def run_benchmarks( fname ):
print '%20s\t%s' % ( 'Test', 'Time')
logger.disable('DEBUG')
if 1:
cleanup()
pygr_parse_fasta(fname )
bio_parse_fasta(fname)
bx_parse_fasta(fname)
cogent_parse_fasta(fname )
print '-' * 20
if 1:
pygr_iter(fname )
bio_iter(fname)
bx_iter(fname)
cogent_iter(fname)
print '-' * 20
if 1:
pygr_slice(fname )
bio_slice(fname)
bx_slice(fname)
cogent_slice(fname)
print '-' * 20
if 1:
pygr_reverse_comp(fname )
bio_reverse_comp(fname)
bx_reverse_comp(fname)
cogent_reverse_comp(fname)
def run_benchmarks(fname):
print '%20s\t%s' % ('Test', 'Time')
logger.disable('DEBUG')
if 1:
cleanup()
pygr_parse_fasta(fname)
bio_parse_fasta(fname)
bx_parse_fasta(fname)
cogent_parse_fasta(fname)
print '-' * 20
if 1:
pygr_iter(fname)
bio_iter(fname)
bx_iter(fname)
cogent_iter(fname)
print '-' * 20
if 1:
pygr_slice(fname)
bio_slice(fname)
bx_slice(fname)
cogent_slice(fname)
print '-' * 20
if 1:
pygr_reverse_comp(fname)
bio_reverse_comp(fname)
bx_reverse_comp(fname)
cogent_reverse_comp(fname)
def __init__(self, **kwargs):
verbosity = kwargs.pop('verbosity', 1)
if verbosity != 2:
logger.disable('DEBUG')
if kwargs.get('testRunner') is None:
kwargs['testRunner'] = PygrTestRunner(verbosity=verbosity)
unittest.TestProgram.__init__(self, **kwargs)
def __init__(self, **kwargs):
verbosity = kwargs.pop('verbosity', 1)
if verbosity < 1:
logger.disable('INFO') # Should implicity disable DEBUG as well
elif verbosity < 2:
logger.disable('DEBUG')
if kwargs.get('testRunner') is None:
kwargs['testRunner'] = PygrTestRunner(verbosity=verbosity)
unittest.TestProgram.__init__(self, **kwargs)
def __init__(self, **kwargs):
verbosity = kwargs.pop('verbosity', 1)
if verbosity < 1:
logger.disable('INFO') # Should implicity disable DEBUG as well
elif verbosity < 2:
logger.disable('DEBUG')
if kwargs.get('testRunner') is None:
kwargs['testRunner'] = PygrTestRunner(verbosity=verbosity)
unittest.TestProgram.__init__(self, **kwargs)
def run(targets, options):
"Imports and runs the modules names that are contained in the 'targets'"
success = errors = skipped = 0
# run the tests by importing the module and getting its test suite
for name in targets:
try:
testutil.info('running tests for module %s' % name)
l = unittest.TestLoader()
suite = l.loadTestsFromName(name)
runner = PygrTestRunner(verbosity=options.verbosity,
descriptions=0)
logger.disable(disable_threshold) # set global override
results = runner.run(suite)
logger.disable(0) # clear global override
# count tests and errors
success += results.testsRun - \
len(results.errors) - \
len(results.failures) - \
len(results.skipped)
errors += len(results.errors) + len(results.failures)
skipped += len(results.skipped)
# if we're in strict mode stop on errors
if options.strict and errors:
testutil.error("strict mode stops on errors")
break
except ImportError:
testutil.error("unable to import module '%s'" % name)
# summarize the run
testutil.info('=' * 59)
testutil.info('''\
%s tests passed, %s tests failed, %s tests skipped; %d total''' % \
(success, errors, skipped, success + errors + skipped))
return (success, errors, skipped)
break
except ImportError:
testutil.error("unable to import module '%s'" % name)
# summarize the run
testutil.info('=' * 59)
testutil.info('''\
%s tests passed, %s tests failed, %s tests skipped; %d total''' % \
(success, errors, skipped, success + errors + skipped))
return (success, errors, skipped)
if __name__ == '__main__':
# Make sure no messages are filtered out at first
logger.disable(0)
# gets the prebuild option parser
parser = testoptions.option_parser()
# parse the options
options, args = parser.parse_args()
# modules: from command line args or all modules
targets = args or all_tests()
# get rid of the .py ending in case full module names were passed in
# the command line
stripped_targets = []
for t in targets:
if t.endswith('.py'):
# same options for all tests (some flags may be ignored)
parser = testoptions.option_parser()
# parse the arguments
options, args = parser.parse_args()
if options.pygrdatapath: # load from specified path
mdb = metabase.MetabaseList(options.pygrdatapath)
else: # use default PYGRDATAPATH
mdb = metabase.MetabaseList()
# disables debug messages at zero verbosity
if options.verbosity == 0:
logger.disable('DEBUG')
# the resources are listed as colon separated names
names = filter(None, options.resources.split(':'))
resources = map(mdb, names) # load the specified resources
# set it to None by default
options.downloadDB = options.downloadDB or None
# create a new server that will serve the resources we just loaded
xmlrpc = metabase.ResourceServer(mdb, 'testy',
withIndex=True,
downloadDB=options.downloadDB,
host='localhost', port=options.port)
# if needed, write out the port information to a file, so that the test runner
for t in targets:
if t.endswith(".py"):
t = t[:-3]
stripped_targets.append(t)
targets = stripped_targets
if options.port:
testutil.default_xmlrpc_port = options.port
# exclusion mode
if options.exclude:
targets = [name for name in all_tests() if name not in targets]
# disables debug messages at < 2 verbosity
if options.verbosity != 2:
logger.disable("DEBUG")
# cleans full entire test directory
if options.clean:
testutil.TEMPROOT.reset()
testutil.TEMPDIR = testutil.TEMPROOT.path # yikes!
# list patterns matching files to be removed here
patterns = [
"*.seqlen",
"*.pureseq",
"*.nin",
"*.pin",
"*.psd",
"*.psi",
"*.psq",
