def main():
desc = """ccp4-python -m ample.testing <command> [<args>]
Available tests include:
integration Integration testing of typical Ample routines
unittest Unittesting of all Ample subroutines
"""
parser = argparse.ArgumentParser(prog="run_tests.py", usage=desc)
# Add options that work on all runtypes
add_core_options(parser)
suboptions = parser.add_subparsers(help="Testing framework options")
integ = suboptions.add_parser("integration", help="Integration testing with examples")
integ.set_defaults(which="integration")
integration_util.add_cmd_options(integ)
add_cluster_submit_options(integ)
unit = suboptions.add_parser("unittest", help="Unittest all functions")
unit.set_defaults(which="unittest")
unittest_util.add_cmd_options(unit)
argd = vars(parser.parse_args())
which_test = argd['which']
if which_test is 'integration':
run_integration(argd)
elif which_test is 'unittest':
run_unittest(argd)
def main():
desc = """ccp4-python -m ample.testing <command> [<args>]
Available tests include:
integration Integration testing of typical Ample routines
unittest Unittesting of all Ample subroutines
"""
parser = argparse.ArgumentParser(prog="run_tests.py", usage=desc)
# Add options that work on all runtypes
add_core_options(parser)
suboptions = parser.add_subparsers(help="Testing framework options")
integ = suboptions.add_parser("integration",
help="Integration testing with examples")
integ.set_defaults(which="integration")
integration_util.add_cmd_options(integ)
add_cluster_submit_options(integ)
unit = suboptions.add_parser("unittest", help="Unittest all functions")
unit.set_defaults(which="unittest")
unittest_util.add_cmd_options(unit)
argd = vars(parser.parse_args())
which_test = argd['which']
if which_test is 'integration':
run_integration(argd)
elif which_test is 'unittest':
run_unittest(argd)
def process_command_line(self,
args=None,
contacts=True,
modelling=True,
mol_rep=True):
"""Process the command-line.
:args: optional argument that can hold the command-line arguments if we
have been called from within python for testing
"""
parser = argparse.ArgumentParser(
description=
"AMPLE: Ab initio Modelling of Proteins for moLEcular replacement",
prefix_chars="-")
argparse_util.add_general_options(parser)
argparse_util.add_cluster_submit_options(parser)
ensembler.add_argparse_options(parser)
if contacts:
argparse_util.add_contact_options(parser)
if mol_rep:
argparse_util.add_mr_options(parser)
if modelling:
argparse_util.add_rosetta_options(parser)
return parser.parse_args(args)
import argparse
import os
import sys
from ample.constants import AMPLE_PKL
from ample import ensembler
from ample.util import ample_util, config_util, exit_util, logging_util, process_models
from ample.util import argparse_util
from ample.util.options_processor import process_ensemble_options
ENSEMBLE_DIRNAME = 'ample_ensemble'
parser = argparse.ArgumentParser(description="AMPLE Ensembling Module")
argparse_util.add_general_options(parser)
argparse_util.add_cluster_submit_options(parser)
argparse_util.add_ensembler_options(parser)
# Get command-line arguments and see if we have a restart_pkl option as this
# is how we pass in an existing ample dictionary when we are running the ensembling
# as a standalone job on a cluster
optd = vars(parser.parse_args())
# Track restart as it determines if we need to unpack models
restart = False
if 'restart_pkl' in optd and optd['restart_pkl']:
if not os.path.isfile(optd['restart_pkl']):
msg = 'Cannot find ensemble pkl file: {0}'.format(optd['restart_pkl'])
exit_util.exit_error(msg)
try:
optd = ample_util.read_amoptd(optd['restart_pkl'])
import argparse
import os
import sys
from ample.constants import AMPLE_PKL
from ample import ensembler
from ample.util import ample_util, config_util, exit_util, logging_util
from ample.util import argparse_util
ENSEMBLE_DIRNAME = 'ample_ensemble'
# Set up the command-line parsing
parser = argparse.ArgumentParser(description="AMPLE Ensembling Module")
# Add options for running as a standalone module
argparse_util.add_general_options(parser)
argparse_util.add_cluster_submit_options(parser)
# Ensemble options
ensembler.add_argparse_options(parser)
# Get command-line arguments and see if we have a restart_pkl option as this
# is how we pass in an existing ample dictionary when we are running the ensembling
# as a standalone job on a cluster
args = parser.parse_args()
optd = vars(args)
# Track restart as it determines if we need to unpack models
restart = False
if 'restart_pkl' in optd and optd['restart_pkl']:
if not os.path.isfile(optd['restart_pkl']):
msg = 'Cannot find ensemble pkl file: {0}'.format(optd['restart_pkl'])
exit_util.exit_error(msg)