text stringlengths 89 104k | code_tokens list | avg_line_len float64 7.91 980 | score float64 0 630 |
|---|---|---|---|
def gff3_to_dataframe(path, attributes=None, region=None, score_fill=-1,
phase_fill=-1, attributes_fill='.', tabix='tabix', **kwargs):
"""Load data from a GFF3 into a pandas DataFrame.
Parameters
----------
path : string
Path to input file.
attributes : list of strings... | [
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def to_gexf(graph, output_path):
"""Writes graph to `GEXF <http://gexf.net>`_.
Uses the NetworkX method
`write_gexf <http://networkx.lanl.gov/reference/generated/networkx.readwrite.gexf.write_gexf.html>`_.
Parameters
----------
graph : networkx.Graph
The Graph to be exported to GEXF.
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def keypair_add(self, name, pubfile=None, pubkey=None):
'''
Add a keypair
'''
nt_ks = self.compute_conn
if pubfile:
with salt.utils.files.fopen(pubfile, 'r') as fp_:
pubkey = salt.utils.stringutils.to_unicode(fp_.read())
if not pubkey:
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def validate(cls, mapper_spec):
"""Validate mapper specification.
Args:
mapper_spec: an instance of model.MapperSpec
Raises:
BadReaderParamsError: if the specification is invalid for any reason such
as missing the bucket name or providing an invalid bucket name.
"""
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def setBendLength(self, x):
""" set bend length
:param x: new bend length to be assigned, [m]
:return: None
"""
if x != self.bend_length:
self.bend_length = x
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def linear_reaction_coefficients(model, reactions=None):
"""Coefficient for the reactions in a linear objective.
Parameters
----------
model : cobra model
the model object that defined the objective
reactions : list
an optional list for the reactions to get the coefficients for. All... | [
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def _rand_sparse(m, n, density, format='csr'):
"""Construct base function for sprand, sprandn."""
nnz = max(min(int(m*n*density), m*n), 0)
row = np.random.randint(low=0, high=m-1, size=nnz)
col = np.random.randint(low=0, high=n-1, size=nnz)
data = np.ones(nnz, dtype=float)
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def __set_config_value(self, key, value):
"""Sets a value for a room config"""
self.check_owner()
params = {"room": self.room_id, "config": to_json({key: value})}
resp = self.conn.make_api_call("setRoomConfig", params)
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def append_search_summary(xmldoc, process, shared_object = "standalone", lalwrapper_cvs_tag = "", lal_cvs_tag = "", comment = None, ifos = None, inseg = None, outseg = None, nevents = 0, nnodes = 1):
"""
Append search summary information associated with the given process
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def _get_chat(self) -> Dict:
"""
As Telegram changes where the chat object is located in the response,
this method tries to be smart about finding it in the right place.
"""
if 'callback_query' in self._update:
query = self._update['callback_query']
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def load_dict_from_yaml(path):
"""
Loads a dictionary from a yaml file
:param path: the absolute path of the target yaml file
:return:
"""
f = file(path, 'r')
dictionary = yaml.load(f)
f.close()
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def tokenize(self):
"""
Tokenizes the string stored in the parser object into a list
of tokens.
"""
self.token_list = []
ps = self.parse_string.strip()
i = 0
last_token = None
while i < len(ps) and ps[i].isspace():
i += 1
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def end_output (self, **kwargs):
"""Write edges and end of checking info as gml comment."""
self.write_edges()
self.end_graph()
if self.has_part("outro"):
self.write_outro()
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def viewport(self):
"""Rect: The drawing area for rendering on the current target."""
viewport = rect.Rect(0, 0, 0, 0)
check_int_err(lib.SDL_RenderGetViewport(self._ptr, viewport._ptr))
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def _mapping(self):
"""Fetch the entire mapping for the specified index.
Returns:
dict: The full mapping for the index.
"""
return (self.__search_client.get(
"/unstable/index/{}/mapping".format(mdf_toolbox.translate_index(self.index)))
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def match_color_index(self, color):
"""Takes an "R,G,B" string or wx.Color and returns a matching xlwt
color.
