def _status(self, final=False):
if not final:
new = (green(len(self._completed)),
white(len(self._running)),
yellow(len(self._queued)),
green('finished'),
white('running'),
yellow('queued'))
if hasattr(self, 'last_status') and new == self.last_status:
return
self.last_status = (green(len(self._completed)),
white(len(self._running)),
yellow(len(self._queued)),
green('finished'),
white('running'),
yellow('queued'))
print WHIPE, "[%s/%s/%s] %s, %s, %s" % new
else:
print "\n[ %s OK / %s ERROR ] in %s seconds" % (
green(self._num_of_jobs - self._errors, True),
red(self._errors),
time.time() - self._time_start)
if self._errors:
print red("Failures:", True)
for job in self._completed:
if job.exitcode != 0:
print red(job.name)
sys.stdout.flush()
def open(self):
os.system("clear")
print blue("Welcome to %s" % green(self.name))
print blue("========================")
while True:
print red("How may I help you?")
print yellow("1. Buy a ticket\n"
" 2. Book a ticket by phone\n"
" 3. Book a ticket\n"
" 4. Cancel booking\n"
" 5. See how many money do you have\n"
" 6. Goodbye!\n")
option = raw_input(green("I want to: "))
if option == "1":
self.buy_ticket()
if option == "2":
self.book_ticket_by_phone()
if option == "3":
self.book_ticket()
if option == "4":
self.cancel_booking()
if option == "5":
self.money()
if option == "6":
break
def show_diff(old, new):
for k, v in new.iteritems():
if k in old.keys() and v == old[k]:
continue
if k in old.keys() and v != old[k]:
red(" - ['{}'] = {}".format(k, old[k]))
green(" + ['{}'] = {}".format(k, v))
def start(self):
os.system("clear")
while True:
print green("How can I help you, %s?" % self.user)
print yellow("1. Transfer some money\n"
" 2. Pay\n"
" 3. Retrieve\n"
" 4. Show balance\n"
" 5. Logout\n")
option = int(raw_input(blue("I want to: ")))
if option == 1 or option == 2:
to = raw_input(red("to: "))
money = raw_input(red("sum: "))
try:
print self.bank.transfer_from(self.user, to, money)
except ValueError as ve:
print red(ve)
elif option == 3:
money = raw_input(red("sum: "))
try:
if self.bank.transfer_from(self.user, self.name, money):
print green("Operation finished with success!\n")
else:
print red("Something went wrong...try again later\n")
except ValueError as ve:
print red(ve)
elif option == 4:
print self.bank.show_balance(self.user)
elif option == 5:
self.user = None
return
def run(self):
if self.is_negative:
if self._from != 10:
self.log.error(red("I dont know how to convert negative numbers if"
" there are not in decimal base"))
return False
else:
number = self.transform_negative()
else:
number = self.transform_positive()
print green("Your number is %s" % red(number))
def login(self):
print "\n\n"
username = raw_input(green("username: "))
password = getpass(green("password: "))
with open("db/clients.txt", "r") as f:
clients = f.read()
credentials = "%s:%s" % (username, sha1(password).hexdigest())
if credentials in clients:
print green("Welcome!")
self.user = username
self.start()
else:
print red("Wrong credentials!")
