positive stringlengths 100 30.3k | anchor stringlengths 1 15k |
|---|---|
def apply_patch(patchfile,cwd=None,posix=False,level=0):
"""call 'patch -p[level] [--posix] < arg1'
posix mode is sometimes necessary. It keeps empty files so that
dpkg-source removes their contents.
"""
if not os.path.exists(patchfile):
raise RuntimeError('patchfile "%s" does not exist'%patchfile)
fd = open(patchfile,mode='r')
level_str = '-p%d'%level
args = ['/usr/bin/patch',level_str]
if posix:
args.append('--posix')
log.info('PATCH COMMAND: %s < %s', ' '.join(args), patchfile)
log.info(' PATCHING in dir: %s', cwd)
# print >> sys.stderr, 'PATCH COMMAND:',' '.join(args),'<',patchfile
# print >> sys.stderr, ' PATCHING in dir:',cwd
res = subprocess.Popen(
args, cwd=cwd,
stdin=fd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True
)
returncode=None
while returncode is None:
returncode = res.poll()
ready = select.select( [res.stdout,res.stderr],[],[],0.1)
# XXX figure out how to do this without reading byte-by-byte
if res.stdout in ready[0]:
sys.stdout.write(res.stdout.read(1))
sys.stdout.flush()
if res.stderr in ready[0]:
sys.stderr.write(res.stderr.read(1))
sys.stderr.flush()
# finish outputting file
sys.stdout.write(res.stdout.read())
sys.stdout.flush()
sys.stderr.write(res.stderr.read())
sys.stderr.flush()
if returncode:
log.error('ERROR running: %s', ' '.join(args))
log.error('ERROR in %s', cwd)
# print >> sys.stderr, 'ERROR running: %s'%(' '.join(args),)
# print >> sys.stderr, 'ERROR in',cwd
raise RuntimeError('returncode %d'%returncode) | call 'patch -p[level] [--posix] < arg1'
posix mode is sometimes necessary. It keeps empty files so that
dpkg-source removes their contents. |
def rank(self, n, mu, sigma, crit=.5, upper=10000, xtol=1):
"""%(super)s
Additional Parameters
----------------------
{0}
"""
return _make_rank(self, n, mu, sigma, crit=crit, upper=upper,
xtol=xtol) | %(super)s
Additional Parameters
----------------------
{0} |
async def cellAuthToHive(dirn, auth):
'''
Migrate old cell Auth() data into a HiveAuth().
'''
logger.warning('migrating old cell auth to hive')
path = os.path.join(dirn, 'auth.lmdb')
lenv = lmdb.open(path, max_dbs=128)
userdb = lenv.open_db(b'users')
roledb = lenv.open_db(b'roles')
migrated_roles = False
migrated_users = False
with lenv.begin() as xact:
with xact.cursor(db=roledb) as curs:
for lkey, lval in curs.iternext():
name = lkey.decode('utf8')
info = s_msgpack.un(lval)
logger.info(f'Migrating role: {name}')
role = auth.getRoleByName(name)
if role is None:
logger.info(f'Creating role: {name}')
role = await auth.addRole(name)
rules = info.get('rules', ())
await role.setRules(rules)
migrated_roles = True
if not migrated_roles: # pragma: no cover
logger.info('No roles were migrated.')
with xact.cursor(db=userdb) as curs:
for lkey, lval in curs.iternext():
name = lkey.decode('utf8')
info = s_msgpack.un(lval)
logger.info(f'Migrating user: {name}')
user = auth.getUserByName(name)
if user is None:
logger.info(f'Creating user: {name}')
user = await auth.addUser(name)
if info.get('admin', False):
await user.setAdmin(True)
if info.get('locked', False):
await user.setLocked(True)
# set this directly since we only have the shadow
shadow = info.get('shadow')
if shadow is not None:
await user.info.set('passwd', shadow)
rules = info.get('rules', ())
await user.setRules(rules)
for name in info.get('roles', ()):
await user.grant(name)
migrated_users = True
if not migrated_users: # pragma: no cover
logger.info('No users were migrated.')
lenv.sync()
lenv.close() | Migrate old cell Auth() data into a HiveAuth(). |
def cached_get(timeout, *params):
"""Decorator applied specifically to a view's get method"""
def decorator(view_func):
@wraps(view_func, assigned=available_attrs(view_func))
def _wrapped_view(view_or_request, *args, **kwargs):
# The type of the request gets muddled when using a function based
# decorator. We must use a function based decorator so it can be
# used in urls.py.
request = getattr(view_or_request, "request", view_or_request)
if not hasattr(_thread_locals, "ultracache_request"):
setattr(_thread_locals, "ultracache_request", request)
# If request not GET or HEAD never cache
if request.method.lower() not in ("get", "head"):
return view_func(view_or_request, *args, **kwargs)
# If request contains messages never cache
l = 0
try:
l = len(request._messages)
except (AttributeError, TypeError):
pass
if l:
return view_func(view_or_request, *args, **kwargs)
# Compute a cache key
li = [str(view_or_request.__class__), view_func.__name__]
# request.get_full_path is implicitly added it no other request
# path is provided. get_full_path includes the querystring and is
# the more conservative approach but makes it trivially easy for a
# request to bust through the cache.
if not set(params).intersection(set((
"request.get_full_path()", "request.path", "request.path_info"
))):
li.append(request.get_full_path())
if "django.contrib.sites" in settings.INSTALLED_APPS:
li.append(get_current_site_pk(request))
# Pre-sort kwargs
keys = list(kwargs.keys())
keys.sort()
for key in keys:
li.append("%s,%s" % (key, kwargs[key]))
# Extend cache key with custom variables
for param in params:
if not isinstance(param, str):
param = str(param)
li.append(eval(param))
s = ":".join([str(l) for l in li])
hashed = hashlib.md5(s.encode("utf-8")).hexdigest()
cache_key = "ucache-get-%s" % hashed
cached = cache.get(cache_key, None)
if cached is None:
# The get view as outermost caller may bluntly set _ultracache
request._ultracache = []
response = view_func(view_or_request, *args, **kwargs)
content = None
if isinstance(response, TemplateResponse):
content = response.render().rendered_content
elif isinstance(response, HttpResponse):
content = response.content
if content is not None:
headers = getattr(response, "_headers", {})
cache.set(
cache_key,
{"content": content, "headers": headers},
timeout
)
cache_meta(request, cache_key)
else:
response = HttpResponse(cached["content"])
# Headers has a non-obvious format
for k, v in cached["headers"].items():
response[v[0]] = v[1]
return response
return _wrapped_view
return decorator | Decorator applied specifically to a view's get method |
def _create_metadata_converter_action(self):
"""Create action for showing metadata converter dialog."""
icon = resources_path('img', 'icons', 'show-metadata-converter.svg')
self.action_metadata_converter = QAction(
QIcon(icon),
self.tr('InaSAFE Metadata Converter'),
self.iface.mainWindow())
self.action_metadata_converter.setStatusTip(self.tr(
'Convert metadata from version 4.3 to version 3.5.'))
self.action_metadata_converter.setWhatsThis(self.tr(
'Use this tool to convert metadata 4.3 to version 3.5'))
self.action_metadata_converter.triggered.connect(
self.show_metadata_converter)
self.add_action(
self.action_metadata_converter, add_to_toolbar=self.full_toolbar) | Create action for showing metadata converter dialog. |
def _orientation_ok_to_bridge_contigs(self, start_hit, end_hit):
'''Returns True iff the orientation of the hits means that the query contig of both hits can bridge the reference contigs of the hits'''
assert start_hit.qry_name == end_hit.qry_name
if start_hit.ref_name == end_hit.ref_name:
return False
if (
(self._is_at_ref_end(start_hit) and start_hit.on_same_strand())
or (self._is_at_ref_start(start_hit) and not start_hit.on_same_strand())
):
start_hit_ok = True
else:
start_hit_ok = False
if (
(self._is_at_ref_start(end_hit) and end_hit.on_same_strand())
or (self._is_at_ref_end(end_hit) and not end_hit.on_same_strand())
):
end_hit_ok = True
else:
end_hit_ok = False
return start_hit_ok and end_hit_ok | Returns True iff the orientation of the hits means that the query contig of both hits can bridge the reference contigs of the hits |
def get_value(self, **kwargs):
"""Return the value for a specific key."""
key = tuple(kwargs[group] for group in self.groups)
if key not in self.data:
self.data[key] = 0
return self.data[key] | Return the value for a specific key. |
def get_one_parameter(self, regex_exp, parameters):
"""
Get three parameters from a given regex expression
Raise an exception if more than three were found
:param regex_exp:
:param parameters:
:return:
"""
Rx, other = self.get_parameters(regex_exp, parameters)
if other is not None and other.strip():
raise iarm.exceptions.ParsingError("Extra arguments found: {}".format(other))
return Rx.upper() | Get three parameters from a given regex expression
Raise an exception if more than three were found
:param regex_exp:
:param parameters:
:return: |
def silent_execute(self, code):
"""Execute code in the kernel without increasing the prompt"""
try:
self.kernel_client.execute(to_text_string(code), silent=True)
except AttributeError:
pass | Execute code in the kernel without increasing the prompt |
def check_out_item(self, expiration):
"""Get the highest-priority item out of this queue.
Returns the item, or None if no items are available. The item
must be either ``return_item()`` or ``renew_item()`` before
``expiration`` seconds pass, or it will become available to
future callers. The item will be marked as being owned by
``worker_id``.
"""
conn = redis.StrictRedis(connection_pool=self.pool)
self._run_expiration(conn)
expiration += time.time()
script = conn.register_script("""
local item = redis.call("zrevrange", KEYS[1], 0, 0)
if #item == 0 then return nil end
item = item[1]
redis.call("zrem", KEYS[1], item)
redis.call("zadd", KEYS[2], ARGV[1], item)
redis.call("hset", KEYS[3], "i" .. item, "w" .. ARGV[2])
redis.call("hset", KEYS[3], "w" .. ARGV[2], "i" .. item)
return item
""")
result = script(keys=[self._key_available(), self._key_expiration(),
self._key_workers()],
args=[expiration, self._get_worker_id(conn)])
return result | Get the highest-priority item out of this queue.
Returns the item, or None if no items are available. The item
must be either ``return_item()`` or ``renew_item()`` before
``expiration`` seconds pass, or it will become available to
future callers. The item will be marked as being owned by
``worker_id``. |
def application_adapter(obj, request):
"""
Adapter for rendering a :class:`pyramid_urireferencer.models.ApplicationResponse` to json.
:param pyramid_urireferencer.models.ApplicationResponse obj: The response to be rendered.
:rtype: :class:`dict`
"""
return {
'title': obj.title,
'uri': obj.uri,
'service_url': obj.service_url,
'success': obj.success,
'has_references': obj.has_references,
'count': obj.count,
'items': [{
'uri': i.uri,
'title': i.title
} for i in obj.items] if obj.items is not None else None
} | Adapter for rendering a :class:`pyramid_urireferencer.models.ApplicationResponse` to json.
:param pyramid_urireferencer.models.ApplicationResponse obj: The response to be rendered.
:rtype: :class:`dict` |
def store_sentry(self, username, sentry_bytes):
"""
Store sentry bytes under a username
:param username: username
:type username: :class:`str`
:return: Whenver the operation succeed
:rtype: :class:`bool`
"""
filepath = self._get_sentry_path(username)
if filepath:
try:
with open(filepath, 'wb') as f:
f.write(sentry_bytes)
return True
except IOError as e:
self._LOG.error("store_sentry: %s" % str(e))
return False | Store sentry bytes under a username
:param username: username
:type username: :class:`str`
:return: Whenver the operation succeed
:rtype: :class:`bool` |
def Freqs(self,jr,jphi,jz,**kwargs):
"""
NAME:
Freqs
PURPOSE:
return the frequencies corresponding to a torus
INPUT:
jr - radial action (scalar)
jphi - azimuthal action (scalar)
jz - vertical action (scalar)
tol= (object-wide value) goal for |dJ|/|J| along the torus
OUTPUT:
(OmegaR,Omegaphi,Omegaz)
HISTORY:
2015-08-07 - Written - Bovy (UofT)
"""
out= actionAngleTorus_c.actionAngleTorus_Freqs_c(\
self._pot,
jr,jphi,jz,
tol=kwargs.get('tol',self._tol))
if out[3] != 0:
warnings.warn("actionAngleTorus' AutoFit exited with non-zero return status %i: %s" % (out[3],_autofit_errvals[out[3]]),
galpyWarning)
return out | NAME:
Freqs
PURPOSE:
return the frequencies corresponding to a torus
INPUT:
jr - radial action (scalar)
jphi - azimuthal action (scalar)
jz - vertical action (scalar)
tol= (object-wide value) goal for |dJ|/|J| along the torus
OUTPUT:
(OmegaR,Omegaphi,Omegaz)
HISTORY:
2015-08-07 - Written - Bovy (UofT) |
def __dbfRecord(self, record):
"""Writes the dbf records."""
f = self.__getFileObj(self.dbf)
if self.recNum == 0:
# first records, so all fields should be set
# allowing us to write the dbf header
# cannot change the fields after this point
self.__dbfHeader()
# begin
self.recNum += 1
if not self.fields[0][0].startswith("Deletion"):
f.write(b' ') # deletion flag
for (fieldName, fieldType, size, deci), value in zip(self.fields, record):
fieldType = fieldType.upper()
size = int(size)
if fieldType in ("N","F"):
# numeric or float: number stored as a string, right justified, and padded with blanks to the width of the field.
if value in MISSING:
value = b"*"*size # QGIS NULL
elif not deci:
# force to int
try:
# first try to force directly to int.
# forcing a large int to float and back to int
# will lose information and result in wrong nr.
value = int(value)
except ValueError:
# forcing directly to int failed, so was probably a float.
value = int(float(value))
value = format(value, "d")[:size].rjust(size) # caps the size if exceeds the field size
else:
value = float(value)
value = format(value, ".%sf"%deci)[:size].rjust(size) # caps the size if exceeds the field size
elif fieldType == "D":
# date: 8 bytes - date stored as a string in the format YYYYMMDD.
if isinstance(value, date):
value = '{:04d}{:02d}{:02d}'.format(value.year, value.month, value.day)
elif isinstance(value, list) and len(value) == 3:
value = '{:04d}{:02d}{:02d}'.format(*value)
elif value in MISSING:
value = b'0' * 8 # QGIS NULL for date type
elif is_string(value) and len(value) == 8:
pass # value is already a date string
else:
raise ShapefileException("Date values must be either a datetime.date object, a list, a YYYYMMDD string, or a missing value.")
elif fieldType == 'L':
# logical: 1 byte - initialized to 0x20 (space) otherwise T or F.
if value in MISSING:
value = b' ' # missing is set to space
elif value in [True,1]:
value = b'T'
elif value in [False,0]:
value = b'F'
else:
value = b' ' # unknown is set to space
else:
# anything else is forced to string, truncated to the length of the field
value = b(value, self.encoding, self.encodingErrors)[:size].ljust(size)
if not isinstance(value, bytes):
# just in case some of the numeric format() and date strftime() results are still in unicode (Python 3 only)
value = b(value, 'ascii', self.encodingErrors) # should be default ascii encoding
if len(value) != size:
raise ShapefileException(
"Shapefile Writer unable to pack incorrect sized value"
" (size %d) into field '%s' (size %d)." % (len(value), fieldName, size))
f.write(value) | Writes the dbf records. |
def to_python(self, value):
"""
"Called during deserialization and during the clean() method used
from forms.... [s]hould deal gracefully with... (*) an instance of
the correct type; (*) a string; (*) None (if the field allows
null=True)."
