text stringlengths 89 104k | code_tokens list | avg_line_len float64 7.91 980 | score float64 0 630 |
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def _annotate_somatic(data, retriever=None):
"""Annotate somatic calls if we have cosmic data installed.
"""
if is_human(data):
paired = vcfutils.get_paired([data])
if paired:
r = dd.get_variation_resources(data)
if r.get("cosmic") and objectstore.file_exists_or_remot... | [
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def _consumeArgument(self,
memberName,
positionalArgumentKeyValueList,
kwargs,
defaultValue):
"""Returns member's value from kwargs if found or from positionalArgumentKeyValueList if found
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def get_feature_flag_by_name(self, name, check_feature_exists=None):
"""GetFeatureFlagByName.
[Preview API] Retrieve information on a single feature flag and its current states
:param str name: The name of the feature to retrieve
:param bool check_feature_exists: Check if feature exists
... | [
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def pagingRequestType2(MobileId_presence=0):
"""PAGING REQUEST TYPE 2 Section 9.1.23"""
a = L2PseudoLength()
b = TpPd(pd=0x6)
c = MessageType(mesType=0x22) # 00100010
d = PageModeAndChannelNeeded()
f = MobileId()
g = MobileId()
packet = a / b / c / d / f / g
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def generate(num, prompt_default=True):
"""Generates Python file for a problem."""
p = Problem(num)
problem_text = p.text
msg = "Generate file for problem %i?" % num
click.confirm(msg, default=prompt_default, abort=True)
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def _infer_fused_data_format(self, input_batch):
"""Infers the data format for the fused batch norm.
It uses the axis option to infer this information. Specifically, the
axis value (0, 1, 2) corresponds to data format NHWC and the
axis value (0, 2, 3) to data format NCHW.
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def _srvc_extract_file_information(self, kwargs):
"""Extracts file information from kwargs.
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def set_opcode(self, opcode):
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@type opcode: int
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def fugacity_coefficients(self, Z, zs):
r'''Literature formula for calculating fugacity coefficients for each
species in a mixture. Verified numerically. Applicable to most
derivatives of the SRK equation of state as well.
Called by `fugacities` on initialization, or by a solver routine... | [
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def human_to_seconds(string):
"""Convert internal string like 1M, 1Y3M, 3W to seconds.
:type string: str
:param string: Interval string like 1M, 1W, 1M3W4h2s...
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def plot(self, data, height=1000, render_large_data=False):
""" Plots a detail view of data.
Args:
data: a Pandas dataframe.
height: the height of the output.
"""
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def scatter_blocks_2d(x, indices, shape):
"""scatters blocks from x into shape with indices."""
x_shape = common_layers.shape_list(x)
# [length, batch, heads, dim]
x_t = tf.transpose(
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def retinotopy_mesh_field(mesh, mdl,
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def _get_context_key(self, **kwargs):
""" Get value of `self._resource.parent.id_name` from :kwargs: """
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def present(name, Name=None,
ScheduleExpression=None,
EventPattern=None,
Description=None,
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region=None, key=None, keyid=None, profile=None):
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Ensure trail exists.
name
The name of... | [
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def ip_rtm_config_route_static_bfd_bfd_static_route_bfd_interval_attributes_interval(self, **kwargs):
"""Auto Generated Code
"""
config = ET.Element("config")
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def get_base_kwargs(self):
"""Get base kwargs for API call."""
kwargs = {
'HostedZoneId': self.hosted_zone_id
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if self.max_items is not None:
kwargs.update({
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def pip_install_to_target(self, path, requirements="", local_package=None):
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def set_ugi(self, user_name, group_names):
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def save_checkpoint(prefix, epoch, symbol, arg_params, aux_params):
"""Checkpoint the model data into file.
Parameters
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Prefix of model name.
epoch : int
The epoch number of the model.
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def cursor_batch(self,
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def variational_lower_bound(params, t, logprob, sampler, log_density,
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def validate(self):
"""Validate / fix up the current config"""
if not self.get('api_key'):
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def to_cloudformation(self, **kwargs):
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def set_iscsi_initiator_info(self, initiator_iqn):
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:raises: IloError, on an error from iLO.
