text stringlengths 89 104k | code_tokens list | avg_line_len float64 7.91 980 | score float64 0 630 |
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def create_api(app_id=None, login=None, password=None, phone_number=None,
scope='offline', api_version='5.92', http_params=None,
interactive=False, service_token=None, client_secret=None,
two_fa_supported=False, two_fa_force_sms=False):
"""Factory method to explicitly cr... | [
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def clear_distribute_compositions(self):
"""Removes the distribution rights.
raise: NoAccess - ``Metadata.isRequired()`` is ``true`` or
``Metadata.isReadOnly()`` is ``true``
*compliance: mandatory -- This method must be implemented.*
"""
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def _dt_array_cmp(cls, op):
"""
Wrap comparison operations to convert datetime-like to datetime64
"""
opname = '__{name}__'.format(name=op.__name__)
nat_result = opname == '__ne__'
def wrapper(self, other):
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def fullPath(self):
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def _key_parenleft(self, text):
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def wnfetd(window, n):
"""
Fetch a particular interval from a double precision window.
http://naif.jpl.nasa.gov/pub/naif/toolkit_docs/C/cspice/wnfetd_c.html
:param window: Input window
:type window: spiceypy.utils.support_types.SpiceCell
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def _findRedundantProteins(protToPeps, pepToProts, proteins=None):
"""Returns a set of proteins with redundant peptide evidence.
After removing the redundant proteins from the "protToPeps" and "pepToProts"
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def get_port_profile_for_intf_output_interface_port_profile_name(self, **kwargs):
"""Auto Generated Code
"""
config = ET.Element("config")
get_port_profile_for_intf = ET.Element("get_port_profile_for_intf")
config = get_port_profile_for_intf
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def make_2D_samples_gauss(n, m, sigma, random_state=None):
"""return n samples drawn from 2D gaussian N(m,sigma)
Parameters
----------
n : int
number of samples to make
m : np.array (2,)
mean value of the gaussian distribution
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def lookup_sig(cls, sigs, method_name, expr_args, stmt_or_expr, context):
"""
Using a list of args, determine the most accurate signature to use from
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def file_format(self):
"""Formats device filesystem"""
log.info('Formating, can take minutes depending on flash size...')
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def setQuery(self, query):
"""
Sets the query information for this filter widget.
:param query | <orb.Query> || None
"""
if query is None:
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def get_slide_seg_list_belonged(dt_str, seg_duration, slide_step=1,
fmt='%Y-%m-%d %H:%M:%S'):
"""
获取该时刻所属的所有时间片列表
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def publish(ctx, test=False):
"""Publish to the cheeseshop."""
clean(ctx)
if test:
run('python setup.py register -r test sdist bdist_wheel', echo=True)
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def add_value_event(self, event_value, func, event_type=None, parameters=None, **kwargs):
"""
Add a function that is called when the value reach or pass the event_value.
:param event_value:
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def _parse(self):
"""! @brief SWO parser as generator function coroutine.
The generator yields every time it needs a byte of SWO data. The caller must use the
generator's send() method to provide the next byte.
"""
timestamp = 0
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def askForPreviousFutures(self):
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def renames(self, new):
""" .. seealso:: :func:`os.renames` """
os.renames(self, new)
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Enable or disable prompt
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def build_precache_map(config):
"""
Build a mapping of contexts and models from the configuration
"""
precache_map = {}
ss_name = config['ores']['scoring_system']
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def Baroczy(x, rhol, rhog, mul, mug):
r'''Calculates void fraction in two-phase flow according to the model of
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.. math::
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def deprecated_opts_signature(args, kwargs):
"""
Utility to help with the deprecation of the old .opts method signature
Returns whether opts.apply_groups should be used (as a bool) and the
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"""
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groups = set(Options._option_groups)
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def _set_esp_key(self, v, load=False):
"""
Setter method for esp_key, mapped from YANG variable /routing_system/interface/ve/ipv6/interface_ospfv3_conf/authentication/ipsec_auth_key_config/esp_key (ipsec-authentication-hexkey-string)
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def get_pending_boot_mode(self):
"""Retrieves the pending boot mode of the server.
