text stringlengths 89 104k | code_tokens list | avg_line_len float64 7.91 980 | score float64 0 630 |
|---|---|---|---|
def add_reads(self, reads):
"""
Create another VariantSequence with more supporting reads.
"""
if len(reads) == 0:
return self
new_reads = self.reads.union(reads)
if len(new_reads) > len(self.reads):
return VariantSequence(
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def convert_html_to_xml(self):
"""
Parses the HTML parsed texts and converts its tags to XML valid tags.
:returns: HTML enabled text in a XML valid format.
:rtype: str
"""
if hasattr(self, 'content') and self.content != '':
regex = r'<(?!/)(?!!)'
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def set_control_scheme(self, index):
"""Sets the control scheme for the agent. See :obj:`ControlSchemes`.
Args:
index (int): The control scheme to use. Should be set with an enum from :obj:`ControlSchemes`.
"""
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def _from_dict(cls, _dict):
"""Initialize a DocumentAccepted object from a json dictionary."""
args = {}
if 'document_id' in _dict:
args['document_id'] = _dict.get('document_id')
if 'status' in _dict:
args['status'] = _dict.get('status')
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def assert_no_current_path(self, path, **kwargs):
"""
Asserts that the page doesn't have the given path.
Args:
path (str | RegexObject): The string or regex that the current "path" should match.
**kwargs: Arbitrary keyword arguments for :class:`CurrentPathQuery`.
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def _generate_base_svm_classifier_spec(model):
"""
Takes an SVM classifier produces a starting spec using the parts. that are
shared between all SVMs.
"""
if not(_HAS_SKLEARN):
raise RuntimeError('scikit-learn not found. scikit-learn conversion API is disabled.')
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def define(self):
"""Defines a new server."""
self.server_def = self.consul.define_server(
self.name,
self.server_tpl,
self.server_tpl_rev,
self.instance_type,
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def multiple(layer: int, limit: int) -> Set[str]:
"""Returns a set of strings to be used as Slots with Pabianas default Clock.
Args:
layer: The layer in the hierarchy this Area is placed in.
Technically, the number specifies how many of the Clocks signals are relevant to the Area.
Between 1 and limit.
limi... | [
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def _calculate_aes_cipher(key):
"""
Determines if the key is a valid AES 128, 192 or 256 key
:param key:
A byte string of the key to use
:raises:
ValueError - when an invalid key is provided
:return:
A unicode string of the AES variation - "aes128", "aes192" or "aes256"
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def do_upgrade(self):
"""Implement your upgrades here."""
sql = text('delete from upgrade where upgrade = :upgrade')
db.engine.execute(
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def all_coplanar(triangles):
"""
Check to see if a list of triangles are all coplanar
Parameters
----------------
triangles: (n, 3, 3) float
Vertices of triangles
Returns
---------------
all_coplanar : bool
True if all triangles are coplanar
"""
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def fullversion():
'''
Shows installed version of dnsmasq and compile options.
CLI Example:
.. code-block:: bash
salt '*' dnsmasq.fullversion
'''
cmd = 'dnsmasq -v'
out = __salt__['cmd.run'](cmd).splitlines()
comps = out[0].split()
version_num = comps[2]
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def calc_mass(nu_max, delta_nu, teff):
""" asteroseismic scaling relations """
NU_MAX = 3140.0 # microHz
DELTA_NU = 135.03 # microHz
TEFF = 5777.0
return (nu_max/NU_MAX)**3 * (delta_nu/DELTA_NU)**(-4) * (teff/TEFF)**1.5 | [
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def range_compress(ol):
'''
#only support sorted-ints or sorted-ascii
l = [1,5,6,7,8,13,14,18,30,31,32,33,34]
range_compress(l)
l = [1,5,6,7,8,13,14,18,30,31,32,33,34,40]
range_compress(l)
l = ['a','b','c','d','j','k','l','m','n','u','y','z']
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def transform_data(self, data):
'''Transform Pandas Timeseries into JSON format
Parameters
----------
data: DataFrame or Series
Pandas DataFrame or Series must have datetime index
Returns
-------
JSON to object.json_data
Example
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"'''Type check values for JSON serialization. Native Python JSON\n serialization will not recognize some Numpy data types properly,\n so they must be explictly ... | 34.276596 | 19.723404 |
def convert_uv(pinyin):
"""ü 转换，还原原始的韵母
ü行的韵跟声母j，q，x拼的时候，写成ju(居)，qu(区)，xu(虚)，
ü上两点也省略；但是跟声母n，l拼的时候，仍然写成nü(女)，lü(吕)。
"""
return UV_RE.sub(
lambda m: ''.join((m.group(1), UV_MAP[m.group(2)], m.group(3))),
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def disconnect(self):
"""Gracefully disconnect from the server."""
