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
