code stringlengths 75 104k | docstring stringlengths 1 46.9k |
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def enable_backups(self, table_name, model):
"""Calls UpdateContinuousBackups on the table according to model.Meta["continuous_backups"]
:param table_name: The name of the table to enable Continuous Backups on
:param model: The model to get Continuous Backups settings from
"""
s... | Calls UpdateContinuousBackups on the table according to model.Meta["continuous_backups"]
:param table_name: The name of the table to enable Continuous Backups on
:param model: The model to get Continuous Backups settings from |
def _producer_wrapper(f, port, addr='tcp://127.0.0.1'):
"""A shim that sets up a socket and starts the producer callable.
Parameters
----------
f : callable
Callable that takes a single argument, a handle
for a ZeroMQ PUSH socket. Must be picklable.
port : int
The port on wh... | A shim that sets up a socket and starts the producer callable.
Parameters
----------
f : callable
Callable that takes a single argument, a handle
for a ZeroMQ PUSH socket. Must be picklable.
port : int
The port on which the socket should connect.
addr : str, optional
... |
def rigid_transform_from_ros(from_frame, to_frame, service_name='rigid_transforms/rigid_transform_listener', namespace=None):
"""Gets transform from ROS as a rigid transform
Requires ROS rigid_transform_publisher service to be running. Assuming autolab_core is installed as a catkin package,
... | Gets transform from ROS as a rigid transform
Requires ROS rigid_transform_publisher service to be running. Assuming autolab_core is installed as a catkin package,
this can be done with: roslaunch autolab_core rigid_transforms.launch
Parameters
----------
from_fr... |
def copy(self, **replacements):
"""Returns a clone of this M2Coordinate with the given replacements kwargs overlaid."""
cls = type(self)
kwargs = {'org': self.org, 'name': self.name, 'ext': self.ext, 'classifier': self.classifier, 'rev': self.rev}
for key, val in replacements.items():
kwargs[key] ... | Returns a clone of this M2Coordinate with the given replacements kwargs overlaid. |
def _SignedVarintEncoder():
"""Return an encoder for a basic signed varint value (does not include
tag)."""
def EncodeSignedVarint(write, value):
if value < 0:
value += (1 << 64)
bits = value & 0x7f
value >>= 7
while value:
write(six.int2byte(0x80|bits))
bits = value & 0x7f
... | Return an encoder for a basic signed varint value (does not include
tag). |
def generate_graphs(result, topic, aspect, for_doc=False):
""" genrate graphs from result file
Parameters
----------
result : str
path to result file
topic : str
benchmark topic; for example "Open file" or "Save file"
aspect : str
performance indiitemsor; can be "ram" (R... | genrate graphs from result file
Parameters
----------
result : str
path to result file
topic : str
benchmark topic; for example "Open file" or "Save file"
aspect : str
performance indiitemsor; can be "ram" (RAM memory usage) or "time" (elapsed time)
for_doc : bool
... |
def parse_item(self, response):
"""
Get basic information about a page, so that it can be passed to the
`pa11y` tool for further testing.
@url https://www.google.com/
@returns items 1 1
@returns requests 0 0
@scrapes url request_headers accessed_at page_title
... | Get basic information about a page, so that it can be passed to the
`pa11y` tool for further testing.
@url https://www.google.com/
@returns items 1 1
@returns requests 0 0
@scrapes url request_headers accessed_at page_title |
def draw_interface(objects, callback, callback_text):
"""
Draws a ncurses interface. Based on the given object list, every object should have a "string" key, this is whats displayed on the screen, callback is called with the selected object.
Rest of the code is modified from:
https://stackov... | Draws a ncurses interface. Based on the given object list, every object should have a "string" key, this is whats displayed on the screen, callback is called with the selected object.
Rest of the code is modified from:
https://stackoverflow.com/a/30834868 |
def _ensure_batch_is_sufficiently_small(
self,
batch_instances: Iterable[Instance],
excess: Deque[Instance]) -> List[List[Instance]]:
"""
If self._maximum_samples_per_batch is specified, then split the batch
into smaller sub-batches if it exceeds the maximum s... | If self._maximum_samples_per_batch is specified, then split the batch
into smaller sub-batches if it exceeds the maximum size.
Parameters
----------
batch_instances : ``Iterable[Instance]``
A candidate batch.
excess : ``Deque[Instance]``
Instances that we... |
def runlist_list(**kwargs):
"""
Show uploaded runlists.
"""
ctx = Context(**kwargs)
ctx.execute_action('runlist:list', **{
'storage': ctx.repo.create_secure_service('storage'),
}) | Show uploaded runlists. |
def CheckVersion(problems, latest_version=None):
"""
Check if there is a newer version of transitfeed available.
Args:
problems: if a new version is available, a NewVersionAvailable problem will
be added
latest_version: if specified, override the latest version read from the
project page
""... | Check if there is a newer version of transitfeed available.