"""
from jcvi.utils.webcolors import color_diff
if isinstance(color, int):
return color
if color:
if isinstance(color, six.string_types):
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def bind_super(self, opr):
""" 为超级管理员授权所有权限
"""
for path in self.routes:
route = self.routes.get(path)
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def _get_member_file_data(member_data, id_filename=False):
"""
Helper function to get file data of member of a project.
:param member_data: This field is data related to member in a project.
"""
file_data = {}
for datafile in member_data['data']:
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def set_border(self, thickness, color="black"):
"""
Sets the border thickness and color.
:param int thickness:
The thickenss of the border.
:param str color:
The color of the border.
"""
self._set_tk_config("highlightthickness", thickness)
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def _rainbow_lines(
self, text, freq=0.1, spread=3.0, offset=0, movefactor=0,
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""" Create rainbow text, using the same offset for each line.
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def destroy_vm(self, vm, logger):
"""
destroy the given vm
:param vm: virutal machine pyvmomi object
:param logger:
"""
self.power_off_before_destroy(logger, vm)
logger.info(("Destroying VM {0}".format(vm.name)))
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def FoldByteStream(self, mapped_value, **unused_kwargs): # pylint: disable=redundant-returns-doc
"""Folds the data type into a byte stream.
Args:
mapped_value (object): mapped value.
Returns:
bytes: byte stream.
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def is_correct(self):
"""Check if the Daterange is correct : weekdays are valid
:return: True if weekdays are valid, False otherwise
:rtype: bool
"""
valid = True
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def _build_command(self):
"""
Command to start the Dynamips hypervisor process.
(to be passed to subprocess.Popen())
"""
command = [self._path]
command.extend(["-N1"]) # use instance IDs for filenames
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def _extract_log_probs(num_states, dist):
"""Tabulate log probabilities from a batch of distributions."""
states = tf.reshape(tf.range(num_states),
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def image(self, height=1, module_width=1, add_quiet_zone=True):
"""Get the barcode as PIL.Image.
By default the image is one pixel high and the number of modules pixels wide, with 10 empty modules added to
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def main():
'''Calculate the distance of an object in centimeters using a HCSR04 sensor
and a Raspberry Pi. This script allows for a quicker reading by
decreasing the number of samples and forcing the readings to be
taken at quicker intervals.'''
trig_pin = 17
echo_pin = 27
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def resource_of_node(resources, node):
""" Returns resource of node.
"""
for resource in resources:
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def update_membercard(self, code, card_id, **kwargs):
"""
更新会员信息
详情请参见
https://mp.weixin.qq.com/wiki?t=resource/res_main&id=mp1451025283
注意事项：
1.开发者可以同时传入add_bonus和bonus解决由于同步失败带来的幂等性问题。同时传入add_bonus和bonus时
add_bonus作为积分变动消息中的变量值，而bonus作为卡面上的总积分额度显示。余额变动同理。
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def process(self):
"""
This method handles the actual processing of Modules and Transforms
"""
self.modules.sort(key=lambda x: x.priority)
for module in self.modules:
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def file_change_history(self, branch='master', limit=None, days=None, ignore_globs=None, include_globs=None):
"""
Returns a DataFrame of all file changes (via the commit history) for the specified branch. This is similar to
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"i... | 44.654321 | 24.703704 |
def create(self, recording_status_callback_event=values.unset,
recording_status_callback=values.unset,
recording_status_callback_method=values.unset, trim=values.unset,
recording_channels=values.unset):
"""
Create a new RecordingInstance
:param unico... | [
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def process_schema(doc, resource, df):
"""Add schema entiries to a metatab doc from a dataframe"""
from rowgenerators import SourceError
from requests.exceptions import ConnectionError
from metapack.cli.core import extract_path_name, alt_col_name, type_map
from tableintuit import TypeIntuiter
f... | [
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def find(self, *args, **kwargs):
" new query builder on current db"
return Query(*args, db=self, schema=self.schema) | [
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def draw(title, subtitle, author, cover_width=400, cover_height=600):
"""
Main drawing function, which generates a cover of the given dimension and
renders title, author, and graphics.
"""
# Based on some initial constants and the title+author strings, generate a base
# background color and a s... | [
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def OIDC_UNAUTHENTICATED_SESSION_MANAGEMENT_KEY(self):
"""
OPTIONAL. Supply a fixed string to use as browser-state key for unauthenticated clients.
