code stringlengths 75 104k | docstring stringlengths 1 46.9k |
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def transmit(self, payload, **kwargs):
"""
Send a completion status call to SAP SuccessFactors using the client.
Args:
payload: The learner completion data payload to send to SAP SuccessFactors
"""
kwargs['app_label'] = 'sap_success_factors'
kwargs['model_nam... | Send a completion status call to SAP SuccessFactors using the client.
Args:
payload: The learner completion data payload to send to SAP SuccessFactors |
def _actor_from_game_image(self, name, game_image):
"""Return an actor object matching the one in the game image.
Note:
Health and mana are based on measured percentage of a fixed maximum
rather than the actual maximum in the game.
Arguments:
name: must be 'player' or '... | Return an actor object matching the one in the game image.
Note:
Health and mana are based on measured percentage of a fixed maximum
rather than the actual maximum in the game.
Arguments:
name: must be 'player' or 'opponent'
game_image: opencv image of the main game are... |
def get_iterator(self, query, **options):
"""Returns an event iterator for the given query (and optional 'sync' token)"""
return EventsPageIterator(self.client, '/events', query, options).items() | Returns an event iterator for the given query (and optional 'sync' token) |
def fetch(self):
"""
Fetch a ExecutionContextInstance
:returns: Fetched ExecutionContextInstance
:rtype: twilio.rest.studio.v1.flow.execution.execution_context.ExecutionContextInstance
"""
params = values.of({})
payload = self._version.fetch(
'GET',
... | Fetch a ExecutionContextInstance
:returns: Fetched ExecutionContextInstance
:rtype: twilio.rest.studio.v1.flow.execution.execution_context.ExecutionContextInstance |
def close_cursor(self, cursor_id, address=None):
"""DEPRECATED - Send a kill cursors message soon with the given id.
Raises :class:`TypeError` if `cursor_id` is not an instance of
``(int, long)``. What closing the cursor actually means
depends on this client's cursor manager.
T... | DEPRECATED - Send a kill cursors message soon with the given id.
Raises :class:`TypeError` if `cursor_id` is not an instance of
``(int, long)``. What closing the cursor actually means
depends on this client's cursor manager.
This method may be called from a :class:`~pymongo.cursor.Curs... |
def output(self):
"""
Returns a ElasticsearchTarget representing the inserted dataset.
Normally you don't override this.
"""
return ElasticsearchTarget(
host=self.host,
port=self.port,
http_auth=self.http_auth,
index=self.index,
... | Returns a ElasticsearchTarget representing the inserted dataset.
Normally you don't override this. |
def save(self, filename):
"""
Save host keys into a file, in the format used by openssh. The order of
keys in the file will be preserved when possible (if these keys were
loaded from a file originally). The single exception is that combined
lines will be split into individual k... | Save host keys into a file, in the format used by openssh. The order of
keys in the file will be preserved when possible (if these keys were
loaded from a file originally). The single exception is that combined
lines will be split into individual key lines, which is arguably a bug.
@p... |
def build_response(description, resource=None):
"""
Build a response definition.
"""
response = swagger.Response(
description=description,
)
if resource is not None:
response.schema = swagger.JsonReference({
"$ref": "#/definitions/{}".format(type_name(name_for(resour... | Build a response definition. |
def get_pid_from_file(self):
"""Get the pid from the pid file.
If the pid file doesn't exist a :exc:`PIDFileError` is raised.
"""
pid_file = os.path.join(self.profile_dir.pid_dir, self.name + u'.pid')
if os.path.isfile(pid_file):
with open(pid_file, 'r') as f:
... | Get the pid from the pid file.
If the pid file doesn't exist a :exc:`PIDFileError` is raised. |
def add_signal_receiver(self, callback_fn, signal, user_arg):
"""
Add a signal receiver callback with user argument
See also :py:meth:`remove_signal_receiver`,
:py:exc:`.ConnSignalNameNotRecognisedException`
:param func callback_fn:
User-defined callback function to... | Add a signal receiver callback with user argument
See also :py:meth:`remove_signal_receiver`,
:py:exc:`.ConnSignalNameNotRecognisedException`
:param func callback_fn:
User-defined callback function to call when signal triggers
:param str signal:
Signal name e.g.... |
def cleanupmem(initial_memory):
""" Cleans up initial memory. Each label must be
ALONE. Each instruction must have an space, etc...
"""
i = 0
while i < len(initial_memory):
tmp = initial_memory[i]
match = RE_LABEL.match(tmp)
if not match:
i += 1
contin... | Cleans up initial memory. Each label must be
ALONE. Each instruction must have an space, etc... |
def cleanup_files(self):
"""Clean up files, remove builds."""
logger.debug('Cleaning up...')
with indent_log():
for req in self.reqs_to_cleanup:
req.remove_temporary_source()
if self._pip_has_created_build_dir():
logger.debug('Removing tem... | Clean up files, remove builds. |
def List(self):
"""
Lists the keys and values.
"""
print()
for key in list(self.keys()):
print(key,'=',self[key])
print() | Lists the keys and values. |
def decimate(self, method, a, maxpoints=10000, **kwargs):
"""Decimate data *a* to *maxpoints* using *method*.