Gets the boot mode to be set on next reset.
:returns: either LEGACY or UEFI.
:raises: IloError, on an error from iLO.
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def exists(self, obj_id, obj_type=None):
"""
Return whether the given object exists in the search index.
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def validate_username(self, value):
"""
Verify that the username has a matching user.
"""
try:
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def build_ref_list(refs):
"""
Given parsed references build a list of ref objects
"""
ref_list = []
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# Publcation Type
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def hit(self, code, line, duration):
"""
A line has finished executing.
code (code)
container function's code object
line (int)
line number of just executed line
duration (float)
duration of the line, in seconds
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def endpoint(f):
"""This decorator marks this method as an endpoint. It is responsible for
the request workflow and will call each relevant method in turn."""
def check_authentication(self, **kwargs):
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def add_to_configs(self, configs):
"""Add configurations to all tomodirs
Parameters
----------
configs : :class:`numpy.ndarray`
Nx4 numpy array with abmn configurations
"""
for f, td in self.tds.items():
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def find(self, key):
"Exact matching (returns value)"
index = self.follow_bytes(key, self.ROOT)
if index is None:
return -1
if not self.has_value(index):
return -1
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def triangle_normal(a, b, c):
"""Return a vector orthogonal to the given triangle
Arguments:
a, b, c -- three 3D numpy vectors
"""
normal = np.cross(a - c, b - c)
norm = np.linalg.norm(normal)
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def generate_molecule_object_dict(source, format, values):
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def netconf_config_change_changed_by_server_or_user_by_user_session_id(self, **kwargs):
"""Auto Generated Code
"""
config = ET.Element("config")
netconf_config_change = ET.SubElement(config, "netconf-config-change", xmlns="urn:ietf:params:xml:ns:yang:ietf-netconf-notifications")
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def delete_exchange(self, vhost, name):
"""
Delete the named exchange from the named vhost. The API returns a 204
on success, in which case this method returns True, otherwise the
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def unperturbed_hamiltonian(states):
r"""Return the unperturbed atomic hamiltonian for given states.
We calcualte the atomic hamiltonian in the basis of the ground states of \
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>>> g = State("Rb", 87, 5, 0, 1/Integer(2))
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def is_data_from_channel(channel=4): # function factory
'''Selecting FE data from given channel.
Parameters
----------
channel : int
Channel number (4 is default channel on Single Chip Card).
Returns
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def _scope_and_enforce_robots(self, site, parent_page, outlinks):
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Returns tuple (
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def _postprocess(self, x, out=None):
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C2C: use ``tmp_f`` (C2C operation)
R2C: use ``tmp_f`` (C2C operation)
HALFC: use ``tmp_f`` (C2C operation)
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def _set_link_oam_interface(self, v, load=False):
"""
Setter method for link_oam_interface, mapped from YANG variable /interface/ethernet/link_oam_interface (container)
If this variable is read-only (config: false) in the
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def run_remove_system(name, token, org, system, prompt):
"""
Removes a system from the repo.
"""
repo = get_repo(token=token, org=org, name=name)
try:
label = repo.get_label(name=system.strip())
label.delete()
click.secho("Successfully deleted {}".format(system), fg="green")
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def update_notification_list(self, apps=None, schema_editor=None, verbose=False):
"""Updates the notification model to ensure all registered
notifications classes are listed.
Typically called from a post_migrate signal.
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def to_dict(self, get_value=None):
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self.trim()
result = {}
for key, value in iteritems(self.counters):
if get_value is not None:
value = getattr(value, get_value)
r = result
for _key in key[:-1]:
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def title(content, new_line_replacement=' ', tab_replacement=' '):
"""
Underlines content with '='. New lines and tabs will be replaced
:param str content:
:param str new_line_replacement:
:param str tab_replacement:
:return: unicode
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def _topology_from_residue(res):
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Parameters
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res : openmm.app.Topology.Residue
An individual residue in an openmm.app.Topology
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-------
topology : openmm.app.Topology
The generated topology
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def set_title(self, title):
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Set terminal title.
