text stringlengths 89 104k | code_tokens list | avg_line_len float64 7.91 980 | score float64 0 630 |
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def int_check(*args, func=None):
"""Check if arguments are integrals."""
func = func or inspect.stack()[2][3]
for var in args:
if not isinstance(var, numbers.Integral):
name = type(var).__name__
raise ComplexError(
f'Function {func} expected integral number, {... | [
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def calculate(self, where, calcExpression, sqlFormat="standard"):
"""
The calculate operation is performed on a feature service layer
resource. It updates the values of one or more fields in an
existing feature service layer based on SQL expressions or scalar
values. The calculat... | [
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def create_bmi_config_file(self, filename: str = "bmi_config.txt") -> None:
""" Create a BMI config file to initialize the model.
Args:
filename: The filename with which the config file should be saved.
"""
s0 = self.construct_default_initial_state()
s0.to_csv(filena... | [
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def serialize_operator_match(self, op):
"""
Serializer for :meth:`SpiffWorkflow.operators.NotEqual`.
Example::
<matches>
<value>text</value>
<value><attribute>foobar</attribute></value>
</matches>
"""
elem = etree.Element(... | [
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def perform_command(self):
"""
Perform command and return the appropriate exit code.
:rtype: int
"""
if len(self.actual_arguments) < 2:
return self.print_help()
input_file_path = self.actual_arguments[0]
output_file_path = self.actual_arguments[1]
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def now(cls, tzinfo=None):
"""[tz] -> new datetime with tz's local day and time."""
obj = cls.utcnow()
if tzinfo is None:
tzinfo = localtz()
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def print_loopy(self, as_url=True):
"""Return
Parameters
----------
out_file : Optional[str]
A file name in which the Loopy network is saved.
Returns
-------
full_str : str
The string representing the Loopy network.
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def _read_bands(self):
""" Reads a band with rasterio """
bands = []
try:
for i, band in enumerate(self.bands):
bands.append(rasterio.open(self.bands_path[i]).read_band(1))
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async def kickban(self, channel, target, reason=None, range=0):
"""
Kick and ban user from channel.
"""
await self.ban(channel, target, range)
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def _set_global_defaults(xmlglobals):
"""Sets the default attributes on tags that were specified in <global>
tags in the XML file."""
for key, val in xmlglobals.items():
if key != "defaults":
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def _compute(self, inputs, outputs):
"""
Run one iteration of TMRegion's compute
"""
#if self.topDownMode and (not 'topDownIn' in inputs):
# raise RuntimeError("The input topDownIn must be linked in if "
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def complete_func(self, findstart, base):
"""Handle omni completion."""
self.log.debug('complete_func: in %s %s', findstart, base)
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def from_unknown_text(text, strict=False):
"""
Detect crs string format and parse into crs object with appropriate function.
Arguments:
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def trace_grad(fn, args):
"""Trace a function, and return a VJP and the function's output."""
from tensorflow.python.eager.backprop import make_vjp
result, vjp = make_vjp(fn)(*args)
return result, vjp | [
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def get_label_set(self, type_str=None):
"""Get a set of label_str for the tree rooted at this node.
Args:
type_str:
SUBJECT_NODE_TAG, TYPE_NODE_TAG or None. If set, only include
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def index_firstnot(ol,value):
'''
from elist.elist import *
ol = [1,'a',3,'a',4,'a',5]
index_firstnot(ol,'a')
####index_firstnot, array_indexnot, indexOfnot are the same
array_indexnot(ol,'a')
indexOfnot(ol,'a')
'''
length = ol.__len__()
for i in range(0,... | [
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def prep_jid(nocache=False, passed_jid=None, recurse_count=0):
'''
Return a job id and prepare the job id directory.
This is the function responsible for making sure jids don't collide (unless
it is passed a jid).