"For ``to_python()``, if anything goes wrong during value conversion,
you should raise a ``ValidationError`` exception."
"""
if value is None:
return value
if not isinstance(value, str):
return value
try:
return json_decode(value)
except Exception as err:
raise ValidationError(repr(err)) | "Called during deserialization and during the clean() method used
from forms.... [s]hould deal gracefully with... (*) an instance of
the correct type; (*) a string; (*) None (if the field allows
null=True)."
"For ``to_python()``, if anything goes wrong during value conversion,
you should raise a ``ValidationError`` exception." |
def value(self):
"""returns the object as dictionary"""
if self._outline is None:
return {
"type" : "esriSMS",
"style" : self._style,
"color" : self._color.value,
"size" : self._size,
"angle" : self._angle,
"xoffset" : self._xoffset,
"yoffset" : self._yoffset
}
else:
return {
"type" : "esriSMS",
"style" : self._style,
"color" : self._color.value,
"size" : self._size,
"angle" : self._angle,
"xoffset" : self._xoffset,
"yoffset" : self._yoffset,
"outline" : {
"width" : self._outline['width'],
"color" : self._color.value
}
} | returns the object as dictionary |
def getAggregation(self):
"""Returns:
str : URIRef of the Aggregation entity
"""
self._check_initialized()
return [
o for o in self.subjects(predicate=rdflib.RDF.type, object=ORE.Aggregation)
][0] | Returns:
str : URIRef of the Aggregation entity |
def connect(self,
fedora_url,
data=None,
method='Get'):
"""Method attempts to connect to REST servers of the Fedora
Commons repository using optional data parameter.
Args:
fedora_url(string): Fedora URL
data(dict): Data to through to REST endpoint
method(str): REST Method, defaults to GET
Returns:
result(string): Response string from Fedora
"""
if data is None:
data = {}
if not fedora_url.startswith("http"):
fedora_url = urllib.parse.urljoin(self.base_url, fedora_url)
request = urllib.request.Request(fedora_url,
method=method)
request.add_header('Accept', 'text/turtle')
request.add_header('Content-Type', 'text/turtle')
if len(data) > 0:
request.data = data
try:
response = urllib.request.urlopen(request)
except urllib.error.URLError as err:
if hasattr(err, 'reason'):
print("failed to reach server at {} with {} method".format(
fedora_url,
request.method))
print("Reason: ", err.reason)
print("Data: ", data)
elif hasattr(err, 'code'):
print("Server error {}".format(err.code))
raise err
return response | Method attempts to connect to REST servers of the Fedora
Commons repository using optional data parameter.
Args:
fedora_url(string): Fedora URL
data(dict): Data to through to REST endpoint
method(str): REST Method, defaults to GET
Returns:
result(string): Response string from Fedora |
def padding(self):
"""Returns the padding algorithm used, if this is the same for all dims.
Use `.paddings` if you want a tuple with the padding algorithm used for each
dimension.
Returns:
The padding algorithm used, if this is the same for all dimensions.
Raises:
ValueError: If different padding algorithms are used for different
dimensions.
"""
# This is for backwards compatibility -- previously only a single
# padding setting was supported across all dimensions.
if all(p == self._padding[0] for p in self._padding):
return self._padding[0]
else:
raise ValueError("This layer uses different paddings for different "
"dimensions. Use .paddings if you want a tuple of "
"per-dimension padding settings.") | Returns the padding algorithm used, if this is the same for all dims.
Use `.paddings` if you want a tuple with the padding algorithm used for each
dimension.
Returns:
The padding algorithm used, if this is the same for all dimensions.
Raises:
ValueError: If different padding algorithms are used for different
dimensions. |
def __detect_cl_tool(env, chainkey, cdict, cpriority=None):
"""
Helper function, picks a command line tool from the list
and initializes its environment variables.
"""
if env.get(chainkey,'') == '':
clpath = ''
if cpriority is None:
cpriority = cdict.keys()
for cltool in cpriority:
if __debug_tool_location:
print("DocBook: Looking for %s"%cltool)
clpath = env.WhereIs(cltool)
if clpath:
if __debug_tool_location:
print("DocBook: Found:%s"%cltool)
env[chainkey] = clpath
if not env[chainkey + 'COM']:
env[chainkey + 'COM'] = cdict[cltool]
break | Helper function, picks a command line tool from the list
and initializes its environment variables. |
def clean_requires_python(candidates):
"""Get a cleaned list of all the candidates with valid specifiers in the `requires_python` attributes."""
all_candidates = []
sys_version = ".".join(map(str, sys.version_info[:3]))
from packaging.version import parse as parse_version
py_version = parse_version(os.environ.get("PIP_PYTHON_VERSION", sys_version))
for c in candidates:
from_location = attrgetter("location.requires_python")
requires_python = getattr(c, "requires_python", from_location(c))
if requires_python:
# Old specifications had people setting this to single digits
# which is effectively the same as '>=digit,<digit+1'
if requires_python.isdigit():
requires_python = ">={0},<{1}".format(
requires_python, int(requires_python) + 1
)
try:
specifierset = SpecifierSet(requires_python)
except InvalidSpecifier:
continue
else:
if not specifierset.contains(py_version):
continue
all_candidates.append(c)
return all_candidates | Get a cleaned list of all the candidates with valid specifiers in the `requires_python` attributes. |
def acquire(self, host: str, port: int, use_ssl: bool=False,
host_key: Optional[Any]=None) \
-> Union[Connection, SSLConnection]:
'''Return an available connection.
Args:
host: A hostname or IP address.
port: Port number.
use_ssl: Whether to return a SSL connection.
host_key: If provided, it overrides the key used for per-host
connection pooling. This is useful for proxies for example.
Coroutine.
'''
assert isinstance(port, int), 'Expect int. Got {}'.format(type(port))
assert not self._closed
yield from self._process_no_wait_releases()
if use_ssl:
connection_factory = functools.partial(
self._ssl_connection_factory, hostname=host)
else:
connection_factory = functools.partial(
self._connection_factory, hostname=host)
connection_factory = functools.partial(
HappyEyeballsConnection, (host, port), connection_factory,
self._resolver, self._happy_eyeballs_table,
is_ssl=use_ssl
)
key = host_key or (host, port, use_ssl)
with (yield from self._host_pools_lock):
if key not in self._host_pools:
host_pool = self._host_pools[key] = HostPool(
connection_factory,
max_connections=self._max_host_count
)
self._host_pool_waiters[key] = 1
else:
host_pool = self._host_pools[key]
self._host_pool_waiters[key] += 1
_logger.debug('Check out %s', key)
connection = yield from host_pool.acquire()
connection.key = key
# TODO: Verify this assert is always true
# assert host_pool.count() <= host_pool.max_connections
# assert key in self._host_pools
# assert self._host_pools[key] == host_pool
with (yield from self._host_pools_lock):
self._host_pool_waiters[key] -= 1
return connection | Return an available connection.
Args:
host: A hostname or IP address.
port: Port number.
use_ssl: Whether to return a SSL connection.
host_key: If provided, it overrides the key used for per-host
connection pooling. This is useful for proxies for example.
Coroutine. |
def add_methods(source_class, blacklist=()):
"""Add wrapped versions of the `api` member's methods to the class.
Any methods passed in `blacklist` are not added.
Additionally, any methods explicitly defined on the wrapped class are
not added.
"""
def wrap(wrapped_fx):
"""Wrap a GAPIC method; preserve its name and docstring."""
# If this is a static or class method, then we need to *not*
# send self as the first argument.
#
# Similarly, for instance methods, we need to send self.api rather
# than self, since that is where the actual methods were declared.
instance_method = True
# If this is a bound method it's a classmethod.
self = getattr(wrapped_fx, "__self__", None)
if issubclass(type(self), type):
instance_method = False
# Okay, we have figured out what kind of method this is; send
# down the correct wrapper function.
if instance_method:
fx = lambda self, *a, **kw: wrapped_fx(self.api, *a, **kw) # noqa
return functools.wraps(wrapped_fx)(fx)
fx = lambda *a, **kw: wrapped_fx(*a, **kw) # noqa
return staticmethod(functools.wraps(wrapped_fx)(fx))
def actual_decorator(cls):
# Reflectively iterate over most of the methods on the source class
# (the GAPIC) and make wrapped versions available on this client.
for name in dir(source_class):
# Ignore all private and magic methods.
if name.startswith("_"):
continue
# Ignore anything on our blacklist.
if name in blacklist:
continue
# Retrieve the attribute, and ignore it if it is not callable.
attr = getattr(source_class, name)
if not callable(attr):
continue
# Add a wrapper method to this object.
fx = wrap(getattr(source_class, name))
setattr(cls, name, fx)
# Return the augmented class.
return cls
# Simply return the actual decorator; this is returned from this method
# and actually used to decorate the class.
return actual_decorator | Add wrapped versions of the `api` member's methods to the class.
Any methods passed in `blacklist` are not added.
Additionally, any methods explicitly defined on the wrapped class are
not added. |
def sendDocument(self, chat_id, document,
thumb=None,
caption=None,
parse_mode=None,
disable_notification=None,
reply_to_message_id=None,
reply_markup=None):
"""
See: https://core.telegram.org/bots/api#senddocument
:param document: Same as ``photo`` in :meth:`amanobot.Bot.sendPhoto`
"""
p = _strip(locals(), more=['document'])
return self._api_request_with_file('sendDocument', _rectify(p), 'document', document) | See: https://core.telegram.org/bots/api#senddocument
:param document: Same as ``photo`` in :meth:`amanobot.Bot.sendPhoto` |
def handle_verification_form(form):
"""Handle email sending verification form."""
form.process(formdata=request.form)
if form.validate_on_submit():
send_confirmation_instructions(current_user)
# NOTE: Flash message.
flash(_("Verification email sent."), category="success") | Handle email sending verification form. |
def build_tree(self, data, tagname, attrs=None, depth=0):
r"""Build xml tree.
:param data: data for build xml.
:param tagname: element tag name.
:param attrs: element attributes. Default：``None``.
:type attrs: dict or None
:param depth: element depth of the hierarchy. Default：``0``.
:type depth: int
"""
if data is None:
data = ''
indent = ('\n%s' % (self.__options['indent'] * depth)) if self.__options['indent'] else ''
if isinstance(data, utils.DictTypes):
if self.__options['hasattr'] and self.check_structure(data.keys()):
attrs, values = self.pickdata(data)
self.build_tree(values, tagname, attrs, depth)
else:
self.__tree.append('%s%s' % (indent, self.tag_start(tagname, attrs)))
iter = data.iteritems()
if self.__options['ksort']:
iter = sorted(iter, key=lambda x:x[0], reverse=self.__options['reverse'])
for k, v in iter:
attrs = {}
if self.__options['hasattr'] and isinstance(v, utils.DictTypes) and self.check_structure(v.keys()):
attrs, v = self.pickdata(v)
self.build_tree(v, k, attrs, depth+1)
self.__tree.append('%s%s' % (indent, self.tag_end(tagname)))
elif utils.is_iterable(data):
for v in data:
self.build_tree(v, tagname, attrs, depth)
else:
self.__tree.append(indent)
data = self.safedata(data, self.__options['cdata'])
self.__tree.append(self.build_tag(tagname, data, attrs)) | r"""Build xml tree.
:param data: data for build xml.
:param tagname: element tag name.
:param attrs: element attributes. Default：``None``.
:type attrs: dict or None
:param depth: element depth of the hierarchy. Default：``0``.
:type depth: int |
def _run_command(
command,
input_data=None,
stdin=None,
out_pipe=subprocess.PIPE,
err_pipe=subprocess.PIPE,
env=None,
uuid=None,
**kwargs
):
"""
Runs a command
Args:
command(list of str): args of the command to execute, including the
command itself as command[0] as `['ls', '-l']`
input_data(str): If passed, will feed that data to the subprocess
through stdin
out_pipe(int or file): File descriptor as passed to
:ref:subprocess.Popen to use as stdout
stdin(int or file): File descriptor as passed to
:ref:subprocess.Popen to use as stdin
err_pipe(int or file): File descriptor as passed to
:ref:subprocess.Popen to use as stderr
env(dict of str:str): If set, will use the given dict as env for the
subprocess
uuid(uuid): If set the command will be logged with the given uuid
converted to string, otherwise, a uuid v4 will be generated.
**kwargs: Any other keyword args passed will be passed to the
:ref:subprocess.Popen call
Returns:
lago.utils.CommandStatus: result of the interactive execution
"""
# add libexec to PATH if needed
if uuid is None:
uuid = uuid_m.uuid4()
if constants.LIBEXEC_DIR not in os.environ['PATH'].split(':'):
os.environ['PATH'
] = '%s:%s' % (constants.LIBEXEC_DIR, os.environ['PATH'])
if input_data and not stdin:
kwargs['stdin'] = subprocess.PIPE
elif stdin:
kwargs['stdin'] = stdin
if env is None:
env = os.environ.copy()
else:
env['PATH'] = ':'.join(
list(
set(
env.get('PATH', '').split(':') + os.environ['PATH']
.split(':')
),
),
)
popen = subprocess.Popen(
' '.join('"%s"' % arg for arg in command),
stdout=out_pipe,
stderr=err_pipe,
shell=True,
env=env,
**kwargs
)
out, err = popen.communicate(input_data)
LOGGER.debug(
'%s: command exit with return code: %d', str(uuid), popen.returncode
)
if out:
LOGGER.debug('%s: command stdout: %s', str(uuid), out)
if err:
LOGGER.debug('%s: command stderr: %s', str(uuid), err)
return CommandStatus(popen.returncode, out, err) | Runs a command
Args:
command(list of str): args of the command to execute, including the
command itself as command[0] as `['ls', '-l']`
input_data(str): If passed, will feed that data to the subprocess
through stdin
out_pipe(int or file): File descriptor as passed to
:ref:subprocess.Popen to use as stdout
stdin(int or file): File descriptor as passed to
:ref:subprocess.Popen to use as stdin
err_pipe(int or file): File descriptor as passed to
:ref:subprocess.Popen to use as stderr
env(dict of str:str): If set, will use the given dict as env for the
subprocess
uuid(uuid): If set the command will be logged with the given uuid
converted to string, otherwise, a uuid v4 will be generated.