with self.lock:
if self.stream:
if self.settings[u"initial_presence"]:
self.send(Presence(stanza_type = "unavailable"))
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def tilequeue_enqueue_random_pyramids(cfg, peripherals, args):
"""enqueue random pyramids"""
from tilequeue.stats import RawrTileEnqueueStatsHandler
from tilequeue.rawr import make_rawr_enqueuer_from_cfg
logger = make_logger(cfg, 'enqueue_random_pyramids')
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def create_attachment(self, container, attachment_file, **kw):
"""Create an Attachment object in the given container
"""
filename = getattr(attachment_file, "filename", "Attachment")
attachment = api.create(container, "Attachment", title=filename)
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def add_inputs(self, inputs):
# type: (Iterable[Address]) -> None
"""
Adds inputs to spend in the bundle.
Note that each input may require multiple transactions, in order
to hold the entire signature.
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def encode(self):
'''
Encode and store a CONNACK control packet.
'''
header = bytearray(1)
varHeader = bytearray(2)
header[0] = 0x20
varHeader[0] = self.session
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def remove(name):
"""Removes a snapshot"""
app = get_app()
snapshot = app.get_snapshot(name)
if not snapshot:
click.echo("Couldn't find snapshot %s" % name)
sys.exit(1)
click.echo("Deleting snapshot %s" % name)
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def assert_in_setup_repo(setup_fpath, name=''):
""" pass in __file__ from setup.py """
setup_dir, setup_fname = split(setup_fpath)
cwd = os.getcwd()
#repo_dname = split(setup_dir)[1]
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def _request(self, *args, **kwargs):
"""Make the request"""
try:
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def get_linked_agenda_items(self) -> List[str]:
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def day_crumb(date):
"""
Crumb for a day.
"""
year = date.strftime('%Y')
month = date.strftime('%m')
day = date.strftime('%d')
return Crumb(day, reverse('zinnia:entry_archive_day',
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def create(
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"""Return a deferred."""
url = cls.class_url()
headers = populate_headers(idempotency_key)
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def firehose(self, **params):
"""Stream statuses/firehose
:param \*\*params: Parameters to send with your stream request
Accepted params found at:
https://dev.twitter.com/docs/api/1.1/get/statuses/firehose
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def preprovision_rbridge_id_wwn(self, **kwargs):
"""Auto Generated Code
"""
config = ET.Element("config")
preprovision = ET.SubElement(config, "preprovision", xmlns="urn:brocade.com:mgmt:brocade-preprovision")
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def get_mean_and_stddevs(self, sites, rup, dists, imt, stddev_types):
"""
See :meth:`superclass method
<.base.GroundShakingIntensityModel.get_mean_and_stddevs>`
for spec of input and result values.
Call super class method with hypocentral depth fixed at 20 km
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... | 36.411765 | 17.823529 |
def connect_euca(host=None, aws_access_key_id=None, aws_secret_access_key=None,
port=8773, path='/services/Eucalyptus', is_secure=False,
**kwargs):
"""
Connect to a Eucalyptus service.
:type host: string
:param host: the host name or ip address of the Eucalyptus server... | [
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def process_data(self, sockets):
"""Called when there is more data to read on connection sockets.
Arguments:
sockets -- A list of socket objects.
See documentation for Reactor.__init__.
"""
with self.mutex:
log.log(logging.DEBUG - 2, "process_data()")
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def clear_values(self, red=0.0, green=0.0, blue=0.0, alpha=0.0, depth=1.0):
"""
Sets the clear values for the window buffer.