def path_exists(self, path, host=None, negate=False):
containers = [self.containers[host]] if host else self.containers.itervalues()
for container in containers:
if negate:
if not path_exists(path, container):
continue
print(utils.red("Found path <{}> on host <{}>".format(path, self.host_from_container(container))))
else:
if path_exists(path, container):
continue
print(utils.red("Path <{}> not found on host <{}>".format(path, self.host_from_container(container))))
return False
return True
def show_unencrypted_diff(diff_part, password_file=None):
intense(get_head(diff_part).strip())
old, new = decrypt_diff(diff_part, password_file)
diff = difflib.unified_diff(old.split('\n'), new.split('\n'), lineterm='')
# ... we'll take the git filenames from git's diff output rather than
# ... difflib
for line in islice(diff, 2, None):
if line.startswith('-'):
red(line)
elif line.startswith('+'):
green(line)
elif line.startswith('@@'):
cyan(line)
else:
print line
def handle(socket, address):
print green("Client connected")
while True:
data = socket.recv(2048)
if not data:
print red("Client disconnected")
return
message = parser(data)
if message is None:
return
if message[0] == "transfer":
transfer(message[1], socket)
def open(self):
os.system("clear")
print blue("Welcome to ") + yellow(self.bank.name)
print blue("========================\n\n")
while True:
print green("Please choose one of the action:")
print red("1. Register\n"
" 2. Login\n\n")
option = int(raw_input(yellow("I want to: ")))
if option == 1:
self.register()
elif option == 2:
self.login()
else:
print red("I dont't understand you! Please repeat")
def run(self):
pid = 0
try:
if self.silent:
self.proc = subprocess.Popen(
[self.path] + self.args,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
else:
self.proc = subprocess.Popen([self.path] + self.args)
pid = self.proc.pid
self.started = True
except Exception as e:
print(utils.red("Process start failed:") + " %s" % self.name)
print(str(e))
sys.exit(1)
try:
while self.proc.poll() is None:
self.started = True
time.sleep(self.interval)
self.started = True
self.retcode = -1 if self.proc is None else self.proc.poll()
self.proc = None
except Exception as e:
return
def main(args = None): opts = docopt.docopt( doc = __doc__, argv = args) try: if opts["--no-color"]: utils.disable_colors() if opts["--verbose"]: utils.enable_tracing() for name in opts["NAMES"]: dist = get_distribution(name) for name in required(dist): raise Error(dist.project_name, "required by", name) for req in dist.requires(): names = filter(lambda name: name != dist.project_name, required(req)) if not names: uninstall(req.project_name, dryrun = opts["--dry-run"]) else: utils.trace(req.project_name, "not uninstalled, used by", names) uninstall(dist.project_name, dryrun = opts["--dry-run"]) # else: # for dist in pip.get_installed_distributions(): # print utils.magenta(dist.project_name), dist.location except utils.Error as exc: raise SystemExit(utils.red(exc))
def register(self):
print "\n\n"
username = raw_input(green("username: "))
password = getpass(green("password: "))
with open("db/clients.txt", "ab+") as f:
clients = f.read()
if "%s:" % username in clients:
print red("Username already taken")
return
f.write("%s:%s\n" % (username, sha1(password).hexdigest()))
initial_deposit = raw_input(green("Initial deposit: "))
with open("clients/%s" % sha1(username).hexdigest(), "w") as g:
g.write(initial_deposit)
print green("Succesfully register!")
self.user = username
self.start()
def get_str(self, models_by_name=None, print_name=True):
s = ''
if print_name:
s = '%s : %s \t<%s>' % (red(self.name.ljust(20)), green(self.superclass.ljust(15)),
blue(self.filename))
for field in self.fields:
s += '\n%s' % field.__repr__()
if self.superclass != 'MTLModel' and models_by_name:
# Also print the fields of the superclass
s += '\n%s' % models_by_name[self.superclass].get_str(models_by_name=models_by_name,
print_name=False)
return s
def on_post_item(self, response, **kwargs):
input_file = kwargs.get('input_file', '')
source = kwargs.get('source', '')
filename = self.format_filename(input_file.replace(source, ''))
if response.success:
self._optimized += 1
self._input_bytes += response.input_size
self._output_bytes += response.output_size
print("%s %16s %37s" % (filename, green("OK"),
response.output_ratio))
else:
self._failed += 1
print("%s %18s %30s" % (filename, red("FAIL"), "-"))
def run(self):
try:
if self.silent:
self.proc = subprocess.Popen([self.path] + self.args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
else:
self.proc = subprocess.Popen([self.path] + self.args)
except Exception as e:
print(utils.red("Process start failed:") + " %s" % self.name)
print(str(e))
sys.exit(1)
try:
while self.proc.poll() is None:
time.sleep(self.interval)
self.proc = None
except:
return
print("Process %s ended" % self.name)
def profile_leaks(shell, queries, count=1, rounds=1, supp_file=None):
report = {}
for name, query in queries.iteritems():
print("Analyzing leaks in query: %s" % query)
# Apply count (optionally run the query several times).
summary = check_leaks(shell, query, count, supp_file)
display = []
for key in summary:
output = summary[key]
if output is not None and output[0] != "0":
# Add some fun colored output if leaking.
if key == "definitely":
output = utils.red(output)
report[name] = "LEAKING"
if key == "indirectly":
output = utils.yellow(output)
report[name] = "WARNING"
else:
report[name] = "SAFE"
display.append("%s: %s" % (key, output))
print(" %s" % "; ".join(display))
return report
def images_delete(self, uproot=False):
func = image_delete_and_containers if uproot else image_delete
for image in self.get_real_images():
print(utils.red("Delete image {}".format(image)))
func(image)
return self
def run(self, platform, precision=None, devices=None,
use_dispersion_correction=True):
"""
Runs the test on the given platform with the given precision model.
