text stringlengths 89 104k | code_tokens list | avg_line_len float64 7.91 980 | score float64 0 630 |
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def _find_and_cache_best_function(self, dispatch_type):
"""Finds the best implementation of this function given a type.
This function caches the result, and uses locking for thread safety.
Returns:
Implementing function, in below order of preference:
1. Explicitly regis... | [
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def recall(self, mode='all'):
"""Recalls from the file specified by :attr:`~SR850.filename`.
:param mode: Specifies the recall mode.
======= ==================================================
Value Description
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def read_tags(filename):
"""Reads values of "magic tags" defined in the given Python file.
:param filename: Python filename to read the tags from
:return: Dictionary of tags
"""
with open(filename) as f:
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def _wrap(func, msg):
"""This is a decorator which can be used to mark functions
as deprecated. It will result in a warning being emitted
when the function is used."""
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def update_variable(self, variable, value) -> None:
"""Assign the given value(s) to the given target or base variable.
If the assignment fails, |ChangeItem.update_variable| raises an
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>>> from hydpy.core.examples import prepare_full_example_2
>>> hp, pu... | [
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def bg_compensate(img, sigma, splinepoints, scale):
'''Reads file, subtracts background. Returns [compensated image, background].'''
from PIL import Image
import pylab
from matplotlib.image import pil_to_array
from centrosome.filter import canny
import matplotlib
img = Image.open(img)
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def infer(self, pattern=False):
"""https://github.com/frictionlessdata/datapackage-py#package
"""
# Files
if pattern:
# No base path
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def build_fptree(self, transactions, root_value,
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"""
Build the FP tree and return the root node.
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root = FPNode(root_value, root_count, None)
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def _process_genotype_backgrounds(self, limit=None):
"""
This table provides a mapping of genotypes to background genotypes
Note that the background_id is also a genotype_id.
Makes these triples:
<ZFIN:genotype_id> GENO:has_reference_part <ZFIN:background_id>
<ZFIN:backg... | [
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def tmatrix_cov(C, row=None):
r"""Covariance tensor for the non-reversible transition matrix ensemble
Normally the covariance tensor cov(p_ij, p_kl) would carry four indices
(i,j,k,l). In the non-reversible case rows are independent so that
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def transforms(self):
"""Return an array of arrays of column transforms.
#The return value is an list of list, with each list being a segment of column transformations, and
#each segment having one entry per column.
"""
tr = []
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def Initialize(self):
"""Open the delegate object."""
if "r" in self.mode:
delegate = self.Get(self.Schema.DELEGATE)
if delegate:
self.delegate = aff4.FACTORY.Open(
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def vm_present(name, vmconfig, config=None):
'''
Ensure vm is present on the computenode
name : string
hostname of vm
vmconfig : dict
options to set for the vm
config : dict
fine grain control over vm_present
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def __find_args_separator(self, decl_string, start_pos):
"""implementation details"""
bracket_depth = 0
for index, ch in enumerate(decl_string[start_pos:]):
if ch not in (self.__begin, self.__end, self.__separator):
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def _nt_on_change(self, key, value, isNew):
"""NetworkTables global listener callback"""
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def phoncontent(self, cls='current', correctionhandling=CorrectionHandling.CURRENT):
"""See :meth:`AbstractElement.phoncontent`"""
if cls == 'original': correctionhandling = CorrectionHandling.ORIGINAL #backward compatibility
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def _get_pydot(self):
"""Return pydot package. Load pydot, if necessary."""
if self.pydot:
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def user(name, id='', user='', priv='', password='', status='active'):
'''
Ensures that a user is configured on the device. Due to being unable to
verify the user password. This is a forced operation.
.. versionadded:: 2019.2.0
name: The name of the module function to execute.
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def get_right_geo_fhs(self, dsid, fhs):
"""Find the right geographical file handlers for given dataset ID *dsid*."""
ds_info = self.ids[dsid]
req_geo, rem_geo = self._get_req_rem_geo(ds_info)
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def _get_bundles_by_type(self, type):
"""Get a dictionary of bundles for requested type.
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def visit_Module(self, node):
"""
Visit the whole module and add all import at the top level.
>> import numpy.linalg
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def split_package(package):
"""
Split package in name, version
arch and build tag.
"""
name = ver = arch = build = []
split = package.split("-")
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def remap_link_target(path, absolute=False):
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def lab_office(self, column=None, value=None, **kwargs):
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def run(self, params):
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def explain_prediction_df(estimator, doc, **kwargs):
# type: (...) -> pd.DataFrame
""" Explain prediction and export explanation to ``pandas.DataFrame``
All keyword arguments are passed to :func:`eli5.explain_prediction`.