"""
# Memoize generated value
if not self._unauthenticated_session_management_key:
self._unauthenticated_session_manage... | [
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def _varargs_checks_gen(self, decorated_function, function_spec, arg_specs):
""" Generate checks for positional variable argument (varargs) testing
:param decorated_function: function decorator
:param function_spec: function inspect information
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def _generate_notebooks_by_category(notebook_object, dict_by_tag):
"""
Internal function that is used for generation of the page "Notebooks by Category".
----------
Parameters
----------
notebook_object : notebook object
Object of "notebook" class where the body will be created.
di... | [
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def _parse_adf_output(self):
"""
Parse the standard ADF output file.
"""
numerical_freq_patt = re.compile(
r"\s+\*\s+F\sR\sE\sQ\sU\sE\sN\sC\sI\sE\sS\s+\*")
analytic_freq_patt = re.compile(
r"\s+\*\s+F\sR\sE\sQ\sU\sE\sN\sC\sY\s+A\sN\sA\sL\sY\sS\sI\sS\s+\*")... | [
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def get_win32_short_path_name(long_name):
"""
Gets the short path name of a given long path.
References:
http://stackoverflow.com/a/23598461/200291
http://stackoverflow.com/questions/23598289/get-win-short-fname-python
Example:
>>> # DISABLE_DOCTEST
>>> from utool.util_... | [
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def merge_required_files(dirnames, out_dir):
"""Merges the required files from each of the directories.
:param dirnames: the list of directories to merge data from.
:param out_dir: the name of the output directory.
:type dirnames: list
:type out_dir: str
"""
# The list of files to merge
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def get_encoder(self, content_type):
"""
Get the encoding function for the provided content type for
this bucket.
:param content_type: the requested media type
:type content_type: str
:param content_type: Content type requested
"""
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def fit(self, x0=None, distribution='lognormal', n=None, **kwargs):
'''Incomplete method to fit experimental values to a curve. It is very
hard to get good initial guesses, which are really required for this.
Differential evolution is promissing. This API is likely to change in
the futur... | [
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def get_queue_obj(session, queue_url, log_url):
"""Checks that all the data that is needed for submit verification is available."""
skip = False
if not queue_url:
logger.error("The queue url is not configured, skipping submit verification")
skip = True
if not session:
logger.err... | [
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def tar_to_bigfile(self, fname, outfile):
"""Convert tar of multiple FASTAs to one file."""
fnames = []
tmpdir = mkdtemp()
# Extract files to temporary directory
with tarfile.open(fname) as tar:
tar.extractall(path=tmpdir)
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def execute_command(parser, config, ext_classes):
"""
Banana banana
"""
res = 0
cmd = config.get('command')
get_private_folder = config.get('get_private_folder', False)
if cmd == 'help':
parser.print_help()
elif cmd == 'run' or get_private_folder: # git.mk backward compat
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def describe(self):
"""Describe the model."""
result = "No description available"
if self.description:
result = "%s" % self.description
else:
if self.__doc__:
s = []
s += [self.__doc__.strip().replace('\n', '').
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def load_internal_cache(cls, pex, pex_info):
"""Possibly cache out the internal cache."""
internal_cache = os.path.join(pex, pex_info.internal_cache)
with TRACER.timed('Searching dependency cache: %s' % internal_cache, V=2):
if os.path.isdir(pex):
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def on_close(self):
''' Clean up when the connection is closed.
'''
log.info('WebSocket connection closed: code=%s, reason=%r', self.close_code, self.close_reason)
if self.connection is not None:
self.application.client_lost(self.connection) | [
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def line(h1: Union[Histogram1D, "HistogramCollection"], ax: Axes, *, errors: bool = False, **kwargs):
"""Line plot of 1D histogram."""
show_stats = kwargs.pop("show_stats", False)
show_values = kwargs.pop("show_values", False)
density = kwargs.pop("density", False)
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def addRecordsFromThread(self, records):
"""
Adds the given record to the system.
:param records | [<orb.Table>, ..]