"""
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self.write_raw('\x1b]2;%s\x07' % title.replace('\x1b', '').replace('\x07', '')) | [
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def c3(x, lag):
"""
This function calculates the value of
.. math::
\\frac{1}{n-2lag} \sum_{i=0}^{n-2lag} x_{i + 2 \cdot lag}^2 \cdot x_{i + lag} \cdot x_{i}
which is
.. math::
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def as_urlpatterns(self):
"""
Creates the appropriate URLs for this object.
"""
urls = []
# for each of our actions
for action in self.actions:
view_class = self.view_for_action(action)
view_pattern = self.pattern_for_view(view_class, action)
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def front(self, *fields):
'''Return the front pair of the structure'''
v, f = tuple(self.irange(0, 0, fields=fields))
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def get_plot(self_or_cls, obj, renderer=None, **kwargs):
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Given a HoloViews Viewable return a corresponding plot instance.
"""
if isinstance(obj, DynamicMap) and obj.unbounded:
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def currentItem( self ):
"""
Returns the current navigation item from the current path.
:return <XNavigationItem> || None
"""
model = self.navigationModel()
if ( not model ):
return None
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def _main(argv):
"""
Handle arguments for the 'lumi-upload' command.
"""
parser = argparse.ArgumentParser(
description=DESCRIPTION,
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser.add_argument(
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def as_ipywidget(self):
""" Provides an IPywidgets player that can be used in a notebook. """
from IPython.display import Audio
return Audio(data=self.y, rate=self.sr) | [
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def on_trial_complete(self,
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def _judeNOtIn(self, raw_str, ele_list):
'''
判断ele是否在原始字符串中
args：
raw_str 源字符串
ele_list 待检查的列表
return
boolean
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def draw_graph(self):
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The central logic for drawing the graph.
Sets self.graph (the 'g' element in the SVG root)
"""
transform = 'translate (%s %s)' % (self.border_left, self.border_top)
self.graph = etree.SubElement(self.root, 'g', transform=transform)
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def count(args):
"""
%prog count *.gz
Count reads based on FASTQC results. FASTQC needs to be run on all the input
data given before running this command.
"""
from jcvi.utils.table import loadtable, write_csv
p = OptionParser(count.__doc__)
p.add_option("--dir",
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def get_ldap_user_membership(self, user_dn):
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membership_filter = self.conf_LDAP_SYNC_GROUP_MEMBERSHIP_FILTER.replace('{distinguishedName}', user_dn.replace('(', "\(").replace(')', "\)"))
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def from_table(cls, table, length, prefix=0, flatten=False):
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Extract from the given table a tree for word length, taking only
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def area(triangles=None, crosses=None, sum=False):
"""
Calculates the sum area of input triangles
Parameters
----------
triangles : (n, 3, 3) float
Vertices of triangles
crosses : (n, 3) float or None
As a speedup don't re- compute cross products
sum : bool
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def glm(data, xseq, **params):
"""
Fit GLM
"""
X = sm.add_constant(data['x'])
Xseq = sm.add_constant(xseq)
init_kwargs, fit_kwargs = separate_method_kwargs(
params['method_args'], sm.GLM, sm.GLM.fit)
model = sm.GLM(data['y'], X, **init_kwargs)
results = model.fit(**fit_kwargs)
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def permission_required(perm, login_url=None):
"""Replacement for django.contrib.auth.decorators.permission_required that
returns 403 Forbidden if the user is already logged in.
"""
return user_passes_test(lambda u: u.has_perm(perm), login_url=login_url) | [
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def _get_prtfmt(self, objgowr, verbose):
"""Get print format containing markers."""
prtfmt = objgowr.get_prtfmt('fmt')
prtfmt = prtfmt.replace('# ', '')
# print('PPPPPPPPPPP', prtfmt)
if not verbose:
prtfmt = prtfmt.replace('{hdr1usr01:2}', '')
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def write_ioc(root, output_dir=None, force=False):
"""
Serialize an IOC, as defined by a set of etree Elements, to a .IOC file.
