text stringlengths 75 104k | code_tokens list | avg_line_len float64 7.91 980 | score float64 0 0.18 |
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def execute_notebook(
input_path,
output_path,
parameters=None,
engine_name=None,
prepare_only=False,
kernel_name=None,
progress_bar=True,
log_output=False,
start_timeout=60,
report_mode=False,
cwd=None,
):
"""Executes a single notebook locally.
Parameters
------... | [
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def get_interface_switchport_output_switchport_default_vlan(self, **kwargs):
"""Auto Generated Code
"""
config = ET.Element("config")
get_interface_switchport = ET.Element("get_interface_switchport")
config = get_interface_switchport
output = ET.SubElement(get_interface_s... | [
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def push(self, item):
'''Push the value item onto the heap, maintaining the heap invariant.
If the item is not hashable, a TypeError is raised.
'''
hash(item)
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def stored_messages_list(context, num_elements=10):
"""
Renders a list of unread stored messages for the current user
"""
if "user" in context:
user = context["user"]
if user.is_authenticated():
qs = Inbox.objects.select_related("message").filter(user=user)
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def send_notification(self, method, args, kwargs):
"""Send a notification."""
msg = dumps([1, method, args, kwargs])
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def get_multiplicon_properties(self, value):
""" Return a dictionary describing multiplicon data:
id, parent, level, number_of_anchorpoints, profile_length,
is_redundant and the contributing genome segments
"""
sql = '''SELECT id, parent, level, number_of_anchorpoints,
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def _get_cpu_info_from_sysinfo_v2():
'''
Returns the CPU info gathered from sysinfo.
Returns {} if sysinfo is not found.
'''
try:
# Just return {} if there is no sysinfo
if not DataSource.has_sysinfo():
return {}
# If sysinfo fails return {}
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def data_period_end_day(self, value=None):
"""Corresponds to IDD Field `data_period_end_day`
Args:
value (str): value for IDD Field `data_period_end_day`
if `value` is None it will not be checked against the
specification and is assumed to be a missing value
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def nth_child_production(self, lexeme, tokens):
"""Parse args and pass them to pclass_func_validator."""
args = self.match(tokens, 'expr')
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if pat.group(5):
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def measure_sidechain_torsion_angles(residue, verbose=True):
"""Calculates sidechain dihedral angles for a residue
Parameters
----------
residue : [ampal.Residue]
`Residue` object.
verbose : bool, optional
If `true`, tells you when a residue does not have any known
dihedral ... | [
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def _GetValue(self, name):
"""Returns the TextFSMValue object natching the requested name."""
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def timespan(self, from_date, to_date=None, span=None, current=False):
"""
Takes a beginning date a filters entries. An optional to_date can be
specified, or a span, which is one of ('month', 'week', 'day').
N.B. - If given a to_date, it does not include that date, only before.
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def calc_ifft_with_PyCUDA(Signalfft):
"""
Calculates the inverse-FFT of the passed FFT-signal by
using the scikit-cuda libary which relies on PyCUDA
Parameters
----------
Signalfft : ndarray
FFT-Signal to be transformed into Real space
Returns
-------
Signal : ndarray
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def tree():
"""Example showing tree progress view"""
#############
# Test data #
#############
# For this example, we're obviously going to be feeding fictitious data
# to ProgressTree, so here it is
leaf_values = [Value(0) for i in range(6)]
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def all_apps(self):
"""Capture a backup of the app."""
cmd = ["heroku", "apps", "--json"]
if self.team:
cmd.extend(["--team", self.team])
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def generate_tolerances(morph1, morph2):
"""Generates all reasonable tolerant particle morphs::
>>> set(generate_tolerances(u'이', u'가'))
set([u'이(가)', u'(이)가', u'가(이)', u'(가)이'])
>>> set(generate_tolerances(u'이면', u'면'))
set([u'(이)면'])
"""
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def _on_connection_open(self, connection):
"""
Callback invoked when the connection is successfully established.
Args:
connection (pika.connection.SelectConnection): The newly-estabilished
connection.