**kwargs: Any other keyword args passed will be passed to the
:ref:subprocess.Popen call
Returns:
lago.utils.CommandStatus: result of the interactive execution |
def check_update ():
"""Return the following values:
(False, errmsg) - online version could not be determined
(True, None) - user has newest version
(True, (version, url string)) - update available
(True, (version, None)) - current version is newer than online version
"""
version, value = get_online_version()
if version is None:
# value is an error message
return False, value
if version == CurrentVersion:
# user has newest version
return True, None
if is_newer_version(version):
# value is an URL linking to the update package
return True, (version, value)
# user is running a local or development version
return True, (version, None) | Return the following values:
(False, errmsg) - online version could not be determined
(True, None) - user has newest version
(True, (version, url string)) - update available
(True, (version, None)) - current version is newer than online version |
def chainproperty(func):
"""Extend sure with a custom chain property."""
func = assertionproperty(func)
setattr(AssertionBuilder, func.fget.__name__, func)
return func | Extend sure with a custom chain property. |
def add_allowance(self, caller):
"""Adds a new allowance for the method.
:param: tuple caller: A tuple indicating where the method was called
:return: The new ``Allowance``.
:rtype: Allowance
"""
allowance = Allowance(self._target, self._method_name, caller)
self._allowances.insert(0, allowance)
return allowance | Adds a new allowance for the method.
:param: tuple caller: A tuple indicating where the method was called
:return: The new ``Allowance``.
:rtype: Allowance |
def load(fnames, tag='', sat_id=None):
""" Load the SuperMAG files
Parameters
-----------
fnames : (list)
List of filenames
tag : (str or NoneType)
Denotes type of file to load. Accepted types are 'indices', 'all',
'stations', and '' (for just magnetometer measurements). (default='')
sat_id : (str or NoneType)
Satellite ID for constellations, not used. (default=None)
Returns
--------
data : (pandas.DataFrame)
Object containing satellite data
meta : (pysat.Meta)
Object containing metadata such as column names and units
"""
# Ensure that there are files to load
if len(fnames) <= 0 :
return pysat.DataFrame(None), pysat.Meta(None)
# Ensure that the files are in a list
if isinstance(fnames, str):
fnames = [fnames]
# Initialise the output data
data = pds.DataFrame()
baseline = list()
# Cycle through the files
for fname in fnames:
fname = fname[:-11] # Remove date index from end of filename
file_type = path.splitext(fname)[1].lower()
# Open and load the files for each file type
if file_type == ".csv":
if tag != "indices":
temp = load_csv_data(fname, tag)
else:
temp, bline = load_ascii_data(fname, tag)
if bline is not None:
baseline.append(bline)
# Save the loaded data in the output data structure
if len(temp.columns) > 0:
data = pds.concat([data, temp], axis=0)
del temp
# If data was loaded, update the meta data
if len(data.columns) > 0:
meta = pysat.Meta()
for cc in data.columns:
meta[cc] = update_smag_metadata(cc)
meta.info = {'baseline':format_baseline_list(baseline)}
else:
meta = pysat.Meta(None)
return data, meta | Load the SuperMAG files
Parameters
-----------
fnames : (list)
List of filenames
tag : (str or NoneType)
Denotes type of file to load. Accepted types are 'indices', 'all',
'stations', and '' (for just magnetometer measurements). (default='')
sat_id : (str or NoneType)
Satellite ID for constellations, not used. (default=None)
Returns
--------
data : (pandas.DataFrame)
Object containing satellite data
meta : (pysat.Meta)
Object containing metadata such as column names and units |
def create(self, name: str, descriptor: str, value: Constant=None) -> Field:
"""
Creates a new field from `name` and `descriptor`. For example::
>>> from jawa.cf import ClassFile
>>> cf = ClassFile.create('BeerCounter')
>>> field = cf.fields.create('BeerCount', 'I')
To automatically create a static field, pass a value::
>>> from jawa.cf import ClassFile
>>> cf = ClassFile.create('BeerCounter')
>>> field = cf.fields.create(
... 'MaxBeer',
... 'I',
... cf.constants.create_integer(99)
... )
:param name: Name of the new field.
:param descriptor: Type descriptor of the new field.
:param value: Optional static value for the field.
"""
field = Field(self._cf)
name = self._cf.constants.create_utf8(name)
descriptor = self._cf.constants.create_utf8(descriptor)
field._name_index = name.index
field._descriptor_index = descriptor.index
field.access_flags.acc_public = True
if value is not None:
field.attributes.create(ConstantValueAttribute, value)
field.access_flags.acc_static = True
self.append(field)
return field | Creates a new field from `name` and `descriptor`. For example::
>>> from jawa.cf import ClassFile
>>> cf = ClassFile.create('BeerCounter')
>>> field = cf.fields.create('BeerCount', 'I')
To automatically create a static field, pass a value::
>>> from jawa.cf import ClassFile
>>> cf = ClassFile.create('BeerCounter')
>>> field = cf.fields.create(
... 'MaxBeer',
... 'I',
... cf.constants.create_integer(99)
... )
:param name: Name of the new field.
:param descriptor: Type descriptor of the new field.
:param value: Optional static value for the field. |
def get_dataset(dataset_id,**kwargs):
"""
Get a single dataset, by ID
"""
user_id = int(kwargs.get('user_id'))
if dataset_id is None:
return None
try:
dataset_rs = db.DBSession.query(Dataset.id,
Dataset.type,
Dataset.unit_id,
Dataset.name,
Dataset.hidden,
Dataset.cr_date,
Dataset.created_by,
DatasetOwner.user_id,
null().label('metadata'),
case([(and_(Dataset.hidden=='Y', DatasetOwner.user_id is not None), None)],
else_=Dataset.value).label('value')).filter(
Dataset.id==dataset_id).outerjoin(DatasetOwner,
and_(DatasetOwner.dataset_id==Dataset.id,
DatasetOwner.user_id==user_id)).one()
rs_dict = dataset_rs._asdict()
#convert the value row into a string as it is returned as a binary
if dataset_rs.value is not None:
rs_dict['value'] = str(dataset_rs.value)
if dataset_rs.hidden == 'N' or (dataset_rs.hidden == 'Y' and dataset_rs.user_id is not None):
metadata = db.DBSession.query(Metadata).filter(Metadata.dataset_id==dataset_id).all()
rs_dict['metadata'] = metadata
else:
rs_dict['metadata'] = []
except NoResultFound:
raise HydraError("Dataset %s does not exist."%(dataset_id))
dataset = namedtuple('Dataset', rs_dict.keys())(**rs_dict)
return dataset | Get a single dataset, by ID |
def lines(self: object, fileids: str, plaintext: bool = True):
"""
Tokenizes documents in the corpus by line
"""
for text in self.texts(fileids, plaintext):
text = re.sub(r'\n\s*\n', '\n', text, re.MULTILINE) # Remove blank lines
for line in text.split('\n'):
yield line | Tokenizes documents in the corpus by line |
def _add_subtitles(self, subtitles):
'''Adds subtitles to playing video.
:param subtitles: A URL to a remote subtitles file or a local filename
for a subtitles file.
.. warning:: You must start playing a video before calling this method
or it will loop for an indefinite length.
'''
# This method is named with an underscore to suggest that callers pass
# the subtitles argument to set_resolved_url instead of calling this
# method directly. This is to ensure a video is played before calling
# this method.
player = xbmc.Player()
for _ in xrange(30):
if player.isPlaying():
break
time.sleep(1)
else:
raise Exception('No video playing. Aborted after 30 seconds.')
player.setSubtitles(subtitles) | Adds subtitles to playing video.
:param subtitles: A URL to a remote subtitles file or a local filename
for a subtitles file.
.. warning:: You must start playing a video before calling this method
or it will loop for an indefinite length. |
def iter_columns(condition):
"""
Yield all columns in the condition or its inner conditions.
Unwraps proxies when the condition's column (or any of its values) include paths.
"""
# Like iter_conditions, this can't live in each condition without going possibly infinite on the
# recursion, or passing the visited set through every call. That makes the signature ugly, so we
# take care of it here. Luckily, it's pretty easy to leverage iter_conditions and just unpack the
# actual columns.
visited = set()
for condition in iter_conditions(condition):
if condition.operation in ("and", "or", "not"):
continue
# Non-meta conditions always have a column, and each of values has the potential to be a column.
# Comparison will only have a list of len 1, but it's simpler to just iterate values and check each
# unwrap proxies created for paths
column = proxied(condition.column)
# special case for None
# this could also have skipped on isinstance(condition, Condition)
# but this is slightly more flexible for users to create their own None-sentinel Conditions
if column is None:
continue
if column not in visited:
visited.add(column)
yield column
for value in condition.values:
if isinstance(value, ComparisonMixin):
if value not in visited:
visited.add(value)
yield value | Yield all columns in the condition or its inner conditions.
Unwraps proxies when the condition's column (or any of its values) include paths. |
def _logging_callback(level, domain, message, data):
""" Callback that outputs libgphoto2's logging message via
Python's standard logging facilities.
:param level: libgphoto2 logging level
:param domain: component the message originates from
:param message: logging message
:param data: Other data in the logging record (unused)
"""
domain = ffi.string(domain).decode()
message = ffi.string(message).decode()
logger = LOGGER.getChild(domain)
if level not in LOG_LEVELS:
return
logger.log(LOG_LEVELS[level], message) | Callback that outputs libgphoto2's logging message via
Python's standard logging facilities.
:param level: libgphoto2 logging level
:param domain: component the message originates from
:param message: logging message
:param data: Other data in the logging record (unused) |
def Sign(self, data, signing_key, verify_key=None):
"""Use the data to sign this blob.
Args:
data: String containing the blob data.
signing_key: The key to sign with.
verify_key: Key to verify with. If None we assume the signing key also
contains the public key.
Returns:
self for call chaining.
"""
if signing_key.KeyLen() < 2048:
logging.warning("signing key is too short.")
self.signature = signing_key.Sign(data)
self.signature_type = self.SignatureType.RSA_PKCS1v15
self.digest = hashlib.sha256(data).digest()
self.digest_type = self.HashType.SHA256
self.data = data
# Test we can verify before we send it off.
if verify_key is None:
verify_key = signing_key.GetPublicKey()
# Verify our own data.
self.Verify(verify_key)
return self | Use the data to sign this blob.
Args:
data: String containing the blob data.
signing_key: The key to sign with.
verify_key: Key to verify with. If None we assume the signing key also
contains the public key.
Returns:
self for call chaining. |
def initializerepo(self):
""" Fill empty directory with products and make first commit """
try:
os.mkdir(self.repopath)
except OSError:
pass
cmd = self.repo.init(bare=self.bare, shared=self.shared)
if not self.bare:
self.write_testing_data([], [])
self.write_training_data([], [])
self.write_classifier(None)
cmd = self.repo.add('training.pkl')
cmd = self.repo.add('testing.pkl')
cmd = self.repo.add('classifier.pkl')
cmd = self.repo.commit(m='initial commit')
cmd = self.repo.tag('initial')
cmd = self.set_version('initial') | Fill empty directory with products and make first commit |
def decimal_year(year, month, day):
"""
Allows to calculate the decimal year for a vector of dates
(TODO this is legacy code kept to maintain comparability with previous
declustering algorithms!)
:param year: year column from catalogue matrix
:type year: numpy.ndarray
:param month: month column from catalogue matrix
:type month: numpy.ndarray
:param day: day column from catalogue matrix
:type day: numpy.ndarray
:returns: decimal year column
:rtype: numpy.ndarray
"""
marker = np.array([0., 31., 59., 90., 120., 151., 181.,
212., 243., 273., 304., 334.])
tmonth = (month - 1).astype(int)
day_count = marker[tmonth] + day - 1.
dec_year = year + (day_count / 365.)
return dec_year | Allows to calculate the decimal year for a vector of dates
(TODO this is legacy code kept to maintain comparability with previous
declustering algorithms!)
:param year: year column from catalogue matrix
:type year: numpy.ndarray
:param month: month column from catalogue matrix
:type month: numpy.ndarray
:param day: day column from catalogue matrix
:type day: numpy.ndarray
:returns: decimal year column
:rtype: numpy.ndarray |
def case(self, case_id=None):
"""Return a Case object
If no case_id is given return one case
Args:
case_id (str): A case id
Returns:
case(Case): A Case object
"""
cases = self.cases()
if case_id:
for case in cases:
if case.case_id == case_id:
return case
else:
if cases:
return cases[0]
return None | Return a Case object
If no case_id is given return one case
Args:
case_id (str): A case id
Returns:
case(Case): A Case object |
def _parseDOM(istack):
"""
Recursively go through element array and create DOM.
Args:
istack (list): List of :class:`.HTMLElement` objects.
Returns:
list: DOM tree as list.
"""
ostack = []
end_tag_index = 0
def neither_nonpair_or_end_or_comment(el):
return not (el.isNonPairTag() or el.isEndTag() or el.isComment())
index = 0
while index < len(istack):
el = istack[index]
# check if this is pair tag
end_tag_index = _indexOfEndTag(istack[index:])
if end_tag_index == 0 and neither_nonpair_or_end_or_comment(el):
el.isNonPairTag(True)
if end_tag_index == 0:
if not el.isEndTag():
ostack.append(el)
else:
el.childs = _parseDOM(istack[index + 1: end_tag_index + index])
el.endtag = istack[end_tag_index + index] # reference to endtag
el.endtag.openertag = el
ostack.append(el)
ostack.append(el.endtag)
index = end_tag_index + index
index += 1
return ostack | Recursively go through element array and create DOM.
Args:
istack (list): List of :class:`.HTMLElement` objects.
Returns:
list: DOM tree as list. |
def create_resource(self, resource_type=None, uri=None):
'''
Convenience method for creating a new resource
Note: A Resource is instantiated, but is not yet created. Still requires resource.create().