:param root: etree Element to write out. Should have the tag 'OpenIOC'
:param output_dir: Directory to write the ioc out to. default is current working directory.
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def uploadFiles(self):
"""
Uploads all the files in 'filesToSync'
"""
for each_file in self.filesToSync:
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def get_im(self, force_update=False):
"""Get the influence map for the model, generating it if necessary.
Parameters
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def messages(self):
'''A generator yielding the :class:`MacIndexMessage`
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def boost(self, boost):
"""Sets boost mode."""
_LOGGER.debug("Setting boost mode: %s", boost)
value = struct.pack('BB', PROP_BOOST, bool(boost))
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def get_conn(self, urlparsed=None):
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def construct_parameter_validators(parameter, context):
"""
Constructs a dictionary of validator functions for the provided parameter
definition.
"""
validators = ValidationDict()
if '$ref' in parameter:
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def head_tail_middle(src):
"""Returns a tuple consisting of the head of a enumerable, the middle
as a list and the tail of the enumerable. If the enumerable is 1 item, the
middle will be empty and the tail will be None.
>>> head_tail_middle([1, 2, 3, 4])
1, [2, 3], 4
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def formatted_prefix(self, **format_info):
"""
Gets a dict with format info, and formats a prefix template with that info. For example:
if our prefix template is:
'some_file_{groups[0]}_{file_number}'
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def fire_event(key, msg, tag, sock_dir, args=None, transport='zeromq'):
'''
Fire deploy action
'''
event = salt.utils.event.get_event(
'master',
sock_dir,
transport,
listen=False)
try:
event.fire_event(msg, tag)
except ValueError:
# We're using at... | [
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def build_request(self):
"""Build a prepared request object."""
clientheaders = {}
if (self.parent_url and
self.parent_url.lower().startswith(HTTP_SCHEMAS)):
clientheaders["Referer"] = self.parent_url
kwargs = dict(
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url=self.u... | [
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def __extract_modules(self, loader, name, is_pkg):
""" if module found load module and save all attributes in the module found """
mod = loader.find_module(name).load_module(name)
""" find the attribute method on each module """
if hasattr(mod, '__method__'):
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def gauss_fit(map_data, chs=None, mode='deg', amplitude=1, x_mean=0, y_mean=0, x_stddev=None, y_stddev=None, theta=None, cov_matrix=None, noise=0, **kwargs):
"""make a 2D Gaussian model and fit the observed data with the model.
Args:
map_data (xarray.Dataarray): Dataarray of cube or single chs.
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def cli(ctx, common_name, directory, blatdb="", genus="", species="", public=False):
"""Add an organism
Output:
a dictionary with information about the new organism
"""
return ctx.gi.organisms.add_organism(common_name, directory, blatdb=blatdb, genus=genus, species=species, public=public) | [
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def getconnections(self, vhost = None):
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if vhost is None:
return list(self.managed_connections)
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def popupWidget(self):
"""
Returns the popup widget for this editor.
:return <skyline.gui.XPopupWidget>
"""
if not self._popup:
btns = QDialogButtonBox.Save | QDialogButtonBox.Cancel
self._popup = XPopupWidget(self, btns)
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def qwarp_align(dset_from,dset_to,skull_strip=True,mask=None,affine_suffix='_aff',suffix='_qwarp',prefix=None):
'''aligns ``dset_from`` to ``dset_to`` using 3dQwarp
Will run ``3dSkullStrip`` (unless ``skull_strip`` is ``False``), ``3dUnifize``,
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def _build_body_schema(serializer, body_parameters):
""" body is built differently, since it's a single argument no matter what. """
description = ""
if isinstance(body_parameters, Param):
schema = serializer.to_json_schema(body_parameters.arginfo.type)
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def synchronous(function, event):
"""
Runs the function synchronously taking care of exceptions.
