text stringlengths 89 104k | code_tokens list | avg_line_len float64 7.91 980 | score float64 0 630 |
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def clone_exception(error, args):
"""
return a new cloned error
when do:
```
try:
do_sth()
except BaseException as e:
handle(e)
def handle(error):
# do sth with error
raise e # <- won't work!
This can ge... | [
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def create_password(self, data):
"""Create a password."""
# http://teampasswordmanager.com/docs/api-passwords/#create_password
log.info('Create new password %s' % data)
NewID = self.post('passwords.json', data).get('id')
log.info('Password has been created with ID %s' % NewID)
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def watch(self, path, action, *args, **kwargs):
"""
Called by the Server instance when a new watch task is requested.
"""
if action is None:
action = _set_changed
event_handler = _WatchdogHandler(self, action)
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def deprecated(comment=None, replacement=None):
"""Flags a function as deprecated. A warning will be emitted.
:param comment: A human-friendly string, such as 'This function
will be removed soon'
:type comment: string
:param replacement: The function to be used instead
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def check(self, check_all=True, do_reload=True):
"""Check whether some modules need to be reloaded."""
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def set_yaxis(self, param, unit=None, label=None):
""" Sets the value of use on the yaxis
:param param: value to use on the yaxis, should be a variable or function of the objects in objectList. ie 'R'
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def _add_supplemental_bams(data):
"""Add supplemental files produced by alignment, useful for structural
variant calling.
"""
file_key = "work_bam"
if data.get(file_key):
for supext in ["disc", "sr"]:
base, ext = os.path.splitext(data[file_key])
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def from_class(metacls, cls, auto_store=True):
"""Create proper PySchema class from cls
Any methods and attributes will be transferred to the
new object
"""
if auto_store:
def wrap(cls):
return cls
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def from_id_gaussian_draw(cls,pst,num_reals):
""" this is an experiemental method to help speed up independent draws
for a really large (>1E6) ensemble sizes.
Parameters
----------
pst : pyemu.Pst
a control file instance
num_reals : int
number of ... | [
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def has_succeed(self):
""" Check if the connection has succeed
Returns:
Returns True if connection has succeed.
False otherwise.
"""
status_code = self._response.status_code
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def _add_to_checksum(self, checksum, value):
"""Add a byte to the checksum."""
checksum = self._byte_rot_left(checksum, 1)
checksum = checksum + value
if (checksum > 255):
checksum = checksum - 255
self._debug(PROP_LOGLEVEL_TRACE, "C: " + str(checksum) + " V: " + str(... | [
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def change_columns(self, model, **fields):
"""Change fields."""
for name, field in fields.items():
old_field = model._meta.fields.get(name, field)
old_column_name = old_field and old_field.column_name
model._meta.add_field(name, field)
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def add_class(self, cls, include_bases=True):
"""Add the specified class (which should be a class object, _not_ a
string). By default all base classes for which is_backup_class returns
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def find_by_id(self, team, params={}, **options):
"""Returns the full record for a single team.
Parameters
----------
team : {Id} Globally unique identifier for the team.
[params] : {Object} Parameters for the request
"""
path = "/teams/%s" % (team)
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def produce_upgrade_operations(
ctx=None, metadata=None, include_symbol=None, include_object=None,
**kwargs):
"""Produce a list of upgrade statements."""
if metadata is None:
# Note, all SQLAlchemy models must have been loaded to produce
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metadata = db.... | [
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def get_subgraph(graph,
seed_method: Optional[str] = None,
seed_data: Optional[Any] = None,
expand_nodes: Optional[List[BaseEntity]] = None,
remove_nodes: Optional[List[BaseEntity]] = None,
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def reset(name, soft=False, call=None):
'''
To reset a VM using its name
.. note::
If ``soft=True`` then issues a command to the guest operating system
asking it to perform a reboot. Otherwise hypervisor will terminate VM and start it again.
Default is soft=False
For ``sof... | [
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def json_rpc_format(self):
"""Return the Exception data in a format for JSON-RPC
"""
error = {
'name': text_type(self.__class__.__name__),
'code': self.code,
'message': '{0}'.format(text_type(self.message)),
'data': self.data
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def commdct2grouplist(gcommdct):
"""extract embedded group data from commdct.
return gdict -> {g1:[obj1, obj2, obj3], g2:[obj4, ..]}"""
gdict = {}
for objidd in gcommdct:
group = objidd[0]['group']
objname = objidd[0]['idfobj']
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def set_image(self):
"""Parses image element and set values"""
temp_soup = self.full_soup
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image = temp_soup.find('image')
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def new(template, target=None, name=None):
"""
Function for creating a template script or tool.