So do what you have to do to make sure that stays the case
'''
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def getOverlayAutoCurveDistanceRangeInMeters(self, ulOverlayHandle):
"""
For high-quality curved overlays only, gets the distance range in meters from the overlay used to automatically curve
the surface around the viewer. Min is distance is when the surface will be most curved. Max is when lea... | [
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def generate_folder_names(name, project):
"""Creates sensible folder names."""
out_data_dir = prms.Paths.outdatadir
project_dir = os.path.join(out_data_dir, project)
batch_dir = os.path.join(project_dir, name)
raw_dir = os.path.join(batch_dir, "raw_data")
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def centered(coordinates):
"""
Centers coordinate distribution with respect to its
mean on all three axes. This is used as the input to
the regression model, so it can be converted easily
into radial coordinates.
"""
coordinates = N.array(coordinates)
means = N.mean(coordinates,axis=0)
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def quit(self):
"""Restore previous stdout/stderr and destroy the window."""
sys.stdout = self._oldstdout
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def cBurkPot(self, R, Rs, rho0, r_core):
"""
:param R: projected distance
:param Rs: scale radius
:param rho0: central core density
:param r_core: core radius
"""
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def on_event(self, evt, is_final):
""" this is invoked from in response to COM PumpWaitingMessages - different thread """
for msg in XmlHelper.message_iter(evt):
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def _loop_use_cache(self, helper_function, num, fragment):
""" Synthesize all fragments using the cache """
self.log([u"Examining fragment %d (cache)...", num])
fragment_info = (fragment.language, fragment.filtered_text)
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def commit_input_confirm_timeout(self, **kwargs):
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def default_filename_decoder():
"""
Creates a decoder which parses CWR filenames following the old or the new
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:return: a CWR filename decoder for the old and the new conventions
"""
factory = default_filename_grammar_factory()
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def _add_plugin_options(self, available_plugins: Set[Type[Plugin]]) -> None:
"""Recovers the list of command line options implemented by the available plugins and adds them to the command
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def loads(s, encoding=None, cls=JSONTreeDecoder, object_hook=None,
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def remote_file_size(self, remote_cmd="", remote_file=None):
"""Get the file size of the remote file."""
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def convert_bb_to_faces(voxel_grid):
""" Converts a voxel grid defined by min and max coordinates to a voxel grid defined by faces.
:param voxel_grid: voxel grid defined by the bounding box of all voxels
:return: voxel grid with face data
"""
new_vg = []
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def decode_and_filter(line: bytes, context: RunContext) -> typing.Optional[str]:
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Decodes a line that was captured from the running process using a given encoding (defaults to UTF8)
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def scan(self, func, sequences=None, outputs=None, non_sequences=None, block=None, **kwargs):
"""
A loop function, the usage is identical with the theano one.
:type block: deepy.layers.Block
"""
results, updates = Scanner(func, sequences, outputs, non_sequences, neural_computatio... | [
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def digest_auth_user(self, realm, user_name, environ):
"""Computes digest hash A1 part."""
user = self._get_realm_entry(realm, user_name)
if user is None:
return False
password = user.get("password")
environ["wsgidav.auth.roles"] = user.get("roles", [])
return... | [
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def _cwl_workflow_template(inputs, top_level=False):
"""Retrieve CWL inputs shared amongst different workflows.
"""
ready_inputs = []
for inp in inputs:
cur_inp = copy.deepcopy(inp)
for attr in ["source", "valueFrom", "wf_duplicate"]:
cur_inp.pop(attr, None)
if top_le... | [
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def apply_option(self, cmd, option, active=True):
"""Apply a command-line option."""
return re.sub(r'{{{}\:(?P<option>[^}}]*)}}'.format(option),
'\g<option>' if active else '', cmd) | [
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def compile_dictionary(self, lang, wordlists, encoding, output):
"""Compile user dictionary."""
cmd = [
self.binary,
'--lang', lang,
'--encoding', codecs.lookup(filters.PYTHON_ENCODING_NAMES.get(encoding, encoding).lower()).name,
'create',
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def make_request(url, method='GET', headers=None, timeout=30, **kwargs):
"""A wrapper around requests to set defaults & call raise_for_status()."""
headers = headers or {}
headers['User-Agent'] = 'treeherder/{}'.format(settings.SITE_HOSTNAME)
# Work around bug 1305768.
if 'queue.taskcluster.net' in ... | [
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def resolve_absolute_name(self, name):
'''
Resolve a field from an absolute name.