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def fit(self, features, target, sample_weight=None, groups=None):
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def _filter_packages(self):
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def _rapply(d, func, *args, **kwargs):
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def btc_is_p2wpkh_address( address ):
"""
Is the given address a p2wpkh address?
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def _handle_results(self):
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def _set_median_session_metrics(session_group, aggregation_metric):
"""Sets the metrics for session_group to those of its "median session".
The median session is the session in session_group with the median value
of the metric given by 'aggregation_metric'. The median is taken over the
subset of sessions in th... | [
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def login(self, user, passwd, bank):
""" Login """
logger.info("login...")
if bank not in self.BANKS:
logger.error("Can't find that bank.")
return False
self.useragent = self.BANKS[bank]["u-a"]
self.bankid = self.BANKS[bank]["id"]
login = json.dump... | [
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def parse_table_schema(json, precise_float):
"""
Builds a DataFrame from a given schema
Parameters
----------
json :
A JSON table schema
precise_float : boolean
Flag controlling precision when decoding string to double values, as
dictated by ``read_json``
Returns
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def index(self, item, **kwargs):
# type: (Any, dict) -> int
"""
Get index of the parameter.
:param item: Item for which get the index.
:return: Index of the parameter in the WeakList.
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def isEquilateral(self):
'''
True if all sides of the triangle are the same length.
All equilateral triangles are also isosceles.
All equilateral triangles are also acute.
'''
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def success_response(field=None, data=None, request_type=""):
"""Return a generic success response."""
data_out = {}
data_out["status"] = "success"
if field:
data_out[field] = data
print("{} request successful.".format(request_type))
js = dumps(data_out, default=date_handler)
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def _qteFindAppletInSplitter(self, appletObj: QtmacsApplet,
split: QtmacsSplitter):
"""
Return the splitter that holds ``appletObj``.
This method recursively searches for ``appletObj`` in the
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def item_id(response):
"""
Parse the item ids, will be available as ``item_0_name``, ``item_1_name``,
``item_2_name`` and so on
"""
dict_keys = ['item_0', 'item_1', 'item_2',
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new_keys = ['item_0_name', 'item_1_name', 'item_2_name',
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def _is_path(s):
"""Return whether an object is a path."""
if isinstance(s, string_types):
try:
return op.exists(s)
except (OSError, ValueError):
return False
else:
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def add_resolved_links(store, drop_defaults):
"""Adds the state of any link models between two models in store"""
for widget_id, widget in Widget.widgets.items(): # go over all widgets
if isinstance(widget, Link) and widget_id not in store:
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def serveUpcoming(self, request):
"""Upcoming events list view."""
myurl = self.get_url(request)
today = timezone.localdate()
monthlyUrl = myurl + self.reverse_subpage('serveMonth',
args=[today.year, today.month])
weekNum = gregor... | [
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def main():
"""Command line entry point."""
def help_exit():
raise SystemExit("usage: ddate [day] [month] [year]")
if "--help" in sys.argv or "-h" in sys.argv:
help_exit()
if len(sys.argv) == 2: # allow for 23-2-2014 style, be lazy/sloppy with it
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def select_single_item(self, option_name, select_name):
"""
Select the named option from select with label (recommended), name or id.
"""
option_box = find_option(world.browser, select_name, option_name)
assert option_box, "Cannot find option '{}'.".format(option_name)
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def set_options(pool_or_cursor,row_instance):
"for connection-level options that need to be set on Row instances"
# todo: move around an Options object instead
for option in ('JSON_READ',): setattr(row_instance,option,getattr(pool_or_cursor,option,None))
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def _init_object(self, catalog_id, proxy, runtime, cat_name, cat_class):
"""Initialize this object as an OsidObject....do we need this??
