text stringlengths 89 104k | code_tokens list | avg_line_len float64 7.91 980 | score float64 0 630 |
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def floats(s):
"""Convert string to float. Handles more string formats that the standard python conversion."""
try:
return float(s)
except ValueError:
s = re.sub(r'(\d)\s*\(\d+(\.\d+)?\)', r'\1', s) # Remove bracketed numbers from end
s = re.sub(r'(\d)\s*±\s*\d+(\.\d+)?', r'\1... | [
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def support_support_param_username(self, **kwargs):
"""Auto Generated Code
"""
config = ET.Element("config")
support = ET.SubElement(config, "support", xmlns="urn:brocade.com:mgmt:brocade-ras")
support_param = ET.SubElement(support, "support-param")
username = ET.SubEleme... | [
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def reset_parameters(self, init_weight):
"""
Sets initial random values for trainable parameters.
"""
stdv = 1. / math.sqrt(self.num_units)
self.linear_att.data.uniform_(-init_weight, init_weight)
if self.normalize:
self.normalize_scalar.data.fill_(stdv)
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def get_SAM(self,min_intron_size=68):
"""Get a SAM object representation of the alignment.
:returns: SAM representation
:rtype: SAM
"""
from seqtools.format.sam import SAM
#ar is target then query
qname = self.alignment_ranges[0][1].chr
flag = 0
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def _process_queue_tasks(self, queue, queue_lock, task_ids, now, log):
"""Process tasks in queue."""
processed_count = 0
# Get all tasks
serialized_tasks = self.connection.mget([
self._key('task', task_id) for task_id in task_ids
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# Parse tasks
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def do_intersect(bb1, bb2):
"""
Helper function that returns True if two bounding boxes overlap.
"""
if bb1[0] + bb1[2] < bb2[0] or bb2[0] + bb2[2] < bb1[0]:
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def pre_render(self):
"""Last things to do before rendering"""
self.add_styles()
self.add_scripts()
self.root.set(
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def volumes_maximum_size_bytes(self):
"""Gets the biggest logical drive
:returns the size in MiB.
"""
return utils.max_safe([member.volumes.maximum_size_bytes
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def send_callback_json_message(value, *args, **kwargs):
"""
useful for sending messages from callbacks as it puts the
result of the callback in the dict for serialization
"""
if value:
kwargs['result'] = value
send_json_message(args[0], args[1], **kwargs)
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def wildcard_import_names(self):
"""The list of imported names when this module is 'wildcard imported'.
It doesn't include the '__builtins__' name which is added by the
current CPython implementation of wildcard imports.
:returns: The list of imported names.
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def _GetDecodedStreamSize(self):
"""Retrieves the decoded stream size.
Returns:
int: decoded stream size.
"""
self._file_object.seek(0, os.SEEK_SET)
self._decoder = self._GetDecoder()
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def write_file(self, target_path, html):
"""
Writes out the provided HTML to the provided path.
"""
logger.debug("Building to {}{}".format(self.fs_name, target_path))
with self.fs.open(smart_text(target_path), 'wb') as outfile:
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def set_nearest_border(self):
"""Snaps the port to the correct side upon state size change
"""
px, py = self._point
nw_x, nw_y, se_x, se_y = self.get_adjusted_border_positions()
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def _logpdf(self, **kwargs):
"""Returns the log of the pdf at the given values. The keyword
arguments must contain all of parameters in self's params. Unrecognized
arguments are ignored.
"""
if kwargs in self:
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def deserialize_duration(attr):
"""Deserialize ISO-8601 formatted string into TimeDelta object.
:param str attr: response string to be deserialized.
:rtype: TimeDelta
:raises: DeserializationError if string format invalid.
"""
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def _create_pattern_set(self, pattern, values):
"""Create a new pattern set."""
type_ = self._get_type(values)
version = self._get_version(values)
comment = values.get(COMMENT)
self._pattern_set = self._spec.new_pattern_set(
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def transform_properties(properties, schema):
"""Transform properties types according to a schema.
Parameters
----------
properties : dict
Properties to transform.
schema : dict
Fiona schema containing the types.