An absolute name is just like unix absolute path,
starts with '/' and each name component is separated by '/'.
:param name: absolute name, e.g. "/container/subcontainer/field"
:return: fiel... | [
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def update_preference_communication_channel_id(self, notification, communication_channel_id, notification_preferences_frequency):
"""
Update a preference.
Change the preference for a single notification for a single communication channel
"""
path = {}
data = {}
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def get_rendered_transform_path(self):
"""
Generates a rendered transform path
that is calculated from all parents.
:return:
"""
path = self.transform_path
parent = self.parent
while parent is not None:
path = "{0}/{1}".format(parent.transform... | [
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def yaml_to_param(obj, name):
"""
Return the top-level element of a document sub-tree containing the
YAML serialization of a Python object.
"""
return from_pyvalue(u"yaml:%s" % name, unicode(yaml.dump(obj))) | [
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def get_athlete(self, athlete_id=None):
"""
Gets the specified athlete; if athlete_id is None then retrieves a
detail-level representation of currently authenticated athlete;
otherwise summary-level representation returned of athlete.
http://strava.github.io/api/v3/athlete/#get-... | [
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def create_index(self, cardinality):
"""
Create an index for the table with the given cardinality.
Parameters
----------
cardinality : int
The cardinality to create a index for.
"""
DatabaseConnector.create_index(self, cardinality)
query = "C... | [
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def regex(regex):
"""Return strategy that generates strings that match given regex.
Regex can be either a string or compiled regex (through `re.compile()`).
You can use regex flags (such as `re.IGNORECASE`, `re.DOTALL` or `re.UNICODE`)
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def cache(self, value):
"""Enable or disable caching of pages/frames. Clear cache if False."""
value = bool(value)
if self._cache and not value:
self._clear()
self._cache = value | [
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def sample(self, signum, frame): #pylint: disable=unused-argument
"""Samples current stack and adds result in self._stats.
Args:
signum: Signal that activates handler.
frame: Frame on top of the stack when signal is handled.
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def as_list_data(self):
"""Return an Element to be used in a list.
Most lists want an element with tag of list_type, and
subelements of id and name.
Returns:
Element: list representation of object.
"""
element = ElementTree.Element(self.list_type)
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def rotate(self, n):
'''Rotate Sequence by n bases.
:param n: Number of bases to rotate.
:type n: int
:returns: The current sequence reoriented at `index`.
:rtype: coral.sequence._sequence.Sequence
:raises: ValueError if applied to linear sequence or `index` is
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def remove_state(self, state):
"""
Remove this conversation from the given state, and potentially
deactivate the state if no more conversations are in it.
The relation name will be interpolated in the state name, and it is
recommended that it be included to avoid conflicts with ... | [
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def set(self, section, option, value=None):
"""Set an option."""
if value:
value = self._interpolation.before_set(self, section, option,
value)
if not section or section == self.default_section:
sectdict = self._defaults
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def get_token_data(self):
""" Get token and data from keystone """
token_data = self._keystone_auth.conn.auth_ref
token = token_data['auth_token']
self.set_token(token)
if self.cache.is_redis_ok():
try:
self.cache.set_cache_token(token_data)
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def _fetch(self, key):
"""Helper function to fetch values from owning section.
Returns a 2-tuple: the value, and the section where it was found.
"""
# switch off interpolation before we try and fetch anything !
save_interp = self.section.main.interpolation
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def deaccent(text):
"""
Remove accentuation from the given string.
"""
norm = unicodedata.normalize("NFD", text)
result = "".join(ch for ch in norm if unicodedata.category(ch) != 'Mn')
return unicodedata.normalize("NFC", result) | [
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def _maybe_decode(self, value, encoding='utf-8'):
"""If a bytes object is passed in, in the Python 3 environment,
decode it using the specified encoding to turn it to a str instance.