Args:
problems: if a new version is available, a NewVersionAvailable problem will
be added
latest_version: if specified, override the latest version read from the
project page |
def normalize_extension(extension):
"""Normalise a file name extension."""
extension = decode_path(extension)
if extension is None:
return
if extension.startswith('.'):
extension = extension[1:]
if '.' in extension:
_, extension = os.path.splitext(extension)
extension = s... | Normalise a file name extension. |
def ok(self, text=u"OK", err=False):
"""Set Ok (success) finalizer to a spinner."""
# Do not display spin text for ok state
self._text = None
_text = to_text(text) if text else u"OK"
err = err or not self.write_to_stdout
self._freeze(_text, err=err) | Set Ok (success) finalizer to a spinner. |
def proxy_alias(alias_name, node_type):
"""Get a Proxy from the given name to the given node type."""
proxy = type(
alias_name,
(lazy_object_proxy.Proxy,),
{
"__class__": object.__dict__["__class__"],
"__instancecheck__": _instancecheck,
},
)
retur... | Get a Proxy from the given name to the given node type. |
def is_vert_aligned(c):
"""Return true if all the components of c are vertically aligned.
Vertical alignment means that the bounding boxes of each Mention of c
shares a similar x-axis value in the visual rendering of the document.
:param c: The candidate to evaluate
:rtype: boolean
"""
ret... | Return true if all the components of c are vertically aligned.
Vertical alignment means that the bounding boxes of each Mention of c
shares a similar x-axis value in the visual rendering of the document.
:param c: The candidate to evaluate
:rtype: boolean |
def get_distance(
self, l_motor: float, r_motor: float, tm_diff: float
) -> typing.Tuple[float, float]:
"""
Given motor values and the amount of time elapsed since this was last
called, retrieves the x,y,angle that the robot has moved. Pass these
values to :meth:`... | Given motor values and the amount of time elapsed since this was last
called, retrieves the x,y,angle that the robot has moved. Pass these
values to :meth:`PhysicsInterface.distance_drive`.
To update your encoders, use the ``l_position`` and ``r_position``
at... |
def transfer(self, receiver_address, amount, from_account):
"""
Transfer tokens from one account to the receiver address.
:param receiver_address: Address of the transfer receiver, str
:param amount: Amount of tokens, int
:param from_account: Sender account, Account
:ret... | Transfer tokens from one account to the receiver address.
:param receiver_address: Address of the transfer receiver, str
:param amount: Amount of tokens, int
:param from_account: Sender account, Account
:return: bool |
def load_core_file(core_fp):
"""
For core OTU data file, returns Genus-species identifier for each data
entry.
:type core_fp: str
:param core_fp: A file containing core OTU data.
:rtype: str
:return: Returns genus-species identifier based on identified taxonomical
level.
"""... | For core OTU data file, returns Genus-species identifier for each data
entry.
:type core_fp: str
:param core_fp: A file containing core OTU data.
:rtype: str
:return: Returns genus-species identifier based on identified taxonomical
level. |
def get_random_proxy(self):
"""Return random proxy"""
idx = randint(0, len(self._list) - 1)
return self._list[idx] | Return random proxy |
def close(self):
"""
Close the internal epoll file descriptor if it isn't closed
:raises OSError:
If the underlying ``close(2)`` fails. The error message matches
those found in the manual page.
"""
with self._close_lock:
epfd = self._epfd
... | Close the internal epoll file descriptor if it isn't closed
:raises OSError:
If the underlying ``close(2)`` fails. The error message matches
those found in the manual page. |
def write_bus_data(self, file):
""" Writes bus data as CSV.
"""
writer = self._get_writer(file)
writer.writerow(BUS_ATTRS)
for bus in self.case.buses:
writer.writerow([getattr(bus, attr) for attr in BUS_ATTRS]) | Writes bus data as CSV. |
def register_blueprint(self, blueprint):
'''
Register given blueprint on curren app.
This method is provided for using inside plugin's module-level
:func:`register_plugin` functions.
:param blueprint: blueprint object with plugin endpoints
:type blueprint: flask.Bluepri... | Register given blueprint on curren app.
This method is provided for using inside plugin's module-level
:func:`register_plugin` functions.
:param blueprint: blueprint object with plugin endpoints
:type blueprint: flask.Blueprint |
def register(self, app, options):
"""Register the blueprint to the mach9 app."""
url_prefix = options.get('url_prefix', self.url_prefix)
# Routes
for future in self.routes:
# attach the blueprint name to the handler so that it can be
# prefixed properly in the r... | Register the blueprint to the mach9 app. |
def update_identity(self, identity, identity_id):
"""UpdateIdentity.
:param :class:`<Identity> <azure.devops.v5_0.identity.models.Identity>` identity:
:param str identity_id:
"""
route_values = {}
if identity_id is not None:
route_values['identityId'] = self._... | UpdateIdentity.
:param :class:`<Identity> <azure.devops.v5_0.identity.models.Identity>` identity:
:param str identity_id: |
def formatdate(timeval=None, localtime=False, usegmt=False):
"""Returns a date string as specified by RFC 2822, e.g.:
Fri, 09 Nov 2001 01:08:47 -0000
Optional timeval if given is a floating point time value as accepted by
gmtime() and localtime(), otherwise the current time is used.
