debugmode", type=int, default=1, help="Debugmode")
parser.add_argument("--verbose", "-V", type=int, default=1, help="Verbose option")
parser.add_argument(
"--preprocess-conf",
type=str,
default=None,
help="The configuration file for the pre-processing",
)
# task related
parser.add_argument(
"--data-json", type=str, help="Json of recognition data for audio and text"
)
parser.add_argument("--utt-text", type=str, help="Text separated into utterances")
# model (parameter) related
parser.add_argument(
"--model", type=str, required=True, help="Model file parameters to read"
)
parser.add_argument(
"--model-conf", type=str, default=None, help="Model config file"
)
parser.add_argument(
"--num-encs", default=1, type=int, help="Number of encoders in the model."
)
# ctc-segmentation related
parser.add_argument(
"--subsampling-factor",
type=int,
default=None,
help="Subsampling factor."
"If the encoder sub-samples its input, the number of frames at the CTC layer is"
" reduced by this factor. For example, a BLSTMP with subsampling 1_2_2_1_1"
" has a subsampling factor of 4.",
)
parser.add_argument(
"--frame-duration",
type=int,
default=None,
help="Non-overlapping duration of a single frame in milliseconds.",
)
parser.add_argument(
"--min-window-size",
type=int,
default=None,
help="Minimum window size considered for utterance.",
)
parser.add_argument(
"--max-window-size",
type=int,
default=None,
help="Maximum window size considered for utterance.",
)
parser.add_argument(
"--use-dict-blank",
type=int,
default=None,
help="Use the Blank character of the model dictionary.",
)
parser.add_argument(
"--output",
type=configargparse.FileType("w"),
required=True,
help="Output segments file",
)
return parser
def _parse_config(args):
def regexp(str_regex):
try:
return re.compile(str_regex)
except re.error as err:
raise configargparse.ArgumentTypeError('Invalid regexp: %r (%s)' %
(str_regex, err.msg))
parser = configargparse.ArgParser(
auto_env_var_prefix='MARGE_',
ignore_unknown_config_file_keys=True, # Don't parse unknown args
config_file_parser_class=configargparse.YAMLConfigFileParser,
formatter_class=configargparse.ArgumentDefaultsRawHelpFormatter,
description=__doc__,
)
parser.add_argument(
'--config-file',
env_var='MARGE_CONFIG_FILE',
type=str,
is_config_file=True,
help='config file path',
)
auth_token_group = parser.add_mutually_exclusive_group(required=True)
auth_token_group.add_argument(
'--auth-token',
type=str,
metavar='TOKEN',
help=
('Your GitLab token.\n'
'DISABLED because passing credentials on the command line is insecure:\n'
'You can still set it via ENV variable or config file, or use "--auth-token-file" flag.\n'
),
)
auth_token_group.add_argument(
'--auth-token-file',
type=configargparse.FileType('rt'),
metavar='FILE',
help='Path to your GitLab token file.\n',
)
parser.add_argument(
'--gitlab-url',
type=str,
required=True,
metavar='URL',
help='Your GitLab instance, e.g. "https://gitlab.example.com".\n',
)
ssh_key_group = parser.add_mutually_exclusive_group(required=True)
ssh_key_group.add_argument(
'--ssh-key',
type=str,
metavar='KEY',
help=
('The private ssh key for marge so it can clone/push.\n'
'DISABLED because passing credentials on the command line is insecure:\n'
'You can still set it via ENV variable or config file, or use "--ssh-key-file" flag.\n'
),
)
ssh_key_group.add_argument(
'--ssh-key-file',
type=str, # because we want a file location, not the content
metavar='FILE',
help='Path to the private ssh key for marge so it can clone/push.\n',
)
parser.add_argument(
'--embargo',
type=interval.IntervalUnion.from_human,
metavar='INTERVAL[,..]',
help=
'Time(s) during which no merging is to take place, e.g. "Friday 1pm - Monday 9am".\n',
)
experimental_group = parser.add_mutually_exclusive_group(required=False)
experimental_group.add_argument(
'--use-merge-strategy',
action='store_true',