Args:
uri (rdflib.term.URIRef, str): uri of resource to create
resource_type (NonRDFSource (Binary), BasicContainer, DirectContainer, IndirectContainer): resource type to create
Returns:
(NonRDFSource (Binary), BasicContainer, DirectContainer, IndirectContainer): instance of appropriate type
'''
if resource_type in [NonRDFSource, Binary, BasicContainer, DirectContainer, IndirectContainer]:
return resource_type(self, uri)
else:
raise TypeError("expecting Resource type, such as BasicContainer or NonRDFSource") | Convenience method for creating a new resource
Note: A Resource is instantiated, but is not yet created. Still requires resource.create().
Args:
uri (rdflib.term.URIRef, str): uri of resource to create
resource_type (NonRDFSource (Binary), BasicContainer, DirectContainer, IndirectContainer): resource type to create
Returns:
(NonRDFSource (Binary), BasicContainer, DirectContainer, IndirectContainer): instance of appropriate type |
def list_():
'''
Return a list of accepted, denied, unaccepted and rejected keys.
This is the same output as `salt-key -L`
CLI Example:
.. code-block:: bash
salt 'master' minion.list
'''
pki_dir = __salt__['config.get']('pki_dir', '')
# We have to replace the minion/master directories
pki_dir = pki_dir.replace('minion', 'master')
# The source code below is (nearly) a copy of salt.key.Key.list_keys
key_dirs = _check_minions_directories(pki_dir)
ret = {}
for dir_ in key_dirs:
ret[os.path.basename(dir_)] = []
try:
for fn_ in salt.utils.data.sorted_ignorecase(os.listdir(dir_)):
if not fn_.startswith('.'):
if os.path.isfile(os.path.join(dir_, fn_)):
ret[os.path.basename(dir_)].append(fn_)
except (OSError, IOError):
# key dir kind is not created yet, just skip
continue
return ret | Return a list of accepted, denied, unaccepted and rejected keys.
This is the same output as `salt-key -L`
CLI Example:
.. code-block:: bash
salt 'master' minion.list |
def get_port_vendor_info(port=None):
""" Return vendor informations of a usb2serial device.
It may depends on the Operating System.
:param string port: port of the usb2serial device
:Example:
Result with a USB2Dynamixel on Linux:
In [1]: import pypot.dynamixel
In [2]: pypot.dynamixel.get_port_vendor_info('/dev/ttyUSB0')
Out[2]: 'USB VID:PID=0403:6001 SNR=A7005LKE' """
port_info_dict = dict((x[0], x[2]) for x in serial.tools.list_ports.comports())
return port_info_dict[port] if port is not None else port_info_dict | Return vendor informations of a usb2serial device.
It may depends on the Operating System.
:param string port: port of the usb2serial device
:Example:
Result with a USB2Dynamixel on Linux:
In [1]: import pypot.dynamixel
In [2]: pypot.dynamixel.get_port_vendor_info('/dev/ttyUSB0')
Out[2]: 'USB VID:PID=0403:6001 SNR=A7005LKE' |
def debug_dump(message, file_prefix="dump"):
"""
Utility while developing to dump message data to play with in the
interpreter
"""
global index
index += 1
with open("%s_%s.dump" % (file_prefix, index), 'w') as f:
f.write(message.SerializeToString())
f.close() | Utility while developing to dump message data to play with in the
interpreter |
def process(self, request, item):
"""Do a direct payment."""
warn_untested()
from paypal.pro.helpers import PayPalWPP
wpp = PayPalWPP(request)
# Change the model information into a dict that PayPal can understand.
params = model_to_dict(self, exclude=self.ADMIN_FIELDS)
params['acct'] = self.acct
params['creditcardtype'] = self.creditcardtype
params['expdate'] = self.expdate
params['cvv2'] = self.cvv2
params.update(item)
# Create recurring payment:
if 'billingperiod' in params:
return wpp.createRecurringPaymentsProfile(params, direct=True)
# Create single payment:
else:
return wpp.doDirectPayment(params) | Do a direct payment. |
def date_to_um_dump_date(date):
"""
Convert a time date object to a um dump format date which is
<decade><year><month><day>0
To accommodate two digit months and days the UM uses letters. e.g. 1st oct
is writing 01a10.
"""
assert(date.month <= 12)
decade = date.year // 10
# UM can only handle 36 decades then goes back to the beginning.
decade = decade % 36
year = date.year % 10
month = date.month
day = date.day
um_d = string.digits + string.ascii_letters[:26]
um_dump_date = (
'{decade}{year}{month}{day}0'.format(
decade=um_d[decade],
year=um_d[year],
month=um_d[month],
day=um_d[day]
)
)
return um_dump_date | Convert a time date object to a um dump format date which is
<decade><year><month><day>0
To accommodate two digit months and days the UM uses letters. e.g. 1st oct
is writing 01a10. |
def clausulae_analysis(prosody):
"""
Return dictionary in which the key is a type of clausula and the value is its frequency.
:param prosody: the prosody of a prose text (must be in the format of the scansion produced by the scanner classes.
:return: dictionary of prosody
"""
prosody = ''.join(prosody)
return {
'cretic + trochee': prosody.count('¯˘¯¯x'),
'4th paeon + trochee': prosody.count('˘˘˘¯¯x'),
'1st paeon + trochee': prosody.count('¯˘˘˘¯x'),
'substituted cretic + trochee': prosody.count('˘˘˘˘˘¯x'),
'1st paeon + anapest': prosody.count('¯˘˘˘˘˘x'),
'double cretic': prosody.count('¯˘¯¯˘x'),
'4th paeon + cretic': prosody.count('˘˘˘¯¯˘x'),
'molossus + cretic': prosody.count('¯¯¯¯˘x'),
'double trochee': prosody.count('¯˘¯x'),
'molossus + double trochee': prosody.count('¯¯¯¯˘¯x'),
'cretic + double trochee': prosody.count('¯˘¯¯˘¯x'),
'dactyl + double trochee': prosody.count('¯˘˘¯˘¯x'),
'choriamb + double trochee': prosody.count('¯˘˘¯¯˘¯x'),
'cretic + iamb': prosody.count('¯˘¯˘x'),
'molossus + iamb': prosody.count('¯¯¯˘x'),
'double spondee': prosody.count('¯¯¯x'),
'cretic + double spondee': prosody.count('¯˘¯¯¯¯x'),
'heroic': prosody.count('¯˘˘¯x')
} | Return dictionary in which the key is a type of clausula and the value is its frequency.
:param prosody: the prosody of a prose text (must be in the format of the scansion produced by the scanner classes.
:return: dictionary of prosody |
def load_config(self):
"""Load the config from the config file or template."""
config = Config()
self.config_obj = config.load('awsshellrc')
self.config_section = self.config_obj['aws-shell']
self.model_completer.match_fuzzy = self.config_section.as_bool(
'match_fuzzy')
self.enable_vi_bindings = self.config_section.as_bool(
'enable_vi_bindings')
self.show_completion_columns = self.config_section.as_bool(
'show_completion_columns')
self.show_help = self.config_section.as_bool('show_help')
self.theme = self.config_section['theme'] | Load the config from the config file or template. |
def datacenter_configured(name):
'''
Makes sure a datacenter exists.
If the state is run by an ``esxdatacenter`` minion, the name of the
datacenter is retrieved from the proxy details, otherwise the datacenter
has the same name as the state.
Supported proxies: esxdatacenter
name:
Datacenter name. Ignored if the proxytype is ``esxdatacenter``.
'''
proxy_type = __salt__['vsphere.get_proxy_type']()
if proxy_type == 'esxdatacenter':
dc_name = __salt__['esxdatacenter.get_details']()['datacenter']
else:
dc_name = name
log.info('Running datacenter_configured for datacenter \'%s\'', dc_name)
ret = {'name': name,
'changes': {},
'result': None,
'comment': 'Default'}
comments = []
si = None
try:
si = __salt__['vsphere.get_service_instance_via_proxy']()
dcs = __salt__['vsphere.list_datacenters_via_proxy'](
datacenter_names=[dc_name], service_instance=si)
if not dcs:
if __opts__['test']:
comments.append('State will create '
'datacenter \'{0}\'.'.format(dc_name))
else:
log.debug('Creating datacenter \'%s\'', dc_name)
__salt__['vsphere.create_datacenter'](dc_name, si)
comments.append('Created datacenter \'{0}\'.'.format(dc_name))
log.info(comments[-1])
ret['changes'].update({'new': {'name': dc_name}})
else:
comments.append('Datacenter \'{0}\' already exists. Nothing to be '
'done.'.format(dc_name))
log.info(comments[-1])
__salt__['vsphere.disconnect'](si)
ret['comment'] = '\n'.join(comments)
ret['result'] = None if __opts__['test'] and ret['changes'] else True
return ret
except salt.exceptions.CommandExecutionError as exc:
log.error('Error: %s', exc)
if si:
__salt__['vsphere.disconnect'](si)
ret.update({
'result': False if not __opts__['test'] else None,
'comment': six.text_type(exc)})
return ret | Makes sure a datacenter exists.
If the state is run by an ``esxdatacenter`` minion, the name of the
datacenter is retrieved from the proxy details, otherwise the datacenter
has the same name as the state.
Supported proxies: esxdatacenter
name:
Datacenter name. Ignored if the proxytype is ``esxdatacenter``. |
def get_host_ipv4(name=None, mac=None, allow_array=False, **api_opts):
'''
Get ipv4 address from host record.
Use `allow_array` to return possible multiple values.
CLI Examples:
.. code-block:: bash
salt-call infoblox.get_host_ipv4 host=localhost.domain.com
salt-call infoblox.get_host_ipv4 mac=00:50:56:84:6e:ae
'''
data = get_host(name=name, mac=mac, **api_opts)
if data and 'ipv4addrs' in data:
l = []
for a in data['ipv4addrs']:
if 'ipv4addr' in a:
l.append(a['ipv4addr'])
if allow_array:
return l
if l:
return l[0]
return None | Get ipv4 address from host record.
Use `allow_array` to return possible multiple values.
CLI Examples:
.. code-block:: bash
salt-call infoblox.get_host_ipv4 host=localhost.domain.com
salt-call infoblox.get_host_ipv4 mac=00:50:56:84:6e:ae |
def has_integration(self, path, method):
"""
Checks if an API Gateway integration is already present at the given path/method
:param string path: Path name
:param string method: HTTP method
:return: True, if an API Gateway integration is already present
"""
method = self._normalize_method_name(method)
path_dict = self.get_path(path)
return self.has_path(path, method) and \
isinstance(path_dict[method], dict) and \
self.method_has_integration(path_dict[method]) | Checks if an API Gateway integration is already present at the given path/method
:param string path: Path name
:param string method: HTTP method
:return: True, if an API Gateway integration is already present |
def pop(self, key, resource_type):
"""
Extract an object from the list.
If the key is not in the cache, this will raise a KeyError.
If the list is empty, method will return None
"""
with self._objects_queue_lock:
objects = self._objects_queue[key].get(resource_type, [])
return objects.pop() if objects else None | Extract an object from the list.
If the key is not in the cache, this will raise a KeyError.
If the list is empty, method will return None |
def get_sci_segs_for_ifo(ifo, cp, start_time, end_time, out_dir, tags=None):
"""
Obtain science segments for the selected ifo
Parameters
-----------
ifo : string
The string describing the ifo to obtain science times for.
start_time : gps time (either int/LIGOTimeGPS)
The time at which to begin searching for segments.
end_time : gps time (either int/LIGOTimeGPS)
The time at which to stop searching for segments.
out_dir : path
The directory in which output will be stored.
tag : string, optional (default=None)
Use this to specify a tag. This can be used if this module is being
called more than once to give call specific configuration (by setting
options in [workflow-datafind-${TAG}] rather than [workflow-datafind]).
This is also used to tag the Files returned by the class to uniqueify
the Files and uniqueify the actual filename.
Returns
--------
sci_segs : ligo.segments.segmentlist
The segmentlist generated by this call
sci_xml_file : pycbc.workflow.core.SegFile
The workflow File object corresponding to this science segments file.
out_sci_seg_name : string
The name of the output segment list in the output XML file.
"""
if tags is None:
tags = []
seg_valid_seg = segments.segment([start_time,end_time])
sci_seg_name = cp.get_opt_tags(
"workflow-segments", "segments-%s-science-name" %(ifo.lower()), tags)
sci_seg_url = cp.get_opt_tags(
"workflow-segments", "segments-database-url", tags)
# NOTE: ligolw_segment_query returns slightly strange output. The output
# segment list is put in with name "RESULT". So this is hardcoded here
out_sci_seg_name = "RESULT"
if tags:
sci_xml_file_path = os.path.join(
out_dir, "%s-SCIENCE_SEGMENTS_%s.xml" \
%(ifo.upper(), '_'.join(tags)))
tag_list=tags + ['SCIENCE']
else:
sci_xml_file_path = os.path.join(
out_dir, "%s-SCIENCE_SEGMENTS.xml" %(ifo.upper()) )
tag_list = ['SCIENCE']
if file_needs_generating(sci_xml_file_path, cp, tags=tags):
seg_find_call = [ resolve_url(cp.get("executables","segment_query"),
permissions=stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR),
"--query-segments",
"--segment-url", sci_seg_url,
"--gps-start-time", str(start_time),
"--gps-end-time", str(end_time),
"--include-segments", sci_seg_name,
"--output-file", sci_xml_file_path ]
make_external_call(seg_find_call, out_dir=os.path.join(out_dir,'logs'),
out_basename='%s-science-call' %(ifo.lower()) )
# Yes its yucky to generate a file and then read it back in.
sci_xml_file_path = os.path.abspath(sci_xml_file_path)
sci_xml_file = SegFile.from_segment_xml(sci_xml_file_path, tags=tag_list,
valid_segment=seg_valid_seg)
# NOTE: ligolw_segment_query returns slightly strange output. The output
# segment_summary output does not use RESULT. Therefore move the
# segment_summary across.
sci_xml_file.seg_summ_dict[ifo.upper() + ":" + out_sci_seg_name] = \
sci_xml_file.seg_summ_dict[':'.join(sci_seg_name.split(':')[0:2])]
sci_segs = sci_xml_file.return_union_seglist()
return sci_segs, sci_xml_file, out_sci_seg_name | Obtain science segments for the selected ifo
Parameters
-----------
ifo : string
The string describing the ifo to obtain science times for.
start_time : gps time (either int/LIGOTimeGPS)
The time at which to begin searching for segments.
end_time : gps time (either int/LIGOTimeGPS)
The time at which to stop searching for segments.
out_dir : path
The directory in which output will be stored.
tag : string, optional (default=None)
Use this to specify a tag. This can be used if this module is being
called more than once to give call specific configuration (by setting
options in [workflow-datafind-${TAG}] rather than [workflow-datafind]).
