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 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",