If *a* is a 1D array then it is promoted to a (2, N) array
where the first column simply contains the index.
If the array contains fewer than *maxpoints* points or if
*... | Decimate data *a* to *maxpoints* using *method*.
If *a* is a 1D array then it is promoted to a (2, N) array
where the first column simply contains the index.
If the array contains fewer than *maxpoints* points or if
*maxpoints* is ``None`` then it is returned as it is. The
defa... |
def attribute(self):
"""Set or reset attributes"""
paint = {
"bold": self.ESC + "1" + self.END,
1: self.ESC + "1" + self.END,
"dim": self.ESC + "2" + self.END,
2: self.ESC + "2" + self.END,
"underlined": self.ESC + "4" + self.END,
... | Set or reset attributes |
def pos_tag(
words: List[str], engine: str = "perceptron", corpus: str = "orchid"
) -> List[Tuple[str, str]]:
"""
Part of Speech tagging function.
:param list words: a list of tokenized words
:param str engine:
* unigram - unigram tagger
* perceptron - perceptron tagger (default)
... | Part of Speech tagging function.
:param list words: a list of tokenized words
:param str engine:
* unigram - unigram tagger
* perceptron - perceptron tagger (default)
* artagger - RDR POS tagger
:param str corpus:
* orchid - annotated Thai academic articles (default)
... |
def fastaReadHeaders(fasta):
"""Returns a list of fasta header lines, excluding
"""
headers = []
fileHandle = open(fasta, 'r')
line = fileHandle.readline()
while line != '':
assert line[-1] == '\n'
if line[0] == '>':
headers.append(line[1:-1])
line = fileHandl... | Returns a list of fasta header lines, excluding |
def do_dock6_flexible(self, ligand_path, force_rerun=False):
"""Dock a ligand to the protein.
Args:
ligand_path (str): Path to ligand (mol2 format) to dock to protein
force_rerun (bool): If method should be rerun even if output file exists
"""
log.debug('{}: run... | Dock a ligand to the protein.
Args:
ligand_path (str): Path to ligand (mol2 format) to dock to protein
force_rerun (bool): If method should be rerun even if output file exists |
def get_tile_geometry(path, origin_espg, tolerance=500):
""" Calculate the data and tile geometry for sentinel-2 tiles """
with rasterio.open(path) as src:
# Get tile geometry
b = src.bounds
tile_shape = Polygon([(b[0], b[1]), (b[2], b[1]), (b[2], b[3]), (b[0], b[3]), (b[0], b[1])])
... | Calculate the data and tile geometry for sentinel-2 tiles |
def png_data_uri(self, **kw):
"""\
Converts the QR Code into a PNG data URI.
Uses the same keyword parameters as the usual PNG serializer.
:rtype: str
"""
return writers.as_png_data_uri(self.matrix, self._version, **kw) | \
Converts the QR Code into a PNG data URI.
Uses the same keyword parameters as the usual PNG serializer.
:rtype: str |
def srbt(bt_address, pkts, inter=0.1, *args, **kargs):
"""send and receive using a bluetooth socket"""
if "port" in kargs:
s = conf.BTsocket(bt_address=bt_address, port=kargs.pop("port"))
else:
s = conf.BTsocket(bt_address=bt_address)
a, b = sndrcv(s, pkts, inter=inter, *args, **kargs)
... | send and receive using a bluetooth socket |
def paste(self, key, data):
"""Pastes data into grid
Parameters
----------
key: 2-Tuple of Integer
\tTop left cell
data: String or wx.Bitmap
\tTab separated string of paste data
\tor paste data image
"""
data_gen = self._get_paste_data_g... | Pastes data into grid
Parameters
----------
key: 2-Tuple of Integer
\tTop left cell
data: String or wx.Bitmap
\tTab separated string of paste data
\tor paste data image |
def send_audio(self, url, name, **audioinfo):
"""Send a pre-uploaded audio to the room.
See http://matrix.org/docs/spec/client_server/r0.2.0.html#m-audio
for audioinfo
Args:
url (str): The mxc url of the audio.
name (str): The filename of the audio.
... | Send a pre-uploaded audio to the room.
See http://matrix.org/docs/spec/client_server/r0.2.0.html#m-audio
for audioinfo
Args:
url (str): The mxc url of the audio.
name (str): The filename of the audio.
audioinfo (): Extra information about the audio. |
def country_bank_code(self):
"""str or None: The country specific bank-code associated with the BIC."""
entry = registry.get('bic').get(self.compact)
if entry:
return entry.get('bank_code') | str or None: The country specific bank-code associated with the BIC. |
def fromcols(selection, n_sessions, eqdata, **kwargs):
"""
Generate features from selected columns of a dataframe.
Parameters
----------
selection : list or tuple of str
Columns to be used as features.
n_sessions : int
Number of sessions over which to create features.
eqda... | Generate features from selected columns of a dataframe.