:param mixed value: The value to possibly decode
:param str encoding: The encoding to use
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def all(
self,
count=500,
offset=0,
type=None,
inactive=None,
emailFilter=None,
tag=None,
messageID=None,
fromdate=None,
todate=None,
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"""
Returns many bounces.
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def set_hostname(hostname=None, **kwargs):
'''
Set the device's hostname
hostname
The name to be set
comment
Provide a comment to the commit
dev_timeout : 30
The NETCONF RPC timeout (in seconds)
confirm
Provide time in minutes for commit confirmation. If this op... | [
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def read_and_save_data(info_df, raw_dir, sep=";", force_raw=False,
force_cellpy=False,
export_cycles=False, shifted_cycles=False,
export_raw=True,
export_ica=False, save=True, use_cellpy_stat_file=False,
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def GetExpirationTime(self):
"""Computes the timestamp at which this breakpoint will expire."""
# TODO(emrekultursay): Move this to a common method.
if '.' not in self.definition['createTime']:
fmt = '%Y-%m-%dT%H:%M:%S%Z'
else:
fmt = '%Y-%m-%dT%H:%M:%S.%f%Z'
create_datetime = datetime.s... | [
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def tab(self, netloc=None, url=None, extra_id=None, use_tid=False):
'''
Get a chromium tab from the pool, optionally one that has an association with a specific netloc/URL.
If no url or netloc is specified, the per-thread identifier will be used.
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def get(self, nb=0):
"""Get the history as a dict of list"""
return {i: self.stats_history[i].history_raw(nb=nb) for i in self.stats_history} | [
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def case(self, case_id):
"""Fetch a case from the database."""
case_obj = self.query(Case).filter_by(case_id=case_id).first()
return case_obj | [
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def allow_migrate(self, db, model):
"""
Make sure self._apps go to their own db
"""
if model._meta.app_label in self._apps:
return getattr(model, '_db_alias', model._meta.app_label) == db
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def supports_card_actions(channel_id: str, button_cnt: int = 100) -> bool:
"""Determine if a number of Card Actions are supported by a Channel.
Args:
channel_id (str): The Channel to check if the Card Actions are supported in.
button_cnt (int, optional): Defaults to 100. The num... | [
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def load_cov(name):
'''Load a datafile with coverage file structure.
'''
content = np.genfromtxt(name, skip_header=1, skip_footer=1, usecols=([2]))
return content | [
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def intercept_(self):
"""
Intercept (bias) property
.. note:: Intercept is defined only for linear learners
Intercept (bias) is only defined when the linear model is chosen as base
learner (`booster=gblinear`). It is not defined for other base learner types, such
... | [
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def stop(self):
"""Stop the background emulation loop."""
if self._started is False:
raise ArgumentError("EmulationLoop.stop() called without calling start()")
self.verify_calling_thread(False, "Cannot call EmulationLoop.stop() from inside the event loop")
if self._thread.... | [
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def no_intersection(to_validate, constraint, violation_cfg):
"""
Returns violation message if validated and constraint sets have no intersection
:param to_validate:
:param constraint:
:param violation_cfg:
:return:
"""
if len(constraint) == 0 or len(set(constraint).intersection(to_valida... | [
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def new_noncomment(self, start_lineno, end_lineno):
""" We are transitioning from a noncomment to a comment.
