def run_ec_on_bin(*args):
cloneset, mismatch_rate, confidence, max_Q = args
try:
gc.disable()
seqlen = len(next(iter(cloneset)).seq)
logger.info("Starting QMerge on cloneset: seqlen: %s, \
#clones: %s, #sequences: %s, #bases: %s, #mutation_count: %s"%(seqlen,
len(cloneset), cloneset.sequence_count, cloneset.base_count,
cloneset.mutation_count))
cloneset = run_qmerge_on_bin(cloneset, mismatch_rate, confidence,
max_Q)
logger.info("Starting IMerge on cloneset: seqlen: %s, \
#clones: %s, #sequences: %s, #bases: %s, #mutation_count: %s"%(seqlen,
len(cloneset), cloneset.sequence_count, cloneset.base_count,
cloneset.mutation_count))
cloneset = run_imerge_on_bin(cloneset, mismatch_rate, confidence)
finally:
gc.enable()
return cloneset, mismatch_rate
python类disable()的实例源码
def test_load_refcount():
# Check that objects returned by np.load are directly freed based on
# their refcount, rather than needing the gc to collect them.
f = BytesIO()
np.savez(f, [1, 2, 3])
f.seek(0)
assert_(gc.isenabled())
gc.disable()
try:
gc.collect()
np.load(f)
# gc.collect returns the number of unreachable objects in cycles that
# were found -- we are checking that no cycles were created by np.load
n_objects_in_cycles = gc.collect()
finally:
gc.enable()
assert_equal(n_objects_in_cycles, 0)
def timeit(self, number=default_number):
"""Time 'number' executions of the main statement.
To be precise, this executes the setup statement once, and
then returns the time it takes to execute the main statement
a number of times, as a float measured in seconds. The
argument is the number of times through the loop, defaulting
to one million. The main statement, the setup statement and
the timer function to be used are passed to the constructor.
"""
if itertools:
it = itertools.repeat(None, number)
else:
it = [None] * number
gcold = gc.isenabled()
gc.disable()
try:
timing = self.inner(it, self.timer)
finally:
if gcold:
gc.enable()
return timing
def sig_vtalrm(self, *args):
self.hndl_called = True
if self.hndl_count > 3:
# it shouldn't be here, because it should have been disabled.
raise signal.ItimerError("setitimer didn't disable ITIMER_VIRTUAL "
"timer.")
elif self.hndl_count == 3:
# disable ITIMER_VIRTUAL, this function shouldn't be called anymore
signal.setitimer(signal.ITIMER_VIRTUAL, 0)
if test_support.verbose:
print("last SIGVTALRM handler call")
self.hndl_count += 1
if test_support.verbose:
print("SIGVTALRM handler invoked", args)
def test_free_from_gc(self):
# Check that freeing of blocks by the garbage collector doesn't deadlock
# (issue #12352).
# Make sure the GC is enabled, and set lower collection thresholds to
# make collections more frequent (and increase the probability of
# deadlock).
if not gc.isenabled():
gc.enable()
self.addCleanup(gc.disable)
thresholds = gc.get_threshold()
self.addCleanup(gc.set_threshold, *thresholds)
gc.set_threshold(10)
# perform numerous block allocations, with cyclic references to make
# sure objects are collected asynchronously by the gc
for i in range(5000):
a = multiprocessing.heap.BufferWrapper(1)
b = multiprocessing.heap.BufferWrapper(1)
# circular references
a.buddy = b
b.buddy = a
#
#
#
def test_del_newclass(self):
# __del__ methods can trigger collection, make this to happen
thresholds = gc.get_threshold()
gc.enable()
gc.set_threshold(1)
class A(object):
def __del__(self):
dir(self)
a = A()
del a
gc.disable()
gc.set_threshold(*thresholds)
# The following two tests are fragile:
# They precisely count the number of allocations,
# which is highly implementation-dependent.
# For example:
# - disposed tuples are not freed, but reused
# - the call to assertEqual somehow avoids building its args tuple
def test_main():
enabled = gc.isenabled()
gc.disable()
assert not gc.isenabled()
debug = gc.get_debug()
gc.set_debug(debug & ~gc.DEBUG_LEAK) # this test is supposed to leak
try:
gc.collect() # Delete 2nd generation garbage
run_unittest(GCTests, GCTogglingTests)
finally:
gc.set_debug(debug)
# test gc.enable() even if GC is disabled by default
if verbose:
print "restoring automatic collection"
# make sure to always test gc.enable()
gc.enable()
assert gc.isenabled()
if not enabled:
gc.disable()
def timeit(self, number=default_number):
"""Time 'number' executions of the main statement.