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def convert_site_dm3_table_intensity(sites_df):
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sites_df : pandas DataFrame
sites information
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def dump_TDDFT_data_in_GW_run(self, TDDFT_dump=True):
"""
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def totz(when, tz=None):
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def visitShapeExprDecl(self, ctx: ShExDocParser.ShapeExprDeclContext):
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def title(self):
"""
The title of the course. If no entry in the namemap of the configuration is found a new entry is created with name=$STUD.IP_NAME + $SEMESTER_NAME
"""
name = c.namemap_lookup(self.id)
if name is None:
name = self._title + " " + client.get_semester_... | [
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def get_constant_state(self):
"""Read state that was written in "first_part" mode.
Returns:
a structure
"""
ret = self.constant_states[self.next_constant_state]
self.next_constant_state += 1
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def _stream_annotation(file_name, pb_dir):
"""
Stream an entire remote annotation file from physiobank
Parameters
----------
file_name : str
The name of the annotation file to be read.
pb_dir : str
The physiobank directory where the annotation file is located.
"""
# Ful... | [
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def retarget_with_change_points(song, cp_times, duration):
"""Create a composition of a song of a given duration that reaches
music change points at specified times. This is still under
construction. It might not work as well with more than
2 ``cp_times`` at the moment.
Here's an example of retarge... | [
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def serialize(obj, **options):
'''
Serialize Python data to YAML.
:param obj: the data structure to serialize
:param options: options given to lower yaml module.
'''
options.setdefault('Dumper', Dumper)
try:
response = yaml.dump(obj, **options)
if response.endswith('\n...\n... | [
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def parse_qc(self, qc_file):
"""
Parse phantompeakqualtools (spp) QC table and return quality metrics.
:param str qc_file: Path to phantompeakqualtools output file, which
contains sample quality measurements.
"""
import pandas as pd
series = pd.Series()
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def get_user_data(self, subid, params=None):
''' /v1/server/get_user_data
GET - account
Retrieves the (base64 encoded) user-data for this subscription.
Link: https://www.vultr.com/api/#server_get_user_data
'''
params = update_params(params, {'SUBID': subid})
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def get_color_map(name):
"""
Return a colormap as (redmap, greenmap, bluemap)
Arguments:
name -- the name of the colormap. If unrecognized, will default to 'jet'.
"""
redmap = [0]
greenmap = [0]
bluemap = [0]
if name == 'white':
# essentially a noop
redmap = [0, 1]
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def trigger_arbitrary_job(repo_name, builder, revision, auth, files=None, dry_run=False,
extra_properties=None):
"""
Request buildapi to trigger a job for us.
We return the request or None if dry_run is True.
Raises BuildapiAuthError if credentials are invalid.
"""
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def workspace_backup_undo(ctx):
"""
Restore the last backup
"""
backup_manager = WorkspaceBackupManager(Workspace(ctx.resolver, directory=ctx.directory, mets_basename=ctx.mets_basename, automatic_backup=ctx.automatic_backup))
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def agent_key_info_from_key_id(key_id):
"""Find a matching key in the ssh-agent.
@param key_id {str} Either a private ssh key fingerprint, e.g.
'b3:f0:a1:6c:18:3b:42:63:fd:6e:57:42:74:17:d4:bc', or the path to
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def summaries(self):
"""Yield (name, (value, value, ...)) for each summary in the file."""
length = self.summary_length
step = self.summary_step
for record_number, n_summaries, summary_data in self.summary_records():
name_data = self.read_record(record_number + 1)
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def setup_TreeRegression(self, covariation=True):
"""instantiate a TreeRegression object and set its tip_value and branch_value function
to defaults that are sensible for treetime instances.
Parameters
----------
covariation : bool, optional
account for phylogenetic ... | [
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def _from_pointer(pointer, incref):
"""Wrap an existing :c:type:`cairo_scaled_font_t *` cdata pointer.
:type incref: bool
:param incref:
Whether increase the :ref:`reference count <refcounting>` now.
:return: A new :class:`ScaledFont` instance.
"""
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def pcapname(dev):
"""Get the device pcap name by device name or Scapy NetworkInterface
"""
if isinstance(dev, NetworkInterface):
if dev.is_invalid():
return None
return dev.pcap_name
try:
return IFACES.dev_from_name(dev).pcap_name
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def arcs(self):
"""Get information about the arcs available in the code.
Returns a sorted list of line number pairs. Line numbers have been
normalized to the first line of multiline statements.