Parameters
----------
selection : list or tuple of str
Columns to be used as features.
n_sessions : int
Number of sessions over which to create features.
eqdata : DataFrame
Data from which to generate feature set. Mus... |
def intern(self, sym: sym.Symbol, var: Var, force: bool = False) -> Var:
"""Intern the Var given in this namespace mapped by the given Symbol.
If the Symbol already maps to a Var, this method _will not overwrite_
the existing Var mapping unless the force keyword argument is given
and is ... | Intern the Var given in this namespace mapped by the given Symbol.
If the Symbol already maps to a Var, this method _will not overwrite_
the existing Var mapping unless the force keyword argument is given
and is True. |
def _reflect_table(self):
"""Load the tables definition from the database."""
with self.db.lock:
try:
self._table = SQLATable(self.name,
self.db.metadata,
schema=self.db.schema,
... | Load the tables definition from the database. |
def get_fit_auto(self, CentralFreq, MaxWidth=15000, MinWidth=500, WidthIntervals=500, MakeFig=True, show_fig=True, silent=False):
"""
Tries a range of regions to search for peaks and runs the one with the least error
and returns the parameters with the least errors.
Parameters
-... | Tries a range of regions to search for peaks and runs the one with the least error
and returns the parameters with the least errors.
Parameters
----------
CentralFreq : float
The central frequency to use for the fittings.
MaxWidth : float, optional
The ma... |
def Serialize(self, writer):
"""
Serialize object.
Args:
writer (neo.IO.BinaryWriter):
"""
writer.WriteUInt32(self.Version)
writer.WriteUInt64(self.Services)
writer.WriteUInt32(self.Timestamp)
writer.WriteUInt16(self.Port)
writer.Write... | Serialize object.
Args:
writer (neo.IO.BinaryWriter): |
def set_ext_param(self, ext_key, param_key, val):
'''
Set the provided parameter in a set of extension parameters.
'''
if not self.extensions[ext_key]:
self.extensions[ext_key] = defaultdict(lambda: None)
self.extensions[ext_key][param_key] = val | Set the provided parameter in a set of extension parameters. |
def post_message(name,
channel,
from_name,
message,
api_key=None,
icon=None):
'''
Send a message to a Slack channel.
.. code-block:: yaml
slack-message:
slack.post_message:
- channel: '#gener... | Send a message to a Slack channel.
.. code-block:: yaml
slack-message:
slack.post_message:
- channel: '#general'
- from_name: SuperAdmin
- message: 'This state was executed successfully.'
- api_key: peWcBiMOS9HrZG15peWcBiMOS9HrZG15
The followi... |
def managed(name, peers=None, servers=None):
'''
Manages the configuration of NTP peers and servers on the device, as specified in the state SLS file.
NTP entities not specified in these lists will be removed whilst entities not configured on the device will be set.
SLS Example:
.. code-block:: y... | Manages the configuration of NTP peers and servers on the device, as specified in the state SLS file.
NTP entities not specified in these lists will be removed whilst entities not configured on the device will be set.
SLS Example:
.. code-block:: yaml
netntp_example:
netntp.managed:
... |
def gauge(name, value, rate=1, tags=None):
"""Set the value for a gauge.
>>> import statsdecor
>>> statsdecor.gauge('my.metric', 10)
"""
client().gauge(name, value, rate, tags) | Set the value for a gauge.
>>> import statsdecor
>>> statsdecor.gauge('my.metric', 10) |
def get_file(self, filename):
"""Get a file from the repo.
Returns a file-like stream with the data.
"""
log.debug('[%s]: reading: //%s/%s', self.name, self.name, filename)
try:
blob = self.repo.head.commit.tree/filename
return blob.data_stream
ex... | Get a file from the repo.
Returns a file-like stream with the data. |
def process_reply(self, reply, status=None, description=None):
"""
Re-entry for processing a successful reply.
Depending on how the ``retxml`` option is set, may return the SOAP
reply XML or process it and return the Python object representing the
returned value.
@param... | Re-entry for processing a successful reply.
Depending on how the ``retxml`` option is set, may return the SOAP
reply XML or process it and return the Python object representing the
returned value.
@param reply: The SOAP reply envelope.
@type reply: I{bytes}
@param statu... |
def _folder_get_content_iter(self, folder_key=None):
"""Iterator for api.folder_get_content"""
lookup_params = [
{'content_type': 'folders', 'node': 'folders'},
{'content_type': 'files', 'node': 'files'}
]
for param in lookup_params:
more_chunks = Tr... | Iterator for api.folder_get_content |
def notify_dispatch_request(self, request):
# type: (Request) -> None
"""Will be called when a context passed to a hooked function is about
to dispatch a request"""
if isinstance(request, Put) and request.path[0] == self.mri:
# This means the context we were passed has just m... | Will be called when a context passed to a hooked function is about
to dispatch a request |
def can_view(self, user=None, access_code=None):
''' Returns true if the accessing user is allowed to view this invoice,
or if the given access code matches this invoice's user's access code.
'''
if user == self.invoice.user:
return True
if user.is_staff:
... | Returns true if the accessing user is allowed to view this invoice,
or if the given access code matches this invoice's user's access code. |
def transfer(self, rights_assignment_data=None, *, from_user, to_user,
rights_assignment_format='jsonld'):
"""Transfer this Right to another owner on the backing
persistence layer.