help=
('Use git merge instead of git rebase to update the *source* branch (EXPERIMENTAL)\n'
'If you need to use a strict no-rebase workflow (in most cases\n'
'you don\'t want this, even if you configured gitlab to use merge requests\n'
'to use merge commits on the *target* branch (the default).)'),
)
parser.add_argument(
'--add-tested',
action='store_true',
help=
'Add "Tested: marge-bot <$MR_URL>" for the final commit on branch after it passed CI.\n',
)
parser.add_argument(
'--batch',
action='store_true',
help='Enable processing MRs in batches\n',
)
parser.add_argument(
'--add-part-of',
action='store_true',
help='Add "Part-of: <$MR_URL>" to each commit in MR.\n',
)
parser.add_argument(
'--add-reviewers',
action='store_true',
help=
'Add "Reviewed-by: $approver" for each approver of MR to each commit in MR.\n',
)
parser.add_argument(
'--impersonate-approvers',
action='store_true',
help='Marge-bot pushes effectively don\'t change approval status.\n',
)
parser.add_argument(
'--approval-reset-timeout',
type=time_interval,
default='0s',
help=
('How long to wait for approvals to reset after pushing.\n'
'Only useful with the "new commits remove all approvals" option in a project\'s settings.\n'
'This is to handle the potential race condition where approvals don\'t reset in GitLab\n'
'after a force push due to slow processing of the event.\n'),
)
parser.add_argument(
'--project-regexp',
type=regexp,
default='.*',
help=
"Only process projects that match; e.g. 'some_group/.*' or '(?!exclude/me)'.\n",
)
parser.add_argument(
'--ci-timeout',
type=time_interval,
default='15min',
help='How long to wait for CI to pass.\n',
)
parser.add_argument(
'--max-ci-time-in-minutes',
type=int,
default=None,
help='Deprecated; use --ci-timeout.\n',
)
parser.add_argument('--git-timeout',
type=time_interval,
default='120s',
help='How long a single git operation can take.\n')
parser.add_argument(
'--branch-regexp',
type=regexp,
default='.*',
help=
'Only process MRs whose target branches match the given regular expression.\n',
)
parser.add_argument(
'--debug',
action='store_true',
help='Debug logging (includes all HTTP requests etc).\n',
)
config = parser.parse_args(args)
if config.use_merge_strategy and config.batch:
raise MargeBotCliArgError(
'--use-merge-strategy and --batch are currently mutually exclusive'
)
if config.use_merge_strategy and config.add_tested:
raise MargeBotCliArgError(
'--use-merge-strategy and --add-tested are currently mutually exclusive'
)
cli_args = []
# pylint: disable=protected-access
for _, (_, value) in parser._source_to_settings.get(
configargparse._COMMAND_LINE_SOURCE_KEY, {}).items():
cli_args.extend(value)
for bad_arg in ['--auth-token', '--ssh-key']:
if bad_arg in cli_args:
raise MargeBotCliArgError(
'"%s" can only be set via ENV var or config file.' % bad_arg)
return config
default_config_files=[
os.path.join(camsa.root_dir, "utils", "grimm",
"grimm2camsa_points.ini"),
os.path.join(camsa.root_dir, "logging.ini")
])
parser.add_argument(
"grimm",
nargs="+",
help=
"A list of paths to files, that in GRIMM format contain information about scaffold assemblies."
)
parser.add_argument("--o-format", type=str, help="")
parser.add_argument(
"-o",
"--output",
type=configargparse.FileType("wt"),
default=sys.stdout,
help=
"Path to the file, where converted assembly points will be stored.\nDEFAULT: stdout"
)
parser.add_argument("--o-delimiter", default="\t", type=str, help="")
parser.add_argument(
"--no-trim-names",
dest="trim_names",
default=True,
action="store_false",
help=
"A flag to indicate, that genome names from grimm file need not to be trimmed by the first \".\"\nDEFAULT: true"
)
parser.add_argument(
"--trimmer-char",
def parseArguments(self):
self.parser.add('-c',
'--config',
is_config_file=True,
help='config file path (default is ' +
",".join(default_cnf_files) + ').')