"""
_log.info("Successfully opened connection to %... | [
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def ec_init(spec):
"""
Initiate a key bundle with an elliptic curve key.
:param spec: Key specifics of the form::
{"type": "EC", "crv": "P-256", "use": ["sig"]}
:return: A KeyBundle instance
"""
kb = KeyBundle(keytype="EC")
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def renumber_atoms(lines):
'''
Takes in a list of PDB lines and renumbers the atoms appropriately
'''
new_lines = []
current_number = 1
for line in lines:
if line.startswith('ATOM') or line.startswith('HETATM'):
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def branches(config, searchstring=""):
"""List all branches. And if exactly 1 found, offer to check it out."""
repo = config.repo
branches_ = list(find(repo, searchstring))
if branches_:
merged = get_merged_branches(repo)
info_out("Found existing branches...")
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def read(self, n):
'''read some bytes'''
if len(self.buf) == 0:
self._recv()
if len(self.buf) > 0:
if n > len(self.buf):
n = len(self.buf)
ret = self.buf[:n]
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def build(cls, value: object, binary: bool = False,
fallback: object = None) -> Union[Nil, 'String']:
"""Produce either a :class:`QuotedString` or :class:`LiteralString`
based on the contents of ``data``. This is useful to improve
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def get_all_server_credentials(self, authorization, **kwargs): # noqa: E501
"""Fetch all (Bootstrap and LwM2M) server credentials. # noqa: E501
This REST API is intended to be used by customers to fetch all (Bootstrap and LwM2M) server credentials that they will need to use with their clients to conn... | [
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def watch_from_file(connection, file_name):
""" Start watching a new volume
:type connection: boto.ec2.connection.EC2Connection
:param connection: EC2 connection object
:type file_name: str
:param file_name: path to config file
:returns: None
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def deploy(target):
"""Deploys the package and documentation.
Proceeds in the following steps:
1. Ensures proper environment variables are set and checks that we are on Circle CI
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def spkw08(handle, body, center, inframe, first, last, segid, degree, n, states,
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# see libspice args for solution to array[][N] problem
"""
Write a type 8 segment to an SPK file.
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def dispatch(self, request, *args, **kwargs):
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Most views in a CMS require a login, so this is the default setup.
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def show_hc(kwargs=None, call=None):
'''
Show the details of an existing health check.
CLI Example:
.. code-block:: bash
salt-cloud -f show_hc gce name=hc
'''
if call != 'function':
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def cp(src_path, dst_path, follow_links=False, recursive=True):
"""Copy source to destination.
>>> if cp('/tmp/one', '/tmp/two'):
... print('OK')
OK
"""
successful = False
try:
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src_path = os.path.realpath(src_path)
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def zip_columns(columns):
"""
Zip together multiple columns.
Args:
columns (WeldObject / Numpy.ndarray): lust of columns
Returns:
A WeldObject representing this computation
"""
weld_obj = WeldObject(encoder_, decoder_)
column_vars = []
for column in columns:
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def log_config(log_level: Union[str, int]) -> dict:
"""
Setup default config. for dictConfig.
:param log_level: str name or django debugging int
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"""
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def removeComponent(self, index):
"""Removes the component at *index* from the model. If the two last
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def get_hosts_unfinished(self, scan_id):
""" Get a list of finished hosts."""
unfinished_hosts = list()
for target in self.scans_table[scan_id]['finished_hosts']:
unfinished_hosts.extend(target_str_to_list(target))
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def setColumns( self, columns ):
"""
Sets the columns for this gantt widget's tree to the inputed list of
columns.
:param columns | {<str>, ..]
"""
self.treeWidget().setColumns(columns)
item = self.treeWidget().headerItem()
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def eventFilter( self, object, event ):
"""
Filters the object for particular events.
:param object | <QObject>
event | <QEvent>
:return <bool> | consumed
"""
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def getIcon( data ):
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import cStringIO
stream = cStringIO.StringIO(data)
image = wx.ImageFromStream(stream)
icon = wx.EmptyIcon()
icon.CopyFromBitmap(wx.BitmapFromImage(image))
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def set_color_in_session(intent, session):
""" Sets the color in the session and prepares the speech to reply to the
user.
