def generate_coverage(func, path, *args, **kwds): """ Generates code coverage for the function and places the results in the path """ import figleaf from figleaf import annotate_html if os.path.isdir(path): shutil.rmtree(path) # execute the function itself return_vals = func(*args, **kwds) logger.info('generating coverage') coverage = figleaf.get_data().gather_files() annotate_html.prepare_reportdir(path) # skip python modules and the test modules regpatt = lambda patt: re.compile(patt, re.IGNORECASE) patterns = map(regpatt, ['python', 'tests']) annotate_html.report_as_html(coverage, path, exclude_patterns=patterns, files_list='') return return_vals
def generate_coverage(func, path, *args, **kwds): """ Generates code coverage for the function and places the results in the path """ import figleaf from figleaf import annotate_html if os.path.isdir(path): shutil.rmtree(path) # execute the function itself return_vals = func(*args, **kwds) logger.info('generating coverage') coverage = figleaf.get_data().gather_files() annotate_html.prepare_reportdir(path) # skip python modules and the test modules regpatt = lambda patt: re.compile(patt, re.IGNORECASE) patterns = map(regpatt, [ 'python', 'tests' ]) annotate_html.report_as_html(coverage, path, exclude_patterns=patterns, files_list='') return return_vals
def get_multiblast_results(self): """return saved results or generate them if needed; results are saved so we only do this time-consuming operation once""" global _multiblast_results if not testutil.blast_enabled(): raise SkipTest("no BLAST installed") if not _multiblast_results: logger.info("running expensive multiblast") blastmap = blast.BlastMapping(self.prot, verbose=False) al = cnestedlist.NLMSA("blasthits", "memory", pairwiseMode=True, bidirectional=False) blastmap(al=al, queryDB=self.prot) # all vs all al.build() # construct the alignment indexes results = [al[seq] for seq in self.prot.values()] _multiblast_results = reformat_results(results, pair_identity_tuple) return _multiblast_results
figleaf.start() if options.coverage: start_coverage() ### try: # try to import the main pygr module import pygr from pygr import logger # we have a logger now logger.info("importing pygr from %s" % pygr.__file__) # try to import an extension module from pygr import cnestedlist except ImportError, exc: stop(""" %s Error: '%s' Possible solutions: 1. build the extension modules in place with: python setup.py build_ext -i
root.removeHandler(hand) figleaf.start() if options.coverage: start_coverage() ### try: # try to import the main pygr module import pygr from pygr import logger # we have a logger now logger.info("importing pygr from %s" % pygr.__file__) # try to import an extension module from pygr import cnestedlist except ImportError, exc: stop(""" %s Error: '%s' Possible solutions: 1. build the extension modules in place with: python setup.py build_ext -i