Optional loca... | Returns a date string as specified by RFC 2822, e.g.:
Fri, 09 Nov 2001 01:08:47 -0000
Optional timeval if given is a floating point time value as accepted by
gmtime() and localtime(), otherwise the current time is used.
Optional localtime is a flag that when True, interprets timeval, and
returns ... |
def p_DefaultValue_string(p):
"""DefaultValue : STRING"""
p[0] = model.Value(type=model.Value.STRING, value=p[1]) | DefaultValue : STRING |
def get_error(self, block=False, timeout=None):
"""Removes and returns an error from self._errors
Args:
block(bool): if True block until a RTMMessage is available,
else it will return None when self._inbox is empty
timeout(int): it blocks at most timeout... | Removes and returns an error from self._errors
Args:
block(bool): if True block until a RTMMessage is available,
else it will return None when self._inbox is empty
timeout(int): it blocks at most timeout seconds
Returns:
error if inbox is no... |
def _find_set_members(set):
'''
Return list of members for a set
'''
cmd = '{0} list {1}'.format(_ipset_cmd(), set)
out = __salt__['cmd.run_all'](cmd, python_shell=False)
if out['retcode'] > 0:
# Set doesn't exist return false
return False
_tmp = out['stdout'].split('\n')
... | Return list of members for a set |
def rps_at(self, t):
'''Return rps for second t'''
if 0 <= t <= self.duration:
return self.minrps + \
float(self.maxrps - self.minrps) * t / self.duration
else:
return 0 | Return rps for second t |
def put_archive(self, path, data):
"""
Insert a file or folder in this container using a tar archive as
source.
Args:
path (str): Path inside the container where the file(s) will be
extracted. Must exist.
data (bytes): tar data to be extracted
... | Insert a file or folder in this container using a tar archive as
source.
Args:
path (str): Path inside the container where the file(s) will be
extracted. Must exist.
data (bytes): tar data to be extracted
Returns:
(bool): True if the call suc... |
def nvrtcGetPTX(self, prog):
"""
Returns the compiled PTX for the NVRTC program object.
"""
size = c_size_t()
code = self._lib.nvrtcGetPTXSize(prog, byref(size))
self._throw_on_error(code)
buf = create_string_buffer(size.value)
code = self._lib.nvrtcGetPT... | Returns the compiled PTX for the NVRTC program object. |
def outdict(self, ndigits=3):
"""Return dictionary structure rounded to a given precision."""
output = self.__dict__.copy()
for item in output:
output[item] = round(output[item], ndigits)
return output | Return dictionary structure rounded to a given precision. |
def AutorizarAnticipo(self):
"Autorizar Anticipo de una Liquidación Primaria Electrónica de Granos"
# extraer y adaptar los campos para el anticipo
anticipo = {"liquidacion": self.liquidacion}
liq = anticipo["liquidacion"]
liq["campaniaPpal"] = self.liquidacion["campaniaPPal"]
... | Autorizar Anticipo de una Liquidación Primaria Electrónica de Granos |
def logtrace(logger, msg, *args, **kwargs):
'''
If esgfpid.defaults.LOG_TRACE_TO_DEBUG, messages are treated
like debug messages (with an added [trace]).
Otherwise, they are ignored.
'''
if esgfpid.defaults.LOG_TRACE_TO_DEBUG:
logdebug(logger, '[trace] %s' % msg, *args, **kwargs)
els... | If esgfpid.defaults.LOG_TRACE_TO_DEBUG, messages are treated
like debug messages (with an added [trace]).
Otherwise, they are ignored. |
def _sendDDEcommand(self, cmd, timeout=None):
"""Send command to DDE client"""
reply = self.conversation.Request(cmd, timeout)
if self.pyver > 2:
reply = reply.decode('ascii').rstrip()
return reply | Send command to DDE client |
def listIterators(self, login, tableName):
"""
Parameters:
- login
- tableName
"""
self.send_listIterators(login, tableName)
return self.recv_listIterators() | Parameters:
- login
- tableName |
def write(self, nb, fp, **kwargs):
"""Write a notebook to a file like object"""
return fp.write(self.writes(nb,**kwargs)) | Write a notebook to a file like object |
def unpack_fixed8(src):
"""Get a FIXED8 value."""
dec_part = unpack_ui8(src)
int_part = unpack_ui8(src)
return int_part + dec_part / 256 | Get a FIXED8 value. |
def _start_of_century(self):
"""
Reset the date to the first day of the century.
:rtype: Date
"""
year = self.year - 1 - (self.year - 1) % YEARS_PER_CENTURY + 1
return self.set(year, 1, 1) | Reset the date to the first day of the century.
:rtype: Date |
def just(*args):
''' this works as an infinite loop that yields
the given argument(s) over and over
'''
assert len(args) >= 1, 'generators.just needs at least one arg'
if len(args) == 1: # if only one arg is given
try:
# try to cycle in a set for iteration speedup
... | this works as an infinite loop that yields
the given argument(s) over and over |
def create_key(file_):
"""
Create a key and save it into ``file_``.
Note that ``file`` must be opened in binary mode.
"""
pkey = crypto.PKey()
pkey.generate_key(crypto.TYPE_RSA, 2048)
file_.write(crypto.dump_privatekey(crypto.FILETYPE_PEM, pkey))
file_.flush() | Create a key and save it into ``file_``.