"""
card_title = intent['name']
session_attributes = {}
should_end_session = False
if 'Color' in intent['slots']:
favorite_color = intent['slots']['Color']['va... | [
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def default_qai(qareport):
"""QAI = 2 * (TP * (PT/PNC) * COV) / (1 + exp(MSE/tau))
Where:
TP: If all tests passes is 1, 0 otherwise.
PT: Processors and commands tested.
PCN: The number number of processors (Loader, Steps and Alerts)
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def find_period(data,
min_period=0.2, max_period=32.0,
coarse_precision=1e-5, fine_precision=1e-9,
periodogram=Lomb_Scargle,
period_jobs=1):
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def adaptStandardLogging(loggerName, logCategory, targetModule):
"""
Make a logger from the standard library log through the Flumotion logging
system.
@param loggerName: The standard logger to adapt, e.g. 'library.module'
@type loggerName: str
@param logCategory: The Flumotion log category to u... | [
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def commit(self):
"""
Insert the text at the current cursor position.
"""
# Backup and remove the currently selected text (may be none).
tc = self.qteWidget.textCursor()
self.selText = tc.selection().toHtml()
self.selStart = tc.selectionStart()
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def get(self, sid):
"""
Constructs a FeedbackSummaryContext
:param sid: A string that uniquely identifies this feedback summary resource
:returns: twilio.rest.api.v2010.account.call.feedback_summary.FeedbackSummaryContext
:rtype: twilio.rest.api.v2010.account.call.feedback_summ... | [
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def render_inline_styles(self):
"Hard-code the styles into the SVG XML if style sheets are not used."
if not self.css_inline:
# do nothing
return
styles = self.parse_css()
for node in self.root.xpath('//*[@class]'):
cl = '.' + node.attrib['class']
if cl not in styles:
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def asDictionary(self):
"""returns object as a dictionary"""
if self._json_dict is None:
self.__init(url=self._url)
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def extract_paths_dead(self, paths, *args, **kwargs):
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Thin method that just uses the provider
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def get_compiler(compiler, **compiler_attrs):
"""get and customize a compiler"""
if compiler is None or isinstance(compiler, str):
cc = ccompiler.new_compiler(compiler=compiler, verbose=0)
customize_compiler(cc)
if cc.compiler_type == 'mingw32':
customize_mingw(cc)
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def dlog(msg, log_path=DEFAULT_LOG_PATH):
"""A handy log utility for debugging multi-process, multi-threaded activities."""
with open(log_path, 'a') as f:
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def quantile(x, q, weights=None):
"""
Compute (weighted) quantiles from an input set of samples.
Parameters
----------
x : `~numpy.ndarray` with shape (nsamps,)
Input samples.
q : `~numpy.ndarray` with shape (nquantiles,)
The list of quantiles to compute from `[0., 1.]`.
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def maskInMicrolensRegion(ch, col, row, padding=0):
"""Is a target in the K2C9 superstamp, including padding?
This function is identical to pixelInMicrolensRegion, except it takes
the extra `padding` argument. The coordinate must be within the K2C9
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def _convert_variant_file_to_dict(varfile):
"""
Converts tsv to dicts with this structure
{
'patient_1': {
'variant-id': {
'build': 'hg19'
'chromosome': 'chr7',
'reference_allele': 'A',
'v... | [
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def pipelines(self):
"""
Property for accessing :class:`PipelineManager` instance, which is used to manage pipelines.
:rtype: yagocd.resources.pipeline.PipelineManager
"""
if self._pipeline_manager is None:
self._pipeline_manager = PipelineManager(session=self._sessi... | [
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def guard_assign(analysis):
"""Return whether the transition "assign" can be performed or not
"""
# Only if the request was done from worksheet context.
if not is_worksheet_context():
return False
# Cannot assign if the Sample has not been received
if not analysis.isSampleReceived():
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def ancovan(dv=None, covar=None, between=None, data=None,
export_filename=None):
"""ANCOVA with n covariates.