self.parser.add('--master',
'-M',
default=default_master,
help='Name of the master node (default: ' +
default_master + ')'),
self.parser.add('--drumbeat',
'-D',
default=default_drumbeat,
help='Name of the drumbeat node (default: ' +
default_drumbeat + ')'),
self.parser.add('--node',
'-n',
default=default_node,
help='Name of this node (default: ' + default_node +
')'),
self.parser.add('-s',
'--secret',
default=default_secret,
help='Master node shared secret (default: ' +
default_secret + ')'),
self.parser.add('--machine',
'-a',
default=default_machine,
help='Machine (default :' + default_machine + ')'),
self.parser.add('-m',
'--mqtthost',
default=default_host,
help='MQTT host (default :' + default_host + ')'),
self.parser.add('--mqttprotocol',
default=default_protocol,
help='MQTT protocol (default :' + default_protocol +
')'),
self.parser.add(
'--topic',
'-t',
default=default_sub,
help=
'MQTT topic to subcribe to for replies from the master (default: '
+ default_sub + ').'),
self.parser.add('--verbose',
'-v',
action='count',
default=0,
help='Verbose on (default off)')
self.parser.add('--debug',
'-d',
action='count',
default=0,
help='Debuging on; implies verbose (default off)')
self.parser.add(
'--no-mqtt-log',
action='count',
help='Disable logging to MQTT log channel (default on)'),
self.parser.add('--no-syslog', help='Disable syslogging (defautl on)'),
self.parser.add(
'-l',
'--logfile',
type=configargparse.FileType('w+'),
help='Append log entries to specified file (default: none)'),
self.parser.add('--ignorebeat',
help='Ignore the beat (default is to follow)')
self.parser.add('--leeway',
action='store',
default=default_leeway,
type=int,
help='Beat leeway, in seconds (default: ' +
str(default_leeway) + ' seconds).')
self.cnf = self.parser.parse_args()
self.cnf.follower = not self.cnf.ignorebeat
information="For more information refer to {docs}".format(docs=camsa.CAMSA_DOCS_URL),
contact=camsa.CONTACT)
full_description = "=" * 80 + "\n" + full_description + "=" * 80 + "\n"
parser = configargparse.ArgParser(description=full_description, formatter_class=configargparse.RawTextHelpFormatter,
default_config_files=[os.path.join(camsa.root_dir, "logging.ini")])
parser.add_argument("-c", "--config", is_config_file=True, help="Config file overwriting some of the default settings as well as any flag starting with \"--\".")
parser.add_argument("--version", action="version", version=camsa.VERSION)
parser.add_argument("ragout_coords", type=str, help="A path to ragout coords file")
parser.add_argument("--filter-indels", action="store_true", dest="filter_indels", default=False)
parser.add_argument("--no-fragment-stats", action="store_false", dest="fragment_stats", default=True)
parser.add_argument("--no-genome-stats", action="store_false", dest="genome_stats", default=True)
parser.add_argument("--filter-duplications", action="store_true", dest="filter_duplications", default=False)
parser.add_argument("--good-genomes", type=str, default="", help="A coma separated list of genome names, to be processed and conversed.\nDEFAULT: \"\" (i.e., all genomes are good)")
parser.add_argument("--bad-genomes", type=str, default="", help="A coma separated list of genome names, to be excluded from processing and conversion.\nDEFAULT: \"\" (i.e., no genomes are bad)")
parser.add_argument("-o", "--output", type=configargparse.FileType("wt"), default=sys.stdout)
parser.add_argument("--c-logging-level", dest="c_logging_level", default=logging.INFO, type=int,
choices=[logging.NOTSET, logging.DEBUG, logging.INFO, logging.WARNING, logging.ERROR, logging.CRITICAL],
help="Logging level for the converter.\nDEFAULT: {info}".format(info=logging.INFO))
parser.add_argument("--c-logging-formatter-entry",
help="Format string for python logger.")