Args:
rights_assignment_data (dict): Model data for the resulting
:cl... | Transfer this Right to another owner on the backing
persistence layer.
Args:
rights_assignment_data (dict): Model data for the resulting
:class:`~.RightsAssignment`
from_user (any, keyword): A user based on the model specified
by the persistence l... |
def _run_suite(self, test_suite):
""" run tests in test_suite
Args:
test_suite: unittest.TestSuite()
Returns:
list: tests_results
"""
tests_results = []
for testcase in test_suite:
testcase_name = testcase.config.get("name")
... | run tests in test_suite
Args:
test_suite: unittest.TestSuite()
Returns:
list: tests_results |
def _open(self, filename):
"""
Open the input file. Set self._fp to point to it. Read the first
line of parameters.
@param filename: A C{str} filename containing JSON BLAST records.
@raise ValueError: if the first line of the file isn't valid JSON,
if the input file ... | Open the input file. Set self._fp to point to it. Read the first
line of parameters.
@param filename: A C{str} filename containing JSON BLAST records.
@raise ValueError: if the first line of the file isn't valid JSON,
if the input file is empty, or if the JSON does not contain an
... |
def from_pint(cls, arr, unit_registry=None):
"""
Convert a Pint "Quantity" to a unyt_array or unyt_quantity.
Parameters
----------
arr : Pint Quantity
The Quantity to convert from.
unit_registry : yt UnitRegistry, optional
A yt unit registry to us... | Convert a Pint "Quantity" to a unyt_array or unyt_quantity.
Parameters
----------
arr : Pint Quantity
The Quantity to convert from.
unit_registry : yt UnitRegistry, optional
A yt unit registry to use in the conversion. If one is not
supplied, the defa... |
def iterable_validator(iterable_type, member_type):
"""Validator for ``attrs`` that performs deep type checking of iterables."""
def _validate_tuple(instance, attribute, value):
# pylint: disable=unused-argument
"""Validate that a dictionary is structured as expected.
:raises TypeError... | Validator for ``attrs`` that performs deep type checking of iterables. |
def make_twitter_request(url, user_id, params={}, request_type='GET'):
""" Generically make a request to twitter API using a particular user's authorization """
if request_type == "GET":
return requests.get(url, auth=get_twitter_auth(user_id), params=params)
elif request_type == "POST":
retu... | Generically make a request to twitter API using a particular user's authorization |
def append_child(self, name, child): # type: (str, typing.Any) -> ArTree
"""Append new child and return it."""
temp = ArTree(name, child)
self._array.append(temp)
return temp | Append new child and return it. |
def clean_streak(image, stat="pmode1", maxiter=15, sigrej=2.0,
lower=None, upper=None, binwidth=0.3, mask=None,
rpt_clean=0, atol=0.01, verbose=True):
"""
Apply destriping algorithm to input array.
Parameters
----------
image : `StripeArray` object
Arrays a... | Apply destriping algorithm to input array.
Parameters
----------
image : `StripeArray` object
Arrays are modifed in-place.
stat : str
Statistics for background computations
(see :py:func:`clean` for more details)
mask : `numpy.ndarray`
Mask array. Pixels with zero ... |
def on_message(self, msg=None):
"""
Poll the websocket for a new packet.
`Client.listen()` calls this.
:param msg (string(byte array)): Optional. Parse the specified message
instead of receiving a packet from the socket.
"""
if msg is None:
try:
... | Poll the websocket for a new packet.
`Client.listen()` calls this.
:param msg (string(byte array)): Optional. Parse the specified message
instead of receiving a packet from the socket. |
def count(self):
"""
This method retrieve the total of records resulting from a given query.
This attribute can be used compounded with query, filter,
sort, order and facet methods.
Examples:
>>> from crossref.restful import Works
>>> Works().query('zika... | This method retrieve the total of records resulting from a given query.
This attribute can be used compounded with query, filter,
sort, order and facet methods.
Examples:
>>> from crossref.restful import Works
>>> Works().query('zika').count()
3597
... |
def font(self):
"""
The |Font| object that provides access to the text properties for
these data labels, such as bold, italic, etc.
"""
defRPr = self._element.defRPr
font = Font(defRPr)
return font | The |Font| object that provides access to the text properties for
these data labels, such as bold, italic, etc. |
def convert_from_file(file):
"""
Reads the content of file in IDX format, converts it into numpy.ndarray and
returns it.
file is a file-like object (with read() method) or a file name.
"""
if isinstance(file, six_string_types):
with open(file, 'rb') as f:
return _internal_con... | Reads the content of file in IDX format, converts it into numpy.ndarray and
returns it.
file is a file-like object (with read() method) or a file name. |
def _flatten_beam_dim(tensor):
"""Reshapes first two dimensions in to single dimension.
Args:
tensor: Tensor to reshape of shape [A, B, ...]
Returns:
Reshaped tensor of shape [A*B, ...]