Parameters
----------
platform : str
Name of the OpenMM platform to use (CPU, Reference, CUDA, or OpenCL)
precision : str
Precision model to use for CUDA or OpenCL (single, double, or mixed)
devices : int or tuple of ints
Which GPUs to run on (a tuple will run in parallel)
"""
if not platform in ('CPU', 'Reference', 'CUDA', 'OpenCL'):
raise ValueError('Platform %s not recognized.' % platform)
# Define our platform and our platform properties
plat = mm.Platform.getPlatformByName(platform)
properties = None
if platform == 'CUDA':
if not precision in ('mixed', 'double', 'single'):
raise ValueError('You must set the precision to single, '
'double, or mixed for the CUDA platform.')
properties = dict(CudaPrecision=precision)
if devices is not None:
properties['CudaDeviceIndex'] = str(devices)
elif platform == 'OpenCL':
if not precision in ('mixed', 'double', 'single'):
raise ValueError('You must set the precision to single, '
'double, or mixed for the CUDA platform.')
properties = dict(OpenCLPrecision=precision)
if devices is not None:
properties['OpenCLDeviceIndex'] = str(devices)
# Create a new system with no charges so we can compare vdW and EEL
# energies to Amber
parmcopy = copy(self.parm)
for i in range(len(parmcopy.parm_data['CHARGE'])):
parmcopy.parm_data['CHARGE'][i] = 0.0
system = parmcopy.createSystem(nonbondedCutoff=8.0*u.angstroms,
nonbondedMethod=app.PME)
system.setDefaultPeriodicBoxVectors(*self.parm.box_vectors)
# Test serialization
xmlsys = mm.XmlSerializer.deserialize(
mm.XmlSerializer.serialize(self.system)
)
# Loop through all systems and turn on or off the dispersion correction
print 'Trying to set PME parameters...',
succeeded = None
for sysmod in (self.system, self.systemapp, system, xmlsys):
for force in sysmod.getForces():
if isinstance(force, mm.NonbondedForce):
force.setUseDispersionCorrection(use_dispersion_correction)
# See if we can set the PME parameters
try:
force.setPMEParameters(3.285326106/u.nanometers,
60, 64, 60)
succeeded = True
except AttributeError:
# This version of OpenMM does not support setting PME
# parameters
succeeded = False
if succeeded:
print 'Changed.'
elif succeeded is None:
print 'No NonbondedForce detected.'
else:
print 'OpenMM is too old. Could not change PME parameters.'
# Define some integrators
dummyint1 = mm.VerletIntegrator(1.0e-6*u.picoseconds)
dummyint2 = mm.VerletIntegrator(1.0e-6*u.picoseconds)
dummyint3 = mm.VerletIntegrator(1.0e-6*u.picoseconds)
dummyint4 = mm.VerletIntegrator(1.0e-6*u.picoseconds)
# Define the contexts
if properties is None:
context1 = mm.Context(self.system, dummyint1, plat)
context2 = mm.Context(system, dummyint2, plat)
context3 = mm.Context(self.systemapp, dummyint3, plat)
context4 = mm.Context(xmlsys, dummyint4, plat)
else:
context1 = mm.Context(self.system, dummyint1, plat, properties)
context2 = mm.Context(system, dummyint2, plat, properties)
context3 = mm.Context(self.systemapp, dummyint3, plat,
properties)
context4 = mm.Context(xmlsys, dummyint4, plat, properties)
# Set the context positions
context1.setPositions(self.parm.positions)
context2.setPositions(self.parm.positions)
context3.setPositions(self.crdapp.getPositions())
context4.setPositions(self.parm.positions)
# Get the energies
eunit = u.kilocalories_per_mole
state = context1.getState(getEnergy=True, getForces=True,
enforcePeriodicBox=True)
funit = eunit / u.angstrom
forces = state.getForces().value_in_unit(funit)
tote = state.getPotentialEnergy().value_in_unit(eunit)
state = context3.getState(getEnergy=True, enforcePeriodicBox=True)
toteapp = state.getPotentialEnergy().value_in_unit(eunit)
state = context4.getState(getEnergy=True, enforcePeriodicBox=True)
xmltote = state.getPotentialEnergy().value_in_unit(eunit)