Note that ``file`` must be opened in binary mode. |
def decode_source(source_bytes):
"""Decode bytes representing source code and return the string.
Universal newline support is used in the decoding.
"""
# source_bytes_readline = io.BytesIO(source_bytes).readline
# encoding, _ = detect_encoding(source_bytes_readline)
newline_decoder = io.Incremen... | Decode bytes representing source code and return the string.
Universal newline support is used in the decoding. |
def unhook_wnd_proc(self):
"""Restore previous Window message handler"""
if not self.__local_wnd_proc_wrapped:
return
SetWindowLong(self.__local_win_handle,
GWL_WNDPROC,
self.__old_wnd_proc)
## Allow the ctypes wrapper ... | Restore previous Window message handler |
def percentile(self, p):
"""
Computes the percentile of a specific value in [0,100].
"""
if not (0 <= p <= 100):
raise ValueError("p must be between 0 and 100, inclusive.")
p = float(p)/100.
p *= self.n
c_i = None
t = 0
if p == 0:
... | Computes the percentile of a specific value in [0,100]. |
def _unpack(c, tmp, package, version, git_url=None):
"""
Download + unpack given package into temp dir ``tmp``.
Return ``(real_version, source)`` where ``real_version`` is the "actual"
version downloaded (e.g. if a Git master was indicated, it will be the SHA
of master HEAD) and ``source`` is the s... | Download + unpack given package into temp dir ``tmp``.
Return ``(real_version, source)`` where ``real_version`` is the "actual"
version downloaded (e.g. if a Git master was indicated, it will be the SHA
of master HEAD) and ``source`` is the source directory (relative to
unpacked source) to import into ... |
def get_dataframe_from_variable(nc, data_var):
""" Returns a Pandas DataFrame of the data.
This always returns positive down depths
"""
time_var = nc.get_variables_by_attributes(standard_name='time')[0]
depth_vars = nc.get_variables_by_attributes(axis=lambda v: v is not None and v.lower() == 'z... | Returns a Pandas DataFrame of the data.
This always returns positive down depths |
def copy(self):
"""
Make a copy of the SegmentList.
:return: A copy of the SegmentList instance.
:rtype: angr.analyses.cfg_fast.SegmentList
"""
n = SegmentList()
n._list = [ a.copy() for a in self._list ]
n._bytes_occupied = self._bytes_occupied
... | Make a copy of the SegmentList.
:return: A copy of the SegmentList instance.
:rtype: angr.analyses.cfg_fast.SegmentList |
def update(self, slug):
'''
Update the page.
'''
post_data = self.get_post_data()
post_data['user_name'] = self.userinfo.user_name
pageinfo = MWiki.get_by_uid(slug)
cnt_old = tornado.escape.xhtml_unescape(pageinfo.cnt_md).strip()
cnt_new = post_data['c... | Update the page. |
def handle_response (response):
"""
Handle a response from the newton API
"""
response = json.loads(response.read())
# Was the expression valid?
if 'error' in response:
raise ValueError(response['error'])
else:
# Some of the strings returned can be parsed to integer... | Handle a response from the newton API |
def enable_directory_service(self, check_peer=False):
"""Enable the directory service.
:param check_peer: If True, enables server authenticity
enforcement. If False, enables directory
service integration.
:type check_peer: bool, optional
... | Enable the directory service.
:param check_peer: If True, enables server authenticity
enforcement. If False, enables directory
service integration.
:type check_peer: bool, optional
:returns: A dictionary describing the status of the directo... |
def _get_on_name(self, func):
"""Return `eventname` when the function name is `on_<eventname>()`."""
r = re.match("^on_(.+)$", func.__name__)
if r:
event = r.group(1)
else:
raise ValueError("The function name should be "
"`on_<eventnam... | Return `eventname` when the function name is `on_<eventname>()`. |
def update_thesis_information(self):
"""501 degree info - move subfields."""
fields_501 = record_get_field_instances(self.record, '502')
for field in fields_501:
new_subs = []
for key, value in field[0]:
if key == 'b':
new_subs.append((... | 501 degree info - move subfields. |
def get(self, name):
"""Returns a Notification by name.
"""
if not self.loaded:
raise RegistryNotLoaded(self)
if not self._registry.get(name):
raise NotificationNotRegistered(
f"Notification not registered. Got '{name}'."
)
retu... | Returns a Notification by name. |
def ungrist (value):
""" Returns the value without grist.
If value is a sequence, does it for every value and returns the result as a sequence.
"""
assert is_iterable_typed(value, basestring) or isinstance(value, basestring)
def ungrist_one (value):
stripped = __re_grist_content.match (v... | Returns the value without grist.
If value is a sequence, does it for every value and returns the result as a sequence. |
def _relative_attention_inner(x, y, z, transpose):
"""Relative position-aware dot-product attention inner calculation.
This batches matrix multiply calculations to avoid unnecessary broadcasting.
Args:
x: Tensor with shape [batch_size, heads, length or 1, length or depth].
y: Tensor with shape [batch_si... | Relative position-aware dot-product attention inner calculation.