"""
shape = _shape_list(tensor)
shape[0] *= shape[1]
shape.pop(1) # Remove beam dim
return tf.reshape(tenso... | Reshapes first two dimensions in to single dimension.
Args:
tensor: Tensor to reshape of shape [A, B, ...]
Returns:
Reshaped tensor of shape [A*B, ...] |
def _get_fault_type_dummy_variables(self, rup):
"""
The original classification considers four style of faulting categories
(normal, strike-slip, reverse-oblique and reverse).
"""
Fn, Fr = 0, 0
if rup.rake >= -112.5 and rup.rake <= -67.5:
# normal
... | The original classification considers four style of faulting categories
(normal, strike-slip, reverse-oblique and reverse). |
def _generate_ccitt_header(self, data):
"""Construct a CCITT G3 or G4 header from the PDF metadata"""
# https://stackoverflow.com/questions/2641770/
# https://www.itu.int/itudoc/itu-t/com16/tiff-fx/docs/tiff6.pdf
if not self.decode_parms:
raise ValueError("/CCITTFaxDecode wi... | Construct a CCITT G3 or G4 header from the PDF metadata |
def _ast_op_concat_to_code(self, opr, *, ignore_whitespace, **kwargs):
"""Convert an AST concatenate op to python source code."""
hoist_target = OP_CONCAT if ignore_whitespace else OP_WS_CONCAT
operands = self._hoist_operands(opr.operands, lambda t: isinstance(t, OptreeNode) and t.opnode.operator is hoist_t... | Convert an AST concatenate op to python source code. |
def copy_graph(subject, existing_graph):
"""Function takes a subject and an existing graph, returns a new graph with
all predicate and objects of the existing graph copied to the new_graph with
subject as the new subject
Args:
subject(rdflib.URIRef): A URIRef subject
existing_graph(rdfl... | Function takes a subject and an existing graph, returns a new graph with
all predicate and objects of the existing graph copied to the new_graph with
subject as the new subject
Args:
subject(rdflib.URIRef): A URIRef subject
existing_graph(rdflib.Graph): A rdflib.Graph
Returns:
... |
def check_visitors(cls):
"""Check that a checker's visitors are correctly named.
A checker has methods named visit_NODETYPE, but it's easy to mis-name
a visit method, and it will never be called. This decorator checks
the class to see that all of its visitors are named after an existing
node class... | Check that a checker's visitors are correctly named.
A checker has methods named visit_NODETYPE, but it's easy to mis-name
a visit method, and it will never be called. This decorator checks
the class to see that all of its visitors are named after an existing
node class. |
def metricCompute(self, sensorToBody, bodyToSpecificObject):
"""
Compute the
"sensor's location relative to a specific object"
from the
"body's location relative to a specific object"
and the
"sensor's location relative to body"
@param sensorToBody (numpy array)
Active cells o... | Compute the
"sensor's location relative to a specific object"
from the
"body's location relative to a specific object"
and the
"sensor's location relative to body"
@param sensorToBody (numpy array)
Active cells of a single module that represents the sensor's location
relative to t... |
def drop_debug_privileges(cls, bIgnoreExceptions = False):
"""
Drops debug privileges.
This may be needed to avoid being detected
by certain anti-debug tricks.
@type bIgnoreExceptions: bool
@param bIgnoreExceptions: C{True} to ignore any exceptions that may be
... | Drops debug privileges.
This may be needed to avoid being detected
by certain anti-debug tricks.
@type bIgnoreExceptions: bool
@param bIgnoreExceptions: C{True} to ignore any exceptions that may be
raised when dropping debug privileges.
@rtype: bool
@retu... |
def _handle_magic_exception(self, mod, exc):
"""
Beginning with Ansible >2.6, some modules (file.py) install a
sys.excepthook which is a closure over AnsibleModule, redirecting the
magical exception to AnsibleModule.fail_json().
For extra special needs bonus points, the class is... | Beginning with Ansible >2.6, some modules (file.py) install a
sys.excepthook which is a closure over AnsibleModule, redirecting the
magical exception to AnsibleModule.fail_json().
For extra special needs bonus points, the class is not defined in
module_utils, but is defined in the modul... |
def fcoe_get_interface_output_fcoe_intf_list_fcoe_intf_tx_ls_rjt(self, **kwargs):
"""Auto Generated Code
"""
config = ET.Element("config")
fcoe_get_interface = ET.Element("fcoe_get_interface")
config = fcoe_get_interface
output = ET.SubElement(fcoe_get_interface, "output"... | Auto Generated Code |
def _process_data_var(string):
"""Transform datastring to key, values pair.
All values are transformed to floating point values.
Parameters
----------
string : str
Returns
-------
Tuple[Str, Str]
key, values pair
"""
key, var = string.split("<-")
if "structure" in ... | Transform datastring to key, values pair.
All values are transformed to floating point values.
Parameters
----------
string : str
Returns
-------
Tuple[Str, Str]
key, values pair |
def configure(self, options, config):
"""Configure the set of plugins with the given options
and config instance. After configuration, disabled plugins
are removed from the plugins list.