"""
all_arcs = []
for l1, l2 in self.byte_parser._all_arcs():
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def process(self, config, grains):
'''
Process the configured beacons
The config must be a list and looks like this in yaml
.. code_block:: yaml
beacons:
inotify:
- files:
- /etc/fstab: {}
- /var/cache/fo... | [
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def _HasOOOWrite(self, path):
"""Returns whether the path has had an out-of-order write."""
# Check the sizes of each path before the current one.
size = tf.io.gfile.stat(path).length
old_size = self._finalized_sizes.get(path, None)
if size != old_size:
if old_size is None:
logger.erro... | [
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def pformat(self, consumed_capacity=None):
""" Pretty format for insertion into table pformat """
consumed_capacity = consumed_capacity or {}
lines = []
parts = ["GLOBAL", self.index_type, "INDEX", self.name]
if self.status != "ACTIVE":
parts.insert(0, "[%s]" % self.s... | [
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def _input_as_multifile(self, data):
"""For use with the -profile option
This input handler expects data to be a tuple containing two
filenames. Index 0 will be set to -in1 and index 1 to -in2
"""
if data:
try:
filename1, filename2 = data
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def get_xy(self, yidx, xidx=0):
"""
Return stored data for the given indices for plot
:param yidx: the indices of the y-axis variables(1-indexing)
:param xidx: the index of the x-axis variables
:return: None
"""
assert isinstance(xidx, int)
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def average(self, projection=None):
"""
Takes the average of elements in the sequence
>>> seq([1, 2]).average()
1.5
>>> seq([('a', 1), ('b', 2)]).average(lambda x: x[1])
:param projection: function to project on the sequence before taking the average
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def get_tag_names(self):
"""Returns the set of tag names present in the XML."""
root = etree.fromstring(self.xml_full_text.encode('utf-8'))
return self.get_children_tag_names(root) | [
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def fileChunkIter(file_object, file_chunk_size=65536):
"""
Return an iterator to a file-like object that yields fixed size chunks
:param file_object: a file-like object
:param file_chunk_size: maximum size of chunk
"""
while True:
chunk = file_object.read(file_chunk_size)
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def get_matching_session(self, session, db_session, timediff=5):
"""
Tries to match a session with it's counterpart. For bait session it will try to match it with honeypot sessions
and the other way around.
:param session: session object which will be used as base for query.
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def calc_model_cosine(self, decimate=None, mode='err'):
"""
Calculates the cosine of the residuals with the model.
Parameters
----------
decimate : Int or None, optional
Decimate the residuals by `decimate` pixels. If None, no
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def brew_query_parts(self):
""" Make columns, group_bys, filters, havings
"""
columns, group_bys, filters, havings = [], [], set(), set()
for ingredient in self.ingredients():
if ingredient.query_columns:
columns.extend(ingredient.query_columns)
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def load_installed_plugins(self):
""" :rtype: list of Plugin """
result = []
plugin_dirs = [d for d in os.listdir(self.plugin_path) if os.path.isdir(os.path.join(self.plugin_path, d))]
settings = constants.SETTINGS
for d in plugin_dirs:
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def get_headline(self, name):
"""Get stored messages for a service.
Args:
name (string): The name of the service to get messages from.
Returns:
ServiceMessage: the headline or None if no headline has been set
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def get_min_row_num(mention):
"""Return the lowest row number that a Mention occupies.
:param mention: The Mention to evaluate. If a candidate is given, default
to its first Mention.
:rtype: integer or None
"""
span = _to_span(mention)
if span.sentence.is_tabular():
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def list_workers(config, *, filter_by_queues=None):
""" Return a list of all available workers.
Args:
config (Config): Reference to the configuration object from which the
settings are retrieved.
filter_by_queues (list): Restrict the returned workers to workers that listen to
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def downloaded(name,
version=None,
pkgs=None,
fromrepo=None,
ignore_epoch=None,
**kwargs):
'''
.. versionadded:: 2017.7.0
Ensure that the package is downloaded, and that it is the correct version
(if specified).
Currently s... | [
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def interpolate_nearest(self, xi, yi, zdata):
"""
Nearest-neighbour interpolation.
Calls nearnd to find the index of the closest neighbours to xi,yi
Parameters
----------
xi : float / array of floats, shape (l,)
x coordinates on the Cartesian plane
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def compute_stop_stats(
feed: "Feed",
dates: List[str],
stop_ids: Optional[List[str]] = None,
headway_start_time: str = "07:00:00",
headway_end_time: str = "19:00:00",
*,
split_directions: bool = False,
) -> DataFrame:
"""
Compute stats for all stops for the given dates.