args = parser.parse_args()
start_time = datetime.datetime.now()
logger = logging.getLogger("CAMSA.utils.ragout_coords2fasta")
ch = logging.StreamHandler()
ch.setLevel(args.c_logging_level)
logger.setLevel(args.c_logging_level)
logger.addHandler(ch)
logger.info(full_description)
def __init__(self,
objects=(),
description="""Run the Pypelid bypass simulation of
Euclid observations."""):
""" Parse arguments """
parser = configargparse.ArgumentParser(
description=description,
args_for_setting_config_path=['-c', '--conf'],
formatter_class=configargparse.ArgumentDefaultsHelpFormatter)
parser.register('type', 'bool', str_to_bool)
parser.add_argument("-w",
metavar='filename',
nargs='?',
const=sys.stdout,
type=configargparse.FileType('w'),
help="write out config file and exit",
is_write_out_config_file_arg=True)
# self.parser.add_argument('--version', action='version', version='%s'%str(misc.GitEnv()), help="show git hash and exit")
param_list = []
objs = []
for o in objects:
try:
for dep in o._dependencies:
objects.append(dep)
except AttributeError:
pass
if o not in objs:
objs.append(o)
for o in objs:
if isinstance(o, Defaults):
default_params = o
else:
try:
default_params = o._default_params
except:
continue
arg_group = parser.add_argument_group(o.__name__)
for p in default_params:
if p.name in param_list:
continue
try:
if p.hidden:
continue
except AttributeError:
pass
param_list.append(p.name)
a = {}
for k in self.argparse_keys:
try:
a[k] = p.__dict__[k]
except KeyError:
pass
args = ["--%s" % p.name]
try:
args.append("-%s" % p.__dict__['alias'])
except:
pass
arg_group.add_argument(*args, **a)
self.__dict__['_parser'] = parser
self.__dict__['_args'] = parser.parse_args()
# Run validation in each class
for o in objs:
try:
o.check_config(self._args.__dict__)
except AttributeError:
pass
def main():
secret_santa_config_dir = Path('~/.secret_santa').expanduser()
parser = configargparse.ArgParser(description='Send secret Santa emails',
default_config_files=[
'/etc/secret_santa/*.conf',
str(secret_santa_config_dir /
'*.conf')
])
parser.add_argument('--names',
'-n',
metavar='NAMES.yaml',
default=str(secret_santa_config_dir / 'names.yaml'),
type=configargparse.FileType('r'),
help='yaml file containing participant data')
parser.add_argument(
'--debug',
action='store_true',
help='print out hidden data such as the secret santa choices')
parser.add_argument('--dry_run',
action='store_true',
help='dry run mode which does not send emails')
parser.add_argument('--dry_run_email',
type=str,
default=None,
help='dry run mode which does not send emails address')
parser.add_argument('--password',
type=str,
required=True,
help='Email Password')
parser.add_argument('--username',
type=str,
required=True,
help='Email Username')
parser.add_argument('--font',
type=str,
default='RobotoSlab-VariableFont_wght.ttf',
help='Font Name Username')
parser.add_argument('--font_path',
type=str,
default='/usr/local/Caskroom/font-arial/2.82/',
help='Font Path')
args = parser.parse_args()
config, credentials, images = {}, {}, {}
credentials['password'] = args.password
credentials['username'] = args.username
images['font'] = args.font
images['font_path'] = args.font_path
config['email'] = credentials
config['images'] = images
config = Box(config)
names = load(args.names.read(), Loader=FullLoader)
names_graph = create_graph(names)
plt.subplot(121)
nx.draw_circular(names_graph, with_labels=True, font_weight='bold')
selection_graph = graph_select(names_graph)
plt.subplot(122)
nx.draw_networkx(selection_graph, with_labels=True, font_weight='bold')
for edge in selection_graph.edges:
(sender, recipient) = edge
email = args.dry_run_email or selection_graph.nodes[sender]['email']
exclude = ', '.join(selection_graph.nodes[sender]['exclude']
or ['anyone'])
if args.debug:
print(f"Emailing {sender} <{email}>: {recipient}")
else:
print(f"Emailing {sender} <{email}>: HIDDEN")
if not args.dry_run:
santa_email(sender, email, recipient, exclude, config=config)
if args.debug:
plt.show()
def parse_options():
'''Handle command-line options
Return parser object and list of arguments
'''
parser = configargparse.ArgumentParser()
parser.add_argument('-p', '--profile', required=False)
parser.add_argument('-r', '--region', required=False)
parser.add_argument('--version',
action='version',
version=__about__.__version__)
subparsers = parser.add_subparsers(title='available subcommands',
dest='subcommand')
parser_resources = subparsers.add_parser('resources',
help='List stack resources')
parser_resources.add_argument('name', help='Stack name')
parser_resources.add_argument(
'logical_id',
nargs='?',
default=None,
help='Logical resource id. Returns physical_resource_id.')