"""
log.debug("Configuring plugins")
self.config = config
cfg = PluginProxy('... | Configure the set of plugins with the given options
and config instance. After configuration, disabled plugins
are removed from the plugins list. |
def total_reads_from_grabix(in_file):
"""Retrieve total reads in a fastq file from grabix index.
"""
gbi_file = _get_grabix_index(in_file)
if gbi_file:
with open(gbi_file) as in_handle:
next(in_handle) # throw away
num_lines = int(next(in_handle).strip())
assert ... | Retrieve total reads in a fastq file from grabix index. |
def determine_min_cell(disordered_structure):
"""
Determine the smallest supercell that is able to enumerate
the provided structure with the given order parameter
"""
def lcm(n1, n2):
"""
Find least common multiple of two numbers
"""
... | Determine the smallest supercell that is able to enumerate
the provided structure with the given order parameter |
def defaultStorable(self, python_type=None, storable_type=None, version=None, **kwargs):
"""
Generate a default storable instance.
Arguments:
python_type (type): Python type of the object.
storable_type (str): storable type name.
version (tuple): version n... | Generate a default storable instance.
Arguments:
python_type (type): Python type of the object.
storable_type (str): storable type name.
version (tuple): version number of the storable handler.
Returns:
StorableHandler: storable instance.
Ex... |
def oauth_register(form):
"""Register user if possible.
:param form: A form instance.
:returns: A :class:`invenio_accounts.models.User` instance.
"""
if form.validate():
data = form.to_dict()
if not data.get('password'):
data['password'] = ''
user = register_user... | Register user if possible.
:param form: A form instance.
:returns: A :class:`invenio_accounts.models.User` instance. |
def concat_ws(sep, *cols):
"""
Concatenates multiple input string columns together into a single string column,
using the given separator.
>>> df = spark.createDataFrame([('abcd','123')], ['s', 'd'])
>>> df.select(concat_ws('-', df.s, df.d).alias('s')).collect()
[Row(s=u'abcd-123')]
"""
... | Concatenates multiple input string columns together into a single string column,
using the given separator.
>>> df = spark.createDataFrame([('abcd','123')], ['s', 'd'])
>>> df.select(concat_ws('-', df.s, df.d).alias('s')).collect()
[Row(s=u'abcd-123')] |
def sget_timestamp(self, cycle, step, dataset_number=None):
"""Returns timestamp for cycle, step.
Convinience function; same as issuing
dfdata[(dfdata[cycle_index_header] == cycle) &
(dfdata[step_index_header] == step)][timestamp_header]
Args:
cycle: cyc... | Returns timestamp for cycle, step.
Convinience function; same as issuing
dfdata[(dfdata[cycle_index_header] == cycle) &
(dfdata[step_index_header] == step)][timestamp_header]
Args:
cycle: cycle number
step: step number
dataset_number: the... |
def update(self, *data, **kwargs) -> 'Entity':
"""Update a Record in the repository.
Also performs unique validations before creating the entity.
Supports both dictionary and keyword argument updates to the entity::
dog.update({'age': 10})
dog.update(age=10)
... | Update a Record in the repository.
Also performs unique validations before creating the entity.
Supports both dictionary and keyword argument updates to the entity::
dog.update({'age': 10})
dog.update(age=10)
:param data: Dictionary of values to be updated for the en... |
def _parse_json(self, doc, exactly_one):
"""
Parse JSON response body.
"""
places = doc.get('geonames', [])
self._raise_for_error(doc)
if not len(places):
return None
def parse_code(place):
"""
Parse each record.
""... | Parse JSON response body. |
def is_integer(value,
coerce_value = False,
minimum = None,
maximum = None,
base = 10,
**kwargs):
"""Indicate whether ``value`` contains a whole number.
:param value: The value to evaluate.
:param coerce_value: If ``True``, will re... | Indicate whether ``value`` contains a whole number.
:param value: The value to evaluate.
:param coerce_value: If ``True``, will return ``True`` if ``value`` can be coerced
to whole number. If ``False``, will only return ``True`` if ``value`` is already
a whole number (regardless of type). Defaults... |
def add_incomplete_penetrance(genes, alias_genes, hpo_lines):
"""Add information of incomplete penetrance"""
LOG.info("Add incomplete penetrance info")
for hgnc_symbol in get_incomplete_penetrance_genes(hpo_lines):
for hgnc_id in get_correct_ids(hgnc_symbol, alias_genes):
genes[hgnc_id][... | Add information of incomplete penetrance |
def delete_a(name=None, ipv4addr=None, allow_array=False, **api_opts):
'''
Delete A record
If the A record is used as a round robin you can set ``allow_array=True`` to
delete all records for the hostname.
CLI Examples:
.. code-block:: bash
salt-call infoblox.delete_a name=abc.example... | Delete A record
If the A record is used as a round robin you can set ``allow_array=True`` to
delete all records for the hostname.
CLI Examples:
.. code-block:: bash
salt-call infoblox.delete_a name=abc.example.com
salt-call infoblox.delete_a ipv4addr=192.168.3.5
salt-call inf... |
def subdivide_with(self, branches, join_function, name='mixed'):
"""Branches this pretty tensor and uses an explicit join function.