Args:
red (float): red compoent
green (float): green compoent
blue (float): blue compoent
alpha (float): alpha compoent
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def overlay_gateway_attach_rbridge_id(self, **kwargs):
"""Configure Overlay Gateway attach rbridge id
Args:
gw_name: Name of Overlay Gateway <WORD:1-32>
rbridge_id: Single or range of rbridge id to be added/removed
get (bool): Get config instead of editing config. ... | [
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def get_re_experiment(case, minor=1):
""" Returns an experiment that uses the Roth-Erev learning method.
"""
gen = case.generators
profile = array([1.0])
maxSteps = len(profile)
experimentation = 0.55
recency = 0.3
tau = 100.0
decay = 0.99#9995
market = pyreto.SmartMarket(case,... | [
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def user(self, base_dn, samaccountname, attributes=(), explicit_membership_only=False):
"""Produces a single, populated ADUser object through the object factory.
Does not populate attributes for the caller instance.
:param str base_dn: The base DN to search within
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def mutate(self, node, index):
"""Modify the numeric value on `node`."""
assert index < len(OFFSETS), 'received count with no associated offset'
assert isinstance(node, parso.python.tree.Number)
val = eval(node.value) + OFFSETS[index] # pylint: disable=W0123
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def TypeFactory(type_):
"""
This function creates a standard form type from a simplified form.
>>> from datetime import date, datetime
>>> from pyws.functions.args import TypeFactory
>>> from pyws.functions.args import String, Integer, Float, Date, DateTime
>>> TypeFactory(str) == String
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def num_lines(self):
"""
Lazy evaluation of the number of lines.
Returns None for stdin input currently.
"""
if self.from_stdin:
return None
if not self._num_lines:
self._iterate_lines()
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def get_arp_output_arp_entry_mac_address(self, **kwargs):
"""Auto Generated Code
"""
config = ET.Element("config")
get_arp = ET.Element("get_arp")
config = get_arp
output = ET.SubElement(get_arp, "output")
arp_entry = ET.SubElement(output, "arp-entry")
ip_... | [
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def Sign(self, context):
"""
Sign the verifiable items ( Transaction, Block, etc ) in the context with the Keypairs in this wallet.
Args:
context (ContractParameterContext): the context to sign.
Returns:
bool: if signing is successful for all contracts in this w... | [
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def get_init_container(self,
init_command,
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env_vars,
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"""Pod init container for sett... | [
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def query(function,
api_key=None,
args=None,
method='GET',
header_dict=None,
data=None,
opts=None):
'''
Slack object method function to construct and execute on the API URL.
:param api_key: The Slack api key.
:param function: The Slack ... | [
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def requires_auth(f):
""" Class decorator for XML-RPC functions that requires auth
"""
@wraps(f)
def decorated(self, *args, **kwargs):
"""
"""
# Fetch auth options from args
auth_options = {}
nipap_args = {}
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def pos_tag(sentence, format=None):
"""
Vietnamese POS tagging
Parameters
==========
sentence: {unicode, str}
Raw sentence
Returns
=======
tokens: list of tuple with word, pos tag
tagged sentence
Examples
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>>> # -*- coding: utf-8 -*-
>>> from un... | [
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def get_speaker_muted(self):
"""Return whether or not the speaker is muted."""
if not self.camera_extended_properties:
return None
speaker = self.camera_extended_properties.get('speaker')
if not speaker:
return None
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def run(self):
"""
Runs the optimization using the previously loaded elements.
"""
space = self._get_space()
obj_func = self._get_obj(space)
model = self._get_model()
acq = self._get_acquisition(model, space)
acq_eval = self._get_acq_evaluator(acq)
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def purchase_ip(self, debug=False):
"""
Return an ip object representing a new bought IP
@param debug [Boolean] if true, request and response will be printed
@return (Ip): Ip object
"""
json_scheme = self.gen_def_json_scheme('SetPurchaseIpAddress')
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def _request(self, url, method = u"get", data = None, headers=None, **kwargs):
"""
does the request via requests
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- use basic auth please
"""
# if self.access_token:
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def is_main_process():
""" Check if this is the main control process and may handle one time tasks
"""
try:
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
return rank == 0
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def to_add(self, citiao):
'''
To Add page.