This batches matrix multiply calculations to avoid unnecessary broadcasting.
Args:
x: Tensor with shape [batch_size, heads, length or 1, length or depth].
y: Tensor with shape [batch_size, heads, length or 1, depth].
z: Tensor with shape... |
def _download_initial_config(self):
"""Loads the initial config."""
_initial_config = self._download_running_config() # this is a bit slow!
self._last_working_config = _initial_config
self._config_history.append(_initial_config)
self._config_history.append(_initial_config) | Loads the initial config. |
def receive_request(self, transaction):
"""
Handle requests coming from the udp socket.
:param transaction: the transaction created to manage the request
"""
with transaction:
transaction.separate_timer = self._start_separate_timer(transaction)
self._b... | Handle requests coming from the udp socket.
:param transaction: the transaction created to manage the request |
def get_or_create_namespace(self, url: str) -> Union[Namespace, Dict]:
"""Insert the namespace file at the given location to the cache.
If not cachable, returns the dict of the values of this namespace.
:raises: pybel.resources.exc.ResourceError
"""
result = self.get_namespace_... | Insert the namespace file at the given location to the cache.
If not cachable, returns the dict of the values of this namespace.
:raises: pybel.resources.exc.ResourceError |
def quotation_markers(self, value):
"""
Setter for **self.__quotation_markers** attribute.
:param value: Attribute value.
:type value: tuple or list
"""
if value is not None:
assert type(value) in (tuple, list), "'{0}' attribute: '{1}' type is not 'tuple' or... | Setter for **self.__quotation_markers** attribute.
:param value: Attribute value.
:type value: tuple or list |
def set_meta_rdf(self, rdf, fmt='n3'):
"""Set the metadata for this Thing in RDF fmt
Advanced users who want to manipulate the RDF for this Thing directly without the
[ThingMeta](ThingMeta.m.html#IoticAgent.IOT.ThingMeta.ThingMeta) helper object
Raises [IOTException](./Exceptions.m.htm... | Set the metadata for this Thing in RDF fmt
Advanced users who want to manipulate the RDF for this Thing directly without the
[ThingMeta](ThingMeta.m.html#IoticAgent.IOT.ThingMeta.ThingMeta) helper object
Raises [IOTException](./Exceptions.m.html#IoticAgent.IOT.Exceptions.IOTException)
... |
def object_ref(self):
"""Return the reference of the changed object."""
return ImmutableDict(type=self.type, category_id=self.category_id, event_id=self.event_id,
session_id=self.session_id, contrib_id=self.contrib_id, subcontrib_id=self.subcontrib_id) | Return the reference of the changed object. |
def indices2one_hot(indices, nb_classes):
"""
Convert an iterable of indices to one-hot encoded list.
You might also be interested in sklearn.preprocessing.OneHotEncoder
Parameters
----------
indices : iterable
iterable of indices
nb_classes : int
Number of classes
dtyp... | Convert an iterable of indices to one-hot encoded list.
You might also be interested in sklearn.preprocessing.OneHotEncoder
Parameters
----------
indices : iterable
iterable of indices
nb_classes : int
Number of classes
dtype : type
Returns
-------
one_hot : list
... |
def _on_apply_button_clicked(self, *args):
"""Apply button clicked: Apply the configuration
"""
refresh_required = self.core_config_model.apply_preliminary_config()
refresh_required |= self.gui_config_model.apply_preliminary_config()
if not self.gui_config_model.config.get_confi... | Apply button clicked: Apply the configuration |
def d3logpdf_dlink3(self, link_f, y, Y_metadata=None):
"""
Third order derivative log-likelihood function at y given link(f) w.r.t link(f)
.. math::
\\frac{d^{3} \\ln p(y_{i}|\lambda(f_{i}))}{d^{3}\\lambda(f)} = -\\beta^{3}\\frac{d^{2}\\Psi(\\alpha_{i})}{d\\alpha_{i}}\\\\
... | Third order derivative log-likelihood function at y given link(f) w.r.t link(f)
.. math::
\\frac{d^{3} \\ln p(y_{i}|\lambda(f_{i}))}{d^{3}\\lambda(f)} = -\\beta^{3}\\frac{d^{2}\\Psi(\\alpha_{i})}{d\\alpha_{i}}\\\\
\\alpha_{i} = \\beta y_{i}
:param link_f: latent variables link(... |
def fit(self, choosers, alternatives, current_choice):
"""
Fit and save model parameters based on given data.
Parameters
----------
choosers : pandas.DataFrame
Table describing the agents making choices, e.g. households.
alternatives : pandas.DataFrame
... | Fit and save model parameters based on given data.
Parameters
----------
choosers : pandas.DataFrame
Table describing the agents making choices, e.g. households.
alternatives : pandas.DataFrame
Table describing the things from which agents are choosing,
... |
def validate_json(data, validator):
"""Validate data against a given JSON schema (see https://json-schema.org).
data: JSON-serializable data to validate.
validator (jsonschema.DraftXValidator): The validator.
RETURNS (list): A list of error messages, if available.
"""
errors = []
for err in... | Validate data against a given JSON schema (see https://json-schema.org).
data: JSON-serializable data to validate.
validator (jsonschema.DraftXValidator): The validator.