# Now get the decomposed energies from both the system and the
# deserialized system to check that serialization and deserialization
# behave as expected with these force objects and force groups
state = context1.getState(getEnergy=True, enforcePeriodicBox=True,
groups=2**self.parm.BOND_FORCE_GROUP)
bonde = state.getPotentialEnergy().value_in_unit(eunit)
state = context4.getState(getEnergy=True, enforcePeriodicBox=True,
groups=2**self.parm.BOND_FORCE_GROUP)
xmlbonde = state.getPotentialEnergy().value_in_unit(eunit)
state = context1.getState(getEnergy=True, enforcePeriodicBox=True,
groups=2**self.parm.ANGLE_FORCE_GROUP)
anglee = state.getPotentialEnergy().value_in_unit(eunit)
state = context4.getState(getEnergy=True, enforcePeriodicBox=True,
groups=2**self.parm.ANGLE_FORCE_GROUP)
xmlanglee = state.getPotentialEnergy().value_in_unit(eunit)
state = context1.getState(getEnergy=True, enforcePeriodicBox=True,
groups=2**self.parm.DIHEDRAL_FORCE_GROUP)
dihede = state.getPotentialEnergy().value_in_unit(eunit)
state = context4.getState(getEnergy=True, enforcePeriodicBox=True,
groups=2**self.parm.DIHEDRAL_FORCE_GROUP)
xmldihede = state.getPotentialEnergy().value_in_unit(eunit)
state = context1.getState(getEnergy=True, enforcePeriodicBox=True,
groups=2**self.parm.NONBONDED_FORCE_GROUP)
nonbe = state.getPotentialEnergy().value_in_unit(eunit)
state = context4.getState(getEnergy=True, enforcePeriodicBox=True,
groups=2**self.parm.NONBONDED_FORCE_GROUP)
xmlnonbe = state.getPotentialEnergy().value_in_unit(eunit)
state = context2.getState(getEnergy=True, enforcePeriodicBox=True,
groups=2**self.parm.NONBONDED_FORCE_GROUP)
vdwe = state.getPotentialEnergy().value_in_unit(eunit)
eele = nonbe - vdwe
# Now get the sander forces and compare them
traj = netcdf_file(get_fn('sander_pme.nc'), 'r')
sander_forces = traj.variables['forces'][0]
maxdif = [abs(ofrc-sfrc)
for ofrc, sfrc in zip(forces[0], sander_forces[0])]
maxrel = [abs(ofrc-sfrc)/sfrc
for ofrc, sfrc in zip(forces[0], sander_forces[0])]
avgdif = [0, 0, 0]
avgrel = [0, 0, 0]
n = 0
for ofrcs, sfrcs in zip(forces, sander_forces):
for i, sfrc in enumerate(sfrcs):
ofrc = ofrcs[i]
dif = abs(ofrc-sfrc)
rel = dif/sfrc
maxdif[i] = max(maxdif[i], dif)
maxrel[i] = max(maxrel[i], rel)
avgdif[i] += dif
avgrel[i] += rel
n += 1
avgdif = [x/n for x in avgdif]
avgrel = [x/n for x in avgrel]
# The sander energies are:
# Etot = -69285.4160 EKtot = 0.0000 EPtot = -69285.4160
# BOND = 404.9439 ANGLE = 1003.4499 DIHED = 2231.7367
# 1-4 NB = 440.7084 1-4 EEL = 3818.2959 VDWAALS = 8271.5191
# EELEC = -85456.0701 EHBOND = 0.0000 RESTRAINT = 0.0000
sander = dict(bond=404.9439, angle=1003.4499, dihedral=2231.7367,
vdw=8271.5191+440.7084, eel=-85456.0701+3818.2959,
total=-69285.4160)
if not use_dispersion_correction:
# Without the long-range dispersion correction, VDWAALS = 8943.8420
sander['total'] -= sander['vdw']
sander['vdw'] = 8943.8420 + 440.7084
sander['total'] += sander['vdw']
bonddif = bonde - sander['bond']
angledif = anglee - sander['angle']
diheddif = dihede - sander['dihedral']
vdwdif = vdwe - sander['vdw'] # includes 1-4 also
eeldif = eele - sander['eel'] # Includes 1-4 also
totaldif = tote - sander['total']
appdif = tote - toteapp
print 'Energy differences compared to sander/Amber (kcal/mol)'
print ' Absolute Relative sander'
print '------------------------------------------------------'
print 'Bond =', colorize_error(bonddif), \
colorize_error(bonddif/sander['bond'], 1e-6), \
'%12.4f'%sander['bond']
print 'Angle =', colorize_error(angledif), \
colorize_error(angledif/sander['angle'], 1e-6), \
'%12.4f'%sander['angle']
print 'Dihedral =', colorize_error(diheddif), \
colorize_error(diheddif/sander['dihedral'], 1e-6), \
'%12.4f'%sander['dihedral']
if use_dispersion_correction:
# The dispersion correction in Amber neglects the repulsive part of
# the correction, but OpenMM does not. Therefore, when we are using
# the dispersion correction we should allow for a slightly larger
# energy difference.
print 'vdWaals =', colorize_error(vdwdif, 1.0), \
colorize_error(vdwdif/sander['vdw'], 1e-4), \
'%12.4f'%sander['vdw']
else:
print 'vdWaals =', colorize_error(vdwdif, 1e-2), \
colorize_error(vdwdif/sander['vdw'], 1e-6), \
'%12.4f'%sander['vdw']
print 'Elec =', colorize_error(eeldif, 4e0), \
colorize_error(eeldif/sander['eel'], 1e-3), '%12.4f'%sander['eel']
print 'Total =', colorize_error(totaldif, 4e0), \
colorize_error(totaldif/sander['total'], 1e-3), \
'%12.4f'%sander['total']
print ''
print 'Difference b/w ParmEd and OpenMM App layer'
print '------------------------------------------'
print 'Total =', colorize_error(appdif, tolerance=5e-3)
print ''
print 'Difference b/w sander and OpenMM forces'
print '---------------------------------------'
print 'Maximum deviation = [%12s, %12s, %12s]' % colorize_list(maxdif,2e0)
print 'Maximum rel. dev. = [%12s, %12s, %12s]' % colorize_list(maxrel,2e0)
print 'Average deviation = [%12s, %12s, %12s]' % colorize_list(avgdif,1e-1)
print 'Average rel. dev. = [%12s, %12s, %12s]' % colorize_list(avgrel,5e-1)
# Now test serialization
CUTOFF = 1e-5
CUTOFFNB = 1e-2
print ''
print 'Serialization tests'
print '-------------------'
print 'Bond........',
if abs(xmlbonde - bonde) < CUTOFF:
print green('OK')
else:
dif = xmlbonde - bonde
print red('off by %.4e (%f%%)' % (dif, 100*dif/(bonde or xmlbonde)))
print 'Angle.......',
if abs(xmlanglee - anglee) < CUTOFF:
print green('OK')
else:
dif = xmlanglee - anglee
print red('off by %.4e (%f%%)' % (dif,100*dif/(anglee or xmlanglee)))
print 'Dihedral....',
if abs(xmldihede - dihede) < CUTOFF:
print green('OK')
else:
dif = xmldihede - dihede
print red('off by %.4e (%f%%)' % (dif,100*dif/(dihede or xmldihede)))
print 'Nonbonded...',
if abs(xmlnonbe - nonbe) < CUTOFFNB:
print green('OK')
else:
dif = xmlnonbe - nonbe
print red('off by %.4e (%f%%)' % (dif,100*dif/(nonbe or xmlnonbe)))
def _dump_data(name, data):
try:
with open(name, 'wb') as fh: fh.write(data)
print "Wrote: %s" % (red(name))
except Exception, e:
print "Error: could not write (%s), (%s)." % (name, str(e))
for match in call[crawler].crawl_full():
with matchfile(match) as fw:
fw.write(str(match) + '\n')
if 0 < match.tostart < 3600 and not tbd in match.teams:
pool[match.webpage] = match
except KeyboardInterrupt:
sys.exit(0)
except Exception as e:
cooldown[crawler] = time.time() + cd
print('{0} cooldowned for {1}s for exception'.format(crawler, cd))
print(e)
cd += 0
with open('httpalias', 'a') as fw:
G = networkx.Graph()
print('{0} matches start <1h'.format(len(G)))
for s1, s2 in itertools.combinations(pool.values(), 2):
if domain(s1) == domain(s2) or not s1 == s2:
continue
G.add_edge(s1.webpage, s2.webpage)
for idx, c in enumerate(networkx.connected_components(G)):
fw.write(' '.join(c) + '\n')
print('###MATCHED### {0}: '.format(idx) + ' '.join(c))
profit = (max([pool[w].returns[0] for w in c]) - 1) * (max([pool[w].returns[1] for w in c]) - 1) - 1
if profit < profit_trs:
continue
print(red(' PROFIT {0:.3}'.format(profit)))
for w in c:
s = pool[w]
print(red(' {0} {1} ({2}): {3}/{4} {5} {6}'.format(s.teams[0], s.teams[1], s.series, s.returns, s.poolsize, domain(s), s.tostart)))
time.sleep(5)