This should be used in a with statement, for example to fork and join with
a sum:
with pt.subdivide_with(2, tf.add_n) as [a, b]:
a...
b...
Ar... | Branches this pretty tensor and uses an explicit join function.
This should be used in a with statement, for example to fork and join with
a sum:
with pt.subdivide_with(2, tf.add_n) as [a, b]:
a...
b...
Args:
branches: The number of branches.
join_function: A funct... |
def initialize():
"""
Method to parse and check configurations of FORD, get the project's
global documentation, and create the Markdown reader.
"""
try:
import multiprocessing
ncpus = '{0}'.format(multiprocessing.cpu_count())
except (ImportError, NotImplementedError):
nc... | Method to parse and check configurations of FORD, get the project's
global documentation, and create the Markdown reader. |
def sort(polylines):
"""
sort points within polyline
p0-p1-p2...
"""
for n, c in enumerate(polylines):
l = len(c)
if l > 2:
# DEFINE FIRST AND LAST INDEX A THOSE TWO POINTS THAT
# HAVE THE BIGGEST DIFFERENCE FROM A MIDDLE:
mid = c.mean(axis=0)
... | sort points within polyline
p0-p1-p2... |
def show(what='contents', calc_id=-1, extra=()):
"""
Show the content of a datastore (by default the last one).
"""
datadir = datastore.get_datadir()
if what == 'all': # show all
if not os.path.exists(datadir):
return
rows = []
for calc_id in datastore.get_calc_i... | Show the content of a datastore (by default the last one). |
def is_module_has_decorated(path,decorator_module,decorator_name):
'''
Finds out if a python module uses a given decorator.
Args :
loaded_module : The loaded module to be scanned.
decorator_module : Then name of the module defining the decorator.
decora... | Finds out if a python module uses a given decorator.
Args :
loaded_module : The loaded module to be scanned.
decorator_module : Then name of the module defining the decorator.
decorator_name : The name of the decorator. |
def val_to_bin(edges, x):
"""Convert axis coordinate to bin index."""
ibin = np.digitize(np.array(x, ndmin=1), edges) - 1
return ibin | Convert axis coordinate to bin index. |
def _gen_packet_setcolor(self, sequence, hue, sat, bri, kel, fade):
""" Generate "setcolor" packet payload. """
hue = min(max(hue, HUE_MIN), HUE_MAX)
sat = min(max(sat, SATURATION_MIN), SATURATION_MAX)
bri = min(max(bri, BRIGHTNESS_MIN), BRIGHTNESS_MAX)
kel = min(max(kel, TEMP_MI... | Generate "setcolor" packet payload. |
def rename(self, old_key, new_key):
"""Rename a file.
:param old_key: Old key that holds the object.
:param new_key: New key that will hold the object.
:returns: The object that has been renamed.
"""
assert new_key not in self
assert old_key != new_key
f... | Rename a file.
:param old_key: Old key that holds the object.
:param new_key: New key that will hold the object.
:returns: The object that has been renamed. |
def push(self):
"""
Pushes updated plot data via the Comm.
"""
if self.comm is None:
raise Exception('Renderer does not have a comm.')
diff = self.renderer.diff(self)
self.comm.send(diff) | Pushes updated plot data via the Comm. |
def generate_jobs_pending_widget():
"""Generates a jobs_pending progress bar widget.
"""
pbar = widgets.IntProgress(
value=0,
min=0,
max=50,
description='',
orientation='horizontal', layout=widgets.Layout(max_width='180px'))
pbar.style.bar_color = '#71cddd'
p... | Generates a jobs_pending progress bar widget. |
def ngram_count(text,N=1,keep_punct=False):
''' if N=1, return a dict containing each letter along with how many times the letter occurred.
if N=2, returns a dict containing counts of each bigram (pair of letters)
etc.
There is an option to remove all spaces and punctuation prior to processi... | if N=1, return a dict containing each letter along with how many times the letter occurred.
if N=2, returns a dict containing counts of each bigram (pair of letters)
etc.
There is an option to remove all spaces and punctuation prior to processing |
def add_files(self, files):
"""Add files and/or folders to transfer.
If :class:`Transfer.compress` attribute is set to ``True``, files
will get packed into a zip file before sending.
:param files: Files or folders to send
:type files: str, list
"""
if isinstance... | Add files and/or folders to transfer.
If :class:`Transfer.compress` attribute is set to ``True``, files
will get packed into a zip file before sending.
:param files: Files or folders to send
:type files: str, list |
def multi_evaluate(self, x, out=None):
"""Evaluate log of the density to propose ``x``, namely log(q(x))
for each row in x.
:param x:
Matrix-like array; the proposed points. Expect i-th accessible
as ``x[i]``.
:param out:
Vector-like array, length=... | Evaluate log of the density to propose ``x``, namely log(q(x))
for each row in x.
:param x:
Matrix-like array; the proposed points. Expect i-th accessible
as ``x[i]``.