This is an internal function. The main call to this function should be done
by the :py:func:`pingouin.ancova` function.
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dv : string
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def stop_process(self):
"""Request the module process to stop and release it
:return: None
"""
if not self.process:
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logger.info("I'm stopping module %r (pid=%d)", self.name, self.process.pid)
self.kill()
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def remove_tcp_port(self, port):
"""
Removes an associated TCP port number from this project.
:param port: TCP port number
"""
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def requires(self):
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Returns the default workflow requirements in an ordered dictionary, which is updated with
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reqs = OrderedDict()
reqs.update(self.task.workflow_requires())
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def find_scraperclasses(comic, multiple_allowed=False):
"""Get a list comic scraper classes. Can return more than one entries if
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if not comic:
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def import_key(kwargs=None, call=None):
'''
List the keys available
CLI Example:
.. code-block:: bash
salt-cloud -f import_key joyent keyname=mykey keyfile=/tmp/mykey.pub
'''
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Registers a type name so that it may be used to send and receive packages.
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def jwks_to_keyjar(jwks, iss=''):
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Convert a JWKS to a KeyJar instance.
:param jwks: String representation of a JWKS
:return: A :py:class:`oidcmsg.key_jar.KeyJar` instance
"""
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def logic_subset(self, op=None):
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def matrix(self, x=(0, 0), y=(0, 0) , z=(0, 0)):
"""
Copy the ``pyny.Polygon`` along a 3D matrix given by the
three tuples x, y, z:
:param x: Number of copies and distance between them in this
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def create_surface_grid(nr_electrodes=None, spacing=None,
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depth=None,
left=None,
right=None,
char_lengths=None,
lines=None,
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def config_status():
""" Check config status in an account.
"""
s = boto3.Session()
client = s.client('config')
channels = client.describe_delivery_channel_status()[
'DeliveryChannelsStatus']
for c in channels:
print(yaml.safe_dump({
c['name']: dict(
s... | [
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... | 36.833333 | 0.001471 |
def load_project(self, filename, overwrite=False):
r"""
Loads a Project from the specified 'pnm' file
The loaded project is added to the Workspace . This will *not* delete
any existing Projects in the Workspace and will rename any Projects
being loaded if necessary.
Par... | [
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def setHoverForeground( self, column, brush ):
"""
Returns the brush to use when coloring when the user hovers over
the item for the given column.
:param column | <int>
brush | <QtGui.QBrush>
"""
self._hoverForeground[column] = Q... | [
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def blocks(self, blocksize=None, overlap=0, frames=-1, dtype='float64',
always_2d=False, fill_value=None, out=None):
"""Return a generator for block-wise reading.
By default, the generator yields blocks of the given
`blocksize` (using a given `overlap`) until the end of the file
... | [
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def _Enum(docstring, *names):
"""Utility to generate enum classes used by annotations.
Args:
docstring: Docstring for the generated enum class.
*names: Enum names.
Returns:
A class that contains enum names as attributes.
"""
enums = dict(zip(names, range(len(names))))
reverse = dict((value, ke... | [
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def add_entity(self, domain, **kwargs):
''' Add a new Entity to tracking. '''
# Set the entity's mapping func if one was specified
map_func = kwargs.get('map_func', None)
if map_func is not None and not callable(kwargs['map_func']):
if self.entity_mapper is None:
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def check_tuple(data: typing.Tuple,
hint: typing.Union[type, typing.TypingMeta]) -> bool:
"""Check argument type & return type of :class:`typing.Tuple`. since it
raises check :class:`typing.Tuple` using `isinstance`, so compare in
diffrent way
:param data: tuple given as a argument
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def _mass_from_knownmass_eta(known_mass, eta, known_is_secondary=False,
force_real=True):
r"""Returns the other component mass given one of the component masses
and the symmetric mass ratio.