'''
kwd = {
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'slug': citiao,
'pager': '',
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self.render('wiki_page/page_add.html',
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def show_colormaps(names=[], N=10, show=True, use_qt=None):
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Parameters
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def get_proxies_from_environ():
"""Get proxies from os.environ."""
proxies = {}
http_proxy = os.getenv('http_proxy') or os.getenv('HTTP_PROXY')
https_proxy = os.getenv('https_proxy') or os.getenv('HTTPS_PROXY')
if http_proxy:
proxies['http'] = http_proxy
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def authenticate(self, dn='', password=''):
"""
Attempt to authenticate given dn and password using a bind operation.
Return True if the bind is successful, and return False there was an
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Parse and clean up argument to user code; separate *args from
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args = []
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self.expression_list = [] # code arrives in dictionary, but is passed in this list
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def check_method_requirements(func):
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"""
@wraps(func)
def wrapper(*args, **kwargs):
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def create_object(container, portal_type, **data):
"""Creates an object slug
:returns: The new created content object
:rtype: object
"""
if "id" in data:
# always omit the id as senaite LIMS generates a proper one
id = data.pop("id")
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def CacheFileSystem(self, path_spec, file_system):
"""Caches a file system object based on a path specification.
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path_spec (PathSpec): path specification.
file_system (FileSystem): file system object.
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identifier = self._GetFileSystemCacheIdentifier(path_spec)
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def kernels_status(self, kernel):
""" call to the api to get the status of a kernel.
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kernel: the kernel to get the status for
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if kernel is None:
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"k... | 38.842105 | 12.368421 |
def patched_get_current(self, request=None):
"""
Monkey patched version of Django's SiteManager.get_current() function.
Returns the current Site based on a given request or the SITE_ID in
the project's settings. If a request is given attempts to match a site
with domain matching request.get_host().... | [
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def dump_info(self, dump=None):
"""Dump all the PE header information into human readable string."""
if dump is None:
dump = Dump()
warnings = self.get_warnings()
if warnings:
dump.add_header('Parsing Warnings')
for warning i... | [
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def initialize_wind_turbine_cluster(example_farm, example_farm_2):
r"""
Initializes a :class:`~.wind_turbine_cluster.WindTurbineCluster` object.
Function shows how to initialize a WindTurbineCluster object. In this case
the cluster only contains two wind farms.
Parameters
----------
exampl... | [
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def validate_parsed_json(obj_json, options=None):
"""
Validate objects from parsed JSON. This supports a single object, or a
list of objects. If a single object is given, a single result is
returned. Otherwise, a list of results is returned.
If an error occurs, a ValidationErrorResults instance ... | [
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def build_collection(df, **kwargs):
'''
Generates a list of Record objects given a DataFrame.
Each Record instance has a series attribute which is a pandas.Series of the same attributes
in the DataFrame.
Optional data can be passed in through kwargs which will be included by the name of each object... | [
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def list_listeners(self, retrieve_all=True, **_params):
"""Fetches a list of all lbaas_listeners for a project."""
return self.list('listeners', self.lbaas_listeners_path,
retrieve_all, **_params) | [
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def sleep(seconds=0):
"""Yield control to another eligible coroutine until at least *seconds* have
elapsed.
*seconds* may be specified as an integer, or a float if fractional seconds
are desired.
"""
loop = evergreen.current.loop
current = Fiber.current()
assert loop.task is not current... | [
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def kld(d1, d2):
"""Return the Kullback-Leibler Divergence (KLD) between two distributions.
Args:
d1 (np.ndarray): The first distribution.
d2 (np.ndarray): The second distribution.
Returns:
float: The KLD of ``d1`` from ``d2``.
