def parse_cli_args():
"""Parse command line arguments"""
parser = argparse.ArgumentParser(
description='Check if a set of files adheres to the PEtab format.')
# General options:
parser.add_argument('-v',
'--verbose',
dest='verbose',
action='store_true',
help='More verbose output')
# Call with set of files
parser.add_argument('-s',
'--sbml',
dest='sbml_file_name',
help='SBML model filename')
parser.add_argument('-m',
'--measurements',
dest='measurement_file_name',
help='Measurement table')
parser.add_argument('-c',
'--conditions',
dest='condition_file_name',
help='Conditions table')
parser.add_argument('-p',
'--parameters',
dest='parameter_file_name',
help='Parameter table')
# or with model name, following default naming
parser.add_argument('-n',
'--model-name',
dest='model_name',
help='Model name where all files are in the working '
'directory and follow PEtab naming convention. '
'Specifying -[smcp] will override defaults')
args = parser.parse_args()
if args.model_name:
if not args.sbml_file_name:
args.sbml_file_name = petab.get_default_sbml_file_name(
args.model_name)
if not args.measurement_file_name:
args.measurement_file_name = \
petab.get_default_measurement_file_name(args.model_name)
if not args.condition_file_name:
args.condition_file_name = petab.get_default_condition_file_name(
args.model_name)
if not args.parameter_file_name:
args.parameter_file_name = petab.get_default_parameter_file_name(
args.model_name)
if not args.model_name and \
(not args.sbml_file_name
or not args.condition_file_name
or not args.measurement_file_name):
# TODO: we should also allow running (limited) tests on a subset of
# files
parser.error('When not specifying a model name, sbml, '
'condition and measurement file must be specified')
return args
def parse_cli_args():
"""Parse command line arguments"""
parser = argparse.ArgumentParser(
description='Import PEtab-format model into AMICI.')
# General options:
parser.add_argument('-v',
'--verbose',
dest='verbose',
action='store_true',
help='More verbose output')
parser.add_argument('-o',
'--output-dir',
dest='model_output_dir',
help='Name of the model directory to create')
parser.add_argument('--no-compile',
action='store_false',
dest='compile',
help='Only generate model code, do not compile')
# Call with set of files
parser.add_argument('-s',
'--sbml',
dest='sbml_file_name',
help='SBML model filename')
parser.add_argument('-m',
'--measurements',
dest='measurement_file_name',
help='Measurement table')
parser.add_argument('-c',
'--conditions',
dest='condition_file_name',
help='Conditions table')
parser.add_argument('-p',
'--parameters',
dest='parameter_file_name',
help='Parameter table')
# or with model name, following default naming
parser.add_argument('-n',
'--model-name',
dest='model_name',
help='Model name where all files are in the working '
'directory and follow PEtab naming convention. '
'Specifying -[smcp] will override defaults')
args = parser.parse_args()
if args.model_name:
if not args.sbml_file_name:
args.sbml_file_name = petab.get_default_sbml_file_name(
args.model_name)
if not args.measurement_file_name:
args.measurement_file_name = \
petab.get_default_measurement_file_name(args.model_name)
if not args.condition_file_name:
args.condition_file_name = petab.get_default_condition_file_name(
args.model_name)
if not args.parameter_file_name:
args.parameter_file_name = petab.get_default_parameter_file_name(
args.model_name)
if not args.model_name and \
(not args.sbml_file_name
or not args.condition_file_name
or not args.measurement_file_name):
parser.error('When not specifying a model name, sbml, '
'condition and measurement file must be specified')
return args
def parse_cli_args():
"""Parse command line arguments"""
parser = argparse.ArgumentParser(
description='Check if a set of files adheres to the PEtab format.')
# General options:
parser.add_argument('-v',
'--verbose',
dest='verbose',
action='store_true',
help='More verbose output')
# Call with set of files
parser.add_argument('-s',
'--sbml',
dest='sbml_file_name',
help='SBML model filename')
parser.add_argument('-o',
'--observables',
dest='observable_file_name',
help='Observable table')
parser.add_argument('-m',
'--measurements',
dest='measurement_file_name',
help='Measurement table')
parser.add_argument('-c',
'--conditions',
dest='condition_file_name',
help='Conditions table')
parser.add_argument('-p',
'--parameters',
dest='parameter_file_name',
help='Parameter table')
group = parser.add_mutually_exclusive_group()
group.add_argument('-y',
'--yaml',
dest='yaml_file_name',
help='PEtab YAML problem filename')
# or with model name, following default naming
group.add_argument('-n',
'--model-name',
dest='model_name',
help='Model name where all files are in the working '
'directory and follow PEtab naming convention. '
'Specifying -[smcp] will override defaults')
parser.add_argument('-d',
'--directory',
dest='directory',
default=os.getcwd())
args = parser.parse_args()
if args.model_name:
if not args.sbml_file_name:
args.sbml_file_name = petab.get_default_sbml_file_name(
args.model_name,
folder=args.directory,
)
if not args.measurement_file_name:
args.measurement_file_name = \
petab.get_default_measurement_file_name(
args.model_name,
folder=args.directory,
)
if not args.condition_file_name:
args.condition_file_name = petab.get_default_condition_file_name(
args.model_name,
folder=args.directory,
)
if not args.parameter_file_name:
args.parameter_file_name = petab.get_default_parameter_file_name(
args.model_name,
folder=args.directory,
)
if (args.yaml_file_name and any(
(args.sbml_file_name, args.condition_file_name,
args.measurement_file_name, args.parameter_file_name))):
parser.error('When providing a yaml file, no other files may '
'be specified.')
if (not args.model_name and not any([
args.sbml_file_name, args.condition_file_name,
args.measurement_file_name, args.parameter_file_name,
args.observable_file_name, args.yaml_file_name
])):
parser.error('Neither model name nor any filename specified. '
'What shall I do?')
return args