From the Mongo learning impl, but seems unnecessary for Handcar"""
self._catalog_identifier = None
self._init_proxy_and_runtime(proxy, runtime)
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def new(cls):
''' a method to generate the current datetime as a labDT object
:return: labDT object
'''
dT = datetime.utcnow().replace(tzinfo=pytz.utc)
dt_kwargs = {
'year': dT.year,
'month': dT.month,
'day': dT.day,
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def tarzip_data(root_dir, output_file):
"""
Given a root directory, adds all its children to a tarball (compressed)
:param root_dir:
:param output_file:
:return:
"""
if root_dir is None:
raise ValueError('Must be a valid directory path', root_dir)
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def bcesboot_backup(y1,y1err,y2,y2err,cerr,nsim=10000):
"""
Does the BCES with bootstrapping.
Usage:
>>> a,b,aerr,berr,covab=bcesboot(x,xerr,y,yerr,cov,nsim)
:param x,y: data
:param xerr,yerr: measurement errors affecting x and y
:param cov: covariance between the measurement errors (all are arrays)
:param nsim: n... | [
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def weight(self):
"""
Current weight of the Node (with respect to the parent).
"""
if self.root.stale:
self.root.update(self.root.now, None)
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def make_traceback(exc_info, source_hint=None):
"""Creates a processed traceback object from the exc_info."""
exc_type, exc_value, tb = exc_info
if isinstance(exc_value, TemplateSyntaxError):
exc_info = translate_syntax_error(exc_value, source_hint)
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async def get_tracks(self, *, limit=20, offset=0) -> List[Track]:
"""Get a list of the songs saved in the current Spotify user’s ‘Your Music’ library.
Parameters
----------
limit : Optional[int]
The maximum number of items to return. Default: 20. Minimum: 1. Maximum: 50.
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def create_server(self, server):
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Create a server and its storages based on a (locally created) Server object.
Populates the given Server instance with the API response.
0.3.0: also supports giving the entire POST body as a dict that is directly
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def remove_ancestors_of(self, node):
"""Remove all of the ancestor operation nodes of node."""
if isinstance(node, int):
warnings.warn('Calling remove_ancestors_of() with a node id is deprecated,'
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def cublasZsyr(handle, uplo, n, alpha, x, incx, A, lda):
"""
Rank-1 operation on complex symmetric matrix.
"""
status = _libcublas.cublasZsyr_v2(handle,
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def run(data, samples, force, ipyclient):
"""
Check all samples requested have been clustered (state=6), make output
directory, then create the requested outfiles. Excluded samples are already
removed from samples.
"""
## prepare dirs
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def data2schemacls(_data, **kwargs):
"""Convert a data to a schema cls.
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:return: schema class.
:rtype: type
"""
content = {}
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def scan_threads(self):
"""
Populates the snapshot with running threads.
"""
# Ignore special process IDs.
# PID 0: System Idle Process. Also has a special meaning to the
# toolhelp APIs (current process).
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def _set_id_field(new_class):
"""Lookup the id field for this entity and assign"""
# FIXME What does it mean when there are no declared fields?
# Does it translate to an abstract entity?
if new_class.meta_.declared_fields:
try:
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def snapshots(self):
"""
Provides access to snapshot management methods for the given content type.
API reference: https://www.contentful.com/developers/docs/references/content-management-api/#/reference/snapshots/content-type-snapshots-collection
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def update_workspace(self,
workspace_id,
name=None,
description=None,
language=None,
metadata=None,
learning_opt_out=None,
system_settings=None,
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def get_image_performance_info(self, userid):
"""Get CPU and memory usage information.
:userid: the zvm userid to be queried
"""
pi_dict = self.image_performance_query([userid])
return pi_dict.get(userid, None) | [
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def _remove_sig(signature, idempotent=False):
"""
Remove the signature node from its parent, keeping any tail element.
This is needed for eneveloped signatures.
:param signature: Signature to remove from payload
:type signature: XML ElementTree Element
:param idempotent:
If True, don't ... | [
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def free_chunks(self):
"""
Returns an iterator over all the free chunks in the heap.
"""
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def verify_path(self, mold_id_path):
"""
Lookup and verify path.
"""
try:
path = self.lookup_path(mold_id_path)
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raise KeyError
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raise_os_error(ENOENT)
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def fit_predict(self, X, y=None, **kwargs):
"""Compute cluster centroids and predict cluster index for each sample.
Convenience method; equivalent to calling fit(X) followed by
predict(X).
