text stringlengths 75 104k | code_tokens list | avg_line_len float64 7.91 980 | score float64 0 0.18 |
|---|---|---|---|
def set_mean(self, col, row, mean):
"""
Sets the mean at this location (if valid location).
:param col: the 0-based column index
:type col: int
:param row: the 0-based row index
:type row: int
:param mean: the mean to set
:type mean: float
"""
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def update_show_function(self, show_name, show_func):
"""
Modifies/overwrites an existing show function in the
locally cached DesignDocument shows dictionary.
:param show_name: Name used to identify the show function.
:param show_func: Javascript show function.
"""
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def securitycli():
"""
Entry point for the runner defined in setup.py.
"""
parser = argparse.ArgumentParser(description="Runner for security test suite")
parser.add_argument("-l", "--list-test-groups", action="store_true",
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def send_with_template(message,
api_key=None,
secure=None,
test=None,
**request_args):
'''Send a message.
:param message: Message to send.
:type message: `dict` or :class:`Message`
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def mac(self, algorithm, key, data):
"""
Generate message authentication code.
Args:
algorithm(CryptographicAlgorithm): An enumeration specifying the
algorithm for which the MAC operation will use.
key(bytes): secret key used in the MAC operation
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def adam7_generate(width, height):
"""
Generate the coordinates for the reduced scanlines
of an Adam7 interlaced image
of size `width` by `height` pixels.
Yields a generator for each pass,
and each pass generator yields a series of (x, y, xstep) triples,
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def apply_network_settings(**settings):
'''
Apply global network configuration.
CLI Example:
.. code-block:: bash
salt '*' ip.apply_network_settings
'''
if __grains__['lsb_distrib_id'] == 'nilrt':
raise salt.exceptions.CommandExecutionError('Not supported in this version.')
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def to_find(self):
'''
Todo: the name should be changed.
list the infors.
'''
kwd = {'pager': ''}
self.render('user/info_list/most.html',
topmenu='',
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def associate(self, eip_or_aid,
instance_id='', network_interface_id='', private_ip=''):
"""Associate an EIP with a given instance or network interface. If
the EIP was allocated for a VPC instance, an AllocationId(aid) must
be provided instead of a PublicIp.
"""
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def popone(self, key, *default):
"""Remove first of given key and return corresponding value.
If key is not found, default is returned if given.
>>> m = MutableMultiMap([('a', 1), ('b', 2), ('b', 3), ('c', 4)])
>>> m.popone('b')
2
>>> m.items()
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def to_string(type):
"""
Converts a TypeCode into its string name.
:param type: the TypeCode to convert into a string.
:return: the name of the TypeCode passed as a string value.
"""
if type == None:
return "unknown"
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def applymap(self, func, subset=None, **kwargs):
"""
Apply a function elementwise, updating the HTML
representation with the result.
Parameters
----------
func : function
``func`` should take a scalar and return a scalar
subset : IndexSlice
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def add_get(self, path, controller, template, raw=False):
"""
Setup a route of type GET
Args:
path (str): URL to listen to
controller (coroutine): the coroutine to handle the request
template (str): the template to render the response or None if it is a JSON respon... | [
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def save_data(self, *, data_filter=None, redownload=False, max_threads=None, raise_download_errors=False):
"""
Saves data to disk. If ``redownload=True`` then the data is redownloaded using ``max_threads`` workers.
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def get_paginated_response(data, request):
"""
Update pagination links in course catalog data and return DRF Response.
Arguments:
data (dict): Dictionary containing catalog courses.
request (HttpRequest): Current request object.
Returns:
(Response): DRF response object containi... | [
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def get_sdb_secret_version_paths(self, sdb_id):
""" Get SDB secret version paths. This function takes the sdb_id """
sdb_resp = get_with_retry(str.join('', [self.cerberus_url, '/v1/sdb-secret-version-paths/', sdb_id]),
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def js(request):
"""Returns the javascript needed to run persona"""
userid = authenticated_userid(request)
user = markupsafe.Markup("'%s'")%userid if userid else "null"
redirect_paramater = request.registry['persona.redirect_url_parameter']
came_from = '%s%s' % (request.host_url,
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def sanitize_command_options(options):
"""
Sanitizes command options.