RETURNS (list): A list of error messages, if available. |
def match(self, s):
""" Matching the pattern to the input string, returns True/False and
saves the matched string in the internal list
"""
if self.re.match(s):
self.list.append(s)
return True
else: return False | Matching the pattern to the input string, returns True/False and
saves the matched string in the internal list |
def minimize(bed_file):
"""
strip a BED file down to its three necessary columns: chrom start end
"""
if not bed_file:
return bed_file
else:
sorted_bed = bt.BedTool(bed_file).cut(range(3)).sort()
if not sorted_bed.fn.endswith(".bed"):
return sorted_bed.moveto(sort... | strip a BED file down to its three necessary columns: chrom start end |
def _GetAccessToken(self):
"""Gets oauth2 access token for Gitkit API using service account.
Returns:
string, oauth2 access token.
"""
d = {
'assertion': self._GenerateAssertion(),
'grant_type': 'urn:ietf:params:oauth:grant-type:jwt-bearer',
}
try:
body = parse.url... | Gets oauth2 access token for Gitkit API using service account.
Returns:
string, oauth2 access token. |
def available_state(self, state: State) -> Tuple[State, ...]:
""" Return the state reachable from a given state. """
result = []
for gene in self.genes:
result.extend(self.available_state_for_gene(gene, state))
if len(result) > 1 and state in result:
result.remove... | Return the state reachable from a given state. |
def validate(self, document, schema=None, update=False, normalize=True):
""" Normalizes and validates a mapping against a validation-schema of
defined rules.
:param document: The document to normalize.
:type document: any :term:`mapping`
:param schema: The validation schema. Def... | Normalizes and validates a mapping against a validation-schema of
defined rules.
:param document: The document to normalize.
:type document: any :term:`mapping`
:param schema: The validation schema. Defaults to :obj:`None`. If not
provided here, the schema must ha... |
def transition_matrix_reversible_pisym(C, return_statdist=False, **kwargs):
r"""
Estimates reversible transition matrix as follows:
..:math:
p_{ij} = c_{ij} / c_i where c_i = sum_j c_{ij}
\pi_j = \sum_j \pi_i p_{ij}
x_{ij} = \pi_i p_{ij} + \pi_j p_{ji}
p^{rev}_{ij} = x_{ij} ... | r"""
Estimates reversible transition matrix as follows:
..:math:
p_{ij} = c_{ij} / c_i where c_i = sum_j c_{ij}
\pi_j = \sum_j \pi_i p_{ij}
x_{ij} = \pi_i p_{ij} + \pi_j p_{ji}
p^{rev}_{ij} = x_{ij} / x_i where x_i = sum_j x_{ij}
In words: takes the nonreversible transition... |
def slice_begin(self, tensor_shape, pnum):
"""Begin position for the tensor slice for the given processor.
Args:
tensor_shape: Shape.
pnum: int <= self.size.
Returns:
list of integers with length tensor_shape.ndims.
"""
tensor_layout = self.tensor_layout(tensor_shape)
coordin... | Begin position for the tensor slice for the given processor.
Args:
tensor_shape: Shape.
pnum: int <= self.size.
Returns:
list of integers with length tensor_shape.ndims. |
def get_sorted_hdrgo2usrgos(self, hdrgos, flat_list=None, hdrgo_prt=True, hdrgo_sort=True):
"""Return GO IDs sorting using go2nt's namedtuple."""
# Return user-specfied sort or default sort of header and user GO IDs
sorted_hdrgos_usrgos = []
h2u_get = self.grprobj.hdrgo2usrgos.get
... | Return GO IDs sorting using go2nt's namedtuple. |
def cmd_ping(ip, interface, count, timeout, wait, verbose):
"""The classic ping tool that send ICMP echo requests.
\b
# habu.ping 8.8.8.8
IP / ICMP 8.8.8.8 > 192.168.0.5 echo-reply 0 / Padding
IP / ICMP 8.8.8.8 > 192.168.0.5 echo-reply 0 / Padding
IP / ICMP 8.8.8.8 > 192.168.0.5 echo-reply 0 / ... | The classic ping tool that send ICMP echo requests.
\b
# habu.ping 8.8.8.8
IP / ICMP 8.8.8.8 > 192.168.0.5 echo-reply 0 / Padding
IP / ICMP 8.8.8.8 > 192.168.0.5 echo-reply 0 / Padding
IP / ICMP 8.8.8.8 > 192.168.0.5 echo-reply 0 / Padding
IP / ICMP 8.8.8.8 > 192.168.0.5 echo-reply 0 / Padding |
def _add_explicit_includes(lines, dependencies=None, extralinks=None):
"""Adds any relevant libraries that need to be explicitly included according
to the fortpy configuration file. Libraries are appended to the specified
collection of lines. Returns true if relevant libraries were added.