"""
block = NonComment(start_lineno, end_lineno)
self.blocks.append(block)
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def or_fault(a, b, out, fault):
"""Returns True if OR(a, b) == out and fault == 0 or OR(a, b) != out and fault == 1."""
if (a or b) == out:
return fault == 0
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def known_author_patterns(self, val):
''' val must be a dictionary or list of dictionaries
e.g., {'attrribute': 'name', 'value': 'my-pubdate', 'content': 'datetime'}
or [{'attrribute': 'name', 'value': 'my-pubdate', 'content': 'datetime'},
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def incr_obj(obj, **attrs):
"""Increments context variables
"""
for name, value in attrs.iteritems():
v = getattr(obj, name, None)
if not hasattr(obj, name) or v is None:
v = 0
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def issueBatchJob(self, jobNode):
"""
Issues the following command returning a unique jobID. Command is the string to run, memory
is an int giving the number of bytes the job needs to run in and cores is the number of cpus
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def register_routes(app):
"""Register routes."""
from . import controllers
from flask.blueprints import Blueprint
for module in _import_submodules_from_package(controllers):
bp = getattr(module, 'bp')
if bp and isinstance(bp, Blueprint):
app.register_blueprint(bp) | [
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def serialize(self, dt):
"""
Converts the date to a string using the :py:attr:`~_DateParameterBase.date_format`.
"""
if dt is None:
return str(dt)
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def get_pubmed_citation_response(pubmed_identifiers: Iterable[str]):
"""Get the response from PubMed E-Utils for a given list of PubMed identifiers.
:param pubmed_identifiers:
:rtype: dict
"""
pubmed_identifiers = list(pubmed_identifiers)
url = EUTILS_URL_FMT.format(','.join(
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def _create_column(values, dtype):
"Creates a column from values with dtype"
if str(dtype) == "tensor(int64)":
return numpy.array(values, dtype=numpy.int64)
elif str(dtype) == "tensor(float)":
return numpy.array(values, dtype=numpy.float32)
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def find_max_and_min_frequencies(name, mass_range_params, freqs):
"""
ADD DOCS
"""
cutoff_fns = pnutils.named_frequency_cutoffs
if name not in cutoff_fns.keys():
err_msg = "%s not recognized as a valid cutoff frequency choice." %name
err_msg += "Recognized choices: " + " ".join(cuto... | [
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def failover(self, name):
"""Force a failover of a named master."""
fut = self.execute(b'FAILOVER', name)
return wait_ok(fut) | [
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def _open_for_write(self):
"""open the file in write mode"""
def put_request(body):
"""
:param body:
"""
ownerid, datasetid = parse_dataset_key(self._dataset_key)
response = requests.put(
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def fit_transform(self, X, y=None):
"""
Fit the imputer and then transform input `X`
Note: all imputations should have a `fit_transform` method,
but only some (like IterativeImputer) also support inductive mode
using `fit` or `fit_transform` on `X_train` and then `transform`
... | [
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def extract_views_from_urlpatterns(self, urlpatterns, base='', namespace=None):
"""
Return a list of views from a list of urlpatterns.
Each object in the returned list is a three-tuple: (view_func, regex, name)
"""
views = []
for p in urlpatterns:
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def surround_parse(self, node, pre_char, post_char):
"""Parse the subnodes of a given node. Subnodes with tags in the
`ignore` list are ignored. Prepend `pre_char` and append `post_char` to
the output in self.pieces."""
self.add_text(pre_char)
self.subnode_parse(node)
sel... | [
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def decompress(self, value: bytes, max_length: int = 0) -> bytes:
"""Decompress a chunk, returning newly-available data.
Some data may be buffered for later processing; `flush` must
be called when there is no more input data to ensure that
all data was processed.
If ``max_lengt... | [
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def get_name(self):
"""Get name based on 4 class attributes
Each attribute is substituted by '' if attribute does not exist
:return: dependent_host_name/dependent_service_description..host_name/service_description
:rtype: str
TODO: Clean this function (use format for string)
... | [
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def merge_lines(top, bot, icod="top"):
"""
Merges two lines (top and bot) in the way that the overlapping make senses.
Args:
top (str): the top line
bot (str): the bottom line
icod (top or bot): in case of doubt, which line should have priority? Default: "top"... | [
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def merge(self, base, head, message=''):
"""Perform a merge from ``head`` into ``base``.