parser_outputs = subparsers.add_parser('outputs',
help='List stack outputs')
parser_outputs.add_argument('name', help='Stack name')
parser_outputs.add_argument('output_name',
nargs='?',
default=None,
help='Output name. Returns output value.')
parser_config = subparsers.add_parser('config',
help='Print config properties')
parser_config.add_argument('-e', '--env', env_var='STACKS_ENV')
parser_config.add_argument('-o',
'--output',
default='text',
choices=['text', 'yaml', 'json'],
dest='output_format',
help='Output format')
parser_config.add_argument('-c',
'--config',
default='config.yaml',
env_var='STACKS_CONFIG',
required=False,
type=_is_file)
parser_config.add_argument('--config-dir',
default='config.d',
env_var='STACKS_CONFIG_DIR',
required=False,
type=_is_dir)
parser_config.add_argument('property_name', nargs='?', default=None)
parser_list = subparsers.add_parser('list', help='List stacks')
parser_list.add_argument('-v', '--verbose', action='store_true')
parser_list.add_argument('name',
default='*',
nargs='?',
help='Stack name or unix shell-style pattern')
parser_create = subparsers.add_parser('create', help='Create a new stack')
parser_create.add_argument('-t',
'--template',
required=True,
type=configargparse.FileType())
parser_create.add_argument('-c',
'--config',
default='config.yaml',
env_var='STACKS_CONFIG',
required=False,
type=_is_file)
parser_create.add_argument('--config-dir',
default='config.d',
env_var='STACKS_CONFIG_DIR',
required=False,
type=_is_dir)
parser_create.add_argument('name', nargs='?', default=None)
parser_create.add_argument('-e',
'--env',
env_var='STACKS_ENV',
required=True)
parser_create.add_argument('-P',
'--property',
required=False,
action='append')
parser_create.add_argument('-d', '--dry-run', action='store_true')
parser_create.add_argument('-f',
'--follow',
dest='events_follow',
help='Follow stack events',
action='store_true')
parser_update = subparsers.add_parser('update',
help='Update an existing stack')
parser_update.add_argument('-t',
'--template',
required=True,
type=configargparse.FileType())
parser_update.add_argument('-c',
'--config',
env_var='STACKS_CONFIG',
default='config.yaml',
required=False,
type=_is_file)
parser_update.add_argument('--config-dir',
default='config.d',
env_var='STACKS_CONFIG_DIR',
required=False,
type=_is_dir)
parser_update.add_argument('name', nargs='?', default=None)
parser_update.add_argument('-e',
'--env',
env_var='STACKS_ENV',
required=True)
parser_update.add_argument('-P',
'--property',
required=False,
action='append')
parser_update.add_argument('-d', '--dry-run', action='store_true')
parser_update.add_argument('--create',
dest='create_on_update',
help='Create if stack does not exist.',
action='store_true')
parser_update.add_argument('-f',
'--follow',
dest='events_follow',
help='Follow stack events',
action='store_true')
parser_delete = subparsers.add_parser('delete',
help='Delete an existing stack')
parser_delete.add_argument('-f',
'--follow',
dest='events_follow',
help='Follow stack events',
action='store_true')
parser_delete.add_argument('-y',
'--yes',
help='Confirm stack deletion.',
action='store_true')
parser_delete.add_argument('name')
parser_events = subparsers.add_parser('events',
help='List events from a stack')
parser_events.add_argument('name')
parser_events.add_argument('-f',
'--follow',
dest='events_follow',
action='store_true',
help='Poll for new events until stopped.')