"""
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def extract_current_routine(page, stations):
'''Extract current routine information from page.
:param page: crawled page.
:param stations: bus stations list. See `~extract_stations`.
'''
current_routines = CURRENT_ROUTINE_PATTERN.findall(page.text())
if not current_routines:
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def remove_observer(self, observer, callble=None):
"""
Either (if callble is None) remove all callables,
which were added alongside observer,
or remove callable `callble` which was added alongside
the observer `observer`.
"""
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def update_all(self):
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self.update_points()
self.update_vertex_list()
self.update_anchor()
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pyglet.gl.glLineWidth(self.line_width)
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def action(cls, action, game, rosters, inning_number, inning_id):
"""
action data
:param action: action object(type:Beautifulsoup)
:param game: MLBAM Game object
:param rosters: Game Rosters
:param inning_number: Inning Number
:param inning_id: Inning Id(0:home 1:... | [
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def experimental_designs(df, filepath=None):
"""
For each experimental design it plot all the corresponding
experimental conditions in a different plot
Parameters
----------
df: `pandas.DataFrame`_
DataFrame with columns `id` and starting with `TR:`
filepath: str
Absolute p... | [
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def get_banks_by_assessment_part(self, assessment_part_id):
"""Gets the ``Banks`` mapped to an ``AssessmentPart``.
arg: assessment_part_id (osid.id.Id): ``Id`` of an
``AssessmentPart``
return: (osid.assessment.BankList) - list of banks
raise: NotFound - ``assessment_... | [
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def _get_pkg_install_time(pkg, arch=None):
'''
Return package install time, based on the /var/lib/dpkg/info/<package>.list
:return:
'''
iso_time = iso_time_t = None
loc_root = '/var/lib/dpkg/info'
if pkg is not None:
locations = []
if arch is not None and arch != 'all':
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def spherical_galaxy_orbit(
orbit_x,
orbit_y,
orbit_z,
N_stars=100,
sigma_r=1,
orbit_visible=False,
orbit_line_interpolate=5,
N_star_orbits=10,
color=[255, 220, 200],
size_star=1,
scatter_kwargs={},
):
"""Create a fake galaxy around the points orbit_x/y/z with N_stars aro... | [
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def _format_strings(self):
""" we by definition have DO NOT have a TZ """
values = self.values
if not isinstance(values, DatetimeIndex):
values = DatetimeIndex(values)
if self.formatter is not None and callable(self.formatter):
return [self.formatter(x) for x i... | [
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def assets(self, asset_type=None):
"""
Gets the assets of a Victim
Args:
asset_type:
Yields: asset json
"""
if not self.can_update():
self._tcex.handle_error(910, [self.type])
if not asset_type:
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def _record_offset(self):
"""Stores the current file pointer position"""
offset = self.blob_file.tell()
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def _create_ring(self, nodes):
"""Generate a ketama compatible continuum/ring.
"""
for node_name, node_conf in nodes:
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def disable(self):
"""
Disable the plugin.
Raises:
:py:class:`docker.errors.APIError`
If the server returns an error.
"""
self.client.api.disable_plugin(self.name)
self.reload() | [
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def add_text_item(self, collection_uri, name, metadata, text, title=None):
"""Add a new item to a collection containing a single
text document.
The full text of the text document is specified as the text
argument and will be stored with the same name as the
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def get_date_type(calendar):
"""Return the cftime date type for a given calendar name."""
try:
import cftime
except ImportError:
raise ImportError(
'cftime is required for dates with non-standard calendars')
else:
calendars = {
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def display_hook(prompt, session, context, matches, longest_match_len):
# type: (str, ShellSession, BundleContext, List[str], int) -> None
"""
Displays the available services matches and the service details
:param prompt: Shell prompt string
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def osx_clipboard_get():
""" Get the clipboard's text on OS X.
"""
p = subprocess.Popen(['pbpaste', '-Prefer', 'ascii'],
stdout=subprocess.PIPE)
text, stderr = p.communicate()
# Text comes in with old Mac \r line endings. Change them to \n.
text = text.replace('\r', '\n')
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def can_cast_to(v: Literal, dt: str) -> bool:
""" 5.4.3 Datatype Constraints
Determine whether "a value of the lexical form of n can be cast to the target type v per
XPath Functions 3.1 section 19 Casting[xpath-functions]."