"""
multiples = [
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for option in multiples:
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def _child_list(element, child_tagname):
"""
Return list containing the direct children of *element* having
*child_tagname*.
"""
xpath = './%s' % child_tagname
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def transform(self, trans):
"""
Compute a transformation in place using a 4x4 transform.
Parameters
----------
trans : vtk.vtkMatrix4x4, vtk.vtkTransform, or np.ndarray
Accepts a vtk transformation object or a 4x4 transformation matrix.
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def average(arr):
"""average of the values, must have more than 0 entries.
:param arr: list of numbers
:type arr: number[] a number array
:return: average
:rtype: float
"""
if len(arr) == 0:
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def TYPEDEF(self, _cursor_type):
"""
Handles TYPEDEF statement.
"""
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def download_attachments(self):
""" Downloads this message attachments into memory.
Need a call to 'attachment.save' to save them on disk.
:return: Success / Failure
:rtype: bool
"""
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def _bfill(arr, n=None, axis=-1):
'''inverse of ffill'''
import bottleneck as bn
arr = np.flip(arr, axis=axis)
# fill
arr = bn.push(arr, axis=axis, n=n)
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def is_ternary(self, keyword):
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def compress(self, setup):
"""
Returns the compressed graph according to the given experimental setup
Parameters
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setup : :class:`caspo.core.setup.Setup`
Experimental setup used to compress the graph
Returns
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def disable(self, msgid, scope="package", line=None, ignore_unknown=False):
"""don't output message of the given id"""
self._set_msg_status(
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def get_groups_from_category(self, category) -> typing.Iterator['Group']:
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def in_nested_list(nested_list, obj):
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def ack(self, msg):
"""Processes the received message. I don't need to
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def t_IDENTIFIER(t):
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def passthrough_proc(self, inputstring, **kwargs):
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... | 38.638298 | 0.003222 |
def converge(self, playbook=None, **kwargs):
"""
Executes ``ansible-playbook`` against the converge playbook unless
specified otherwise and returns a string.
:param playbook: An optional string containing an absolute path to a
playbook.
:param kwargs: An optional keywor... | [
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def add_options(parser):
"""
Add optional arguments to the parser
"""
partial_action = common.partial_append_action
file_mods = parser.add_argument_group("Sequence File Modification")
file_mods.add_argument('--line-wrap', dest='line_wrap', metavar='N',
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def download_supplementary_files(self, directory='series',
download_sra=True, email=None,
sra_kwargs=None, nproc=1):
"""Download supplementary data.
.. warning::
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def x509_rsa_load(txt):
""" So I get the same output format as loads produces
:param txt:
:return:
"""
pub_key = import_rsa_key(txt)
if isinstance(pub_key, rsa.RSAPublicKey):
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def add_feature_values(self, features):
"""
Adds feature values of feature 'feature' to all fixations in
the calling fixmat.
For fixations out of the image boundaries, NaNs are returned.
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string in featu... | [
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def _find_pair(self, protocol, remote_candidate):
"""
Find a candidate pair in the check list.
"""
for pair in self._check_list:
if (pair.protocol == protocol and pair.remote_candidate == remote_candidate):
return pair
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def named_config(self, func):
"""
Decorator to turn a function into a named configuration.
See :ref:`named_configurations`.
"""
config_scope = ConfigScope(func)
self._add_named_config(func.__name__, config_scope)
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def get_membership_cache(self, group_ids=None, is_active=True):
"""
Build a dict cache with the group membership info. Keyed off the group id and the values are
a 2 element list of entity id and entity kind id (same values as the membership model). If no group ids
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def demonstrate_colored_logging():
"""Interactively demonstrate the :mod:`coloredlogs` package."""