This is also used to tag the Files returned by the class to uniqueify
the Files and uniqueify the actual filename.
Returns
--------
sci_segs : ligo.segments.segmentlist
The segmentlist generated by this call
sci_xml_file : pycbc.workflow.core.SegFile
The workflow File object corresponding to this science segments file.
out_sci_seg_name : string
The name of the output segment list in the output XML file. |
def unserialize(jsonstr):
'''
Unserialize a JSON string representation of a topology
'''
topod = json.loads(jsonstr)
G = json_graph.node_link_graph(topod)
for n,ndict in G.nodes(data=True):
if 'nodeobj' not in ndict or 'type' not in ndict:
raise Exception("Required type information is not present in serialized node {} :{}".format(n, ndict))
nobj = ndict['nodeobj']
cls = eval(ndict['type'])
ndict['nodeobj'] = cls(**dict(nobj))
t = Topology(nxgraph=G)
return t | Unserialize a JSON string representation of a topology |
def temp_dir(sub_dir='work'):
"""Obtain the temporary working directory for the operating system.
An inasafe subdirectory will automatically be created under this and
if specified, a user subdirectory under that.
.. note:: You can use this together with unique_filename to create
a file in a temporary directory under the inasafe workspace. e.g.
tmpdir = temp_dir('testing')
tmpfile = unique_filename(dir=tmpdir)
print tmpfile
/tmp/inasafe/23-08-2012/timlinux/testing/tmpMRpF_C
If you specify INASAFE_WORK_DIR as an environment var, it will be
used in preference to the system temp directory.
:param sub_dir: Optional argument which will cause an additional
subdirectory to be created e.g. /tmp/inasafe/foo/
:type sub_dir: str
:return: Path to the temp dir that is created.
:rtype: str
:raises: Any errors from the underlying system calls.
"""
user = getpass.getuser().replace(' ', '_')
current_date = date.today()
date_string = current_date.isoformat()
if 'INASAFE_WORK_DIR' in os.environ:
new_directory = os.environ['INASAFE_WORK_DIR']
else:
# Following 4 lines are a workaround for tempfile.tempdir()
# unreliabilty
handle, filename = mkstemp()
os.close(handle)
new_directory = os.path.dirname(filename)
os.remove(filename)
path = os.path.join(new_directory, 'inasafe', date_string, user, sub_dir)
if not os.path.exists(path):
# Ensure that the dir is world writable
# Umask sets the new mask and returns the old
old_mask = os.umask(0000)
os.makedirs(path, 0o777)
# Reinstate the old mask for tmp
os.umask(old_mask)
return path | Obtain the temporary working directory for the operating system.
An inasafe subdirectory will automatically be created under this and
if specified, a user subdirectory under that.
.. note:: You can use this together with unique_filename to create
a file in a temporary directory under the inasafe workspace. e.g.
tmpdir = temp_dir('testing')
tmpfile = unique_filename(dir=tmpdir)
print tmpfile
/tmp/inasafe/23-08-2012/timlinux/testing/tmpMRpF_C
If you specify INASAFE_WORK_DIR as an environment var, it will be
used in preference to the system temp directory.
:param sub_dir: Optional argument which will cause an additional
subdirectory to be created e.g. /tmp/inasafe/foo/
:type sub_dir: str
:return: Path to the temp dir that is created.
:rtype: str
:raises: Any errors from the underlying system calls. |
def is_monotonic(full_list):
"""
Determine whether elements in a list are monotonic. ie. unique
elements are clustered together.
ie. [5,5,3,4] is, [5,3,5] is not.
"""
prev_elements = set({full_list[0]})
prev_item = full_list[0]
for item in full_list:
if item != prev_item:
if item in prev_elements:
return False
prev_item = item
prev_elements.add(item)
return True | Determine whether elements in a list are monotonic. ie. unique
elements are clustered together.
ie. [5,5,3,4] is, [5,3,5] is not. |
def _to_protobuf(self):
"""Convert the current query into the equivalent protobuf.
Returns:
google.cloud.firestore_v1beta1.types.StructuredQuery: The
query protobuf.
"""
projection = self._normalize_projection(self._projection)
orders = self._normalize_orders()
start_at = self._normalize_cursor(self._start_at, orders)
end_at = self._normalize_cursor(self._end_at, orders)
query_kwargs = {
"select": projection,
"from": [
query_pb2.StructuredQuery.CollectionSelector(
collection_id=self._parent.id
)
],
"where": self._filters_pb(),
"order_by": orders,
"start_at": _cursor_pb(start_at),
"end_at": _cursor_pb(end_at),
}
if self._offset is not None:
query_kwargs["offset"] = self._offset
if self._limit is not None:
query_kwargs["limit"] = wrappers_pb2.Int32Value(value=self._limit)
return query_pb2.StructuredQuery(**query_kwargs) | Convert the current query into the equivalent protobuf.
Returns:
google.cloud.firestore_v1beta1.types.StructuredQuery: The
query protobuf. |
def center(self):
"""Return footprint center in world coordinates, as GeoVector."""
image_center = Point(self.width / 2, self.height / 2)
return self.to_world(image_center) | Return footprint center in world coordinates, as GeoVector. |
def apply_security_groups(name, security_groups, region=None, key=None,
keyid=None, profile=None):
'''
Apply security groups to ELB.
CLI example:
.. code-block:: bash
salt myminion boto_elb.apply_security_groups myelb '["mysecgroup1"]'
'''
conn = _get_conn(region=region, key=key, keyid=keyid, profile=profile)
if isinstance(security_groups, six.string_types):
security_groups = salt.utils.json.loads(security_groups)
try:
conn.apply_security_groups_to_lb(name, security_groups)
log.info('Applied security_groups on ELB %s', name)
return True
except boto.exception.BotoServerError as e:
log.debug(e)
log.error('Failed to appply security_groups on ELB %s: %s',
name, e.message)
return False | Apply security groups to ELB.
CLI example:
.. code-block:: bash
salt myminion boto_elb.apply_security_groups myelb '["mysecgroup1"]' |
def transfer_learning_tuner(self, additional_parents=None, estimator=None):
"""Creates a new ``HyperparameterTuner`` by copying the request fields from the provided parent to the new
instance of ``HyperparameterTuner``. Followed by addition of warm start configuration with the type as
"TransferLearning" and parents as the union of provided list of ``additional_parents`` and the ``self``.
Also, training image in the new tuner's estimator is updated with the provided ``training_image``.
Args:
additional_parents (set{str}): Set of additional parents along with the self to be used in warm starting
the transfer learning tuner.
estimator (sagemaker.estimator.EstimatorBase): An estimator object that has been initialized with
the desired configuration. There does not need to be a training job associated with this instance.
Returns:
sagemaker.tuner.HyperparameterTuner: ``HyperparameterTuner`` instance which can be used to launch transfer
learning tuning job.
Examples:
>>> parent_tuner = HyperparameterTuner.attach(tuning_job_name="parent-job-1")
>>> transfer_learning_tuner = parent_tuner.transfer_learning_tuner(additional_parents={"parent-job-2"})
Later On:
>>> transfer_learning_tuner.fit(inputs={})
"""
return self._create_warm_start_tuner(additional_parents=additional_parents,
warm_start_type=WarmStartTypes.TRANSFER_LEARNING,
estimator=estimator) | Creates a new ``HyperparameterTuner`` by copying the request fields from the provided parent to the new
instance of ``HyperparameterTuner``. Followed by addition of warm start configuration with the type as
"TransferLearning" and parents as the union of provided list of ``additional_parents`` and the ``self``.
Also, training image in the new tuner's estimator is updated with the provided ``training_image``.
Args:
additional_parents (set{str}): Set of additional parents along with the self to be used in warm starting
the transfer learning tuner.
estimator (sagemaker.estimator.EstimatorBase): An estimator object that has been initialized with
the desired configuration. There does not need to be a training job associated with this instance.
Returns:
sagemaker.tuner.HyperparameterTuner: ``HyperparameterTuner`` instance which can be used to launch transfer
learning tuning job.
Examples:
>>> parent_tuner = HyperparameterTuner.attach(tuning_job_name="parent-job-1")
>>> transfer_learning_tuner = parent_tuner.transfer_learning_tuner(additional_parents={"parent-job-2"})
Later On:
>>> transfer_learning_tuner.fit(inputs={}) |
def delete(self, robj, rw=None, r=None, w=None, dw=None, pr=None,
pw=None, timeout=None):
"""
Deletes an object.
"""
raise NotImplementedError | Deletes an object. |
def quadratic_jacobian_polynomial(nodes):
r"""Compute the Jacobian determinant of a quadratic surface.
.. note::
This is used **only** by :meth:`Surface._compute_valid` (which is
in turn used to compute / cache the :attr:`Surface.is_valid`
property).
Converts :math:`\det(J(s, t))` to a polynomial on the reference
triangle and represents it as a surface object.
.. note::
This assumes that ``nodes`` is ``2 x 6`` but doesn't verify this.
(However, the right multiplication by ``_QUADRATIC_JACOBIAN_HELPER``
would fail if ``nodes`` wasn't ``R x 6`` and then the ensuing
determinants would fail if there weren't 2 rows.)
Args:
nodes (numpy.ndarray): A 2 x 6 array of nodes in a surface.
Returns:
numpy.ndarray: 1 x 6 array, coefficients in Bernstein basis.
"""
# First evaluate the Jacobian at each of the 6 nodes.
jac_parts = _helpers.matrix_product(nodes, _QUADRATIC_JACOBIAN_HELPER)
jac_at_nodes = np.empty((1, 6), order="F")
jac_at_nodes[0, 0] = two_by_two_det(jac_parts[:, :2])
jac_at_nodes[0, 1] = two_by_two_det(jac_parts[:, 2:4])
jac_at_nodes[0, 2] = two_by_two_det(jac_parts[:, 4:6])
jac_at_nodes[0, 3] = two_by_two_det(jac_parts[:, 6:8])
jac_at_nodes[0, 4] = two_by_two_det(jac_parts[:, 8:10])
jac_at_nodes[0, 5] = two_by_two_det(jac_parts[:, 10:])
# Convert the nodal values to the Bernstein basis...
bernstein = _helpers.matrix_product(jac_at_nodes, _QUADRATIC_TO_BERNSTEIN)
return bernstein | r"""Compute the Jacobian determinant of a quadratic surface.
.. note::
This is used **only** by :meth:`Surface._compute_valid` (which is
in turn used to compute / cache the :attr:`Surface.is_valid`
property).
Converts :math:`\det(J(s, t))` to a polynomial on the reference
triangle and represents it as a surface object.
.. note::
This assumes that ``nodes`` is ``2 x 6`` but doesn't verify this.
(However, the right multiplication by ``_QUADRATIC_JACOBIAN_HELPER``
would fail if ``nodes`` wasn't ``R x 6`` and then the ensuing
determinants would fail if there weren't 2 rows.)
Args:
nodes (numpy.ndarray): A 2 x 6 array of nodes in a surface.
Returns:
numpy.ndarray: 1 x 6 array, coefficients in Bernstein basis. |
def link(self):
"""Link all the types in this module and all included modules."""
if self.linked:
return self
self.linked = True
included_modules = []
# Link includes
for include in self.includes.values():
included_modules.append(include.link().surface)
self.scope.add_surface('__includes__', tuple(included_modules))
self.scope.add_surface('__thrift_source__', self.thrift_source)
# Link self
for linker in LINKERS:
linker(self.scope).link()
self.scope.add_surface('loads', Deserializer(self.protocol))
self.scope.add_surface('dumps', Serializer(self.protocol))
return self | Link all the types in this module and all included modules. |
def main(league, time, standings, team, live, use12hour, players,
output_format, output_file, upcoming, lookup, listcodes, apikey):
"""
A CLI for live and past football scores from various football leagues.
League codes:
\b
- WC: World Cup
- EC: European Championship
- CL: Champions League
- PL: English Premier League
- ELC: English Championship
- FL1: French Ligue 1
- BL: German Bundesliga
- SA: Serie A
- DED: Eredivisie
- PPL: Primeira Liga
- PD: Primera Division
- BSA: Brazil Serie A
"""
headers = {'X-Auth-Token': apikey}
try:
if output_format == 'stdout' and output_file:
raise IncorrectParametersException('Printing output to stdout and '
'saving to a file are mutually exclusive')
writer = get_writer(output_format, output_file)
rh = RequestHandler(headers, LEAGUE_IDS, TEAM_NAMES, writer)
if listcodes:
list_team_codes()
return
if live:
rh.get_live_scores(use12hour)
return
if standings:
if not league:
raise IncorrectParametersException('Please specify a league. '
'Example --standings --league=PL')
if league == 'CL':
raise IncorrectParametersException('Standings for CL - '
'Champions League not supported')
rh.get_standings(league)
return
if team:
if lookup:
map_team_id(team)
return
if players:
rh.get_team_players(team)
return
else:
rh.get_team_scores(team, time, upcoming, use12hour)
return
rh.get_league_scores(league, time, upcoming, use12hour)
except IncorrectParametersException as e:
click.secho(str(e), fg="red", bold=True) | A CLI for live and past football scores from various football leagues.
League codes:
\b
- WC: World Cup
- EC: European Championship
- CL: Champions League
- PL: English Premier League
- ELC: English Championship
- FL1: French Ligue 1
- BL: German Bundesliga
- SA: Serie A
- DED: Eredivisie
- PPL: Primeira Liga
- PD: Primera Division
- BSA: Brazil Serie A |
def status(*args):
"""
Get the current status of the fragments repository, limited to FILENAME(s) if specified.
Limit output to files with status STATUS, if present.
"""
parser = argparse.ArgumentParser(prog="%s %s" % (__package__, status.__name__), description=status.__doc__)
parser.add_argument('FILENAME', help="files to show status for", nargs="*", default=['.'])
parser.add_argument('-l', '--limit', type=str, dest="STATUS", default='MDAE ', action="store", help="limit to files in STATUS")
args = parser.parse_args(args)
config = FragmentsConfig()
yield "%s configuration version %s.%s.%s" % ((__package__,) + config['version'])
yield "stored in %s" % config.directory
for s, curr_path in _iterate_over_files(args.FILENAME, config, statuses=args.STATUS):
yield _status_to_color.get(s, str)('%s\t%s' % (s, os.path.relpath(curr_path))) | Get the current status of the fragments repository, limited to FILENAME(s) if specified.