"""
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def private_key(self, s):
"""
Parse text as some kind of private key.
Return a subclass of :class:`Key <pycoin.key.Key>`, or None.
"""
s = parseable_str(s)
for f in [self.wif, self.secret_exponent]:
v = f(s)
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def file_handles(self) -> Iterable[IO[str]]:
"""Generates all file handles represented by the analysis.
Callee owns file handle and closes it when the next is yielded or the
generator ends.
"""
if self.file_handle:
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def random_markov_chain(n, k=None, sparse=False, random_state=None):
"""
Return a randomly sampled MarkovChain instance with n states, where
each state has k states with positive transition probability.
Parameters
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n : scalar(int)
Number of states.
k : scalar(int), option... | [
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def ec2_vpc_subnets(self, lookup, default=None):
"""
Args:
lookup - the friendly name of the VPC whose subnets we want
Returns:
A comma-separated list of all subnets in use in the named VPC or default/None if no match found
"""
vpc_id = self.ec2_vpc_vpc_id(lookup)
if vpc_id is None:
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def _extract_header_number(lines):
"""
Extracts the number of header lines from the second line of the ODF file
"""
pair = _extract_header_value(lines[1])
value_list = list(pair.values())
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def srfnrm(method, target, et, fixref, srfpts):
"""
Map array of surface points on a specified target body to
the corresponding unit length outward surface normal vectors.
The surface of the target body may be represented by a triaxial
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def update_appt(self, complex: str, house: str, price: str, square: str, id: str, **kwargs):
"""
Update existing appartment
"""
self.check_house(complex, house)
kwargs['price'] = self._format_decimal(price)
kwargs['square'] = self._format_decimal(square)
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def flatten_nested_hash(hash_table):
"""
Flatten nested dictionary for GET / POST / DELETE API request
"""
def flatten(hash_table, brackets=True):
f = {}
for key, value in hash_table.items():
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def report_exception(self, filename, exc):
"""
This method is used when self.parser raises an Exception so that
we can report a customized :class:`EventReport` object with info the exception.
"""
# Build fake event.
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def safe_listdir(path):
"""
Attempt to list contents of path, but suppress some exceptions.
"""
try:
return os.listdir(path)
except (PermissionError, NotADirectoryError):
pass
except OSError as e:
# Ignore the directory if does not exist, not a directory or
# perm... | [
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def parse_headers(content_disposition, location=None, relaxed=False):
"""Build a ContentDisposition from header values.
"""
LOGGER.debug(
'Content-Disposition %r, Location %r', content_disposition, location)
if content_disposition is None:
return ContentDisposition(location=location)
... | [
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def _get_bounds(self):
'''
Return cached bounds of this Grob.
If bounds are not cached, render to a meta surface, and
keep the meta surface and bounds cached.
'''
if self._bounds:
return self._bounds
record_surface = cairo.RecordingSurface(cairo.CONTE... | [
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... | 33.2 | 20 |
def _collect_data(directory, input_ext, target_ext):
"""Traverses directory collecting input and target files."""
# Directory from string to tuple pair of strings
# key: the filepath to a datafile including the datafile's basename. Example,
# if the datafile was "/path/to/datafile.wav" then the key would be
... | [
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"# if the datafile was \"/path/to/datafile.wav\" then the key would ... | 48.736842 | 14.631579 |
def fw_hex_to_int(hex_str, words):
"""Unpack hex string into integers.
Use little-endian and unsigned int format. Specify number of words to
unpack with argument words.
"""
return struct.unpack('<{}H'.format(words), binascii.unhexlify(hex_str)) | [
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")",
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] | 37 | 17.571429 |
def fit_multinest(self, n_live_points=1000, basename='chains/single-',
verbose=True, refit=False, overwrite=False,
**kwargs):
"""
Fits model using MultiNest, via pymultinest.
:param n_live_points:
Number of live points to use for MultiNe... | [
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... | 36.342466 | 18.479452 |
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