# Determine the available logging levels and order them by numeric value.
decorated_levels = []
defined_levels = coloredlogs.find_defined_levels()
normalizer = coloredlogs.NameNormalizer()
for name... | [
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def _filter_dicts(self):
'''Filters out all the report_dicts that do not pass the cutoffs. If any ref sequence
loses all of its report_dicts, then it is completely removed.'''
keys_to_remove = set()
for ref_name in self.report:
for ctg_name in self.report[ref_name]:
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def segment_radii(neurites, neurite_type=NeuriteType.all):
'''arithmetic mean of the radii of the points in segments in a collection of neurites'''
def _seg_radii(sec):
'''vectorized mean radii'''
pts = sec.points[:, COLS.R]
return np.divide(np.add(pts[:-1], pts[1:]), 2.0)
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def load_cache():
"""
Load cache from the disk.
Return:
set: Deserialized data from disk.
"""
if not os.path.exists(settings.DUP_FILTER_FILE):
return set()
with open(settings.DUP_FILTER_FILE) as f:
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def _clean_xml(self, path_to_xml):
"""Clean MARCXML harvested from OAI.
Allows the xml to be used with BibUpload or BibRecord.
:param xml: either XML as a string or path to an XML file
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def create_enum_option(self, custom_field, params={}, **options):
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def dmol_neg_log_perplexity(predictions,
labels,
weights_fn=None):
"""Average log-perplexity excluding padding 0s. No smoothing."""
del weights_fn # Unused
num, den = common_layers.dml_loss(
predictions, labels, reduce_sum=False)
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def listDatasetArray(self):
"""
API to list datasets in DBS. To be called by datasetlist url with post call.
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def validate_crc(msg):
""" Validate CRC of message.
:param msg: Byte array with message with CRC.
:raise: CRCError.
"""
if not struct.unpack('<H', get_crc(msg[:-2])) ==\
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def generate_colours(n):
"""Return a list of `n` distinct colours, each represented as an RGB
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Based on the code at
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def _find_classes_param(self):
"""
Searches the wrapped model for the classes_ parameter.
"""
for attr in ["classes_"]:
try:
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except AttributeError:
continue
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def addnot(self, action=None, subject=None, **conditions):
"""
Defines an ability which cannot be done.
"""
self.add_rule(Rule(False, action, subject, **conditions)) | [
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def main(unused_argv):
"""Freeze a model to a GraphDef proto."""
if FLAGS.use_tpu:
dual_net.freeze_graph_tpu(FLAGS.model_path)
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def loadWallet(self, fpath):
"""Load wallet from specified localtion.
Returns loaded wallet.
Error cases:
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- ``fpath`` exists and it's a directory - IsADirectoryError raised
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def retry_connect(self):
"""Will be called when new channels in the token network are detected.
If the minimum number of channels was not yet established, it will try
to open new channels.
If the connection manager has no funds, this is a noop.
"""
with self.lock:
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def get_loco_name(self):
"""
Returns the Provider, Product and Engine name.
:return list
"""
ret_str = self.dll.GetLocoName().decode()
if not ret_str:
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return ret_str.split('.:.') | [
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def check_cmake_exists(cmake_command):
"""
Check whether CMake is installed. If not, print
informative error message and quits.
"""
from subprocess import Popen, PIPE
p = Popen(
'{0} --version'.format(cmake_command),
shell=True,
stdin=PIPE,
stdout=PIPE)
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def update_fmt_with_notebook_options(self, metadata):
"""Update format options with the values in the notebook metadata, and record those
options in the notebook metadata"""
# format options in notebook have precedence over that in fmt
for opt in _VALID_FORMAT_OPTIONS:
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def _decode_agents_data(self, block):
"""
decode agents jsons, count diffs
"""
collect = []
if block:
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try:
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prepared_results = {}
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def _check_input_directory_listing(base_directory, listing):
"""
Raises an DirectoryError if files or directories, given in the listing, could not be found in the local filesystem.
