def testArgs(self):
"""
It must be possible to parse command line arguments to create a new
instance of FindParameters.
"""
parser = argparse.ArgumentParser()
FindParameters.addArgsToParser(parser)
args = parser.parse_args([
'--significanceMethod',
'Always',
'--significanceFraction',
'0.4',
'--binScoreMethod',
'MinHashesScore',
'--featureMatchScore',
'5',
'--featureMismatchScore',
'6',
'--weights',
'AlphaHelix 2',
'--deltaScale',
'0.2',
])
# Parsing must do the expected thing.
self.assertEqual('Always', args.significanceMethod)
self.assertEqual(0.4, args.significanceFraction)
self.assertEqual('MinHashesScore', args.binScoreMethod)
self.assertEqual(5, args.featureMatchScore)
self.assertEqual(6, args.featureMismatchScore)
self.assertEqual(0.2, args.deltaScale)
# We must be able to make an instance from the parsed args.
findParams = FindParameters.fromArgs(args)
self.assertEqual('Always', findParams.significanceMethod)
self.assertEqual(0.4, findParams.significanceFraction)
self.assertEqual('MinHashesScore', findParams.binScoreMethod)
self.assertEqual(5, findParams.featureMatchScore)
self.assertEqual(6, findParams.featureMismatchScore)
self.assertEqual(0.2, findParams.deltaScale)
#!/usr/bin/env python
"""
Print all database and find parameters available via the command line,
with their default values (according to argparse).
"""
from __future__ import print_function
import argparse
from light.parameters import DatabaseParameters, FindParameters
dbParams = DatabaseParameters()
parser = argparse.ArgumentParser(
add_help=False, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
dbParams.addArgsToParser(parser)
print('Database parameters:')
# Splitting on 'optional arguments:\n' is a hack that works nicely as the
# first part of the help message is a summary of how to call the program
# and doesn't show descriptions or default values.
print(parser.format_help().split('optional arguments:\n')[1])
findParams = FindParameters()
parser = argparse.ArgumentParser(
add_help=False, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
findParams.addArgsToParser(parser)
print('Find parameters:')
print(parser.format_help().split('optional arguments:\n')[1])
'--printParams',
default=False,
action='store_true',
help=('If given, print the values of all parameters used.'))
parser.add_argument('--description',
default='<not given>',
help='A description of the code being tested.')
parser.add_argument(
'--testIdPrefix',
default=None,
help=('A test id prefix. Tests whose ids do not contain this pattern '
'will not be run. The pattern is case-sensitive.'))
FindParameters.addArgsToParser(parser)
DatabaseParameters.addArgsToParser(parser)
args = parser.parse_args()
# If no parameter sets were specified, use the ones on the command line.
if not args.parameterSets:
args.parameterSets = ['command-line']
if 'command-line' in args.parameterSets:
PARAMETER_SETS['command-line'] = {
'dbParams': DatabaseParameters.fromArgs(args),
'findParams': FindParameters.fromArgs(args),
}
if args.printParams: