code stringlengths 75 104k | docstring stringlengths 1 46.9k |
|---|---|
def configureLogger(self):
"""
Configures the python logging system to log to a debug file and to stdout for warn and above.
:return: the base logger.
"""
baseLogLevel = logging.DEBUG if self.isDebugLogging() else logging.INFO
# create recorder app root logger
log... | Configures the python logging system to log to a debug file and to stdout for warn and above.
:return: the base logger. |
def process_form(self, instance, field, form,
empty_marker=None, emptyReturnsMarker=False):
"""Return a list of dictionaries fit for ReferenceResultsField
consumption. Only services which have float()able entries in result,min
and max field will be included. If any of min, m... | Return a list of dictionaries fit for ReferenceResultsField
consumption. Only services which have float()able entries in result,min
and max field will be included. If any of min, max, or result fields
are blank, the row value is ignored here. |
def serve_forever(self, poll_interval=0.5):
"""
Handle one request at a time until shutdown.
Polls for shutdown every poll_interval seconds. Ignores
self.timeout. If you need to do periodic tasks, do them in
another thread.
"""
self.__is_shut_down.clear()
... | Handle one request at a time until shutdown.
Polls for shutdown every poll_interval seconds. Ignores
self.timeout. If you need to do periodic tasks, do them in
another thread. |
def redirect(self):
""" This is the HTTP-redirect endpoint """
logger.info("--- In SSO Redirect ---")
saml_msg = self.unpack_redirect()
try:
_key = saml_msg["key"]
saml_msg = IDP.ticket[_key]
self.req_info = saml_msg["req_info"]
del IDP.t... | This is the HTTP-redirect endpoint |
def touch(fname, times=None):
"""Creates an empty file at fname, creating path if necessary
Answer taken from Stack Overflow http://stackoverflow.com/a/1160227
User: ephemient http://stackoverflow.com/users/20713
License: CC-BY-SA 3.0 https://creativecommons.org/licenses/by-sa/3.0/
"""
fpath, f ... | Creates an empty file at fname, creating path if necessary
Answer taken from Stack Overflow http://stackoverflow.com/a/1160227
User: ephemient http://stackoverflow.com/users/20713
License: CC-BY-SA 3.0 https://creativecommons.org/licenses/by-sa/3.0/ |
def getTypeByPosition(self, idx):
"""Return ASN.1 type object by its position in fields set.
Parameters
----------
idx: :py:class:`int`
Field index
Returns
-------
:
ASN.1 type
Raises
------
: :class:`~pyasn1.erro... | Return ASN.1 type object by its position in fields set.
Parameters
----------
idx: :py:class:`int`
Field index
Returns
-------
:
ASN.1 type
Raises
------
: :class:`~pyasn1.error.PyAsn1Error`
If given position ... |
def _format_output(kernel_restart, packages, verbose, restartable, nonrestartable, restartservicecommands,
restartinitcommands):
'''
Formats the output of the restartcheck module.
Returns:
String - formatted output.
Args:
kernel_restart: indicates that newer kernel i... | Formats the output of the restartcheck module.
Returns:
String - formatted output.
Args:
kernel_restart: indicates that newer kernel is instaled
packages: list of packages that should be restarted
verbose: enables extensive output
restartable: list of restartable packag... |
def parse_unknown_args(args):
"""
Parse arguments not consumed by arg parser into a dicitonary
"""
retval = {}
preceded_by_key = False
for arg in args:
if arg.startswith('--'):
if '=' in arg:
key = arg.split('=')[0][2:]
value = arg.split('=')[1... | Parse arguments not consumed by arg parser into a dicitonary |
def chmod(self, path, mode):
"""
Change the mode (permissions) of a file. The permissions are
unix-style and identical to those used by python's C{os.chmod}
function.
@param path: path of the file to change the permissions of
@type path: str
@param mode: new per... | Change the mode (permissions) of a file. The permissions are
unix-style and identical to those used by python's C{os.chmod}
function.
@param path: path of the file to change the permissions of
@type path: str
@param mode: new permissions
@type mode: int |
def _validate_place_types(self, types):
"""Validate place types and return a mapping for use in requests."""
for pt in types:
if pt not in self.place_types:
raise InvalidPlaceTypeError(pt)
return {'types': ",".join(types)} | Validate place types and return a mapping for use in requests. |
def manhattan_distant(vector1, vector2):
"""曼哈顿距离"""
vector1 = np.mat(vector1)
vector2 = np.mat(vector2)
return np.sum(np.abs(vector1 - vector2)) | 曼哈顿距离 |
def key_value_to_tree(data):
'''
Convert key/value to tree
'''
tree = {}
for flatkey, value in six.iteritems(data):
t = tree
keys = flatkey.split(__opts__['pepa_delimiter'])
for i, key in enumerate(keys, 1):
if i == len(keys):
t[key] = value
... | Convert key/value to tree |
def args_range(min_value, max_value, *args):
"""
检查参数范围
"""
not_null(*args)
if not all(map(lambda v: min_value <= v <= max_value, args)):
raise ValueError("Argument must be between {0} and {1}!".format(min_value, max_value)) | 检查参数范围 |
def _hammer_function_precompute(self,x0, L, Min, model):
"""
Pre-computes the parameters of a penalizer centered at x0.
"""
if x0 is None: return None, None
if len(x0.shape)==1: x0 = x0[None,:]
m = model.predict(x0)[0]
pred = model.predict(x0)[1].copy()
pr... | Pre-computes the parameters of a penalizer centered at x0. |
def apply_bbox(sf,ax):
"""
Use bbox as xlim and ylim in ax
"""
limits = sf.bbox
xlim = limits[0],limits[2]
ylim = limits[1],limits[3]
ax.set_xlim(xlim)
ax.set_ylim(ylim) | Use bbox as xlim and ylim in ax |
def run_gblocks(align_fasta_file, **kwargs):
"""
remove poorly aligned positions and divergent regions with Gblocks
"""
cl = GblocksCommandline(aln_file=align_fasta_file, **kwargs)
r, e = cl.run()
print("Gblocks:", cl, file=sys.stderr)
if e:
print("***Gblocks could not run", file=s... | remove poorly aligned positions and divergent regions with Gblocks |
def get_file_courses(self, id, course_id, include=None):
"""
Get file.
Returns the standard attachment json object
"""
path = {}
data = {}
params = {}
# REQUIRED - PATH - course_id
"""ID"""
path["course_id"] = course_id
... | Get file.
Returns the standard attachment json object |
def tables_get(self, table_name):
"""Issues a request to retrieve information about a table.
Args:
table_name: a tuple representing the full name of the table.
Returns:
A parsed result object.
Raises:
Exception if there is an error performing the operation.
"""
url = Api._ENDP... | Issues a request to retrieve information about a table.
Args:
table_name: a tuple representing the full name of the table.
Returns:
A parsed result object.
Raises:
Exception if there is an error performing the operation. |
def set_opt(self, name, value):
""" Set option.
"""
self.cache['opts'][name] = value
if name == 'compress':
self.cache['delims'] = self.def_delims if not value else (
'',
'',
'') | Set option. |
def watch(self, path, recursive=False):
"""Watch for files in a directory and apply normalizations.
Watch for new or changed files in a directory and apply
normalizations over them.
Args:
path: Path to the directory.
recursive: Whether to find files recursively ... | Watch for files in a directory and apply normalizations.
Watch for new or changed files in a directory and apply
normalizations over them.
Args:
path: Path to the directory.
recursive: Whether to find files recursively or not. |
def wait_script(name,
source=None,
template=None,
onlyif=None,
unless=None,
cwd=None,
runas=None,
shell=None,
env=None,
stateful=False,
umask=None,
... | Download a script from a remote source and execute it only if a watch
statement calls it.
source
The source script being downloaded to the minion, this source script is
hosted on the salt master server. If the file is located on the master
in the directory named spam, and is called egg... |
def list_view_on_selected(self, widget, selected_item_key):
""" The selection event of the listView, returns a key of the clicked event.
You can retrieve the item rapidly
"""
self.lbl.set_text('List selection: ' + self.listView.children[selected_item_key].get_text()) | The selection event of the listView, returns a key of the clicked event.
You can retrieve the item rapidly |
def _lab_to_rgb(labs):
"""Convert Nx3 or Nx4 lab to rgb"""
# adapted from BSD-licensed work in MATLAB by Mark Ruzon
# Based on ITU-R Recommendation BT.709 using the D65
labs, n_dim = _check_color_dim(labs)
# Convert Lab->XYZ (silly indexing used to preserve dimensionality)
y = (labs[:, 0] + 16.... | Convert Nx3 or Nx4 lab to rgb |
def gen_df_state(
list_table: list,
set_initcond: set,
set_runcontrol: set,
set_input_runcontrol: set)->pd.DataFrame:
'''generate dataframe of all state variables used by supy
Parameters
----------
list_table : list
csv files for site info: `SUEWS_xx.csv` on gith... | generate dataframe of all state variables used by supy
Parameters
----------
list_table : list
csv files for site info: `SUEWS_xx.csv` on github SUEWS-docs repo
set_initcond : set
initial condition related variables
set_runcontrol : set
runcontrol related variables
set_i... |
def parse_reports(self):
""" Find RSeQC junction_saturation frequency reports and parse their data """
# Set up vars
self.junction_saturation_all = dict()
self.junction_saturation_known = dict()
self.junction_saturation_novel = dict()
# Go through files and parse data
for f in self.find_lo... | Find RSeQC junction_saturation frequency reports and parse their data |
def most_even(number, group):
"""Divide a number into a list of numbers as even as possible."""
count, rest = divmod(number, group)
counts = zip_longest([count] * group, [1] * rest, fillvalue=0)
chunks = [sum(one) for one in counts]
logging.debug('chunks: %s', chunks)
return chunks | Divide a number into a list of numbers as even as possible. |
def unique(seen, *iterables):
"""
Get the unique items in iterables while preserving order. Note that this
mutates the seen set provided only when the returned generator is used.
Args:
seen (set): either an empty set, or the set of things already seen
*iterables: one or more iterable l... | Get the unique items in iterables while preserving order. Note that this
mutates the seen set provided only when the returned generator is used.
Args:
seen (set): either an empty set, or the set of things already seen
*iterables: one or more iterable lists to chain together
Returns:
... |
def dump(doc, output_stream=None):
"""
Dump a :class:`.Doc` object into a JSON-encoded text string.
The output will be sent to :data:`sys.stdout` unless an alternative
text stream is given.
To dump to :data:`sys.stdout` just do:
>>> import panflute as pf
>>> doc = pf.Doc(Para(Str(... | Dump a :class:`.Doc` object into a JSON-encoded text string.
The output will be sent to :data:`sys.stdout` unless an alternative
text stream is given.
To dump to :data:`sys.stdout` just do:
>>> import panflute as pf
>>> doc = pf.Doc(Para(Str('a'))) # Create sample document
>>> pf... |
def v1_highlights_get(response, kvlclient, file_id_str, max_elapsed = 300):
'''Obtain highlights for a document POSTed previously to this end
point. See documentation for v1_highlights_post for further
details. If the `state` is still `pending` for more than
`max_elapsed` after the start of the `WorkU... | Obtain highlights for a document POSTed previously to this end
point. See documentation for v1_highlights_post for further
details. If the `state` is still `pending` for more than
`max_elapsed` after the start of the `WorkUnit`, then this reports
an error, although the `WorkUnit` may continue in the b... |
def page(self, course):
""" Get all data and display the page """
if not self.webdav_host:
raise web.notfound()
url = self.webdav_host + "/" + course.get_id()
username = self.user_manager.session_username()
apikey = self.user_manager.session_api_key()
return ... | Get all data and display the page |
def public_key_to_connection_id(self, public_key):
"""
Get stored connection id for a public key.
"""
with self._connections_lock:
for connection_id, connection_info in self._connections.items():
if connection_info.public_key == public_key:
... | Get stored connection id for a public key. |
def get_effective_domain_id(request):
"""Gets the id of the default domain.
If the requests default domain is the same as DEFAULT_DOMAIN,
return None.
"""
default_domain = get_default_domain(request)
domain_id = default_domain.get('id')
domain_name = default_domain.get('name')
return No... | Gets the id of the default domain.
If the requests default domain is the same as DEFAULT_DOMAIN,
return None. |
def get_url_endpoint(self):
"""
Returns the Hypermap endpoint for a layer.
This endpoint will be the WMTS MapProxy endpoint, only for WM we use the original endpoint.
"""
endpoint = self.url
if self.type not in ('Hypermap:WorldMap',):
endpoint = 'registry/%s/l... | Returns the Hypermap endpoint for a layer.
This endpoint will be the WMTS MapProxy endpoint, only for WM we use the original endpoint. |
def kick_job(self, job: JobOrID) -> None:
"""Moves a delayed or buried job into the ready queue.
:param job: The job or job ID to kick.
"""
self._send_cmd(b'kick-job %d' % _to_id(job), b'KICKED') | Moves a delayed or buried job into the ready queue.
:param job: The job or job ID to kick. |
def experiments_predictions_list(self, listing_url, offset=0, limit=-1, properties=None):
"""Get list of experiment resources from a SCO-API.
Parameters
----------
listing_url : string
url for experiments run listing.
offset : int, optional
Starting offse... | Get list of experiment resources from a SCO-API.
Parameters
----------
listing_url : string
url for experiments run listing.
offset : int, optional
Starting offset for returned list items
limit : int, optional
Limit the number of items in the ... |
def res_to_str(res):
"""
:param res: :class:`requests.Response` object
Parse the given request and generate an informative string from it
"""
if 'Authorization' in res.request.headers:
res.request.headers['Authorization'] = "*****"
return """
####################################
url = %... | :param res: :class:`requests.Response` object
Parse the given request and generate an informative string from it |
def plot(feature, mp=None, style_function=None, **map_kwargs):
"""Plots a GeoVector in an ipyleaflet map.
Parameters
----------
feature : telluric.vectors.GeoVector, telluric.features.GeoFeature, telluric.collections.BaseCollection
Data to plot.
mp : ipyleaflet.Map, optional
Map in ... | Plots a GeoVector in an ipyleaflet map.
Parameters
----------
feature : telluric.vectors.GeoVector, telluric.features.GeoFeature, telluric.collections.BaseCollection
Data to plot.
mp : ipyleaflet.Map, optional
Map in which to plot, default to None (creates a new one).
style_function... |
def authenticate(name, remote_addr, password, cert, key, verify_cert=True):
'''
Authenticate with a remote peer.
.. notes:
This function makes every time you run this a connection
to remote_addr, you better call this only once.
remote_addr :
An URL to a remote Server, you also... | Authenticate with a remote peer.
.. notes:
This function makes every time you run this a connection
to remote_addr, you better call this only once.
remote_addr :
An URL to a remote Server, you also have to give cert and key if you
provide remote_addr!
Examples:
... |
def relevant(symbol, token='', version=''):
'''Same as peers
https://iexcloud.io/docs/api/#relevant
Args:
symbol (string); Ticker to request
token (string); Access token
version (string); API version
Returns:
dict: result
'''
_raiseIfNotStr(symbol)
return _g... | Same as peers
https://iexcloud.io/docs/api/#relevant
Args:
symbol (string); Ticker to request
token (string); Access token
version (string); API version
Returns:
dict: result |
def could_be(self, other):
"""Return True if the other PersonName is not explicitly inconsistent."""
# TODO: Some suffix and title differences should be allowed
if type(other) is not type(self):
return NotImplemented
if self == other:
return True
for attr ... | Return True if the other PersonName is not explicitly inconsistent. |
def _coulomb(n1, n2, k, r):
"""Calculates Coulomb forces and updates node data."""
# Get relevant positional data
delta = [x2 - x1 for x1, x2 in zip(n1['velocity'], n2['velocity'])]
distance = sqrt(sum(d ** 2 for d in delta))
# If the deltas are too small, use random values to keep things moving
... | Calculates Coulomb forces and updates node data. |
def to_e164(name, origin=public_enum_domain, want_plus_prefix=True):
"""Convert an ENUM domain name into an E.164 number.
@param name: the ENUM domain name.
@type name: dns.name.Name object.
@param origin: A domain containing the ENUM domain name. The
name is relativized to this domain before being... | Convert an ENUM domain name into an E.164 number.
@param name: the ENUM domain name.
@type name: dns.name.Name object.
@param origin: A domain containing the ENUM domain name. The
name is relativized to this domain before being converted to text.
@type: dns.name.Name object or None
@param want_... |
def until_condition(self, condition, condition_description):
"""
Waits until conditions is True or returns a non-None value.
If any of the trait is still not present after timeout, raises a TimeoutException.
"""
end_time = time.time() + self._timeout
count = 1
whi... | Waits until conditions is True or returns a non-None value.
If any of the trait is still not present after timeout, raises a TimeoutException. |
def userParamFromDict(attributes):
"""Python representation of a mzML userParam = tuple(name, value,
unitAccession, type)
:param attributes: #TODO: docstring
:returns: #TODO: docstring
"""
keys = ['name', 'value', 'unitAccession', 'type']
return tuple(attributes[key] if key in attributes e... | Python representation of a mzML userParam = tuple(name, value,
unitAccession, type)
:param attributes: #TODO: docstring
:returns: #TODO: docstring |
def get_gc_property(value, is_bytes=False):
"""Get `GC` property."""
obj = unidata.ascii_properties if is_bytes else unidata.unicode_properties
if value.startswith('^'):
negate = True
value = value[1:]
else:
negate = False
value = unidata.unicode_alias['generalcategory'].g... | Get `GC` property. |
def name(self):
"""
Algo name.
"""
if self._name is None:
self._name = self.__class__.__name__
return self._name | Algo name. |
def on_state_execution_status_changed_after(self, model, prop_name, info):
""" Show current execution status in the widget
This function specifies what happens if the state machine execution status of a state changes
:param model: the model of the state that has changed (most likely it... | Show current execution status in the widget
This function specifies what happens if the state machine execution status of a state changes
:param model: the model of the state that has changed (most likely its execution status)
:param prop_name: property name that has been changed
... |
def __initialize_node(self, attributes_flags=int(Qt.ItemIsSelectable | Qt.ItemIsEnabled)):
"""
Initializes the node.
:param attributes_flags: Attributes flags.
:type attributes_flags: int
"""
self["traced"] = umbra.ui.nodes.GraphModelAttribute(name="traced",
... | Initializes the node.
:param attributes_flags: Attributes flags.
:type attributes_flags: int |
def redo(self, channel, image):
"""This method is called when an image is set in a channel."""
imname = image.get('name', 'none')
chname = channel.name
# is image in contents tree yet?
in_contents = self.is_in_contents(chname, imname)
# get old highlighted entries for t... | This method is called when an image is set in a channel. |
def GetMessage(self, log_source, lcid, message_identifier):
"""Retrieves a specific message for a specific Event Log source.
Args:
log_source (str): Event Log source.
lcid (int): language code identifier (LCID).
message_identifier (int): message identifier.
Returns:
str: message st... | Retrieves a specific message for a specific Event Log source.
Args:
log_source (str): Event Log source.
lcid (int): language code identifier (LCID).
message_identifier (int): message identifier.
Returns:
str: message string or None if not available. |
def quit(self):
"""
Quit the player, blocking until the process has died
"""
if self._process is None:
logger.debug('Quit was called after self._process had already been released')
return
try:
logger.debug('Quitting OMXPlayer')
proc... | Quit the player, blocking until the process has died |
def sum_dicts(dicts, normalize=False):
"""Sums the given dicts into a single dict mapping each numberic-valued
key to the sum of its mappings in all given dicts. Keys mapping to
non-numeric values retain the last value (by the given order).
Parameters
----------
dicts : list
A list of d... | Sums the given dicts into a single dict mapping each numberic-valued
key to the sum of its mappings in all given dicts. Keys mapping to
non-numeric values retain the last value (by the given order).
Parameters
----------
dicts : list
A list of dict objects mapping each key to an numeric val... |
def set_fraction(self, value):
"""Set the meter indicator. Value should be between 0 and 1."""
if value < 0:
value *= -1
value = min(value, 1)
if self.horizontal:
width = int(self.width * value)
height = self.height
else:
width = se... | Set the meter indicator. Value should be between 0 and 1. |
def ticket_delete(self, id, **kwargs):
"https://developer.zendesk.com/rest_api/docs/core/tickets#delete-ticket"
api_path = "/api/v2/tickets/{id}.json"
api_path = api_path.format(id=id)
return self.call(api_path, method="DELETE", **kwargs) | https://developer.zendesk.com/rest_api/docs/core/tickets#delete-ticket |
def conversion_rate(self):
"""
The percentage of participants that have converted for this variant.
Returns a > 0 float representing a percentage rate.
"""
participants = self.participant_count
if participants == 0:
return 0.0
return self.experiment.c... | The percentage of participants that have converted for this variant.
Returns a > 0 float representing a percentage rate. |
def get_savename_from_varname(
varname, varname_prefix=None,
savename_prefix=None):
"""
Args:
varname(str): a variable name in the graph
varname_prefix(str): an optional prefix that may need to be removed in varname
savename_prefix(str): an optional prefix to append to al... | Args:
varname(str): a variable name in the graph
varname_prefix(str): an optional prefix that may need to be removed in varname
savename_prefix(str): an optional prefix to append to all savename
Returns:
str: the name used to save the variable |
def _update_rs_with_primary_from_member(
sds,
replica_set_name,
server_description):
"""RS with known primary. Process a response from a non-primary.
Pass in a dict of ServerDescriptions, current replica set name, and the
ServerDescription we are processing.
Returns new topolog... | RS with known primary. Process a response from a non-primary.
Pass in a dict of ServerDescriptions, current replica set name, and the
ServerDescription we are processing.
Returns new topology type. |
def fromProfileName(cls, name):
"""Return a `SessionAPI` from a given configuration profile name.
:see: `ProfileStore`.
"""
with profiles.ProfileStore.open() as config:
return cls.fromProfile(config.load(name)) | Return a `SessionAPI` from a given configuration profile name.
:see: `ProfileStore`. |
def as_ordered_dict(self, preference_orders: List[List[str]] = None) -> OrderedDict:
"""
Returns Ordered Dict of Params from list of partial order preferences.
Parameters
----------
preference_orders: List[List[str]], optional
``preference_orders`` is list of partial... | Returns Ordered Dict of Params from list of partial order preferences.
Parameters
----------
preference_orders: List[List[str]], optional
``preference_orders`` is list of partial preference orders. ["A", "B", "C"] means
"A" > "B" > "C". For multiple preference_orders fir... |
def manipulate(self, stored_instance, component_instance):
"""
Stores the given StoredInstance bean.
:param stored_instance: The iPOPO component StoredInstance
:param component_instance: The component instance
"""
# Store the stored instance...
self._ipopo_instan... | Stores the given StoredInstance bean.
:param stored_instance: The iPOPO component StoredInstance
:param component_instance: The component instance |
def hgetall(self, key):
"""
Returns all fields and values of the has stored at `key`.
The underlying redis `HGETALL`_ command returns an array of
pairs. This method converts that to a Python :class:`dict`.
It will return an empty :class:`dict` when the key is not
found.... | Returns all fields and values of the has stored at `key`.
The underlying redis `HGETALL`_ command returns an array of
pairs. This method converts that to a Python :class:`dict`.
It will return an empty :class:`dict` when the key is not
found.
.. note::
**Time compl... |
def is_from_parent(cls, attribute_name, value=None):
# type: (type, str, bool) -> bool
"""
Tests if the current attribute value is shared by a parent of the given
class.
Returns None if the attribute value is None.
:param cls: Child class with the requested attribute
:param attribute_name:... | Tests if the current attribute value is shared by a parent of the given
class.
Returns None if the attribute value is None.
:param cls: Child class with the requested attribute
:param attribute_name: Name of the attribute to be tested
:param value: The exact value in the child class (optional)
... |
def _append_record(test_data, results, test_path):
"""Adds data of single testcase results to results database."""
statuses = test_data.get("statuses")
jenkins_data = test_data.get("jenkins") or {}
data = [
("title", test_data.get("test_name") or _get_testname(test_path)),
("verdict", s... | Adds data of single testcase results to results database. |
def delete_ipv6(self, ipv6_id):
"""
Delete ipv6
"""
uri = 'api/ipv6/%s/' % (ipv6_id)
return super(ApiNetworkIPv6, self).delete(uri) | Delete ipv6 |
def sg_argmin(tensor, opt):
r"""Returns the indices of the minimum values along the specified axis.
See `tf.argin()` in tensorflow.
Args:
tensor: A `Tensor` (automatically given by chain).
opt:
axis: Target axis. Default is the last one.
name: If provided, replace current tenso... | r"""Returns the indices of the minimum values along the specified axis.
See `tf.argin()` in tensorflow.
Args:
tensor: A `Tensor` (automatically given by chain).
opt:
axis: Target axis. Default is the last one.
name: If provided, replace current tensor's name.
Returns:
A ... |
def translate_rgb_to_ansi_code(red, green, blue, offset, colormode):
"""
Translate the given RGB color into the appropriate ANSI escape code
for the given color mode.
The offset is used for the base color which is used.
The ``colormode`` has to be one of:
* 0: no colors / disabled
*... | Translate the given RGB color into the appropriate ANSI escape code
for the given color mode.
The offset is used for the base color which is used.
The ``colormode`` has to be one of:
* 0: no colors / disabled
* 8: use ANSI 8 colors
* 16: use ANSI 16 colors (same as 8 but with bright... |
def wait_until_alert_is_present(self, timeout=None):
"""
Waits for an alert to be present
@type timeout: int
@param timeout: the maximum number of seconds the driver will wait before timing out
@rtype: webdriverwrapper.WebElementWrapper
... | Waits for an alert to be present
@type timeout: int
@param timeout: the maximum number of seconds the driver will wait before timing out
@rtype: webdriverwrapper.WebElementWrapper
@return: Returns the element found |
def execute_all_rules(self, matches, context):
"""
Execute all rules from this rules list. All when condition with same priority will be performed before
calling then actions.
:param matches:
:type matches:
:param context:
:type context:
:return:
... | Execute all rules from this rules list. All when condition with same priority will be performed before
calling then actions.
:param matches:
:type matches:
:param context:
:type context:
:return:
:rtype: |
def _set_gre_ttl(self, v, load=False):
"""
Setter method for gre_ttl, mapped from YANG variable /interface/tunnel/gre_ttl (uint32)
If this variable is read-only (config: false) in the
source YANG file, then _set_gre_ttl is considered as a private
method. Backends looking to populate this variable sh... | Setter method for gre_ttl, mapped from YANG variable /interface/tunnel/gre_ttl (uint32)
If this variable is read-only (config: false) in the
source YANG file, then _set_gre_ttl is considered as a private
method. Backends looking to populate this variable should
do so via calling thisObj._set_gre_ttl() d... |
def _top_element(self):
"""Returns top XML element."""
attrs = {"project-id": self.config["polarion-project-id"]}
document_relative_path = self.config.get("requirements-document-relative-path")
if document_relative_path:
attrs["document-relative-path"] = document_relative_pat... | Returns top XML element. |
def namedb_state_mutation_sanity_check( opcode, op_data ):
"""
Make sure all mutate fields for this operation are present.
Return True if so
Raise exception if not
"""
# sanity check: each mutate field in the operation must be defined in op_data, even if it's null.
missing = []
mutate_... | Make sure all mutate fields for this operation are present.
Return True if so
Raise exception if not |
def to_links_df(regressor_type,
regressor_kwargs,
trained_regressor,
tf_matrix_gene_names,
target_gene_name):
"""
:param regressor_type: string. Case insensitive.
:param regressor_kwargs: dict of key-value pairs that configures the regressor.
... | :param regressor_type: string. Case insensitive.
:param regressor_kwargs: dict of key-value pairs that configures the regressor.
:param trained_regressor: the trained model from which to extract the feature importances.
:param tf_matrix_gene_names: the list of names corresponding to the columns of the tf_ma... |
def plot_variability_thresholds(varthreshpkl,
xmin_lcmad_stdev=5.0,
xmin_stetj_stdev=2.0,
xmin_iqr_stdev=2.0,
xmin_inveta_stdev=2.0,
lcformat='hat-sql',
... | This makes plots for the variability threshold distributions.
Parameters
----------
varthreshpkl : str
The pickle produced by the function above.
xmin_lcmad_stdev,xmin_stetj_stdev,xmin_iqr_stdev,xmin_inveta_stdev : float or np.array
Values of the threshold values to override the ones ... |
def start( self ):
"""
Starts the thread in its own event loop if the local and global thread
options are true, otherwise runs the thread logic in the main event
loop.
"""
if ( self.localThreadingEnabled() and self.globalThreadingEnabled() ):
super(XThread, se... | Starts the thread in its own event loop if the local and global thread
options are true, otherwise runs the thread logic in the main event
loop. |
def estimator_spec_train(self, loss, num_async_replicas=1, use_tpu=False):
"""Constructs `tf.estimator.EstimatorSpec` for TRAIN (training) mode."""
train_op = self.optimize(loss, num_async_replicas=num_async_replicas,
use_tpu=use_tpu)
if use_tpu:
if self._hparams.warm_sta... | Constructs `tf.estimator.EstimatorSpec` for TRAIN (training) mode. |
def get_snpeff_info(snpeff_string, snpeff_header):
"""Make the vep annotations into a dictionaries
A snpeff dictionary will have the snpeff column names as keys and
the vep annotations as values.
The dictionaries are stored in a list.
One dictionary for each transcript.
... | Make the vep annotations into a dictionaries
A snpeff dictionary will have the snpeff column names as keys and
the vep annotations as values.
The dictionaries are stored in a list.
One dictionary for each transcript.
Args:
snpeff_string (string): A string with... |
def udp_messenger(domain_name, UDP_IP, UDP_PORT, sock_timeout, message):
"""Send UDP messages to usage tracker asynchronously
This multiprocessing based messenger was written to overcome the limitations
of signalling/terminating a thread that is blocked on a system call. This
messenger is created as a ... | Send UDP messages to usage tracker asynchronously
This multiprocessing based messenger was written to overcome the limitations
of signalling/terminating a thread that is blocked on a system call. This
messenger is created as a separate process, and initialized with 2 queues,
to_send to receive messages... |
def _add_prefix(self, split_names, start_node, group_type_name):
"""Adds the correct sub branch prefix to a given name.
Usually the prefix is the full name of the parent node. In case items are added
directly to the trajectory the prefixes are chosen according to the matching subbranch.
... | Adds the correct sub branch prefix to a given name.
Usually the prefix is the full name of the parent node. In case items are added
directly to the trajectory the prefixes are chosen according to the matching subbranch.
For example, this could be 'parameters' for parameters or 'results.run_000... |
def get_element_dt(self, el_name, tz=None, el_idx=0):
"""Return the text of the selected element as a ``datetime.datetime`` object.
The element text must be a ISO8601 formatted datetime
Args:
el_name : str
Name of element to use.
tz : datetime.tzinfo
... | Return the text of the selected element as a ``datetime.datetime`` object.
The element text must be a ISO8601 formatted datetime
Args:
el_name : str
Name of element to use.
tz : datetime.tzinfo
Timezone in which to return the datetime.
- Withou... |
def cctop_submit(seq_str):
"""Submit a protein sequence string to CCTOP and return the job ID.
Args:
seq_str (str): Protein sequence as a string
Returns:
dict: Job ID on the CCTOP server
"""
url = 'http://cctop.enzim.ttk.mta.hu/php/submit.php?sequence={}&tmFilter&signalPred'.forma... | Submit a protein sequence string to CCTOP and return the job ID.
Args:
seq_str (str): Protein sequence as a string
Returns:
dict: Job ID on the CCTOP server |
def normalize_per_cell_weinreb16_deprecated(
X,
max_fraction=1,
mult_with_mean=False,
) -> np.ndarray:
"""Normalize each cell [Weinreb17]_.
This is a deprecated version. See `normalize_per_cell` instead.
Normalize each cell by UMI count, so that every cell has the same total
count.
Pa... | Normalize each cell [Weinreb17]_.
This is a deprecated version. See `normalize_per_cell` instead.
Normalize each cell by UMI count, so that every cell has the same total
count.
Parameters
----------
X : np.ndarray
Expression matrix. Rows correspond to cells and columns to genes.
m... |
def _validate_covars(covars, covariance_type, n_components):
"""Do basic checks on matrix covariance sizes and values."""
from scipy import linalg
if covariance_type == 'spherical':
if len(covars) != n_components:
raise ValueError("'spherical' covars have length n_components")
el... | Do basic checks on matrix covariance sizes and values. |
def migrateFileFields(portal):
"""
This function walks over all attachment types and migrates their FileField
fields.
"""
portal_types = [
"Attachment",
"ARImport",
"Instrument",
"InstrumentCertification",
"Method",
"Multifile",
"Report",
... | This function walks over all attachment types and migrates their FileField
fields. |
def get_delta(D, k):
'''Calculate the k-th order trend filtering matrix given the oriented edge
incidence matrix and the value of k.'''
if k < 0:
raise Exception('k must be at least 0th order.')
result = D
for i in range(k):
result = D.T.dot(result) if i % 2 == 0 else D.dot(result)
... | Calculate the k-th order trend filtering matrix given the oriented edge
incidence matrix and the value of k. |
def get_element_ids(self, prefix_id):
"""
Returns a single or a list of element ids, one for each input widget of this field
"""
if isinstance(self.widget, widgets.MultiWidget):
ids = ['{0}_{1}_{2}'.format(prefix_id, self.name, field_name) for field_name in self.widget]
... | Returns a single or a list of element ids, one for each input widget of this field |
def set_cookie( # type: ignore
self,
key: str,
value: AnyStr='',
max_age: Optional[Union[int, timedelta]]=None,
expires: Optional[datetime]=None,
path: str='/',
domain: Optional[str]=None,
secure: bool=False,
ht... | Set a cookie in the response headers.
The arguments are the standard cookie morsels and this is a
wrapper around the stdlib SimpleCookie code. |
def _parse_notes_dict(sbase):
""" Creates dictionary of COBRA notes.
Parameters
----------
sbase : libsbml.SBase
Returns
-------
dict of notes
"""
notes = sbase.getNotesString()
if notes and len(notes) > 0:
pattern = r"<p>\s*(\w+\s*\w*)\s*:\s*([\w|\s]+)<"
matche... | Creates dictionary of COBRA notes.