"""
try:
function(event)
except Exception as error:
logger = get_function_logger(function)
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def hqwe(zsrc, zrec, lsrc, lrec, off, factAng, depth, ab, etaH, etaV, zetaH,
zetaV, xdirect, qweargs, use_ne_eval, msrc, mrec):
r"""Hankel Transform using Quadrature-With-Extrapolation.
*Quadrature-With-Extrapolation* was introduced to geophysics by
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def available(self, src, dst, model):
"""
Iterate over all registered plugins or plugin points and prepare to add
them to database.
"""
for name, point in six.iteritems(src):
inst = dst.pop(name, None)
if inst is None:
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def get_containers_by_name(self, name):
"""
get all task which relative with task name
:param name: :class:`str`, task name
:return: :class:`list`, container list
"""
code, containers = self.get_containers()
if code != httplib.OK:
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def get_object_header(self, ref):
""" Use this method to quickly examine the type and size of the object behind
the given ref.
:note: The method will only suffer from the costs of command invocation
once and reuses the command in subsequent calls.
:return: (hexsha, type_string, size_as_int)"""
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def com_google_fonts_check_name_familyname(ttFont, style, familyname_with_spaces):
""" Check name table: FONT_FAMILY_NAME entries. """
from fontbakery.utils import name_entry_id
failed = False
only_weight = get_only_weight(style)
for name in ttFont['name'].names:
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def fishqq(lon=None, lat=None, di_block=None):
"""
Test whether a distribution is Fisherian and make a corresponding Q-Q plot.
The Q-Q plot shows the data plotted against the value expected from a
Fisher distribution. The first plot is the uniform plot which is the
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def transform(self, photo, **kwds):
"""
Endpoint: /photo/<id>/transform.json
Performs the specified transformations.
eg. transform(photo, rotate=90)
Returns the transformed photo.
"""
result = self._client.post("/photo/%s/transform.json" %
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async def fastStreamedQuery(self, url, *, headers=None, verify=True):
""" Send a GET request with short timeout, do not retry, and return streamed response. """
response = await self.session.get(url,
headers=self._buildHeaders(headers),
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def query(self, sql=None, filename=None, **kwargs):
""" run raw sql from sql or file against.
:param sql: Raw SQL query to pass directly to the connection.
:type sql: string
:param filename: Path to a file containing a SQL query. The path should be relative to CWD.
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def overlay_gateway_monitor_remote_endpoint(self, **kwargs):
"""Auto Generated Code
"""
config = ET.Element("config")
overlay_gateway = ET.SubElement(config, "overlay-gateway", xmlns="urn:brocade.com:mgmt:brocade-tunnels")
name_key = ET.SubElement(overlay_gateway, "name")
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def reopen(self, file_obj):
"""Reopen the file-like object in a safe manner."""
file_obj.open('U')
if sys.version_info[0] <= 2:
return file_obj
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def alias_field(model, field):
"""
Return the prefix name of a field
"""
for part in field.split(LOOKUP_SEP)[:-1]:
model = associate_model(model,part)
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def glibc_version_string():
"Returns glibc version string, or None if not using glibc."
# ctypes.CDLL(None) internally calls dlopen(NULL), and as the dlopen
# manpage says, "If filename is NULL, then the returned handle is for the
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def mismatches(args):
"""
%prog mismatches blastfile
Print out histogram of mismatches of HSPs, usually for evaluating SNP level.
"""
from jcvi.utils.cbook import percentage
from jcvi.graphics.histogram import stem_leaf_plot
p = OptionParser(mismatches.__doc__)
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def get_bibtex_string(self):
"""
Get BibTeX reference from CIF file.
:param data:
:return: BibTeX string
"""
bibtex_keys = {'author': ('_publ_author_name', '_citation_author_name'),
'title': ('_publ_section_title', '_citation_title'),
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def set(self, item_name, item_value):
"""
Sets the value of an option in the configuration.
:param str item_name: The name of the option to set.
:param item_value: The value of the option to set.
"""
if self.prefix:
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