:param str base: (required), where you're merging into
:param str head: (required), where you're merging from
:param str message: (optional), message to be used for the commit
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def get_implicit_depends_on(input_hash, depends_on):
'''
Add DNAnexus links to non-closed data objects in input_hash to depends_on
'''
q = []
for field in input_hash:
possible_dep = get_nonclosed_data_obj_link(input_hash[field])
if possible_dep is not None:
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def _set_is_address_family_v4(self, v, load=False):
"""
Setter method for is_address_family_v4, mapped from YANG variable /isis_state/router_isis_config/is_address_family_v4 (container)
If this variable is read-only (config: false) in the
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def search(self):
"""
Construct the Search object.
"""
s = Search(doc_type=self.doc_types, using=es.client,
index=es.index_name)
# don't return any fields, just the metadata
s = s.fields([])
# Sort from parameters
s = s.sort(*self.sorts)... | [
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def convert_compartment_entry(self, compartment, adjacencies):
"""Convert compartment entry to YAML dict.
Args:
compartment: :class:`psamm.datasource.entry.CompartmentEntry`.
adjacencies: Sequence of IDs or a single ID of adjacent
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def create_rectangular_prism(origin, size):
'''
Return a Mesh which is an axis-aligned rectangular prism. One vertex is
`origin`; the diametrically opposite vertex is `origin + size`.
size: 3x1 array.
'''
from lace.topology import quads_to_tris
lower_base_plane = np.array([
# Lowe... | [
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def visitInlineShapeAtomNodeConstraint(self, ctx: ShExDocParser.InlineShapeAtomNodeConstraintContext):
""" inlineShapeAtomNodeConstraint: nodeConstraint inlineShapeOrRef? # inlineShapeAtomShapeOrRef """
nc = ShexNodeExpressionParser(self.context, self.label)
nc.visit(ctx.nodeConstraint())
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def _set_new_object(self, new_obj, inherited_obj, new_class, superclass,
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"""
Set the object attributes for a single object and resolve the
qualifiers. This sets attributes for Properties, Methods, and
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def fpy_interface(fpy, static, interface, typedict):
"""Splices the full list of subroutines and the module procedure list
into the static.f90 file.
:arg static: the string contents of the static.f90 file.
:arg interface: the name of the interface *field* being replaced.
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def system(*args, **kwargs):
"""Execute the given bash command"""
kwargs.setdefault('stdout', subprocess.PIPE)
proc = subprocess.Popen(args, **kwargs)
out, _ = proc.communicate()
if proc.returncode:
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"out",
",",... | 35.5 | 7.5 |
def check_data(cls, name, dims, is_unstructured):
"""
A validation method for the data shape
Parameters
----------
name: str or list of str
The variable names (one variable per array)
dims: list with length 1 or list of lists with length 1
The dim... | [
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"dim... | 40.538462 | 17.076923 |
def _rate_limit_status(self, api=None, mode=None):
"""
Verifying the API limits
"""
if api == None:
api = self.connectToAPI()
if mode == None:
print json.dumps(api.rate_limit_status(), indent=2)
raw_input("<Press ENTER>")
else:
... | [
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"dumps"... | 52 | 22.307692 |
def update_config(
self, filename="MAGTUNE_PYMAGICC.CFG", top_level_key="nml_allcfgs", **kwargs
):
"""Updates a configuration file for MAGICC
Updates the contents of a fortran namelist in the run directory,
creating a new namelist if none exists.
Parameters
--------... | [
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"(... | 27.578947 | 21.394737 |
def reload_core(host=None, core_name=None):
'''
MULTI-CORE HOSTS ONLY
Load a new core from the same configuration as an existing registered core.
While the "new" core is initializing, the "old" one will continue to accept
requests. Once it has finished, all new request will go to the "new" core,
... | [
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... | 34.888889 | 22.533333 |
def call_workflow_event(instance, event, after=True):
"""Calls the instance's workflow event
"""
if not event.transition:
return False
portal_type = instance.portal_type
wf_module = _load_wf_module('{}.events'.format(portal_type.lower()))
if not wf_module:
return False
# In... | [
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"... | 31.090909 | 18.318182 |
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