This requires finding the roots of the quadratic equation:
.. math::
\eta m... | [
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def get_media_backend(fail_silently=True, handles_media_types=None,
handles_file_extensions=None, supports_thumbnails=None):
"""
Returns the MediaBackend subclass that is configured for use with
media_tree.
"""
backends = app_settings.MEDIA_TREE_MEDIA_BACKENDS
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def parse(self, document, text):
"""Depth-first search over the provided tree.
Implemented as an iterative procedure. The structure of the state
needed to parse each node is also defined in this function.
:param document: the Document context
:param text: the structured text of... | [
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def absent(name, user=None, config=None):
'''
Verifies that the specified host is not known by the given user
name
The host name
Note that only single host names are supported. If foo.example.com
and bar.example.com are the same machine and you need to exclude both,
you wil... | [
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def _get_indexers_coords_and_indexes(self, indexers):
""" Extract coordinates from indexers.
Returns an OrderedDict mapping from coordinate name to the
coordinate variable.
Only coordinate with a name different from any of self.variables will
be attached.
"""
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def proto_0111(theABF):
"""protocol: IC ramp for AP shape analysis."""
abf=ABF(theABF)
abf.log.info("analyzing as an IC ramp")
# AP detection
ap=AP(abf)
ap.detect()
# also calculate derivative for each sweep
abf.derivative=True
# create the multi-plot figure
plt.figure(figsize... | [
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def train_df(self, df):
"""
Train scale from a dataframe
"""
aesthetics = sorted(set(self.aesthetics) & set(df.columns))
for ae in aesthetics:
self.train(df[ae]) | [
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def dolby(word, max_length=-1, keep_vowels=False, vowel_char='*'):
r"""Return the Dolby Code of a name.
This is a wrapper for :py:meth:`Dolby.encode`.
Parameters
----------
word : str
The word to transform
max_length : int
Maximum length of the returned Dolby code -- this also ... | [
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def _rsync_cmd(self):
"""Helper method to generate base rsync command."""
cmd = ['rsync']
if self._identity_file:
cmd += ['-e', 'ssh -i ' + os.path.expanduser(self._identity_file)]
return cmd | [
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def getXlogStatus(self):
"""Returns Transaction Logging or Recovery Status.
@return: Dictionary of status items.
"""
inRecovery = None
if self.checkVersion('9.0'):
inRecovery = self._simpleQuery("SELECT pg_is_in_recovery();")
cur = self._conn... | [
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def default(self, line):
"""Overriding default to get access to any argparse commands we have specified."""
if any((line.startswith(x) for x in self.argparse_names())):
try:
args = self.argparser.parse_args(shlex.split(line))
except Exception: # intentionally ca... | [
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def make_join_request(self, password = None, history_maxchars = None,
history_maxstanzas = None, history_seconds = None,
history_since = None):
"""
Make the presence stanza a MUC room join request.
:Parameters:
- `password`: password to the room.
... | [
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def _prepare_file(self, finder, req_to_install):
"""Prepare a single requirements files.
:return: A list of addition InstallRequirements to also install.
"""
# Tell user what we are doing for this requirement:
# obtain (editable), skipping, processing (local url), collecting
... | [
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def getStrings(lang_dict):
"""
Return a FunctionFS descriptor suitable for serialisation.
lang_dict (dict)
Key: language ID (ex: 0x0409 for en-us)
Value: list of unicode objects
All values must have the same number of items.
"""
field_list = []
kw = {}
try:
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"... | 28.714286 | 0.001375 |
def copy_part_from_key(self, src_bucket_name, src_key_name, part_num,
start=None, end=None):
"""
Copy another part of this MultiPart Upload.
:type src_bucket_name: string
:param src_bucket_name: Name of the bucket containing the source key
:type src_k... | [
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def set_config(self, key, value):
'''set {key:value} paris to self.config'''
self.config = self.read_file()
self.config[key] = value
self.write_file() | [
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def avail_images(call=None):
'''
Return available OpenNebula images.