:param template: template to be used ; one of TEMPLATES
:param target: type of script/tool to be created
:param name: name of the new script/tool
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def _last_of_quarter(self, day_of_week=None):
"""
Modify to the last occurrence of a given day of the week
in the current quarter. If no day_of_week is provided,
modify to the last day of the quarter. Use the supplied consts
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def as_template(value):
"""Convert a simple "shorthand" Python value to a `Template`.
"""
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def get_subnet(context, id, fields=None):
"""Retrieve a subnet.
: param context: neutron api request context
: param id: UUID representing the subnet to fetch.
: param fields: a list of strings that are valid keys in a
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def get_instance(self, payload):
"""
Build an instance of MachineToMachineInstance
:param dict payload: Payload response from the API
:returns: twilio.rest.api.v2010.account.available_phone_number.machine_to_machine.MachineToMachineInstance
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def clouds(opts):
'''
Return the cloud functions
'''
# Let's bring __active_provider_name__, defaulting to None, to all cloud
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functions = LazyLoader(
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def decode(obj, content_type):
# type: (np.array or Iterable or int or float, str) -> np.array
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obj (object): to be decoded.
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def resolve_config(self):
'''Resolve configuration params to native instances'''
conf = self.load_config(self.force_default)
for k in conf['hues']:
conf['hues'][k] = getattr(KEYWORDS, conf['hues'][k])
as_tuples = lambda name, obj: namedtuple(name, obj.keys())(**obj)
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def load_import_keychain( cls, working_dir, namespace_id ):
"""
Get an import keychain from disk.
Return None if it doesn't exist.
"""
# do we have a cached one on disk?
cached_keychain = os.path.join(working_dir, "%s.keychain" % namespace_id)
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def parent(self):
""" Return the parent device. """
if self._has_parent is None:
_parent = self._ctx.backend.get_parent(self._ctx.dev)
self._has_parent = _parent is not None
if self._has_parent:
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def fwhm(x, y, k=10): # http://stackoverflow.com/questions/10582795/finding-the-full-width-half-maximum-of-a-peak
"""
Determine full-with-half-maximum of a peaked set of points, x and y.
Assumes that there is only one peak present in the datasset. The function
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def build_attrs(self, *args, **kwargs):
"""Add select2 data attributes."""
attrs = super(Select2Mixin, self).build_attrs(*args, **kwargs)
if self.is_required:
attrs.setdefault('data-allow-clear', 'false')
else:
attrs.setdefault('data-allow-clear', 'true')
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def update(self):
"""Update |KD1| based on |EQD1| and |TInd|.
>>> from hydpy.models.lland import *
>>> parameterstep('1d')
>>> eqd1(0.5)
>>> tind.value = 10.0
>>> derived.kd1.update()
>>> derived.kd1
kd1(5.0)
"""
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def fuzzy(cls, field, value, boost=None, min_similarity=None, prefix_length=None):
'''
http://www.elasticsearch.org/guide/reference/query-dsl/fuzzy-query.html
A fuzzy based query that uses similarity based on Levenshtein (edit distance) algorithm.
'''
instance = cls(fuzzy={field:... | [
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def variants(vcf_fn, region=None, fields=None, exclude_fields=None,
dtypes=None, arities=None, fills=None, transformers=None,
vcf_types=None, count=None, progress=0, logstream=None,
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def build_statusbar(self):
"""construct and return statusbar widget"""
info = {}
cb = self.current_buffer
btype = None
if cb is not None:
info = cb.get_info()
btype = cb.modename
info['buffer_no'] = self.buffers.index(cb)
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def _display_layers(circ: Circuit, qubits: Qubits) -> Circuit:
"""Separate a circuit into groups of gates that do not visually overlap"""
N = len(qubits)
qubit_idx = dict(zip(qubits, range(N)))
gate_layers = DAGCircuit(circ).layers()
layers = []
lcirc = Circuit()
layers.append(lcirc)
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def lines_without_stdlib(self):
"""Filters code from standard library from self.lines."""
prev_line = None
current_module_path = inspect.getabsfile(inspect.currentframe())
for module_path, lineno, runtime in self.lines:
module_abspath = os.path.abspath(module_path)
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def fill(self, name_or_slot, value):
"""Fills an output slot required by this Pipeline.
Args:
name_or_slot: The name of the slot (a string) or Slot record to fill.
value: The serializable value to assign to this slot.