"""
d1, d2 = flatten(d1), flatten(d2)
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def encode(self):
"""
Just iterate over the child elements and append them to the current element
:return: the encoded element
:rtype: xml.etree.ElementTree.Element
"""
element = ElementTree.Element(
self.name,
attrib={'type': FieldConstants.ARRAY... | [
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def set_to_tuple(tokens):
"""Converts set literal tokens to tuples."""
internal_assert(len(tokens) == 1, "invalid set maker tokens", tokens)
if "comp" in tokens or "list" in tokens:
return "(" + tokens[0] + ")"
elif "test" in tokens:
return "(" + tokens[0] + ",)"
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def get_default_config(self):
"""
Returns the default collector settings
"""
config = super(ExampleCollector, self).get_default_config()
config.update({
'path': 'example'
})
return config | [
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def discrete(cats, name='discrete'):
"""Return a class category that shows the encoding"""
import json
ks = list(cats)
for key in ks:
if isinstance(key, bytes):
cats[key.decode('utf-8')] = cats.pop(key)
return 'discrete(' + json.dumps([cats, name]) + ')' | [
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def get_mesh(oqparam):
"""
Extract the mesh of points to compute from the sites,
the sites_csv, or the region.
:param oqparam:
an :class:`openquake.commonlib.oqvalidation.OqParam` instance
"""
global pmap, exposure, gmfs, eids
if 'exposure' in oqparam.inputs and exposure is None:
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def isometric_view_interactive(self):
""" sets the current interactive render window to isometric view """
interactor = self.iren.GetInteractorStyle()
renderer = interactor.GetCurrentRenderer()
renderer.view_isometric() | [
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def set_parent(self, parent):
"""Set parent ``Expression`` for this object.
Args:
parent (Expression): The ``Expression`` which contains this object.
Raises:
FiqlObjectException: Parent must be of type ``Expression``.
"""
if not isinstance(parent, Expres... | [
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def get_preflist(self, bucket, key):
"""
Get the preflist for a bucket/key
:param bucket: Riak Bucket
:type bucket: :class:`~riak.bucket.RiakBucket`
:param key: Riak Key
:type key: string
:rtype: list of dicts
"""
if not self.preflists():
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def run(self):
"""
Ping entries to a directory in a thread.
"""
logger = getLogger('zinnia.ping.directory')
socket.setdefaulttimeout(self.timeout)
for entry in self.entries:
reply = self.ping_entry(entry)
self.results.append(reply)
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def ancestor(self, value):
"""Set the ancestor for the query
:type value: :class:`~google.cloud.datastore.key.Key`
:param value: the new ancestor key
"""
if not isinstance(value, Key):
raise TypeError("Ancestor must be a Key")
self._ancestor = value | [
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def write(version):
# type: (str) -> None
""" Write the given version to the VERSION_FILE """
if not is_valid(version):
raise ValueError("Invalid version: ".format(version))
storage = get_version_storage()
storage.write(version) | [
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def ensure_stopped(self):
"""Idempotent channel stop"""
if not self.active:
return self
self.stop()
self.observer.cancel()
self._manager.remove_routes(self, self.get_routing_keys())
self._active = False
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def paintEvent(self, event):
"""Fills the panel background using QPalette."""
if self.isVisible() and self.position != self.Position.FLOATING:
# fill background
self._background_brush = QBrush(QColor(
self.editor.sideareas_color))
self._foreground_pen ... | [
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def _write_multiplicons(self, filename):
""" Write multiplicons to file.
- filename, (str) location of output file
"""
# Column headers
mhead = '\t'.join(['id', 'genome_x', 'list_x', 'parent', 'genome_y',
'list_y', 'level', 'number_of_anchorpoints'... | [
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def _finalize(self):
""" command to run at the end of sprinter's run """
self.logger.info("Finalizing...")
self.write_manifest()
if self.directory.rewrite_config:
# always ensure .rc is written (sourcing .env)
self.directory.add_to_rc('')
# prepend br... | [
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def get_names(list_of_taxids):
"""
>>> mylist = [3702, 3649, 3694, 3880]
>>> get_names(mylist)
['Arabidopsis thaliana', 'Carica papaya', 'Populus trichocarpa', 'Medicago truncatula']
"""
from jcvi.apps.fetch import batch_taxonomy
list_of_taxids = [str(x) for x in list_of_taxids]
return l... | [
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def new_utterance(self, utterance_idx, track_idx, issuer_idx=None, start=0, end=float('inf')):
"""
Add a new utterance to the corpus with the given data.