parser_events.add_argument(
'-n',
'--lines',
default='10',
type=int,
help=
'Maximum number of lines of CF output returned per 5 second iteration')
return parser, parser.parse_args()
if __name__ == "__main__":
full_description = camsa.full_description_template.format(
names=camsa.CAMSA_AUTHORS,
affiliations=camsa.AFFILIATIONS,
dummy=" ",
tool="Converting FASTA formatted fragments further CAMSA processing.",
information="For more information refer to {docs}".format(docs=camsa.CAMSA_DOCS_URL),
contact=camsa.CONTACT)
full_description = "=" * 80 + "\n" + full_description + "=" * 80 + "\n"
parser = configargparse.ArgParser(description=full_description, formatter_class=configargparse.RawTextHelpFormatter,
default_config_files=[os.path.join(camsa.root_dir, "utils", "fasta", "fasta2camsa_seqi.ini"),
os.path.join(camsa.root_dir, "logging.ini")])
parser.add_argument("--version", action="version", version=camsa.VERSION)
parser.add_argument("-o", "--output-file", metavar="OUTPUT", dest="output", type=configargparse.FileType("wt"), default=sys.stdout,
help="A file to which the CAMSA readable fragments lengths would be written. Standard extension is \".camsa.lengths\".\nDEFAULT: stdout")
parser.add_argument("--o-format", type=str, help="")
parser.add_argument("contigs", nargs="+", metavar="CONTIGS", type=configargparse.FileType("rt"), default=sys.stdin,
help="A list of input *.fasta files with contigs.\nDEFAULT: stdin")
parser.add_argument("--c-logging-level", dest="logging_level", default=logging.INFO, type=int,
choices=[logging.NOTSET, logging.DEBUG, logging.INFO, logging.WARNING, logging.ERROR, logging.CRITICAL],
help="Logging level for the converter.\nDEFAULT: {info}".format(info=logging.INFO))
parser.add_argument("--c-logging-formatter-entry",
help="Format string for python logger.")
parser.add_argument("--o-delimiter", type=str, default="\t",
help="A single character string, used as a delimiter in the output (t)/(c)sv file.\nDEFAULT: \\t")
args = parser.parse_args()
start_time = datetime.datetime.now()
logger = logging.getLogger("CAMSA.utils.fasta2camsa_seqi")
def get_parser():
"""Get default arguments."""
parser = configargparse.ArgumentParser(
description="Align text to audio using CTC segmentation."
"using a pre-trained speech recognition model.",
config_file_parser_class=configargparse.YAMLConfigFileParser,
formatter_class=configargparse.ArgumentDefaultsHelpFormatter,
)
# general configuration
parser.add("--config", is_config_file=True, help="Decoding config file path.")
parser.add_argument(
"--ngpu", type=int, default=0, help="Number of GPUs (max. 1 is supported)"
)
parser.add_argument(
"--dtype",
choices=("float16", "float32", "float64"),
default="float32",
help="Float precision (only available in --api v2)",
)
parser.add_argument(
"--backend",
type=str,
default="pytorch",
choices=["pytorch"],
help="Backend library",
)
parser.add_argument("--debugmode", type=int, default=1, help="Debugmode")
parser.add_argument("--verbose", "-V", type=int, default=1, help="Verbose option")
parser.add_argument(
"--preprocess-conf",
type=str,
default=None,
help="The configuration file for the pre-processing",
)
# task related
parser.add_argument(
"--data-json", type=str, help="Json of recognition data for audio and text"
)
parser.add_argument("--utt-text", type=str, help="Text separated into utterances")
# model (parameter) related
parser.add_argument(
"--model", type=str, required=True, help="Model file parameters to read"
)
parser.add_argument(
"--model-conf", type=str, default=None, help="Model config file"
)
parser.add_argument(
"--num-encs", default=1, type=int, help="Number of encoders in the model."
)
# ctc-segmentation related
parser.add_argument(
"--subsampling-factor",
type=int,
default=None,
help="Subsampling factor."
" If the encoder sub-samples its input, the number of frames at the CTC layer"
" is reduced by this factor. For example, a BLSTMP with subsampling 1_2_2_1_1"
" has a subsampling factor of 4.",
)
parser.add_argument(
"--frame-duration",
type=int,
default=None,
help="Non-overlapping duration of a single frame in milliseconds.",
)
parser.add_argument(
"--min-window-size",
type=int,
default=None,
help="Minimum window size considered for utterance.",
)
parser.add_argument(
"--max-window-size",
type=int,
default=None,
help="Maximum window size considered for utterance.",
)
parser.add_argument(
"--use-dict-blank",
type=int,
default=None,
help="DEPRECATED.",
)
parser.add_argument(
"--set-blank",
type=int,
default=None,
help="Index of model dictionary for blank token (default: 0).",
)
parser.add_argument(
"--gratis-blank",
type=int,
default=None,
help="Set the transition cost of the blank token to zero. Audio sections"
" labeled with blank tokens can then be skipped without penalty. Useful"
" if there are unrelated audio segments between utterances.",
)
parser.add_argument(
"--replace-spaces-with-blanks",
type=int,
default=None,
help="Fill blanks in between words to better model pauses between words."