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def set_ownership(self):
"""Recursivelt set the parent, section and doc for a children"""
assert self.section is not None
for t in self.children:
t.parent = self
t._section = self.section
t.doc = self.doc
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def extend_extents(extents, factor=1.1):
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:param extents: The bound box extents
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def csv_to_map(fields, delimiter=','):
"""
Convert csv to dict
:param delimiter:
:param fields:
:return:
"""
def _csv_to_list(csv_input):
"""
Util function to overcome the use of files by in-memory io buffer
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def on_change_plot_cursor(self,event):
"""
If mouse is over data point making it selectable change the shape of the cursor
@param: event -> the wx Mouseevent for that click
"""
if not self.xdata or not self.ydata: return
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def get_relationship_search_session(self, proxy=None):
"""Gets the ``OsidSession`` associated with the relationship search service.
arg: proxy (osid.proxy.Proxy): a proxy
return: (osid.relationship.RelationshipSearchSession) - a
``RelationshipSearchSession``
raise: N... | [
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def old_streamer(main_method):
"""Open a stream for the first file in arguments, or stdin"""
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def fetch(self, tickers, fields=None, date=None, date_from=None, date_to=None,
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"""Fetch data from TR DWE.
tickers - ticker or list of tickers
fields - list of fields.
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def get_dict_for_class(self, class_name, state=None, base_name='View'):
"""The style dict for a given class and state.
This collects the style attributes from parent classes
and the class of the given object and gives precedence
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def exists(path, **kwargs):
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'''
Check if an environment is exposed by comparing it against a whitelist and
blacklist.
'''
if __opts__['svnfs_env_whitelist']:
salt.utils.versions.warn_until(
'Neon',
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def finish(self):
"""
Restore the original SIGINT handler after finishing.
This should happen regardless of whether the progress display finishes
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"""
super(InterruptibleMixin, self).finish()
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def type_object_attrgetter(obj, attr, *defargs):
"""
This implements an improved attrgetter for type objects (i.e. classes)
that can handle class attributes that are implemented as properties on
a metaclass.
Normally `getattr` on a class with a `property` (say, "foo"), would return
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def doubleMouseButtonLeftWithMods(self, coord, modifiers):
"""Click the left mouse button with modifiers pressed.
Parameters: coordinates to click; modifiers (list)
Returns: None
"""
modFlags = self._pressModifiers(modifiers)
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def collate_data(in_dir, extension='.csv', out_dir=None):
"""
Copy all csvs in nested directroy to single directory.
Function to copy all csvs from a directory, and place
them in a new directory.
Parameters
----------
in_dir : str
Input directory containing csv files in subfolders
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def setContentLen(self, content, len):
"""Replace the content of a node. NOTE: @content is supposed
to be a piece of XML CDATA, so it allows entity references,
but XML special chars need to be escaped first by using
xmlEncodeEntitiesReentrant() resp. xmlEncodeSpecialChars(). """
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def _serialize(
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value, # type: List
state # type: _ProcessorState
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# type: (...) -> None
"""Serialize the array value and add it to the array parent element."""
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def statement_prep(link):
'''
Prepare a statement into a triple ready for rdflib
'''
from rdflib import URIRef, Literal
from rdflib import BNode
s, p, o = link[:3]
if not isinstance(s, BNode): s = URIRef(s)
p = URIRef(p)
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def _get_all(self, *args, **kwargs):
"""If 'force' is in the headers, retrieve the list of keys from S3.
Otherwise, use the list() function to retrieve the keys from MimicDB.