"""
label_mapper = self.labelMapper()
icon_mapper = self.iconMapper()
tree = None
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def add_missing_optional_args_with_value_none(args, optional_args):
'''
Adds key-value pairs to the passed dictionary, so that
afterwards, the dictionary can be used without needing
to check for KeyErrors.
If the keys passed as a second argument are not present,
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def commit_branches(sha1):
# type: (str) -> List[str]
""" Get the name of the branches that this commit belongs to. """
cmd = 'git branch --contains {}'.format(sha1)
return shell.run(
cmd,
capture=True,
never_pretend=True
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def buildIcon(icon):
"""
Builds an icon from the inputed information.
:param icon | <variant>
"""
if icon is None:
return QIcon()
if type(icon) == buffer:
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def get_community_by_name(self, name, token=None):
"""
Get a community based on its name.
:param name: The name of the target community.
:type name: string
:param token: (optional) A valid token for the user in question.
:type token: None | string
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def backprop(self, input_data, df_output, cache=None):
""" Backpropagate through the hidden layer
**Parameters:**
input_data : ``GPUArray``
Input data to compute activations for.
df_output : ``GPUArray``
Gradients with respect to the activations of this layer
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def _fetch_dimensions(self, dataset):
""" Iterate through semesters, counties and municipalities.
"""
yield Dimension(u"school")
yield Dimension(u"year",
datatype="year")
yield Dimension(u"semester",
datatype="academic_term",
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def Matches(self, file_entry):
"""Compares the file entry against the filter collection.
Args:
file_entry (dfvfs.FileEntry): file entry to compare.
Returns:
bool: True if the file entry matches one of the filters. If no filters
are provided or applicable the result will be True.
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def add(self, fig, title, minX, maxX, offsetAdjuster=None,
sequenceFetcher=None):
"""
Find the features for a sequence title. If there aren't too many, add
the features to C{fig}. Return information about the features, as
described below.
@param fig: A matplotlib fig... | [
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def _download_rtd_zip(rtd_version=None, **kwargs):
"""
Download and extract HTML ZIP from RTD to installed doc data path.
Download is skipped if content already exists.
Parameters
----------
rtd_version : str or `None`
RTD version to download; e.g., "latest", "stable", or "v2.6.0".
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def account_following(self, id, max_id=None, min_id=None, since_id=None, limit=None):
"""
Fetch users the given user is following.
Returns a list of `user dicts`_.
"""
id = self.__unpack_id(id)
if max_id != None:
max_id = self.__unpack_id(max_id)
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def _server_property(self, attr_name):
"""An attribute of the current server's description.
If the client is not connected, this will block until a connection is
established or raise ServerSelectionTimeoutError if no server is
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Not threadsafe if used multiple times in... | [
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def information_title_header_element(feature, parent):
"""Retrieve information title header string from definitions."""
_ = feature, parent # NOQA
header = information_title_header['string_format']
return header.capitalize() | [
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def make_output_cf_compliant(self,
simulation_start_datetime,
comid_lat_lon_z_file="",
project_name="Normal RAPID project"):
"""
This function converts the RAPID output to be CF compliant.
This wil... | [
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def get_network_ipv4(self, id_network):
"""
Get networkipv4
:param id_network: Identifier of the Network. Integer value and greater than zero.
:return: Following dictionary:
::
{'network': {'id': < id_networkIpv6 >,
'network_type': < id_tipo_rede >,
... | [
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def update_module_names(cr, namespec, merge_modules=False):
"""Deal with changed module names, making all the needed changes on the
related tables, like XML-IDs, translations, and so on.
:param namespec: list of tuples of (old name, new name)
:param merge_modules: Specify if the operation should be a m... | [
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def get_cmd_output(*args, encoding: str = SYS_ENCODING) -> str:
"""
Returns text output of a command.
"""
log.debug("get_cmd_output(): args = {!r}", args)
p = subprocess.Popen(args, stdout=subprocess.PIPE)
stdout, stderr = p.communicate()
return stdout.decode(encoding, errors='ignore') | [
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def btc_script_deserialize(script):
"""
Given a script (hex or bin), decode it into its list of opcodes and data.
Return a list of strings and ints.
Based on code in pybitcointools (https://github.com/vbuterin/pybitcointools)
by Vitalik Buterin
"""
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def match_names(self, *valist, **kwargs):
"""performs taxonomic name resolution.