"""
from f... | Adds any relevant libraries that need to be explicitly included according
to the fortpy configuration file. Libraries are appended to the specified
collection of lines. Returns true if relevant libraries were added. |
def parse_error(self, tup_tree):
"""
Parse the tuple for an ERROR element:
::
<!ELEMENT ERROR (INSTANCE*)>
<!ATTLIST ERROR
CODE CDATA #REQUIRED
DESCRIPTION CDATA #IMPLIED>
"""
self.check_node(tup_tree, 'ERROR', ('CODE',... | Parse the tuple for an ERROR element:
::
<!ELEMENT ERROR (INSTANCE*)>
<!ATTLIST ERROR
CODE CDATA #REQUIRED
DESCRIPTION CDATA #IMPLIED> |
def extrude(
self,
input_entity,
translation_axis=None,
rotation_axis=None,
point_on_axis=None,
angle=None,
num_layers=None,
recombine=False,
):
"""Extrusion (translation + rotation) of any entity along a given
translation_axis, around ... | Extrusion (translation + rotation) of any entity along a given
translation_axis, around a given rotation_axis, about a given angle. If
one of the entities is not provided, this method will produce only
translation or rotation. |
def setup_address(self, name, address=default, transact={}):
"""
Set up the name to point to the supplied address.
The sender of the transaction must own the name, or
its parent name.
Example: If the caller owns ``parentname.eth`` with no subdomains
and calls this method... | Set up the name to point to the supplied address.
The sender of the transaction must own the name, or
its parent name.
Example: If the caller owns ``parentname.eth`` with no subdomains
and calls this method with ``sub.parentname.eth``,
then ``sub`` will be created as part of thi... |
def create_model( # noqa: C901 (ignore complexity)
model_name: str,
*,
__config__: Type[BaseConfig] = None,
__base__: Type[BaseModel] = None,
__module__: Optional[str] = None,
__validators__: Dict[str, classmethod] = None,
**field_definitions: Any,
) -> BaseModel:
"""
Dynamically cr... | Dynamically create a model.
:param model_name: name of the created model
:param __config__: config class to use for the new model
:param __base__: base class for the new model to inherit from
:param __validators__: a dict of method names and @validator class methods
:param **field_definitions: field... |
def send_response(self, transaction):
"""
Finalize to add the client to the list of observer.
:type transaction: Transaction
:param transaction: the transaction that owns the response
:return: the transaction unmodified
"""
host, port = transaction.request.source... | Finalize to add the client to the list of observer.
:type transaction: Transaction
:param transaction: the transaction that owns the response
:return: the transaction unmodified |
def get(self, alias: str):
"""
Retrieve cache identified by alias. Will return always the same instance
If the cache was not instantiated yet, it will do it lazily the first time
this is called.
:param alias: str cache alias
:return: cache instance
"""
t... | Retrieve cache identified by alias. Will return always the same instance
If the cache was not instantiated yet, it will do it lazily the first time
this is called.
:param alias: str cache alias
:return: cache instance |
def get_field_def(
schema: GraphQLSchema, parent_type: GraphQLObjectType, field_name: str
) -> GraphQLField:
"""Get field definition.
This method looks up the field on the given type definition. It has special casing
for the two introspection fields, `__schema` and `__typename`. `__typename` is
spe... | Get field definition.
This method looks up the field on the given type definition. It has special casing
for the two introspection fields, `__schema` and `__typename`. `__typename` is
special because it can always be queried as a field, even in situations where no
other fields are allowed, like on a Un... |
def intersect_3d(p1, p2):
"""Find the closes point for a given set of lines in 3D.
Parameters
----------
p1 : (M, N) array_like
Starting points
p2 : (M, N) array_like
End points.
Returns
-------
x : (N,) ndarray
Least-squares solution - the closest point of the ... | Find the closes point for a given set of lines in 3D.
Parameters
----------
p1 : (M, N) array_like
Starting points
p2 : (M, N) array_like
End points.
Returns
-------
x : (N,) ndarray
Least-squares solution - the closest point of the intersections.
Raises
--... |
def pred_eq(self, n, val):
"""
Test if a node set with setint or setstr equal a certain value
example::
R = [
__scope__:n
['a' #setint(n, 12) | 'b' #setint(n, 14)]
C
[#eq(n, 12) D]
]
"""
v1 = n.value
v2 = val
if hasattr(val, ... | Test if a node set with setint or setstr equal a certain value
example::
R = [
__scope__:n
['a' #setint(n, 12) | 'b' #setint(n, 14)]
C
[#eq(n, 12) D]
] |
def from_body(cls, body):
"""Create a tunnelling request from a given body of a KNX/IP frame."""
# TODO: Check length
request = cls()
request.channel = body[1]
request.seq = body[2]
request.cemi = body[4:]
return request | Create a tunnelling request from a given body of a KNX/IP frame. |
def insert_code(filename, code, save=True, marker='# ATX CODE END'):
""" Auto append code """
content = ''
found = False
for line in open(filename, 'rb'):
if not found and line.strip() == marker:
found = True
cnt = line.find(marker)
content += line[:cnt] + cod... | Auto append code |
def validate(identifier):
'''Validate a source given its identifier'''
source = actions.validate_source(identifier)
log.info('Source %s (%s) has been validated', source.slug, str(source.id)) | Validate a source given its identifier |
def get_repo(self, repo: str, branch: str, *,
depth: Optional[int]=1,
reference: Optional[Path]=None
) -> Repo:
""" Returns a :class:`Repo <git.repo.base.Repo>` instance for the branch.
See :meth:`run` for arguments descriptions.
"""
gi... | Returns a :class:`Repo <git.repo.base.Repo>` instance for the branch.
See :meth:`run` for arguments descriptions. |
def sleep(seconds=0):
"""Yield control to another eligible coroutine until at least *seconds* have
elapsed.
*seconds* may be specified as an integer, or a float if fractional seconds
are desired.
"""
loop = evergreen.current.loop
current = Fiber.current()
assert loop.task is not current... | Yield control to another eligible coroutine until at least *seconds* have
elapsed.
*seconds* may be specified as an integer, or a float if fractional seconds
are desired. |
def stopped(name=None,
containers=None,
shutdown_timeout=None,
unpause=False,
error_on_absent=True,
**kwargs):
'''
Ensure that a container (or containers) is stopped
name
Name or ID of the container
containers
Run this state o... | Ensure that a container (or containers) is stopped
name
Name or ID of the container
containers
Run this state on more than one container at a time. The following two
examples accomplish the same thing:
.. code-block:: yaml
stopped_containers:
docker_... |
def from_start_and_end(cls, start, end, sequence, phos_3_prime=False):
"""Creates a DNA duplex from a start and end point.
Parameters
----------
start: [float, float, float]
Start of the build axis.
end: [float, float, float]
End o... | Creates a DNA duplex from a start and end point.
Parameters
----------
start: [float, float, float]
Start of the build axis.
end: [float, float, float]
End of build axis.
sequence: str
Nucleotide sequence.
... |
def deserialize(self, buffer=bytes(), index=Index(), **options):
""" De-serializes the `Field` from the byte *buffer* starting at
the begin of the *buffer* or with the given *index* by unpacking the
bytes to the :attr:`value` of the `Field` in accordance with the
decoding *byte order* fo... | De-serializes the `Field` from the byte *buffer* starting at
the begin of the *buffer* or with the given *index* by unpacking the
bytes to the :attr:`value` of the `Field` in accordance with the
decoding *byte order* for the de-serialization and the decoding
:attr:`byte_order` of the `Fi... |
def get_encoded_word(value):
""" encoded-word = "=?" charset "?" encoding "?" encoded-text "?="
"""
ew = EncodedWord()
if not value.startswith('=?'):
raise errors.HeaderParseError(
"expected encoded word but found {}".format(value))
_3to2list1 = list(value[2:].split('?=', 1))
... | encoded-word = "=?" charset "?" encoding "?" encoded-text "?=" |
def _find_errors_param(self):
"""
Searches for the parameter on the estimator that contains the array of
errors that was used to determine the optimal alpha. If it cannot find
the parameter then a YellowbrickValueError is raised.
"""
# NOTE: The order of the search is ve... | Searches for the parameter on the estimator that contains the array of
errors that was used to determine the optimal alpha. If it cannot find
the parameter then a YellowbrickValueError is raised. |
def filter_on_wire_representation(ava, acs, required=None, optional=None):
"""
:param ava: A dictionary with attributes and values
:param acs: List of tuples (Attribute Converter name,
Attribute Converter instance)
:param required: A list of saml.Attributes
:param optional: A list of saml.At... | :param ava: A dictionary with attributes and values
:param acs: List of tuples (Attribute Converter name,
Attribute Converter instance)
:param required: A list of saml.Attributes
:param optional: A list of saml.Attributes
:return: Dictionary of expected/wanted attributes and values |
def load_backend(build_configuration, backend_package):
"""Installs the given backend package into the build configuration.
:param build_configuration the :class:``pants.build_graph.build_configuration.BuildConfiguration`` to
install the backend plugin into.
:param string backend_package: the package name co... | Installs the given backend package into the build configuration.
:param build_configuration the :class:``pants.build_graph.build_configuration.BuildConfiguration`` to
install the backend plugin into.
:param string backend_package: the package name containing the backend plugin register module that
provides... |
def _new_convolution(self, use_bias):
"""Returns new convolution.
Args:
use_bias: Use bias in convolutions. If False, clean_dict removes bias
entries from initializers, partitioners and regularizers passed to
the constructor of the convolution.
"""
def clean_dict(input_dict):
... | Returns new convolution.
Args:
use_bias: Use bias in convolutions. If False, clean_dict removes bias
entries from initializers, partitioners and regularizers passed to
the constructor of the convolution. |
def _generate_union_tag_vars_funcs(self, union):
"""Emits the getter methods for retrieving tag-specific state. Setters throw
an error in the event an associated tag state variable is accessed without
the correct tag state."""
for field in union.all_fields:
if not is_void_typ... | Emits the getter methods for retrieving tag-specific state. Setters throw
an error in the event an associated tag state variable is accessed without
the correct tag state. |
def get_url(request, application, roles, label=None):
""" Retrieve a link that will work for the current user. """
args = []
if label is not None:
args.append(label)
# don't use secret_token unless we have to
if 'is_admin' in roles:
# Administrators can access anything without secre... | Retrieve a link that will work for the current user. |
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