:param out:
Vector-like array, length==``len(x)``, optional; If provided,
th... |
def _get_netengine_backend(self):
"""
returns the netengine backend specified in self.backend
for internal use only
"""
# extract backend class name, eg: AirOS or OpenWRT
backend_class_name = self.backend.split('.')[-1]
# convert to lowercase to get the path
... | returns the netengine backend specified in self.backend
for internal use only |
def visit_yieldfrom(self, node):
""" Return an astroid.YieldFrom node as string. """
yi_val = (" " + node.value.accept(self)) if node.value else ""
expr = "yield from" + yi_val
if node.parent.is_statement:
return expr
return "(%s)" % (expr,) | Return an astroid.YieldFrom node as string. |
def _reset_timeout(self):
"""Reset timeout for date keep alive."""
if self._timeout:
self._timeout.cancel()
self._timeout = self.loop.call_later(self.client.timeout,
self.transport.close) | Reset timeout for date keep alive. |
def _request(self, method, path, server=None, **kwargs):
"""Execute a request to the cluster
A server is selected from the server pool.
"""
while True:
next_server = server or self._get_server()
try:
response = self.server_pool[next_server].reques... | Execute a request to the cluster
A server is selected from the server pool. |
def stop(self):
"""
Stops the Dynamips hypervisor process.
"""
if self.is_running():
log.info("Stopping Dynamips process PID={}".format(self._process.pid))
yield from DynamipsHypervisor.stop(self)
# give some time for the hypervisor to properly stop.
... | Stops the Dynamips hypervisor process. |
def discover(self, start, top_level_directory=None, pattern='test*.py'):
"""Do test case discovery.
This is the top-level entry-point for test discovery.
If the ``start`` argument is a drectory, then ``haas`` will
discover all tests in the package contained in that directory.
... | Do test case discovery.
This is the top-level entry-point for test discovery.
If the ``start`` argument is a drectory, then ``haas`` will
discover all tests in the package contained in that directory.
If the ``start`` argument is not a directory, it is assumed to
be a package ... |
def plot_bargraph (self, data, cats=None, pconfig=None):
""" Depreciated function. Forwards to new location. """
from multiqc.plots import bargraph
if pconfig is None:
pconfig = {}
return bargraph.plot(data, cats, pconfig) | Depreciated function. Forwards to new location. |
def _ssl_PRF(secret, seed, req_len):
"""
Provides the implementation of SSLv3 PRF function:
SSLv3-PRF(secret, seed) =
MD5(secret || SHA-1("A" || secret || seed)) ||
MD5(secret || SHA-1("BB" || secret || seed)) ||
MD5(secret || SHA-1("CCC" || secret || seed)) || ...
req_len sho... | Provides the implementation of SSLv3 PRF function:
SSLv3-PRF(secret, seed) =
MD5(secret || SHA-1("A" || secret || seed)) ||
MD5(secret || SHA-1("BB" || secret || seed)) ||
MD5(secret || SHA-1("CCC" || secret || seed)) || ...
req_len should not be more than 26 x 16 = 416. |
def feature_scaling(x, xmin, xmax, a=0, b=1):
'''Generalized feature scaling (useful for variable error correction rate calculation)'''
return a + float(x - xmin) * (b - a) / (xmax - xmin) | Generalized feature scaling (useful for variable error correction rate calculation) |
def get_authenticated_subjects(cert_pem):
"""Return primary subject and set of equivalents authenticated by certificate.
- ``cert_pem`` can be str or bytes
"""
if isinstance(cert_pem, str):
cert_pem = cert_pem.encode('utf-8')
return d1_common.cert.subjects.extract_subjects(cert_pem) | Return primary subject and set of equivalents authenticated by certificate.
- ``cert_pem`` can be str or bytes |
def run(self):
"""Call self._poll_for_update() in a loop and handle errors."""
while True:
try:
self._poll_for_update()
except RuntimeError as error:
# Note that because logging triggers a call to notify_update(), by
# logging a message, we automatically retry publishing the ... | Call self._poll_for_update() in a loop and handle errors. |
def atlasdb_get_zonefiles_by_name(name, max_index=None, con=None, path=None):
"""
Look up the sequence of zone file records by name, optionally up to a specific zonefile index
Returns [{'zonefile_hash': ..., 'txid': ..., 'inv_index': ..., 'block_height': ..., 'present': ..., 'tried_storage': ...}], in block... | Look up the sequence of zone file records by name, optionally up to a specific zonefile index
Returns [{'zonefile_hash': ..., 'txid': ..., 'inv_index': ..., 'block_height': ..., 'present': ..., 'tried_storage': ...}], in blockchain order |
def _loadFromRow(self, result, fields, cursor):
"""Load from a database row, described by fields.
``fields`` should be the attribute names that
will be set. Note that userclasses will be
created (but not loaded).
"""
position = 0
for elem in fields:
v... | Load from a database row, described by fields.
``fields`` should be the attribute names that
will be set. Note that userclasses will be
created (but not loaded). |
def save(self):
"""
Persist changes on this Samples object back to the One Codex server along with any changes
on its metadata (if it has any).
"""
super(Samples, self).save()
if self.metadata is not None:
self.metadata.save() | Persist changes on this Samples object back to the One Codex server along with any changes
on its metadata (if it has any). |
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