See https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs#match_names
with the exception that "ids" in the API call is referred has the name "id_list" in this function.
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def _remove_wire_nets(block):
""" Remove all wire nodes from the block. """
wire_src_dict = _ProducerList()
wire_removal_set = set() # set of all wirevectors to be removed
# one pass to build the map of value producers and
# all of the nets and wires to be removed
for net in block.logic:
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def fetch(self, url, encoding=None, force_refetch=False, nocache=False, quiet=True):
''' Fetch a HTML file as binary'''
try:
if not force_refetch and self.cache is not None and url in self.cache:
# try to look for content in cache
logging.debug('Retrieving con... | [
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def get(self, endpoint, params=None):
"""Send an HTTP GET request to QuadrigaCX.
:param endpoint: API endpoint.
:type endpoint: str | unicode
:param params: URL parameters.
:type params: dict
:return: Response body from QuadrigaCX.
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def insert(self, point, payload):
"""!
@brief Insert new point with payload to kd-tree.
@param[in] point (list): Coordinates of the point of inserted node.
@param[in] payload (any-type): Payload of inserted node. It can be identificator of the node or
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def clean(self, value):
"""Cleans and returns the given value, or raises a ParameterNotValidError exception"""
if isinstance(value, (list, tuple)):
return [super(FeatureCollectionParameter, self).clean(x) for x in value]
raise ParameterNotValidError | [
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def register_elastic_task(self, *args, **kwargs):
"""Register an elastic task."""
kwargs["task_class"] = ElasticTask
return self.register_task(*args, **kwargs) | [
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def list_nodes_min(call=None):
'''
Return a list of the VMs that are on the provider. Only a list of VM names and
their state is returned. This is the minimum amount of information needed to
check for existing VMs.
.. versionadded:: 2015.8.0
CLI Example:
.. code-block:: bash
salt... | [
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def cache(self):
"""Call a user defined query and cache the results"""
if not self._bucket_width or self._untrusted_time is None:
raise ValueError('QueryCompute must be initialized with a bucket_width '
'and an untrusted_time in order to write to the cache.')
now = datetime.dat... | [
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def supports_export(self, exported_configs, service_intents, export_props):
"""
Method called by rsa.export_service to ask if this
ExportDistributionProvider supports export for given
exported_configs (list), service_intents (list), and
export_props (dict).
If a ExportCo... | [
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def backup(file_name, jail=None, chroot=None, root=None):
'''
Export installed packages into yaml+mtree file
CLI Example:
.. code-block:: bash
salt '*' pkg.backup /tmp/pkg
jail
Backup packages from the specified jail. Note that this will run the
command within the jail, a... | [
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def compare_and_update_config(config, update_config, changes, namespace=''):
'''
Recursively compare two configs, writing any needed changes to the
update_config and capturing changes in the changes dict.
'''
if isinstance(config, dict):
if not update_config:
if config:
... | [
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def deleter(self, func):
"""Register a delete function for the DynamicProperty
This function may only take one argument, self.
"""
if not callable(func):
raise TypeError('deleter must be callable function')
if hasattr(func, '__code__') and func.__code__.co_argcount !... | [
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def do_ams_put(endpoint, path, body, access_token, rformat="json", ds_min_version="3.0;NetFx"):
'''Do a AMS HTTP PUT request and return JSON.
Args:
endpoint (str): Azure Media Services Initial Endpoint.
path (str): Azure Media Services Endpoint Path.
body (str): Azure Media Services Con... | [
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def args(self):
"""Parse args if they have not already been parsed and return the Namespace for args.
.. Note:: Accessing args should only be done directly in the App.
Returns:
(namespace): ArgParser parsed arguments.
"""
if not self._parsed: # only resolve once
... | [
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def message_worker(device):
"""Loop through messages and pass them on to right device"""
_LOGGER.debug("Starting Worker Thread.")
msg_q = device.messages
while True:
if not msg_q.empty():
message = msg_q.get()
data = {}
try:
data = json.load... | [
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def add_service_certificate(self, service_name, data, certificate_format,
password=None):
'''
Adds a certificate to a hosted service.
service_name:
Name of the hosted service.
data:
The base-64 encoded form of the pfx/cer file.