Optional... | [
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def _set_user(self, v, load=False):
"""
Setter method for user, mapped from YANG variable /snmp_server/user (list)
If this variable is read-only (config: false) in the
source YANG file, then _set_user is considered as a private
method. Backends looking to populate this variable should
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... | 142.772727 | 69.090909 |
def evaluate(self, m):
"""Search for comments."""
g = m.groupdict()
if g["strings"]:
self.line_num += g['strings'].count('\n')
elif g["code"]:
self.line_num += g["code"].count('\n')
else:
if g['block']:
self.evaluate_block(g)
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def _sample_template(sample, out_dir):
"""R code to get QC for one sample"""
bam_fn = dd.get_work_bam(sample)
genome = dd.get_genome_build(sample)
if genome in supported:
peaks = sample.get("peaks_files", []).get("main")
if peaks:
r_code = ("library(ChIPQC);\n"
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def check_precondition(self, key, value):
'''
Override to check for timeout
'''
timeout = float(value)
curr_time = self.get_current_time()
if curr_time > timeout:
return True
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def cublasDestroy(handle):
"""
Release CUBLAS resources.
Releases hardware resources used by CUBLAS.
Parameters
----------
handle : void_p
CUBLAS context.
"""
status = _libcublas.cublasDestroy_v2(ctypes.c_void_p(handle))
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def GetCustomJsonFieldMapping(message_type, python_name=None, json_name=None):
"""Return the appropriate remapping for the given field, or None."""
return _FetchRemapping(message_type, 'field',
python_name=python_name, json_name=json_name,
mappings=_JSON_FIE... | [
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def _check_equals_spacing(self, tokens, i):
"""Check the spacing of a single equals sign."""
if self._has_valid_type_annotation(tokens, i):
self._check_space(tokens, i, (_MUST, _MUST))
elif self._inside_brackets("(") or self._inside_brackets("lambda"):
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def is_notifying(cls, user_or_email, instance):
"""Check if the watch created by notify exists."""
return super(InstanceEvent, cls).is_notifying(user_or_email,
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def search(self, tid, seller_nick):
'''taobao.logistics.trace.search 物流流转信息查询
用户根据淘宝交易号查询物流流转信息，如2010-8-10 15：23：00到达杭州集散地'''
request = TOPRequest('taobao.logistics.address.add')
request['tid'] = tid
request['seller_nick'] = seller_nick
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def create_figures(n, *fig_args, **fig_kwargs):
'''Create multiple figures.
Args and Kwargs are passed to `matplotlib.figure.Figure`.
This routine is provided in order to avoid usage of pyplot which
is stateful and not thread safe. As drawing routines in tf-matplotlib
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def load_data_file_to_net(self, filename):
'''
Load Clustergrammer's dat format (saved as JSON).
'''
inst_dat = self.load_json_to_dict(filename)
load_data.load_data_to_net(self, inst_dat) | [
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def all_blocks(self):
status = OrderedDict.fromkeys(parameters.BLOCKS.keys())
status['13AE'] = ['discovery complete', '50', '24.05']
status['13AO'] = ['discovery complete', '36', '24.40']
status['13BL'] = ['discovery complete', '79', '24.48']
status['14BH'] = ['discovery running... | [
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def _can_be_double(x):
"""
Return if the array can be safely converted to double.
That happens when the dtype is a float with the same size of
a double or narrower, or when is an integer that can be safely
converted to double (if the roundtrip conversion works).
"""
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"items... | 37.538462 | 18.461538 |
def create(cls, name, servers=None, time_range='yesterday', all_logs=False,
filter_for_delete=None, comment=None, **kwargs):
"""
Create a new delete log task. Provide True to all_logs to delete
all log types. Otherwise provide kwargs to specify each log by
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def camel_to_underscore(string):
"""Convert camelcase to lowercase and underscore.
Recipe from http://stackoverflow.com/a/1176023
Args:
string (str): The string to convert.
Returns:
str: The converted string.
"""
string = FIRST_CAP_RE.sub(r'\1_\2', string)
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def lookup_character_keycode(self, character):
"""
Looks up the keysym for the character then returns the keycode mapping
for that keysym.
"""
keysym = self.string_to_keysym.get(character, 0)
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def run_preassembly(stmts_in, **kwargs):
"""Run preassembly on a list of statements.
Parameters
----------
stmts_in : list[indra.statements.Statement]
A list of statements to preassemble.
return_toplevel : Optional[bool]
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def _get_mean(self, sites, rup, dists, imt, stddev_types):
"""
See :meth:`superclass method
<.base.GroundShakingIntensityModel.get_mean_and_stddevs>`
for spec of input and result values.