Parameters:
track_idx (str): The track id the utterance is in.
utterance_idx (str): The id to associate with the utte... | [
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def register_directory(self, directory, parent, ensure_uniqueness=False):
"""
Registers given directory in the Model.
:param directory: Directory to register.
:type directory: unicode
:param parent: DirectoryNode parent.
:type parent: GraphModelNode
:param ensure... | [
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def update_external_store(self, project_name, config):
"""
update the logstore meta info
Unsuccessful opertaion will cause an LogException.
:type config: ExternalStoreConfig
:param config : external store config
:return: UpdateExternalStoreResponse
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def extract_boto_args_from_env(env_vars):
"""Return boto3 client args dict with environment creds."""
boto_args = {}
for i in ['aws_access_key_id', 'aws_secret_access_key',
'aws_session_token']:
if env_vars.get(i.upper()):
boto_args[i] = env_vars[i.upper()]
return boto_... | [
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def flush(self):
""" Flush message queue if there's an active connection running """
self._pending_flush = False
if self.handler is None:
return
if self.send_queue.is_empty():
return
self.handler.send_pack('a[%s]' % self.send_queue.get())
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def _gate_height(self, gate):
"""
Return the height to use for this gate.
:param string gate: The name of the gate whose height is desired.
:return: Height of the gate.
:rtype: float
"""
try:
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def plot_max_median_position_concentration(positions, ax=None, **kwargs):
"""
Plots the max and median of long and short position concentrations
over the time.
Parameters
----------
positions : pd.DataFrame
The positions that the strategy takes over time.
ax : matplotlib.Axes, optio... | [
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def recv(self, timeout=None):
"""Overwrite standard recv for timeout calls to catch interrupt errors.
"""
if timeout:
try:
testsock = self._zmq.select([self.socket], [], [], timeout)[0]
except zmq.ZMQError as e:
if e.errno == errno.EINTR:
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... | 36.882353 | 14.529412 |
def invite(self, address, text=None, *,
mode=InviteMode.DIRECT,
allow_upgrade=False):
"""
Invite another entity to the conversation.
:param address: The address of the entity to invite.
:type address: :class:`aioxmpp.JID`
:param text: A reason/accom... | [
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")"... | 44.523077 | 23.938462 |
def _handle_tag_jpegtables(self):
"""Handle the JPEGTables tag."""
obj = _make_object("JPEGTables")
assert self._src.read(2) == b'\xFF\xD8' # SOI marker
eoimark1 = eoimark2 = None
allbytes = [b'\xFF\xD8']
while not (eoimark1 == b'\xFF' and eoimark2 == b'\xD9'):
... | [
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"allby... | 37.266667 | 11.533333 |
def _kpost(url, data):
''' create any object in kubernetes based on URL '''
# Prepare headers
headers = {"Content-Type": "application/json"}
# Make request
log.trace("url is: %s, data is: %s", url, data)
ret = http.query(url,
method='POST',
header_dict=... | [
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def add_vertex(self, v):
""" Add a vertex to the graph
:param v: The vertex name.
"""
self.graph.add_vertex(v)
self.vs.add(v) | [
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def delete_collection_storage_class(self, **kwargs): # noqa: E501
"""delete_collection_storage_class # noqa: E501
delete collection of StorageClass # noqa: E501
This method makes a synchronous HTTP request by default. To make an
asynchronous HTTP request, please pass async_req=True
... | [
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"delete_coll... | 163.655172 | 135.275862 |
def switch(condition, then_expression, else_expression):
"""Switches between two operations depending on a scalar value (int or bool).
Note that both `then_expression` and `else_expression`
should be symbolic tensors of the *same shape*.
# Arguments
condition: scalar tensor.
then_expres... | [
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"condit... | 37.75 | 11.75 |
def _default_headers(self):
"""Set the default header for a Twilio SendGrid v3 API call"""
headers = {
"Authorization": 'Bearer {}'.format(self.api_key),
"User-agent": self.useragent,
"Accept": 'application/json'
}
if self.impersonate_subuser:
... | [
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":",
"'application/json'",... | 36.181818 | 15.545455 |
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