CLI Example:
.. code-block:: bash
salt-cloud --list-images opennebula
salt-cloud --function avail_images opennebula
salt-cloud -f avail_images opennebula
'''
if call == 'action':
raise SaltCl... | [
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def _gradient_descent(objective, p0, it, n_iter,
n_iter_check=1, n_iter_without_progress=300,
momentum=0.8, learning_rate=200.0, min_gain=0.01,
min_grad_norm=1e-7, verbose=0, args=None, kwargs=None):
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def add_graph(self, graph):
"""Adds a `Graph` protocol buffer to the event file."""
event = event_pb2.Event(graph_def=graph.SerializeToString())
self._add_event(event, None) | [
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def find_closest_trackpointLB(self,l,b,D,vlos,pmll,pmbb,interp=True,
usev=False):
"""
NAME:
find_closest_trackpointLB
PURPOSE:
find the closest point on the stream track to a given point in (l,b,...) coordinates
INPUT:
... | [
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def get_full_page_box_list_assigning_media_and_crop(input_doc, quiet=False):
"""Get a list of all the full-page box values for each page. The argument
input_doc should be a PdfFileReader object. The boxes on the list are in the
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def bind_protocol(self, proto):
"""Tries to bind given protocol to this peer.
Should only be called by `proto` trying to bind.
Once bound this protocol instance will be used to communicate with
peer. If another protocol is already bound, connection collision
resolution takes pla... | [
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def visitBuiltinValueType(self, ctx: jsgParser.BuiltinValueTypeContext):
""" valueTypeExpr: JSON_STRING | JSON_NUMBER | JSON_INT | JSON_BOOL | JSON_NULL | JSON_ARRAY | JSON_OBJECT """
self._value_type_text = ctx.getText()
self._typeinfo = self.parserTypeToImplClass[self._value_type_text] | [
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def help_center_article_subscriptions(self, article_id, locale=None, **kwargs):
"https://developer.zendesk.com/rest_api/docs/help_center/subscriptions#list-article-subscriptions"
api_path = "/api/v2/help_center/articles/{article_id}/subscriptions.json"
api_path = api_path.format(article_id=artic... | [
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def background_model(self, ignore_black=True, use_hsv=False, scale=8):
"""Creates a background model for the given image. The background
color is given by the modes of each channel's histogram.
Parameters
----------
ignore_black : bool
If True, the zero pixels will b... | [
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... | 36.481481 | 0.001483 |
def write_iso19115_metadata(layer_uri, keywords, version_35=False):
"""Create metadata object from a layer path and keywords dictionary.
This function will save these keywords to the file system or the database.
:param version_35: If we write keywords version 3.5. Default to False.
:type version_35: ... | [
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"i... | 34.673469 | 0.000572 |
def listener_dict_to_tuple(listener):
'''
Convert an ELB listener dict into a listener tuple used by certain parts of
the AWS ELB API.
CLI example:
.. code-block:: bash
salt myminion boto_elb.listener_dict_to_tuple '{"elb_port":80,"instance_port":80,"elb_protocol":"HTTP"}'
'''
# W... | [
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... | 37.380952 | 0.002484 |
def p_values(self, p):
"""values :
| values value VALUE_SEPARATOR
| values value"""
if len(p) == 1:
p[0] = list()
else:
p[1].append(p[2])
p[0] = p[1] | [
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"]... | 26.333333 | 0.008163 |
def arguments_to_lists(function):
"""
Decorator for a function that converts all arguments to lists.
:param function: target function
:return: target function with only lists as parameters
"""
def l_function(*args, **kwargs):
l_args = [_to_list(arg) for arg in args]
l_kw... | [
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"k... | 29.3125 | 0.002066 |
def logistic(x, a=0., b=1.):
r"""Computes the logistic function with range :math:`\in (a, b)`.
This is given by:
.. math::
\mathrm{logistic}(x; a, b) = \frac{a + b e^x}{1 + e^x}.
Note that this is also the inverse of the logit function with domain
:math:`(a, b)`.
... | [
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] | 26.2 | 0.002454 |
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