Raises:
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def transitively_reduce(self):
"""
Performs a transitive reduction on the graph.
"""
removals = set()
for from_node, neighbors in self._edges.items():
childpairs = \
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def load_plugins(self, plugins):
"""
Loads plugins that match the `Plugin` interface and are instantiated.
:param plugins: A list of plugin instances.
"""
def instantiate(plugin):
return plugin() if inspect.isclass(plugin) else plugin
loaded_plugins = []
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def stream_has_colours(stream):
"""
True if stream supports colours. Python cookbook, #475186
"""
if not hasattr(stream, "isatty"):
return False
if not stream.isatty():
return False # auto color only on TTYs
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import curses
curses.setupterm()
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def list_pool(self):
""" List pools and return JSON encoded result.
"""
# fetch attributes from request.json
attr = XhrController.extract_pool_attr(request.json)
try:
pools = Pool.list(attr)
except NipapError, e:
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def redefined_by_decorator(node):
"""return True if the object is a method redefined via decorator.
For example:
@property
def x(self): return self._x
@x.setter
def x(self, value): self._x = value
"""
if node.decorators:
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def fetch_query_from_pgdb(self, qname, query, con, cxn, limit=None, force=False):
"""
Supply either an already established connection, or connection parameters.
The supplied connection will override any separate cxn parameter
:param qname: The name of the query to save the output to
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def get_history(self, i=None):
"""
Get a history item by index.
You can toggle whether history is recorded using
* :meth:`enable_history`
* :meth:`disable_history`
:parameter int i: integer for indexing (can be positive or
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def max_dimension(cellmap, sheet = None):
"""
This function calculates the maximum dimension of the workbook or optionally the worksheet. It returns a tupple
of two integers, the first being the rows and the second being the columns.
:param cellmap: all the cells that should be used to calculate the ma... | [
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def unlock(self, time=3):
"""
unlock the door\n
thanks to https://github.com/SoftwareHouseMerida/pyzk/
:param time: define delay in seconds
:return: bool
"""
command = const.CMD_UNLOCK
command_string = pack("I",int(time)*10)
cmd_response = self.__... | [
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def status_message(self):
"""Return friendly response from API based on response code. """
msg = None
if self.last_ddns_response in response_messages.keys():
return response_messages.get(self.last_ddns_response)
if 'good' in self.last_ddns_response:
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def makeNetwork(self):
"""Makes graph object from .gdf loaded data"""
if "weight" in self.data_friendships.keys():
self.G=G=x.DiGraph()
else:
self.G=G=x.Graph()
F=self.data_friends
for friendn in range(self.n_friends):
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def _addr_in_exec_memory_regions(self, addr):
"""
Test if the address belongs to an executable memory region.
:param int addr: The address to test
:return: True if the address belongs to an exectubale memory region, False otherwise
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def feed(self, data):
"""
Feed data to the parser.
"""
assert isinstance(data, binary_type)
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def strip_chr(bt):
"""Strip 'chr' from chromosomes for BedTool object
Parameters
----------
bt : pybedtools.BedTool
BedTool to strip 'chr' from.
Returns
-------
out : pybedtools.BedTool
New BedTool with 'chr' stripped from chromosome names.
"""
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def tangle(*args, **kwargs):
"""
Shortcut to create a new, custom Tangle model. Use instead of directly
subclassing `Tangle`.
A new, custom Widget class is created, with each of `kwargs` as a traitlet.
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def compile_ui(self, namespace, unknown):
"""Compile qt designer files
:param namespace: namespace containing arguments from the launch parser
:type namespace: Namespace
:param unknown: list of unknown arguments
:type unknown: list
:returns: None
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def heptad_register(self):
"""Returns the calculated register of the coiled coil and the fit quality."""
base_reg = 'abcdefg'
exp_base = base_reg * (self.cc_len//7+2)
ave_ca_layers = self.calc_average_parameters(self.ca_layers)[0][:-1]
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def ps_ball(radius):
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Creates spherical ball structuring element for morphological operations
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radius : float or int
The desired radius of the structuring element
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strel : 3D-array
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def read(self, prompt='', clean=lambda x: x):
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def get_etree_root(doc, encoding=None):
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Args:
doc: The input XML document. Can be an instance of
``lxml.etree._Element``, ``lxml.etree._ElementTree``, a file-like
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def _diff(self, x, th, eps):
"""
Differentiation function.
Numerical approximation of a Rosenblatt transformation created from
copula formulation.