Limit output to files with status STATUS, if present. |
def verify(self):
'''
Verify the correctness of the region arcs. Throws an VennRegionException if verification fails
(or any other exception if it happens during verification).
'''
# Verify size of arcs list
if (len(self.arcs) < 2):
raise VennRegionException("At least two arcs needed in a poly-arc region")
if (len(self.arcs) > 4):
raise VennRegionException("At most 4 arcs are supported currently for poly-arc regions")
TRIG_TOL = 100*tol # We need to use looser tolerance level here because conversion to angles and back is prone to large errors.
# Verify connectedness of arcs
for i in range(len(self.arcs)):
if not np.all(self.arcs[i-1].end_point() - self.arcs[i].start_point() < TRIG_TOL):
raise VennRegionException("Arcs of an poly-arc-gon must be connected via endpoints")
# Verify that arcs do not cross-intersect except at endpoints
for i in range(len(self.arcs)-1):
for j in range(i+1, len(self.arcs)):
ips = self.arcs[i].intersect_arc(self.arcs[j])
for ip in ips:
if not (np.all(abs(ip - self.arcs[i].start_point()) < TRIG_TOL) or np.all(abs(ip - self.arcs[i].end_point()) < TRIG_TOL)):
raise VennRegionException("Arcs of a poly-arc-gon may only intersect at endpoints")
if len(ips) != 0 and (i - j) % len(self.arcs) > 1 and (j - i) % len(self.arcs) > 1:
# Two non-consecutive arcs intersect. This is in general not good, but
# may occasionally happen when all arcs inbetween have length 0.
pass # raise VennRegionException("Non-consecutive arcs of a poly-arc-gon may not intersect")
# Verify that vertices are ordered so that at each point the direction along the polyarc changes towards the left.
# Note that this test only makes sense for polyarcs obtained using circle intersections & subtractions.
# A "flower-like" polyarc may have its vertices ordered counter-clockwise yet the direction would turn to the right at each of them.
for i in range(len(self.arcs)):
prev_arc = self.arcs[i-1]
cur_arc = self.arcs[i]
if box_product(prev_arc.direction_vector(prev_arc.to_angle), cur_arc.direction_vector(cur_arc.from_angle)) < -tol:
raise VennRegionException("Arcs must be ordered so that the direction at each vertex changes counter-clockwise") | Verify the correctness of the region arcs. Throws an VennRegionException if verification fails
(or any other exception if it happens during verification). |
def rewrite_file_imports(item, vendored_libs):
"""Rewrite 'import xxx' and 'from xxx import' for vendored_libs"""
text = item.read_text(encoding='utf-8')
for lib in vendored_libs:
text = re.sub(
r'(\n\s*)import %s(\n\s*)' % lib,
r'\1from pythonfinder._vendor import %s\2' % lib,
text,
)
text = re.sub(
r'(\n\s*)from %s' % lib,
r'\1from pythonfinder._vendor.%s' % lib,
text,
)
item.write_text(text, encoding='utf-8') | Rewrite 'import xxx' and 'from xxx import' for vendored_libs |
def is_token_annotation_tier(self, tier):
"""
returns True, iff all events in the given tier annotate exactly one
token.
"""
for i, event in enumerate(tier.iter('event')):
if self.indexdelta(event.attrib['end'], event.attrib['start']) != 1:
return False
return True | returns True, iff all events in the given tier annotate exactly one
token. |
def alloc(self):
"""from _mosquitto_packet_alloc."""
byte = 0
remaining_bytes = bytearray(5)
i = 0
remaining_length = self.remaining_length
self.payload = None
self.remaining_count = 0
loop_flag = True
#self.dump()
while loop_flag:
byte = remaining_length % 128
remaining_length = remaining_length / 128
if remaining_length > 0:
byte = byte | 0x80
remaining_bytes[self.remaining_count] = byte
self.remaining_count += 1
if not (remaining_length > 0 and self.remaining_count < 5):
loop_flag = False
if self.remaining_count == 5:
return NC.ERR_PAYLOAD_SIZE
self.packet_length = self.remaining_length + 1 + self.remaining_count
self.payload = bytearray(self.packet_length)
self.payload[0] = self.command
i = 0
while i < self.remaining_count:
self.payload[i+1] = remaining_bytes[i]
i += 1
self.pos = 1 + self.remaining_count
return NC.ERR_SUCCESS | from _mosquitto_packet_alloc. |
def adjust_status(info: dict) -> dict:
"""Apply status mapping to a raw API result."""
modified_info = deepcopy(info)
modified_info.update({
'level':
get_nearest_by_numeric_key(STATUS_MAP, int(info['level'])),
'level2':
STATUS_MAP[99] if info['level2'] is None else
get_nearest_by_numeric_key(STATUS_MAP, int(info['level2']))
})
return modified_info | Apply status mapping to a raw API result. |
def describe_subnet(subnet_id=None, subnet_name=None, region=None,
key=None, keyid=None, profile=None):
'''
Given a subnet id or name, describe its properties.
Returns a dictionary of interesting properties.
.. versionadded:: 2015.8.0
CLI Examples:
.. code-block:: bash
salt myminion boto_vpc.describe_subnet subnet_id=subnet-123456
salt myminion boto_vpc.describe_subnet subnet_name=mysubnet
'''
try:
subnet = _get_resource('subnet', name=subnet_name, resource_id=subnet_id,
region=region, key=key, keyid=keyid, profile=profile)
except BotoServerError as e:
return {'error': __utils__['boto.get_error'](e)}
if not subnet:
return {'subnet': None}
log.debug('Found subnet: %s', subnet.id)
keys = ('id', 'cidr_block', 'availability_zone', 'tags', 'vpc_id')
ret = {'subnet': dict((k, getattr(subnet, k)) for k in keys)}
explicit_route_table_assoc = _get_subnet_explicit_route_table(ret['subnet']['id'],
ret['subnet']['vpc_id'],
conn=None, region=region,
key=key, keyid=keyid, profile=profile)
if explicit_route_table_assoc:
ret['subnet']['explicit_route_table_association_id'] = explicit_route_table_assoc
return ret | Given a subnet id or name, describe its properties.
Returns a dictionary of interesting properties.
.. versionadded:: 2015.8.0
CLI Examples:
.. code-block:: bash
salt myminion boto_vpc.describe_subnet subnet_id=subnet-123456
salt myminion boto_vpc.describe_subnet subnet_name=mysubnet |
def run_cli():
"Command line interface to hiwenet."
features_path, groups_path, weight_method, num_bins, edge_range, \
trim_outliers, trim_percentile, return_networkx_graph, out_weights_path = parse_args()
# TODO add the possibility to process multiple combinations of parameters: diff subjects, diff metrics
# for features_path to be a file containing multiple subjects (one/line)
# -w could take multiple values kldiv,histint,
# each line: input_features_path,out_weights_path
features, groups = read_features_and_groups(features_path, groups_path)
extract(features, groups, weight_method=weight_method, num_bins=num_bins,
edge_range=edge_range, trim_outliers=trim_outliers, trim_percentile=trim_percentile,
return_networkx_graph=return_networkx_graph, out_weights_path=out_weights_path) | Command line interface to hiwenet. |
def iter_commands(self):
"""Iterator returning ImportCommand objects."""
while True:
line = self.next_line()
if line is None:
if b'done' in self.features:
raise errors.PrematureEndOfStream(self.lineno)
break
elif len(line) == 0 or line.startswith(b'#'):
continue
# Search for commands in order of likelihood
elif line.startswith(b'commit '):
yield self._parse_commit(line[len(b'commit '):])
elif line.startswith(b'blob'):
yield self._parse_blob()
elif line.startswith(b'done'):
break
elif line.startswith(b'progress '):
yield commands.ProgressCommand(line[len(b'progress '):])
elif line.startswith(b'reset '):
yield self._parse_reset(line[len(b'reset '):])
elif line.startswith(b'tag '):
yield self._parse_tag(line[len(b'tag '):])
elif line.startswith(b'checkpoint'):
yield commands.CheckpointCommand()
elif line.startswith(b'feature'):
yield self._parse_feature(line[len(b'feature '):])
else:
self.abort(errors.InvalidCommand, line) | Iterator returning ImportCommand objects. |
def pmag_results_extract(res_file="pmag_results.txt", crit_file="", spec_file="",
age_file="", latex=False, grade=False, WD="."):
"""
Generate tab delimited output file(s) with result data.
Save output files and return True if successful.
Possible output files: Directions, Intensities, SiteNfo, Criteria,
Specimens
Optional Parameters (defaults are used if not specified)
----------
res_file : name of pmag_results file (default is "pmag_results.txt")
crit_file : name of criteria file (default is "pmag_criteria.txt")
spec_file : name of specimen file (default is "pmag_specimens.txt")
age_file : name of age file (default is "er_ages.txt")
latex : boolean argument to output in LaTeX (default is False)
WD : path to directory that contains input files and takes output (default is current directory, '.')
"""
# format outfiles
if latex:
latex = 1
file_type = '.tex'
else:
latex = 0
file_type = '.txt'
dir_path = os.path.realpath(WD)
outfile = os.path.join(dir_path, 'Directions' + file_type)
Ioutfile = os.path.join(dir_path, 'Intensities' + file_type)
Soutfile = os.path.join(dir_path, 'SiteNfo' + file_type)
Specout = os.path.join(dir_path, 'Specimens' + file_type)
Critout = os.path.join(dir_path, 'Criteria' + file_type)
# format infiles
res_file = os.path.join(dir_path, res_file)
if crit_file:
crit_file = os.path.join(dir_path, crit_file)
if spec_file:
spec_file = os.path.join(dir_path, spec_file)
else:
grade = False
# open output files
f = open(outfile, 'w')
sf = open(Soutfile, 'w')
fI = open(Ioutfile, 'w')
if crit_file:
cr = open(Critout, 'w')
# set up column headers
Sites, file_type = pmag.magic_read(res_file)
if crit_file:
Crits, file_type = pmag.magic_read(crit_file)
else:
Crits = []
SiteCols = ["Site", "Location",
"Lat. (N)", "Long. (E)", "Age ", "Age sigma", "Units"]
SiteKeys = ["er_site_names", "average_lat", "average_lon", "average_age",
"average_age_sigma", "average_age_unit"]
DirCols = ["Site", 'Comp.', "perc TC", "Dec.", "Inc.", "Nl", "Np", "k ", "R", "a95",
"PLat", "PLong"]
DirKeys = ["er_site_names", "pole_comp_name", "tilt_correction", "average_dec", "average_inc",
"average_n_lines", "average_n_planes", "average_k", "average_r", "average_alpha95",
"vgp_lat", "vgp_lon"]
IntCols = ["Site", "N", "B (uT)", "sigma",
"sigma perc", "VADM", "VADM sigma"]
IntKeys = ["er_site_names", "average_int_n", "average_int", "average_int_sigma",
'average_int_sigma_perc', "vadm", "vadm_sigma"]
AllowedKeys = ['specimen_frac', 'specimen_scat', 'specimen_gap_max', 'measurement_step_min',
'measurement_step_max', 'measurement_step_unit', 'specimen_polarity',
'specimen_nrm', 'specimen_direction_type', 'specimen_comp_nmb', 'specimen_mad',
'specimen_alpha95', 'specimen_n', 'specimen_int_sigma',
'specimen_int_sigma_perc', 'specimen_int_rel_sigma',
'specimen_int_rel_sigma_perc', 'specimen_int_mad', 'specimen_int_n',
'specimen_w', 'specimen_q', 'specimen_f', 'specimen_fvds', 'specimen_b_sigma',
'specimen_b_beta', 'specimen_g', 'specimen_dang', 'specimen_md',
'specimen_ptrm', 'specimen_drat', 'specimen_drats', 'specimen_rsc',
'specimen_viscosity_index', 'specimen_magn_moment', 'specimen_magn_volume',
'specimen_magn_mass', 'specimen_int_ptrm_n', 'specimen_delta', 'specimen_theta',
'specimen_gamma', 'sample_polarity', 'sample_nrm', 'sample_direction_type',
'sample_comp_nmb', 'sample_sigma', 'sample_alpha95', 'sample_n',
'sample_n_lines', 'sample_n_planes', 'sample_k', 'sample_r',
'sample_tilt_correction', 'sample_int_sigma', 'sample_int_sigma_perc',
'sample_int_rel_sigma', 'sample_int_rel_sigma_perc', 'sample_int_n',
'sample_magn_moment', 'sample_magn_volume', 'sample_magn_mass', 'site_polarity',
'site_nrm', 'site_direction_type', 'site_comp_nmb', 'site_sigma',
'site_alpha95', 'site_n', 'site_n_lines', 'site_n_planes', 'site_k', 'site_r',
'site_tilt_correction', 'site_int_sigma', 'site_int_sigma_perc',
'site_int_rel_sigma', 'site_int_rel_sigma_perc', 'site_int_n',
'site_magn_moment', 'site_magn_volume', 'site_magn_mass', 'average_age_min',
'average_age_max', 'average_age_sigma', 'average_age_unit', 'average_sigma',
'average_alpha95', 'average_n', 'average_nn', 'average_k', 'average_r',
'average_int_sigma', 'average_int_rel_sigma', 'average_int_rel_sigma_perc',
'average_int_n', 'average_int_nn', 'vgp_dp', 'vgp_dm', 'vgp_sigma',
'vgp_alpha95', 'vgp_n', 'vdm_sigma', 'vdm_n', 'vadm_sigma', 'vadm_n']
if crit_file:
crit = Crits[0] # get a list of useful keys
for key in list(crit.keys()):
if key not in AllowedKeys:
del(crit[key])
for key in list(crit.keys()):
if (not crit[key]) or (eval(crit[key]) > 1000) or (eval(crit[key]) == 0):
# get rid of all blank or too big ones or too little ones
del(crit[key])
CritKeys = list(crit.keys())
if spec_file:
Specs, file_type = pmag.magic_read(spec_file)
fsp = open(Specout, 'w') # including specimen intensities if desired
SpecCols = ["Site", "Specimen", "B (uT)", "MAD", "Beta", "N", "Q", "DANG", "f-vds",
"DRATS", "T (C)"]
SpecKeys = ['er_site_name', 'er_specimen_name', 'specimen_int', 'specimen_int_mad',
'specimen_b_beta', 'specimen_int_n', 'specimen_q', 'specimen_dang',
'specimen_fvds', 'specimen_drats', 'trange']
Xtra = ['specimen_frac', 'specimen_scat', 'specimen_gmax']
if grade:
SpecCols.append('Grade')
SpecKeys.append('specimen_grade')
for x in Xtra: # put in the new intensity keys if present
if x in list(Specs[0].keys()):
SpecKeys.append(x)
newkey = ""
for k in x.split('_')[1:]:
newkey = newkey + k + '_'
SpecCols.append(newkey.strip('_'))
SpecCols.append('Corrections')
SpecKeys.append('corrections')
# these should be multiplied by 1e6
Micro = ['specimen_int', 'average_int', 'average_int_sigma']
Zeta = ['vadm', 'vadm_sigma'] # these should be multiplied by 1e21
# write out the header information for each output file
if latex: # write out the latex header stuff
sep = ' & '
end = '\\\\'
f.write('\\documentclass{article}\n')
f.write('\\usepackage[margin=1in]{geometry}\n')
f.write('\\usepackage{longtable}\n')
f.write('\\begin{document}\n')
sf.write('\\documentclass{article}\n')
sf.write('\\usepackage[margin=1in]{geometry}\n')
sf.write('\\usepackage{longtable}\n')
sf.write('\\begin{document}\n')
fI.write('\\documentclass{article}\n')
fI.write('\\usepackage[margin=1in]{geometry}\n')
fI.write('\\usepackage{longtable}\n')
fI.write('\\begin{document}\n')
if crit_file:
cr.write('\\documentclass{article}\n')
cr.write('\\usepackage[margin=1in]{geometry}\n')
cr.write('\\usepackage{longtable}\n')
cr.write('\\begin{document}\n')
if spec_file:
fsp.write('\\documentclass{article}\n')
fsp.write('\\usepackage[margin=1in]{geometry}\n')
fsp.write('\\usepackage{longtable}\n')
fsp.write('\\begin{document}\n')
tabstring = '\\begin{longtable}{'
fstring = tabstring
for k in range(len(SiteCols)):
fstring = fstring + 'r'
sf.write(fstring + '}\n')
sf.write('\hline\n')
fstring = tabstring
for k in range(len(DirCols)):
fstring = fstring + 'r'
f.write(fstring + '}\n')
f.write('\hline\n')
fstring = tabstring
for k in range(len(IntCols)):
fstring = fstring + 'r'
fI.write(fstring + '}\n')
fI.write('\hline\n')
fstring = tabstring
if crit_file:
for k in range(len(CritKeys)):
fstring = fstring + 'r'
cr.write(fstring + '}\n')
cr.write('\hline\n')
if spec_file:
fstring = tabstring
for k in range(len(SpecCols)):
fstring = fstring + 'r'
fsp.write(fstring + '}\n')
fsp.write('\hline\n')
else: # just set the tab and line endings for tab delimited
sep = ' \t '
end = ''
# now write out the actual column headers
Soutstring, Doutstring, Ioutstring, Spoutstring, Croutstring = "", "", "", "", ""
for k in range(len(SiteCols)):
Soutstring = Soutstring + SiteCols[k] + sep
Soutstring = Soutstring.strip(sep)
Soutstring = Soutstring + end + '\n'
sf.write(Soutstring)
for k in range(len(DirCols)):
Doutstring = Doutstring + DirCols[k] + sep
Doutstring = Doutstring.strip(sep)
Doutstring = Doutstring + end + '\n'
f.write(Doutstring)
for k in range(len(IntCols)):
Ioutstring = Ioutstring + IntCols[k] + sep
Ioutstring = Ioutstring.strip(sep)
Ioutstring = Ioutstring + end + '\n'
fI.write(Ioutstring)
if crit_file:
for k in range(len(CritKeys)):
Croutstring = Croutstring + CritKeys[k] + sep
Croutstring = Croutstring.strip(sep)
Croutstring = Croutstring + end + '\n'
cr.write(Croutstring)
if spec_file:
for k in range(len(SpecCols)):
Spoutstring = Spoutstring + SpecCols[k] + sep
Spoutstring = Spoutstring.strip(sep)
Spoutstring = Spoutstring + end + "\n"
fsp.write(Spoutstring)
if latex: # put in a horizontal line in latex file
f.write('\hline\n')
sf.write('\hline\n')
fI.write('\hline\n')
if crit_file:
cr.write('\hline\n')
if spec_file:
fsp.write('\hline\n')
# do criteria
if crit_file:
for crit in Crits:
Croutstring = ""
for key in CritKeys:
Croutstring = Croutstring + crit[key] + sep
Croutstring = Croutstring.strip(sep) + end
cr.write(Croutstring + '\n')
# do directions
# get all results with VGPs
VGPs = pmag.get_dictitem(Sites, 'vgp_lat', '', 'F')
VGPs = pmag.get_dictitem(VGPs, 'data_type', 'i',
'T') # get site level stuff
for site in VGPs:
if len(site['er_site_names'].split(":")) == 1:
if 'er_sample_names' not in list(site.keys()):
site['er_sample_names'] = ''
if 'pole_comp_name' not in list(site.keys()):
site['pole_comp_name'] = "A"
if 'average_nn' not in list(site.keys()) and 'average_n' in list(site.keys()):
site['average_nn'] = site['average_n']
if 'average_n_lines' not in list(site.keys()):
site['average_n_lines'] = site['average_nn']
if 'average_n_planes' not in list(site.keys()):
site['average_n_planes'] = ""
Soutstring, Doutstring = "", ""
for key in SiteKeys:
if key in list(site.keys()):
Soutstring = Soutstring + site[key] + sep
Soutstring = Soutstring.strip(sep) + end
sf.write(Soutstring + '\n')
for key in DirKeys:
if key in list(site.keys()):
Doutstring = Doutstring + site[key] + sep
Doutstring = Doutstring.strip(sep) + end
f.write(Doutstring + '\n')
# now do intensities
VADMs = pmag.get_dictitem(Sites, 'vadm', '', 'F')
VADMs = pmag.get_dictitem(VADMs, 'data_type', 'i', 'T')
for site in VADMs: # do results level stuff
if site not in VGPs:
Soutstring = ""
for key in SiteKeys:
if key in list(site.keys()):
Soutstring = Soutstring + site[key] + sep
else:
Soutstring = Soutstring + " " + sep
Soutstring = Soutstring.strip(sep) + end
sf.write(Soutstring + '\n')
if len(site['er_site_names'].split(":")) == 1 and site['data_type'] == 'i':
if 'average_int_sigma_perc' not in list(site.keys()):
site['average_int_sigma_perc'] = "0"
if site["average_int_sigma"] == "":
site["average_int_sigma"] = "0"
if site["average_int_sigma_perc"] == "":
site["average_int_sigma_perc"] = "0"
if site["vadm"] == "":
site["vadm"] = "0"
if site["vadm_sigma"] == "":
site["vadm_sigma"] = "0"
for key in list(site.keys()): # reformat vadms, intensities
if key in Micro:
site[key] = '%7.1f' % (float(site[key]) * 1e6)
if key in Zeta:
site[key] = '%7.1f' % (float(site[key]) * 1e-21)
outstring = ""
for key in IntKeys:
if key not in list(site.keys()):
site[key] = ""
outstring = outstring + site[key] + sep
outstring = outstring.strip(sep) + end + '\n'
fI.write(outstring)
# VDMs=pmag.get_dictitem(Sites,'vdm','','F') # get non-blank VDMs
# for site in VDMs: # do results level stuff
# if len(site['er_site_names'].split(":"))==1:
# if 'average_int_sigma_perc' not in site.keys():site['average_int_sigma_perc']="0"
# if site["average_int_sigma"]=="":site["average_int_sigma"]="0"
# if site["average_int_sigma_perc"]=="":site["average_int_sigma_perc"]="0"
# if site["vadm"]=="":site["vadm"]="0"
# if site["vadm_sigma"]=="":site["vadm_sigma"]="0"
# for key in site.keys(): # reformat vadms, intensities
# if key in Micro: site[key]='%7.1f'%(float(site[key])*1e6)
# if key in Zeta: site[key]='%7.1f'%(float(site[key])*1e-21)
# outstring=""
# for key in IntKeys:
# outstring=outstring+site[key]+sep
# fI.write(outstring.strip(sep)+'\n')
if spec_file:
SpecsInts = pmag.get_dictitem(Specs, 'specimen_int', '', 'F')
for spec in SpecsInts:
spec['trange'] = '%i' % (int(float(spec['measurement_step_min']) - 273)) + \
'-' + '%i' % (int(float(spec['measurement_step_max']) - 273))
meths = spec['magic_method_codes'].split(':')
corrections = ''
for meth in meths:
if 'DA' in meth:
corrections = corrections + meth[3:] + ':'
corrections = corrections.strip(':')
if corrections.strip() == "":
corrections = "None"
spec['corrections'] = corrections
outstring = ""
for key in SpecKeys:
if key in Micro:
spec[key] = '%7.1f' % (float(spec[key]) * 1e6)
if key in Zeta:
spec[key] = '%7.1f' % (float(spec[key]) * 1e-21)
outstring = outstring + spec[key] + sep
fsp.write(outstring.strip(sep) + end + '\n')
#
if latex: # write out the tail stuff
f.write('\hline\n')
sf.write('\hline\n')
fI.write('\hline\n')
f.write('\end{longtable}\n')
sf.write('\end{longtable}\n')
fI.write('\end{longtable}\n')
f.write('\end{document}\n')
sf.write('\end{document}\n')
fI.write('\end{document}\n')
if spec_file:
fsp.write('\hline\n')
fsp.write('\end{longtable}\n')
fsp.write('\end{document}\n')
if crit_file:
cr.write('\hline\n')
cr.write('\end{longtable}\n')
cr.write('\end{document}\n')
f.close()
sf.close()
fI.close()
print('data saved in: ', outfile, Ioutfile, Soutfile)
outfiles = [outfile, Ioutfile, Soutfile]
if spec_file:
fsp.close()
print('specimen data saved in: ', Specout)
outfiles.append(Specout)
if crit_file:
cr.close()
print('Selection criteria saved in: ', Critout)
outfiles.append(Critout)
return True, outfiles | Generate tab delimited output file(s) with result data.
Save output files and return True if successful.
Possible output files: Directions, Intensities, SiteNfo, Criteria,
Specimens
Optional Parameters (defaults are used if not specified)
----------
res_file : name of pmag_results file (default is "pmag_results.txt")
crit_file : name of criteria file (default is "pmag_criteria.txt")
spec_file : name of specimen file (default is "pmag_specimens.txt")
age_file : name of age file (default is "er_ages.txt")
latex : boolean argument to output in LaTeX (default is False)
WD : path to directory that contains input files and takes output (default is current directory, '.') |
def source(self):
"""Source."""
if "source" not in self.attrs.keys():
self.attrs["source"] = "None"
value = self.attrs["source"]
return value if not value == "None" else None | Source. |
def OnRowSize(self, event):
"""Row size event handler"""
row = event.GetRowOrCol()
tab = self.grid.current_table
rowsize = self.grid.GetRowSize(row) / self.grid.grid_renderer.zoom
# Detect for resizing group of rows
rows = self.grid.GetSelectedRows()
if len(rows) == 0:
rows = [row, ]
# Detect for selection of rows spanning all columns
selection = self.grid.selection
num_cols = self.grid.code_array.shape[1]-1
for box in zip(selection.block_tl, selection.block_br):
leftmost_col = box[0][1]
rightmost_col = box[1][1]
if leftmost_col == 0 and rightmost_col == num_cols:
rows += range(box[0][0], box[1][0]+1)
# All row resizing is undone in one click
with undo.group(_("Resize Rows")):
for row in rows:
self.grid.code_array.set_row_height(row, tab, rowsize)
zoomed_rowsize = rowsize * self.grid.grid_renderer.zoom
self.grid.SetRowSize(row, zoomed_rowsize)
# Mark content as changed
post_command_event(self.grid.main_window, self.grid.ContentChangedMsg)
event.Skip()
self.grid.ForceRefresh() | Row size event handler |
def GetBaseFiles(self, diff):
"""Helper that calls GetBase file for each file in the patch.
Returns:
A dictionary that maps from filename to GetBaseFile's tuple. Filenames
are retrieved based on lines that start with "Index:" or
"Property changes on:".
"""
files = {}
for line in diff.splitlines(True):
if line.startswith('Index:') or line.startswith('Property changes on:'):
unused, filename = line.split(':', 1)
# On Windows if a file has property changes its filename uses '\'
# instead of '/'.
filename = to_slash(filename.strip())
files[filename] = self.GetBaseFile(filename)
return files | Helper that calls GetBase file for each file in the patch.
Returns:
A dictionary that maps from filename to GetBaseFile's tuple. Filenames
are retrieved based on lines that start with "Index:" or
"Property changes on:". |
def hse_output(pdb_file, file_type):
"""
The solvent exposure of an amino acid residue is important for analyzing,
understanding and predicting aspects of protein structure and function [73].
A residue's solvent exposure can be classified as four categories: exposed, partly exposed,
buried and deeply buried residues. Hamelryck et al. [73] established a new 2D measure that provides a
different view of solvent exposure, i.e. half-sphere exposure (HSE). By conceptually dividing the sphere
of a residue into two halves- HSE-up and HSE-down, HSE provides a more detailed description of an amino
acid residue's spatial neighborhood. HSE is calculated by the hsexpo module implemented in the BioPython
package [74] from a PDB file.
http://onlinelibrary.wiley.com/doi/10.1002/prot.20379/abstract
Args:
pdb_file:
Returns:
"""
# Get the first model
my_structure = StructureIO(pdb_file)
model = my_structure.first_model
# Calculate HSEalpha
exp_ca = HSExposureCA(model)
# Calculate HSEbeta
exp_cb = HSExposureCB(model)
# Calculate classical coordination number
exp_fs = ExposureCN(model)
return | The solvent exposure of an amino acid residue is important for analyzing,
understanding and predicting aspects of protein structure and function [73].
A residue's solvent exposure can be classified as four categories: exposed, partly exposed,
buried and deeply buried residues. Hamelryck et al. [73] established a new 2D measure that provides a
different view of solvent exposure, i.e. half-sphere exposure (HSE). By conceptually dividing the sphere
of a residue into two halves- HSE-up and HSE-down, HSE provides a more detailed description of an amino
acid residue's spatial neighborhood. HSE is calculated by the hsexpo module implemented in the BioPython
package [74] from a PDB file.
http://onlinelibrary.wiley.com/doi/10.1002/prot.20379/abstract
Args:
pdb_file:
Returns: |
def fix_shapes(self):
"""
Fixes the shape of the data fields on edges. Left edges should be
column vectors, and top edges should be row vectors, for example.