"""
headers = kwargs.get('headers', args[2] if len(args) > 2 else None) or dict()
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def build_additional_match(self, ident, node_set):
"""
handle additional matches supplied by 'has()' calls
"""
source_ident = ident
for key, value in node_set.must_match.items():
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def _insert_data(con, data):
"""
insert line for each cluster
"""
with con:
cur = con.cursor()
cur.execute("DROP TABLE IF EXISTS clusters;")
cur.execute("CREATE TABLE clusters(Id INT, Description TEXT, Locus TEXT, Annotation TEXT, Sequences TEXT, Profile TXT, Precursor TXT)")
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def cns_vwl_pstr_long(self):
"""
Return a new IPAString, containing only:
1. the consonants,
2. the vowels, and
3. the primary stress diacritics, and
4. the long suprasegmental
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def file_find(self, load):
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Convenience function for calls made using the LocalClient
'''
path = load.get('path')
if not path:
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tgt_env = load.get('saltenv', 'base')
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def add(config, username, filename):
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try:
client = Client()
client.prepare_connection()
user_api = UserApi(client)
key_api = API(client)
key_api.add(username, user_api, filename)
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def delete_operation(self, name, options=None):
"""
Deletes a long-running operation. This method indicates that the client is
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def _bfd_rx(self, **kwargs):
"""Return the BFD minimum receive interval XML.
You should not use this method.
You probably want `BGP.bfd`.
Args:
min_rx (str): BFD receive interval in milliseconds (300, 500, etc)
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def _get_meta(model):
"""Return metadata of a model.
Model could be a real model or evaluated metadata."""
if isinstance(model, Model):
w = model.meta
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w = model # Already metadata
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def _maybe_validate_distributions(distributions, dtype_override, validate_args):
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assertions = []
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def create(filename, spec):
"""Create a new segy file.
Create a new segy file with the geometry and properties given by `spec`.
This enables creating SEGY files from your data. The created file supports
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def set_metadata(self, obj, metadata, clear=False, prefix=None):
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def encoder(f, blocksize, seed=None, c=sampler.DEFAULT_C, delta=sampler.DEFAULT_DELTA):
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"""
# Generate seed if not provided
if seed is None:
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def from_api_repr(cls, resource, client):
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def write_str(data, sidx, pnames):
""" Write STRUCTURE format for all SNPs and unlinked SNPs """
## grab snp and bis data from tmparr
start = time.time()
tmparrs = os.path.join(data.dirs.outfiles, "tmp-{}.h5".format(data.name))
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def get(self, key, default) -> Union[Uniform, UniformBlock, Subroutine, Attribute, Varying]:
'''
Returns a Uniform, UniformBlock, Subroutine, Attribute or Varying.
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def add_ubridge_udp_connection(self, bridge_name, source_nio, destination_nio):
"""
Creates an UDP connection in uBridge.
:param bridge_name: bridge name in uBridge
:param source_nio: source NIO instance
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def add_veth(name, interface_name, bridge=None, path=None):
'''
Add a veth to a container.
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name
Name of the container
interface_name
Name of the interface in the container
bridge
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"# Generate a ramdom string for veth and ensure ... | 38.975 | 0.004692 |
def check(self):
"""
Checks the values of the window quads. If any problems are found it
flags the offending window by changing the background colour.
Returns:
status : bool
"""
status = synced = True
xbin = self.xbin.value()
ybin = self.ybin... | [
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"... | 39.37931 | 0.001281 |
def value_type(type_):
"""returns reference to `boost::shared_ptr` \
or `std::shared_ptr` value type"""
if not smart_pointer_traits.is_smart_pointer(type_):
raise TypeError(
'Type "%s" is not an instantiation of \
boost::shared_ptr or std::shared_ptr' ... | [
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"... | 44.25 | 0.00369 |
def _create_fig(
*,
x_sc=bq.LinearScale,
y_sc=bq.LinearScale,
x_ax=bq.Axis,
y_ax=bq.Axis,
fig=bq.Figure,
options={},
params={}
):
"""
Initializes scales and axes for a bqplot figure and returns the resulting
blank figure. Each plot component is passed in as a class. The plot ... | [
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"options"... | 34.368421 | 0.000745 |
def add_member(self, member, dn=False):
"""Add a member to the bound group
Arguments:
member -- the CSHMember object (or distinguished name) of the member
Keyword arguments:
dn -- whether or not member is a distinguished name
"""
if dn:
if self.chec... | [
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"'mem... | 33.846154 | 0.00221 |
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