To be precise, this executes the setup statement once, and
then returns the time it takes to execute the main statement
a number of times, as a float measured in seconds. The
argument is the number of times through the loop, defaulting
to one million. The main statement, the setup statement and
the timer function to be used are passed to the constructor.
"""
if itertools:
it = itertools.repeat(None, number)
else:
it = [None] * number
gcold = gc.isenabled()
gc.disable()
try:
timing = self.inner(it, self.timer)
finally:
if gcold:
gc.enable()
return timing
def sig_vtalrm(self, *args):
self.hndl_called = True
if self.hndl_count > 3:
# it shouldn't be here, because it should have been disabled.
raise signal.ItimerError("setitimer didn't disable ITIMER_VIRTUAL "
"timer.")
elif self.hndl_count == 3:
# disable ITIMER_VIRTUAL, this function shouldn't be called anymore
signal.setitimer(signal.ITIMER_VIRTUAL, 0)
if test_support.verbose:
print("last SIGVTALRM handler call")
self.hndl_count += 1
if test_support.verbose:
print("SIGVTALRM handler invoked", args)
def test_free_from_gc(self):
# Check that freeing of blocks by the garbage collector doesn't deadlock
# (issue #12352).
# Make sure the GC is enabled, and set lower collection thresholds to
# make collections more frequent (and increase the probability of
# deadlock).
if not gc.isenabled():
gc.enable()
self.addCleanup(gc.disable)
thresholds = gc.get_threshold()
self.addCleanup(gc.set_threshold, *thresholds)
gc.set_threshold(10)
# perform numerous block allocations, with cyclic references to make
# sure objects are collected asynchronously by the gc
for i in range(5000):
a = multiprocessing.heap.BufferWrapper(1)
b = multiprocessing.heap.BufferWrapper(1)
# circular references
a.buddy = b
b.buddy = a
#
#
#
def test_del_newclass(self):
# __del__ methods can trigger collection, make this to happen
thresholds = gc.get_threshold()
gc.enable()
gc.set_threshold(1)
class A(object):
def __del__(self):
dir(self)
a = A()
del a
gc.disable()
gc.set_threshold(*thresholds)
# The following two tests are fragile:
# They precisely count the number of allocations,
# which is highly implementation-dependent.
# For example:
# - disposed tuples are not freed, but reused
# - the call to assertEqual somehow avoids building its args tuple
def test_main():
enabled = gc.isenabled()
gc.disable()
assert not gc.isenabled()
debug = gc.get_debug()
gc.set_debug(debug & ~gc.DEBUG_LEAK) # this test is supposed to leak
try:
gc.collect() # Delete 2nd generation garbage
run_unittest(GCTests, GCTogglingTests)
finally:
gc.set_debug(debug)
# test gc.enable() even if GC is disabled by default
if verbose:
print "restoring automatic collection"
# make sure to always test gc.enable()
gc.enable()
assert gc.isenabled()
if not enabled:
gc.disable()
def timeit(self, number=default_number):
"""Time 'number' executions of the main statement.
To be precise, this executes the setup statement once, and
then returns the time it takes to execute the main statement
a number of times, as a float measured in seconds. The
argument is the number of times through the loop, defaulting
to one million. The main statement, the setup statement and
the timer function to be used are passed to the constructor.