Parameters
----------
sbase : libsbml.SBase
Returns
-------
dict of notes |
def to_dict(self):
""" to_dict: puts channel data into the format that Kolibri Studio expects
Args: None
Returns: dict of channel data
"""
return {
"id": self.get_node_id().hex,
"name": self.title,
"thumbnail": self.thumbnail.filename i... | to_dict: puts channel data into the format that Kolibri Studio expects
Args: None
Returns: dict of channel data |
def edit_release_notes():
"""Use the default text $EDITOR to write release notes.
If $EDITOR is not set, use 'nano'."""
from tempfile import mkstemp
import os
import shlex
import subprocess
text_editor = shlex.split(os.environ.get('EDITOR', 'nano'))
fd, ... | Use the default text $EDITOR to write release notes.
If $EDITOR is not set, use 'nano'. |
def canintersect(self, other):
'''
Intersection is not well-defined for all pairs of multipliers.
For example:
{2,3} & {3,4} = {3}
{2,} & {1,7} = {2,7}
{2} & {5} = ERROR
'''
return not (self.max < other.min or other.max < self.min) | Intersection is not well-defined for all pairs of multipliers.
For example:
{2,3} & {3,4} = {3}
{2,} & {1,7} = {2,7}
{2} & {5} = ERROR |
def get_failed_instruments(self):
"""Find invalid instruments
- instruments who have failed QC tests
- instruments whose certificate is out of date
- instruments which are disposed until next calibration test
Return a dictionary with all info about expired/invalid instruments
... | Find invalid instruments
- instruments who have failed QC tests
- instruments whose certificate is out of date
- instruments which are disposed until next calibration test
Return a dictionary with all info about expired/invalid instruments |
def _make_intermediate_dirs(sftp_client, remote_directory):
"""
Create all the intermediate directories in a remote host
:param sftp_client: A Paramiko SFTP client.
:param remote_directory: Absolute Path of the directory containing the file
:return:
"""
if remote_directory == '/':
s... | Create all the intermediate directories in a remote host
:param sftp_client: A Paramiko SFTP client.
:param remote_directory: Absolute Path of the directory containing the file
:return: |
def digests_are_equal(digest1, digest2):
"""
<Purpose>
While protecting against timing attacks, compare the hexadecimal arguments
and determine if they are equal.
<Arguments>
digest1:
The first hexadecimal string value to compare.
digest2:
The second hexadecimal string value to compa... | <Purpose>
While protecting against timing attacks, compare the hexadecimal arguments
and determine if they are equal.
<Arguments>
digest1:
The first hexadecimal string value to compare.
digest2:
The second hexadecimal string value to compare.
<Exceptions>
securesystemslib.exceptio... |
def trim_wav_pydub(in_path: Path, out_path: Path,
start_time: int, end_time: int) -> None:
""" Crops the wav file. """
logger.info(
"Using pydub/ffmpeg to create {} from {}".format(out_path, in_path) +
" using a start_time of {} and an end_time of {}".format(start_time,
... | Crops the wav file. |
def _buildDict(self):
'''
Builds the isle textfile into a dictionary for fast searching
'''
lexDict = {}
with io.open(self.islePath, "r", encoding='utf-8') as fd:
wordList = [line.rstrip('\n') for line in fd]
for row in wordList:
word, pro... | Builds the isle textfile into a dictionary for fast searching |
def ac_viz(acdata):
'''
Adapted from Gerry Harp at SETI.
Slightly massages the autocorrelated calculation result for better visualization.
In particular, the natural log of the data are calculated and the
values along the subband edges are set to the maximum value of the data,
and the t=0 delay of the ... | Adapted from Gerry Harp at SETI.
Slightly massages the autocorrelated calculation result for better visualization.
In particular, the natural log of the data are calculated and the
values along the subband edges are set to the maximum value of the data,
and the t=0 delay of the autocorrelation result are s... |
def ensure_parent_id(self):
"""If current trace_parent has no span_id, generate one, then return it
This is used to generate a span ID which the RUM agent will use to correlate
the RUM transaction with the backend transaction.
"""
if self.trace_parent.span_id == self.id:
... | If current trace_parent has no span_id, generate one, then return it
This is used to generate a span ID which the RUM agent will use to correlate
the RUM transaction with the backend transaction. |
def expected_error_messages(*error_messages):
"""
Decorator expecting defined error messages at the end of test method. As
param use what
:py:meth:`~.WebdriverWrapperErrorMixin.get_error_messages`
returns.
.. versionadded:: 2.0
Before this decorator was called ``ShouldBeError``.
"""... | Decorator expecting defined error messages at the end of test method. As
param use what
:py:meth:`~.WebdriverWrapperErrorMixin.get_error_messages`
returns.
.. versionadded:: 2.0
Before this decorator was called ``ShouldBeError``. |
def run_from_argv(self, argv):
"""Overriden in order to access the command line arguments."""
self.argv_string = ' '.join(argv)
super(EmailNotificationCommand, self).run_from_argv(argv) | Overriden in order to access the command line arguments. |
def install(editable=True):
"""Install this component (or remove and reinstall)"""
try:
__import__(package['name'])
except ImportError:
pass
else:
run("pip uninstall --quiet -y %s" % package['name'], warn=True)
cmd = "pip install --quiet "
cmd += "-e ." if editable else... | Install this component (or remove and reinstall) |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.