" Segments can be misaligned if this option is combined with --gratis-blank."
" May increase length of ground truth.",
)
parser.add_argument(
"--scoring-length",
type=int,
default=None,
help="Changes partitioning length L for calculation of the confidence score.",
)
parser.add_argument(
"--output",
type=configargparse.FileType("w"),
required=True,
help="Output segments file",
)
return parser
def define_args(parser):
""" Define the input, output, scaling, and decimation command-line arguments.
"""
# Would like this to be a mutually-exclusive group with one arg required,
# but those don't have title and description parms and don't group their
# help separately. Mutual exclusion is tested for in _process_args.
input_group = parser.add_argument_group(
title='Inputs',
description='These arguments each specify a different input data '
'source. Use exactly one.')
input_group.add_argument(
'--in_eos_file_base',
metavar='<base path>. ',
help='Read source data points from EOS data <base path>'
'[default: %(default)s]. '
'If this is set, --out_eos_file_base must also be set.')
input_group.add_argument(
'--input_file',
metavar='<path>',
type=configargparse.FileType('r'),
help='Read this input file for source data points')
input_group.add_argument(
'--parabola_in',
action='store_true',
help='(For developer testing) Use the internal noisy input parabola '
'as source data [default: %(default)s]')
input_group.add_argument(
'--predefined_in',
action='store_true',
help='(For developer testing) Use the internal predefined data as '
'source data [default: %(default)s]')
# Would like this to be a mutually-exclusive group, but those don't
# have title and description parms and don't group their help separately.
# Mutual exclusion is tested for in _process_args.
output_group = parser.add_argument_group(
title='Outputs',
description='These arguments each specify where the changed data '
'is written to. Use no more than one.')
output_group.add_argument(
'--out_eos_file_base',
metavar='<base path>',
help='Use the EOS file <base path> for '
'the adjusted/moved data points [default: %(default)s]. '
'If this is set, --in_eos_file_base must also be set.')
output_group.add_argument(
'--output_file_name',
metavar='<path>',
# Not setting "type=argparse.FileType('w')" because that opens the
# file for writing in the argument parser, and that conflicts with
# opening it for writing later:
help='Use this output file for the adjusted/moved data points '
'[default: %(default)s]')
shifts = parser.add_argument_group(
title='Shifts, Limits, and Point Exclusion',
description='These arguments limit, exclude or alter the input data.')
shifts.add_argument(
'--decimate',
metavar='<count>',
type=int,
help='Only use <count> points from the input data, minimum 2 '
'[default: all points]')
shifts.add_argument(
'--step',
metavar='<step>',
type=int,
help='Only use every <step>th input point. e.g. --step 2 only' +
' uses every other point, minimum 1 [default: %(default)s]')
shifts.add_argument(
'--t_step',
metavar='<step>',
type=int,
help='Only use every <step>th isotherm. e.g. --step 2 only' +
' uses every other isotherm, minimum 1 [default: %(default)s]')
shifts.add_argument(
'--x_include',
'--xinclude',
nargs=2,
metavar=('<lo>', '<hi>'),
type=float,
help=
'Only consume input points when <lo> > x > <hi> [default: %(default)s]'
)
shifts.add_argument(
'--x_scale',
'--xscale',
nargs=3,
metavar=('<scale>', '<lo>', '<hi>'),
type=float,
help='Multiply the x value of each input point by <scale> '
'when <lo> > x > <hi> [default: %(default)s] '
'>>NOTE<< applied AFTER --x_include')
shifts.add_argument('--x_shift',
'--xshift',
nargs=3,
type=float,
help='Add <shift> to the x value of each input point '
'when <lo> > x > <hi> [default: %(default)s] '
'>>NOTE<< applied AFTER --x_scale',
metavar=('<shift>', '<lo>', '<hi>'))
shifts.add_argument(
'--y_include',
'--yinclude',
nargs=2,
metavar=('<lo>', '<hi>'),
type=float,
help='Only consume input points when <lo> > y > <hi> [default: '
'%(default)s]')
shifts.add_argument(
'--y_scale',
'--yscale',
nargs=3,
metavar=('<scale>', '<lo>', '<hi>'),
type=float,
help='Multiply the y value of each input point by <scale> '
'when <lo> > x > <hi> [default: %(default)s]. '
'>>NOTE<< uses x to trigger, not y. '
'>>NOTE<< applied BEFORE x adjustments, and AFTER --y_include. ')
shifts.add_argument('--y_shift',
'--yshift',
nargs=3,
metavar=('<shift>', '<lo>', '<hi>'),
type=float,
help='Add <shift> to the y value of each input point '
'when <lo> > x > <hi> [default: %(default)s] '
'>>NOTE<< uses x to trigger, not y. ')
shifts.add_argument(
'--t_include',
'--tinclude',
nargs=2,
metavar=('<lo>', '<hi>'),
type=float,
help='Only consume input points when <lo> > t > <hi> [default: '
'%(default)s]')
shifts.add_argument(
'--v_axis',
action='store_true',
help=
'Use v as x axis instead or rho. Note curve fits don\'t work like this.'