"""
if itertools:
it = itertools.repeat(None, number)
else:
it = [None] * number
gcold = gc.isenabled()
gc.disable()
try:
timing = self.inner(it, self.timer)
finally:
if gcold:
gc.enable()
return timing
def test_main():
min_kb, max_kb = get_bounds()
# This should be the **only** test function here.
gc.disable()
intersect_all()
kb_used_after = memory_profiler.memory_usage(max_usage=True)
if min_kb <= kb_used_after <= max_kb:
status = 0
msg = SUCCESS_TEMPLATE.format(kb_used_after)
print(msg)
else:
status = 1
msg = ERR_TEMPLATE.format(kb_used_after, min_kb, max_kb)
print(msg, file=sys.stderr)
gc.enable()
sys.exit(status)
def test_main():
min_kb, max_kb = get_bounds()
# This should be the **only** test function here.
gc.disable()
intersect_all()
kb_used_after = memory_profiler.memory_usage(max_usage=True)
if min_kb <= kb_used_after <= max_kb:
status = 0
msg = SUCCESS_TEMPLATE.format(kb_used_after)
print(msg)
else:
status = 1
msg = ERR_TEMPLATE.format(kb_used_after, min_kb, max_kb)
print(msg, file=sys.stderr)
gc.enable()
sys.exit(status)
def timeit(self, number=default_number):
"""Time 'number' executions of the main statement.
To be precise, this executes the setup statement once, and
then returns the time it takes to execute the main statement
a number of times, as a float measured in seconds. The
argument is the number of times through the loop, defaulting
to one million. The main statement, the setup statement and
the timer function to be used are passed to the constructor.
"""
it = itertools.repeat(None, number)
gcold = gc.isenabled()
gc.disable()
try:
timing = self.inner(it, self.timer)
finally:
if gcold:
gc.enable()
return timing
def test_free_from_gc(self):
# Check that freeing of blocks by the garbage collector doesn't deadlock
# (issue #12352).
# Make sure the GC is enabled, and set lower collection thresholds to
# make collections more frequent (and increase the probability of
# deadlock).
if not gc.isenabled():
gc.enable()
self.addCleanup(gc.disable)
thresholds = gc.get_threshold()
self.addCleanup(gc.set_threshold, *thresholds)
gc.set_threshold(10)
# perform numerous block allocations, with cyclic references to make
# sure objects are collected asynchronously by the gc
for i in range(5000):
a = multiprocessing.heap.BufferWrapper(1)
b = multiprocessing.heap.BufferWrapper(1)
# circular references
a.buddy = b
b.buddy = a
#
#
#
def test_del_newclass(self):
# __del__ methods can trigger collection, make this to happen
thresholds = gc.get_threshold()
gc.enable()
gc.set_threshold(1)
class A(object):
def __del__(self):
dir(self)
a = A()
del a
gc.disable()
gc.set_threshold(*thresholds)
# The following two tests are fragile:
# They precisely count the number of allocations,
# which is highly implementation-dependent.
# For example, disposed tuples are not freed, but reused.
# To minimize variations, though, we first store the get_count() results
# and check them at the end.
def test_main():
enabled = gc.isenabled()
gc.disable()
assert not gc.isenabled()
debug = gc.get_debug()
gc.set_debug(debug & ~gc.DEBUG_LEAK) # this test is supposed to leak
try:
gc.collect() # Delete 2nd generation garbage
run_unittest(GCTests, GCTogglingTests, GCCallbackTests)
finally:
gc.set_debug(debug)
# test gc.enable() even if GC is disabled by default
if verbose:
print("restoring automatic collection")
# make sure to always test gc.enable()
gc.enable()
assert gc.isenabled()
if not enabled:
gc.disable()
def parse_all_files(self, directory, dictionary, use_chars, cache_file):
"""
parse all files under the given directory into a list of questions,
where each element is in the form of (document, query, answer, filename)
"""
if os.path.exists(cache_file):
gc.disable()
temp = cPickle.load(open(cache_file))
gc.enable()
return temp
all_files = glob.glob(directory + '/*.question')
questions = []
for i, f in enumerate(all_files):
if i % 10000 == 0:
print 'parsing {}'.format(i)
questions.append(self.parse_one_file(f, dictionary, use_chars) + (f,))
questions = self.parse_ner_pos(questions)
cPickle.dump(questions, open(cache_file, 'w'), cPickle.HIGHEST_PROTOCOL)
return questions