"""
foo = lambda y: self.igen(numpy.sum(self.gen(y, th), 0), th)
out1 = out2 = 0.
sign = 1 - 2*(x > .5).T
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def keyPressEvent(self, event):
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if event.key() == Qt.Key_Down:
self.select_row(1)
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def add_to_manifest(dynamodb_client, table_name, run_id):
"""Add run_id into DynamoDB manifest table
Arguments:
dynamodb_client - boto3 DynamoDB client (not service)
table_name - string representing existing table name
run_id - string representing run_id to store
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def is_sms_service_for_region(numobj, region_dialing_from):
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async def unloadmodule(self, module, ignoreDependencies = False):
'''
Unload a module class
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self._logger.debug('Try to unload module %r', module)
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def padded_to_same_length(seq1, seq2, item=0):
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def _get_oauth_params(self, req_kwargs):
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def arrow(self, JOIN, _id):
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def build_bucket(self, name, lifecycle_configuration=False,
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"""
Generate S3 bucket statement
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:param lifecycle_configuration: Additional lifecycle configuration (default=False)
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def location_2_json(self):
"""
transform ariane_clip3 location object to Ariane server JSON obj
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"""
LOGGER.debug("Location.location_2_json")
json_obj = {
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def encode(claims, key, algorithm=ALGORITHMS.HS256, headers=None, access_token=None):
"""Encodes a claims set and returns a JWT string.
JWTs are JWS signed objects with a few reserved claims.
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claims (dict): A claims set to sign
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def _assert_input_is_valid(input_value, # type: Any
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def replace(self, old_patch, new_patch):
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self._check_patch(old_patch)
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def cli(family_file, family_type, to_json, to_madeline, to_ped, to_dict,
outfile, logfile, loglevel):
"""Cli for testing the ped parser."""
from pprint import pprint as pp
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def import_model(self, source):
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def cached(f):
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async def delete(self, key, param=None):
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delete cache corresponding to identity
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identity = self._gen_identity(key, param)
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def goal_update(self, goal_id, data, **kwargs):
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api_path = "/api/v2/goals/{goal_id}"
api_path = api_path.format(goal_id=goal_id)
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def get_series(self, key):
"""Get a series object from TempoDB given its key.
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def datatype(field_decls, superclass_name=None, **kwargs):
"""A wrapper for `namedtuple` that accounts for the type of the object in equality.
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def nvmlDeviceGetInforomImageVersion(handle):
r"""
/**
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def save_sequence_rule(self, sequence_rule_form, *args, **kwargs):
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def play_mode(self, playmode):
"""Set the speaker's mode."""
playmode = playmode.upper()
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def peek(self) -> str:
"""Return the next character without advancing offset.
Raises:
EndOfInput: If past the end of `self.input`.
"""
try:
return self.input[self.offset]
except IndexError:
raise EndOfInput(self) | [
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def _check_data(data):
"""
Check a data object for inconsistencies.
Parameters
----------
data : `pandas.DataFrame`
A `data` object, i.e., a table whose rows store information about
chemical species, indexed by chemical species.
Warns
-----
UserWarning
Warned if... | [
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... | 40.731707 | 23.268293 |
def singleFactor(factors, chart, factor, obj, aspect=None):
"""" Single factor for the table. """
objID = obj if type(obj) == str else obj.id
res = {
'factor': factor,
'objID': objID,
'aspect': aspect
}
# For signs (obj as string) return sign element
if type(obj... | [
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"fa... | 29.75 | 17.454545 |
def should_stop_early(self) -> bool:
"""
Returns true if improvement has stopped for long enough.
"""
if self._patience is None:
return False
else:
return self._epochs_with_no_improvement >= self._patience | [
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def _server_end_response_callback(self, respoonse: Response):
'''Response callback handler.'''
request = self._item_session.request
response = self._item_session.response
_logger.info(__(
_('Fetched ‘{url}’: {status_code} {reason}. '
'Length: {content_length} [... | [
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... | 47.2 | 23.533333 |
def register_child(self, child):
"""
Register a new child that will be closed whenever the current instance
closes.
:param child: The child instance.
"""
if self.closing:
child.close()
else:
self._children.add(child)
child.on_c... | [
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... | 28.75 | 15.916667 |
def discover():
"""
Import all experiments listed in *_PLUGINS_REPORTS.
Tests:
>>> from benchbuild.settings import CFG
>>> from benchbuild.reports import discover
>>> import logging as lg
>>> import sys
>>> l = lg.getLogger('benchbuild')
>>> l.setLevel(lg.DEB... | [
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":",
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":",... | 36.76 | 14.52 |
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