"""
# Zhao et al. 2006 - Vs30 + Rrup
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def renew_token(self):
"""Convenience method: renew Vault token"""
url = _url_joiner(self._vault_url, 'v1/auth/token/renew-self')
resp = requests.get(url, headers=self._headers)
resp.raise_for_status()
data = resp.json()
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def cache_clean(path=None, runas=None, env=None, force=False):
'''
Clean cached NPM packages.
If no path for a specific package is provided the entire cache will be cleared.
path
The cache subpath to delete, or None to clear the entire cache
runas
The user to run NPM with
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def create_order_line_item(cls, order_line_item, **kwargs):
"""Create OrderLineItem
Create a new OrderLineItem
This method makes a synchronous HTTP request by default. To make an
asynchronous HTTP request, please pass async=True
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def rebalance(self, weight, child, base=np.nan, update=True):
"""
Rebalance a child to a given weight.
This is a helper method to simplify code logic. This method is used
when we want to se the weight of a particular child to a set amount.
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def enhance_pubmed_annotations(pubmed: Mapping[str, Any]) -> Mapping[str, Any]:
"""Enhance pubmed namespace IDs
Add additional entity and annotation types to annotations
Use preferred id for namespaces as needed
Add strings from Title, Abstract matching Pubtator BioConcept spans
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def _handle_get(self, request_data):
"""
An OCSP GET request contains the DER-in-base64 encoded OCSP request in the
HTTP request URL.
"""
der = base64.b64decode(request_data)
ocsp_request = self._parse_ocsp_request(der)
return self._build_http_response(ocsp_reques... | [
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def set_vocabulary(self, peer_id, from_dialogue=None, update=False):
"""
Получает вокабулар из функции get_vocabulary и делает его активным.
"""
self.tokens_array = self.get_vocabulary(
peer_id,
from_dialogue,
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def AddFilterOptions(self, argument_group):
"""Adds the filter options to the argument group.
Args:
argument_group (argparse._ArgumentGroup): argparse argument group.
"""
names = ['artifact_filters', 'date_filters', 'filter_file']
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def update_normals(self, normals):
"""
Update the triangle normals.
"""
normals = np.array(normals, dtype=np.float32)
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def stop(self):
"""
trigger clean up by hand, needs to be done when not using
context management via 'with' statement
- will terminate loop process
- show a last progress -> see the full 100% on exit
- releases terminal reservation
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"sh... | 35.375 | 13.541667 |
def copy(tree, source_filename):
""" Copy file in tree, show a progress bar during operations,
and return the sha1 sum of copied file.
"""
#_, ext = os.path.splitext(source_filename)
filehash = sha1()
with printer.progress(os.path.getsize(source_filename)) as update:
with open(source... | [
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... | 48.6 | 16.28 |
def fromDataset(datatype, value, metadata=None, tmap=None):
"""
Return a representation of dataset argument as an instance
of the class corresponding to its datatype
"""
if tmap is None:
tmap = typemap
return tmap[datatype.upper()].fromDataset(value, meta... | [
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"fr... | 36.222222 | 18.222222 |
def latlon(location, throttle=0.5, center=True, round_digits=2):
'''Look up the latitude/longitude coordinates of a given location using the
Google Maps API. The result is cached to avoid redundant API requests.
throttle: send at most one request in this many seconds
center: return the center of th... | [
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... | 38.824561 | 25.245614 |
def add_edge(self, ind_node, dep_node):
""" Add an edge (dependency) between the specified nodes.
Args:
ind_node (str): The independent node to add an edge to.
dep_node (str): The dependent node that has a dependency on the
ind_node.
Raises:
... | [
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def parse_file(self, sg_file=None, data=None):
"""Parse a sensor graph file into an AST describing the file.
This function builds the statements list for this parser.
If you pass ``sg_file``, it will be interpreted as the path to a file
to parse. If you pass ``data`` it will be directl... | [
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"\"You must pass either a path to an sgf file or th... | 40.548387 | 24.096774 |
def info(cwd,
targets=None,
user=None,
username=None,
password=None,
fmt='str'):
'''
Display the Subversion information from the checkout.
cwd
The path to the Subversion repository
targets : None
files, directories, and URLs to pass to the c... | [
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"o... | 22.909091 | 23.236364 |
def _set_config_mode(self, v, load=False):
"""
Setter method for config_mode, mapped from YANG variable /interface/fc_port/config_mode (interface-fc-config-mode-type)
If this variable is read-only (config: false) in the
source YANG file, then _set_config_mode is considered as a private
method. Backe... | [
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"ba... | 98.416667 | 48.208333 |
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