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def process_post_tags(self, bulk_mode, api_post, post_tags):
"""
Create or update Tags related to a post.
:param bulk_mode: If True, minimize db operations by bulk creating post objects
:param api_post: the API data for the post
:param post_tags: a mapping of Tags keyed by post ... | [
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async def communicate(self, data_id=None, run_sync=False, save_settings=True):
"""Scan database for resolving Data objects and process them.
This is submitted as a task to the manager's channel workers.
:param data_id: Optional id of Data object which (+ its
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def _generate_shape(word: str) -> str:
"""
Recreate shape from a token input by user
Args:
word: str
Returns: str
"""
def counting_stars(w) -> List[int]:
count = [1]
for i in range(1, len(w)):
if w[i - 1] == w[i]:
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def fit(self, y, exogenous=None):
"""Fit the transformer
Computes the periods of all the Fourier terms. The values of ``y`` are
not actually used; only the periodicity is used when computing Fourier
terms.
Parameters
----------
y : array-like or None, shape=(n_s... | [
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def log_commit( self, block_id, vtxindex, op, opcode, op_data ):
"""
Log a committed operation
"""
debug_op = self.sanitize_op( op_data )
if 'history' in debug_op:
del debug_op['history']
log.debug("COMMIT %s (%s) at (%s, %s) data: %s", opcode, op, block_id... | [
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def node_has_namespaces(node: BaseEntity, namespaces: Set[str]) -> bool:
"""Pass for nodes that have one of the given namespaces."""
ns = node.get(NAMESPACE)
return ns is not None and ns in namespaces | [
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def _collapse_variants_by_function(graph: BELGraph, func: str) -> None:
"""Collapse all of the given functions' variants' edges to their parents, in-place."""
for parent_node, variant_node, data in graph.edges(data=True):
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def rotation_matrix(angle, direction, point=None):
"""
Returns matrix to rotate about axis defined by point and direction.
Examples:
>>> angle = (random.random() - 0.5) * (2*math.pi)
>>> direc = numpy.random.random(3) - 0.5
>>> point = numpy.random.random(3) - 0.5
>>> R0 = ... | [
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def refresh(self, force: bool = False) -> bool:
"""
Loads the cauldron.json definition file for the project and populates
the project with the loaded data. Any existing data will be overwritten,
if the new definition file differs from the previous one.
If the project has already... | [
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def _add_parser_arguments_git(self, subparsers):
"""Create a sub-parsers for git subcommands.
"""
subparsers.add_parser(
"git-clone",
help="Clone all defined data repositories if they dont exist.")
subparsers.add_parser(
"git-push",
help="... | [
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"\"git-push\"",... | 31.107143 | 21 |
def _get_date_facet_counts(self, timespan, date_field, start_date=None, end_date=None):
'''
Returns Range Facet counts based on
'''
if 'DAY' not in timespan:
raise ValueError("At this time, only DAY date range increment is supported. Aborting..... ")
#Need to ... | [
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def merge(*args):
"""Implements the 'merge' operator for merging lists."""
ret = []
for arg in args:
if isinstance(arg, list) or isinstance(arg, tuple):
ret += list(arg)
else:
ret.append(arg)
return ret | [
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... | 27.777778 | 18.666667 |
def whitespace_around_operator(logical_line):
"""
Avoid extraneous whitespace in the following situations:
- More than one space around an assignment (or other) operator to
align it with another.
"""
line = logical_line
for operator in operators:
found = line.find(' ' + operator)... | [
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... | 35.952381 | 13.47619 |
def _backsearch(self):
"""
Inspect previous peaks from the last detected qrs peak (if any),
using a lower threshold
"""
if self.last_qrs_peak_num is not None:
for peak_num in range(self.last_qrs_peak_num + 1, self.peak_num + 1):
if self._is_qrs(peak_n... | [
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"if",
... | 41.4 | 20.6 |
def getServiceEndpoints(self, yadis_url, service_element):
"""Returns an iterator of endpoint objects produced by the
filter functions."""
endpoints = []
# Do an expansion of the service element by xrd:Type and xrd:URI
for type_uris, uri, _ in expandService(service_element):
... | [
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"servic... | 36.722222 | 19.277778 |
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