)
# TODO: Add the rest of the arguments in alphabetical order, so they come
# out that way in help. (Even though the arguments are defined in different
# modules)
parser.add_argument(
'--background_file',
metavar='<path>',
nargs='+',
type=configargparse.FileType('r'),
help='Use this input file for background (unchanging) data points '
'[default: %(default)s]')
parser.add_argument(
'--curve_output_file_name',
metavar='<path>',
# Not setting "type=argparse.FileType('w')" because that opens the file
# for writing in the argument parser, and that conflicts with opening it
# for writing later.
help='Use this output file for data points generated from the '
'current fit curve [default: %(default)s]')
parser.add_argument('--eos_function',
help='Only read in the data for this function'
'[default: %(default)s]')
parser.add_argument(
'--use_eos_info_file',
action='store_true',
help=
'When EOS is selected as input, read and write the .info file with the'
' same name as the eos data file with extension .info. [default: %(default)s]'
)
# parser.add_argument(
# '--yaml', action='store_true',
# dest='use_yaml_io',
# help='Use YAML format for input and output files [default: %(default)s]')
output_group = parser.add_argument_group(
title='View',
description='Change the view but don\'t change the actual data')
output_group.add_argument('--x_max',
metavar='<num>',
help='Set the maximum x value for the window')
output_group.add_argument('--x_min',
metavar='<num>',
help='Set the minimum x value for the window')
output_group.add_argument('--y_max',
metavar='<num>',
help='Set the maximum y value for the window')
output_group.add_argument('--y_min',
metavar='<num>',
help='Set the minimum y value for the window')
parser.set_defaults(
# Input group:
in_eos_file_base=None,
input_file=None,
parabola_in=False,
predefined_in=False,
# Output group:
out_eos_file_base=None,
output_file_name='moved_points_out.dat',
# Shifts group:
decimate=_NO_DECIMATE,
step=1,
t_step=1,
x_include=[_NEG_INFINITY, _INFINITY],
x_scale=[1.0, _NEG_INFINITY, _INFINITY],
x_shift=[0.0, _NEG_INFINITY, _INFINITY],
y_include=[_NEG_INFINITY, _INFINITY],
y_scale=[1.0, _NEG_INFINITY, _INFINITY],
y_shift=[0.0, _NEG_INFINITY, _INFINITY],
t_include=[_NEG_INFINITY, _INFINITY],
# other:
background_file=[],
curve_output_file_name='fit_curve_out.dat',
use_eos_info_file=False,
use_yaml_io=False,
eos_function='all',
)
default=None,
type=str,
help='comma-separated list of email addresses to send messages to',
env_var="SEND_MESSAGES_TO")
parser.add_argument('--notification_interval',
default=86400,
type=int,
help='time in seconds between status emails',
env_var="NOTIFICATION_INTERVAL")
parser.add_argument('--account',
type=str,
help='Account to perform delegations for',
env_var="ACCOUNT")
parser.add_argument(
'--wif',
type=configargparse.FileType('r'),
help=
'An active WIF for account. The flag expects a path to a file. The environment variable REDEEMER_WIF will be checked for a literal WIF also.'
)
parser.add_argument('--log_level',
type=str,
default='INFO',
env_var="LOG_LEVEL")
parser.add_argument('--dry_run',
type=int,
default=1,
help='Set this to 0 to actually broadcast transactions',
env_var="DRY_RUN")
parser.add_argument(
'--interval',
type=int,