"""
for i in xrange(self.n_chunks):
for side in ['left', 'right', 'top', 'bottom']:
edge = getattr(self, side).ravel()[i]
if side in ['left', 'right']:
shp = [edge.todo.size, 1]
else:
shp = [1, edge.todo.size]
edge.done = edge.done.reshape(shp)
edge.data = edge.data.reshape(shp)
edge.todo = edge.todo.reshape(shp) | Fixes the shape of the data fields on edges. Left edges should be
column vectors, and top edges should be row vectors, for example. |
def send_registered_email(self, user, user_email, request_email_confirmation):
"""Send the 'user has registered' notification email."""
# Verify config settings
if not self.user_manager.USER_ENABLE_EMAIL: return
if not self.user_manager.USER_SEND_REGISTERED_EMAIL: return
# The registered email is sent to a specific user_email.email or user.email
email = user_email.email if user_email else user.email
# Add a request to confirm email if needed
if request_email_confirmation:
# Generate a confirm_email_link
token = self.user_manager.generate_token(user_email.id if user_email else user.id)
confirm_email_link = url_for('user.confirm_email', token=token, _external=True)
else:
confirm_email_link = None
# Render email from templates and send it via the configured EmailAdapter
self._render_and_send_email(
email,
user,
self.user_manager.USER_REGISTERED_EMAIL_TEMPLATE,
confirm_email_link=confirm_email_link,
) | Send the 'user has registered' notification email. |
def _iterate(self, url, params, api_entity):
"""
Args:
url:
params:
api_entity:
Return:
"""
params['resultLimit'] = self.result_limit
should_iterate = True
result_start = 0
while should_iterate:
# params['resultOffset'] = result_offset
params['resultStart'] = result_start
r = self.tcex.session.get(url, params=params)
if not self.success(r):
err = r.text or r.reason
self.tcex.handle_error(950, [r.status_code, err, r.url])
data = r.json().get('data').get(api_entity)
if len(data) < self.result_limit:
should_iterate = False
result_start += self.result_limit
for result in data:
yield result | Args:
url:
params:
api_entity:
Return: |
def _show_annotation_box(self, event):
"""Update an existing box or create an annotation box for an event."""
ax = event.artist.axes
# Get the pre-created annotation box for the axes or create a new one.
if self.display != 'multiple':
annotation = self.annotations[ax]
elif event.mouseevent in self.annotations:
# Avoid creating multiple datacursors for the same click event
# when several artists are selected.
annotation = self.annotations[event.mouseevent]
else:
annotation = self.annotate(ax, **self._annotation_kwargs)
self.annotations[event.mouseevent] = annotation
if self.display == 'single':
# Hide any other annotation boxes...
for ann in self.annotations.values():
ann.set_visible(False)
self.update(event, annotation) | Update an existing box or create an annotation box for an event. |
def send_json_message(address, message, **kwargs):
"""
a shortcut for message sending
"""
data = {
'message': message,
}
if not kwargs.get('subject_id'):
data['subject_id'] = address
data.update(kwargs)
hxdispatcher.send(address, data) | a shortcut for message sending |
def orc(self, path):
"""Loads a ORC file stream, returning the result as a :class:`DataFrame`.
.. note:: Evolving.
>>> orc_sdf = spark.readStream.schema(sdf_schema).orc(tempfile.mkdtemp())
>>> orc_sdf.isStreaming
True
>>> orc_sdf.schema == sdf_schema
True
"""
if isinstance(path, basestring):
return self._df(self._jreader.orc(path))
else:
raise TypeError("path can be only a single string") | Loads a ORC file stream, returning the result as a :class:`DataFrame`.
.. note:: Evolving.
>>> orc_sdf = spark.readStream.schema(sdf_schema).orc(tempfile.mkdtemp())
>>> orc_sdf.isStreaming
True
>>> orc_sdf.schema == sdf_schema
True |
def model_installed(name):
"""Check if spaCy language model is installed.
From https://github.com/explosion/spaCy/blob/master/spacy/util.py
:param name:
:return:
"""
data_path = util.get_data_path()
if not data_path or not data_path.exists():
raise IOError(f"Can't find spaCy data path: {data_path}")
if name in {d.name for d in data_path.iterdir()}:
return True
if Spacy.is_package(name): # installed as package
return True
if Path(name).exists(): # path to model data directory
return True
return False | Check if spaCy language model is installed.
From https://github.com/explosion/spaCy/blob/master/spacy/util.py
:param name:
:return: |
def _update_dPrxy(self):
"""Update `dPrxy`."""
super(ExpCM_fitprefs, self)._update_dPrxy()
if 'zeta' in self.freeparams:
tildeFrxyQxy = self.tildeFrxy * self.Qxy
j = 0
zetaxterm = scipy.ndarray((self.nsites, N_CODON, N_CODON), dtype='float')
zetayterm = scipy.ndarray((self.nsites, N_CODON, N_CODON), dtype='float')
for r in range(self.nsites):
for i in range(N_AA - 1):
zetari = self.zeta[j]
zetaxterm.fill(0)
zetayterm.fill(0)
zetaxterm[r][self._aa_for_x > i] = -1.0 / zetari
zetaxterm[r][self._aa_for_x == i] = -1.0 / (zetari - 1.0)
zetayterm[r][self._aa_for_y > i] = 1.0 / zetari
zetayterm[r][self._aa_for_y == i] = 1.0 / (zetari - 1.0)
self.dPrxy['zeta'][j] = tildeFrxyQxy * (zetayterm + zetaxterm)
_fill_diagonals(self.dPrxy['zeta'][j], self._diag_indices)
j += 1 | Update `dPrxy`. |
def noise_get_fbm(
n: tcod.noise.Noise,
f: Sequence[float],
oc: float,
typ: int = NOISE_DEFAULT,
) -> float:
"""Return the fractal Brownian motion sampled from the ``f`` coordinate.
Args:
n (Noise): A Noise instance.
f (Sequence[float]): The point to sample the noise from.
typ (int): The noise algorithm to use.
octaves (float): The level of level. Should be more than 1.
Returns:
float: The sampled noise value.
"""
return float(
lib.TCOD_noise_get_fbm_ex(n.noise_c, ffi.new("float[4]", f), oc, typ)
) | Return the fractal Brownian motion sampled from the ``f`` coordinate.
Args:
n (Noise): A Noise instance.
f (Sequence[float]): The point to sample the noise from.
typ (int): The noise algorithm to use.
octaves (float): The level of level. Should be more than 1.
Returns:
float: The sampled noise value. |
def safe_write(filename, blob):
"""
A two-step write.
:param filename: full path
:param blob: binary data
:return: None
"""
temp_file = filename + '.saving'
with open(temp_file, 'bw') as f:
f.write(blob)
os.rename(temp_file, filename) | A two-step write.
:param filename: full path
:param blob: binary data
:return: None |
def stop_change(self):
"""Stop changing light level manually"""
self.logger.info("Dimmer %s stop_change", self.device_id)
self.hub.direct_command(self.device_id, '18', '00')
success = self.hub.check_success(self.device_id, '18', '00')
if success:
self.logger.info("Dimmer %s stop_change: Light stopped changing successfully",
self.device_id)
self.hub.clear_device_command_cache(self.device_id)
else:
self.logger.error("Dimmer %s stop_change: Light did not stop",
self.device_id)
return success | Stop changing light level manually |
def _parse_string_host(host_str):
"""
Parse host string into a dictionary host
:param host_str:
:return:
"""
host_str = EsParser._fix_host_prefix(host_str)
parsed_url = urlparse(host_str)
host = {HostParsing.HOST: parsed_url.hostname}
if parsed_url.port:
host[HostParsing.PORT] = parsed_url.port
if parsed_url.scheme == HostParsing.HTTPS:
host[HostParsing.PORT] = parsed_url.port or EsParser.SSL_DEFAULT_PORT
host[HostParsing.USE_SSL] = True
host[HostParsing.SCHEME] = HostParsing.HTTPS
elif parsed_url.scheme:
host[HostParsing.SCHEME] = parsed_url.scheme
if parsed_url.username or parsed_url.password:
host[HostParsing.HTTP_AUTH] = '%s:%s' % (parsed_url.username, parsed_url.password)
if parsed_url.path and parsed_url.path != '/':
host[HostParsing.URL_PREFIX] = parsed_url.path
return host | Parse host string into a dictionary host
:param host_str:
:return: |
def items(self):
"""
Request URL and parse response. Yield a ``Torrent`` for every torrent
on page.
"""
request = get(str(self.url), headers={'User-Agent' : "Magic Browser","origin_req_host" : "thepiratebay.se"})
root = html.fromstring(request.text)
items = [self._build_torrent(row) for row in
self._get_torrent_rows(root)]
for item in items:
yield item | Request URL and parse response. Yield a ``Torrent`` for every torrent
on page. |
def text_color(self, value):
"""
Setter for **self.__text_color** attribute.
:param value: Attribute value.
:type value: int or QColor
"""
if value is not None:
assert type(value) in (Qt.GlobalColor, QColor), \
"'{0}' attribute: '{1}' type is not 'int' or 'QColor'!".format("text_color", value)
self.__text_color = value | Setter for **self.__text_color** attribute.
:param value: Attribute value.
:type value: int or QColor |
def ed25519_public_key_to_string(key):
"""Convert an ed25519 public key to a base64-encoded string.
Args:
key (Ed25519PublicKey): the key to write to the file.
Returns:
str: the key representation as a str
"""
return base64.b64encode(key.public_bytes(
encoding=serialization.Encoding.Raw,
format=serialization.PublicFormat.Raw,
), None).decode('utf-8') | Convert an ed25519 public key to a base64-encoded string.
Args:
key (Ed25519PublicKey): the key to write to the file.
Returns:
str: the key representation as a str |
def to_gremlin(self):
"""Return a unicode object with the Gremlin representation of this block."""
self.validate()
if len(self.start_class) == 1:
# The official Gremlin documentation claims that this approach
# is generally faster than the one below, since it makes using indexes easier.
# http://gremlindocs.spmallette.documentup.com/#filter/has
start_class = list(self.start_class)[0]
return u'g.V({}, {})'.format('\'@class\'', safe_quoted_string(start_class))
else:
start_classes_list = ','.join(safe_quoted_string(x) for x in self.start_class)
return u'g.V.has(\'@class\', T.in, [{}])'.format(start_classes_list) | Return a unicode object with the Gremlin representation of this block. |
def check_forbidden_filename(filename,
destiny_os=os.name,
restricted_names=restricted_names):
'''
Get if given filename is forbidden for current OS or filesystem.
:param filename:
:param destiny_os: destination operative system
:param fs_encoding: destination filesystem filename encoding
:return: wether is forbidden on given OS (or filesystem) or not
:rtype: bool
'''
return (
filename in restricted_names or
destiny_os == 'nt' and
filename.split('.', 1)[0].upper() in nt_device_names
) | Get if given filename is forbidden for current OS or filesystem.
:param filename:
:param destiny_os: destination operative system
:param fs_encoding: destination filesystem filename encoding
:return: wether is forbidden on given OS (or filesystem) or not
:rtype: bool |
def assign_yourself(self):
"""
Assigning the workflow to itself.
The selected job is checked to see if there is an assigned role.
If it does not have a role assigned to it, it takes the job to itself
and displays a message that the process is successful.
If there is a role assigned to it, it does not do any operation
and the message is displayed on the screen.
.. code-block:: python
# request:
{
'task_inv_key': string,
}
"""
task_invitation = TaskInvitation.objects.get(self.task_invitation_key)
wfi = task_invitation.instance
if not wfi.current_actor.exist:
wfi.current_actor = self.current.role
wfi.save()
[inv.delete() for inv in TaskInvitation.objects.filter(instance=wfi) if
not inv == task_invitation]
title = _(u"Successful")
msg = _(u"You have successfully assigned the job to yourself.")
else:
title = _(u"Unsuccessful")
msg = _(u"Unfortunately, this job is already taken by someone else.")
self.current.msg_box(title=title, msg=msg) | Assigning the workflow to itself.
The selected job is checked to see if there is an assigned role.
If it does not have a role assigned to it, it takes the job to itself
and displays a message that the process is successful.
If there is a role assigned to it, it does not do any operation
and the message is displayed on the screen.
.. code-block:: python
# request:
{
'task_inv_key': string,
} |
def eaSimpleConverge(population, toolbox, cxpb, mutpb, ngen, stats=None,
halloffame=None, callback=None, verbose=True):
"""This algorithm reproduce the simplest evolutionary algorithm as
presented in chapter 7 of [Back2000]_.
Modified to allow checking if there is no change for ngen, as a simple
rule for convergence. Interface is similar to eaSimple(). However, in
eaSimple, ngen is total number of iterations; in eaSimpleConverge, we
terminate only when the best is NOT updated for ngen iterations.
"""
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in population if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
if halloffame is not None:
halloffame.update(population)
record = stats.compile(population) if stats else {}
# Begin the generational process
gen = 1
best = (0,)
while True:
# Select the next generation individuals
offspring = toolbox.select(population, len(population))
# Vary the pool of individuals
offspring = varAnd(offspring, toolbox, cxpb, mutpb)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# Update the hall of fame with the generated individuals
if halloffame is not None:
halloffame.update(offspring)
if callback is not None:
callback(halloffame[0], gen)
# Replace the current population by the offspring
population[:] = offspring
# Append the current generation statistics to the logbook
record = stats.compile(population) if stats else {}
current_best = record['max']
if gen % 20 == 0 and verbose:
print("Current iteration {0}: max_score={1}".
format(gen, current_best), file=sys.stderr)
if current_best > best:
best = current_best
updated = gen
gen += 1
if gen - updated > ngen:
break
return population | This algorithm reproduce the simplest evolutionary algorithm as
presented in chapter 7 of [Back2000]_.
Modified to allow checking if there is no change for ngen, as a simple
rule for convergence. Interface is similar to eaSimple(). However, in
eaSimple, ngen is total number of iterations; in eaSimpleConverge, we
terminate only when the best is NOT updated for ngen iterations. |
def signature(self, name, file_name, file_type, file_content, owner=None, **kwargs):
"""
Create the Signature TI object.
Args:
owner:
file_content:
file_name:
file_type:
name:
**kwargs:
Return:
"""
return Signature(self.tcex, name, file_name, file_type, file_content, owner=owner, **kwargs) | Create the Signature TI object.
Args:
owner:
file_content:
file_name:
file_type:
name:
**kwargs:
Return: |
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