"""
new_properties = properties.copy()
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def list_passwords(kwargs=None, call=None):
'''
List all password on the account
.. versionadded:: 2015.8.0
'''
response = _query('support', 'password/list')
ret = {}
for item in response['list']:
if 'server' in item:
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def HA2(credentials, request, algorithm):
"""Create HA2 md5 hash
If the qop directive's value is "auth" or is unspecified, then HA2:
HA2 = md5(A2) = MD5(method:digestURI)
If the qop directive's value is "auth-int" , then HA2 is
HA2 = md5(A2) = MD5(method:digestURI:MD5(entityBody))
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def check_auth(self):
"""Check authentication/authorization of client"""
# access permissions
if self.auth is not None:
return self.auth(self.request)
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def get_digests(self):
'''return a list of layers from a manifest.
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def render_template_with_args_in_file(file, template_file_name, **kwargs):
"""
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def first(pipe, items=1):
''' first is essentially the next() function except it's second argument
determines how many of the first items you want. If items is more than
1 the output is an islice of the generator. If items is 1, the first
item is returned
'''
pipe = iter(pipe)
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def connect(*, dsn, autocommit=False, ansi=False, timeout=0, loop=None,
executor=None, echo=False, after_created=None, **kwargs):
"""Accepts an ODBC connection string and returns a new Connection object.
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def u16le_list_to_byte_list(data):
"""! @brief Convert a halfword array into a byte array"""
byteData = []
for h in data:
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def next(self, acceleration=0.0):
"""Continue rotation in direction of last drag."""
q = quaternion_slerp(self._qpre, self._qnow, 2.0 + acceleration, False)
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def create(self):
"""
Creates the node.
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def upscale(file_name, scale=1.5, margin_x=0, margin_y=0, suffix='scaled', tempdir=None):
"""Upscale a PDF to a large size."""
# Set output file name
if tempdir:
output = NamedTemporaryFile(suffix='.pdf', dir=tempdir, delete=False).name
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def copy_file(stream, target, maxread=-1, buffer_size=2*16):
''' Read from :stream and write to :target until :maxread or EOF. '''
size, read = 0, stream.read
while 1:
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def propertySearch(self, pid, getall=0):
"""
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def generate_nonce_timestamp():
""" Generate unique nonce with counter, uuid and rng."""
global count
rng = botan.rng().get(30)
uuid4 = uuid.uuid4().bytes # 16 byte
tmpnonce = (bytes(str(count).encode('utf-8'))) + uuid4 + rng
nonce = tmpnonce[:41] # 41 byte (328 bit)
count += 1
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def _update_record(self, identifier, rtype=None, name=None, content=None):
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def create_config_file(filename):
"""
Create main configuration file if it doesn't exist.
"""
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def association_pivot(self, association_resource):
"""Pivot point on association for this resource.
This method will return all *resources* (group, indicators, task, victims, etc) for this
resource that are associated with the provided resource.
**Example Endpoints URI's**
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def _retrieve_page(self, page_index):
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def constant(interval=1):
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def get_missing_params_message(self, parameter_state):
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Get a user-friendly message indicating a missing parameter for the API endpoint.
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def create(self, using=None, **kwargs):
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def request(req=None, method=None, requires_response=True):
"""Call function req and then emit its results to the LSP server."""
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def _populate_cmd_lists(self):
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def get_shutit_pexpect_session_from_child(self, shutit_pexpect_child):
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"""
shutit_global.shutit_global_object.yield_to_draw()
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def check_submission_successful(self, submission_id=None):
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def parse_end_date(self, request, start_date):
"""
Return period in days after the start date to show event occurrences,
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def main():
"""
upload a package to pypi or gemfury
:return:
"""
setup_main()
config = ConfigData(clean=True)
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config.upload()
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Pastes text from the clipboard.
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def get_git_remote_url(path='.', remote='origin'):
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def cli(verbose):
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Floyd CLI interacts with FloydHub server and executes your commands.
More help is available under each command listed below.
"""
floyd.floyd_host = floyd.floyd_web_host = "https://dev.floydhub.com"
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Read header info of the windaq file
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def _get_major_minor_revision(self, version_string):
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This is complicated by the fact that a version string can be
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def estimate_hmm(observations, nstates, lag=1, initial_model=None, output=None,
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mincount_connectivity=1e-2):
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def make_python_patterns(additional_keywords=[], additional_builtins=[]):
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kw = r"\b" + any("keyword", kwlist + additional_keywords) + r"\b"
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self.perform_bulk_pubmed_query()
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def imshow(self, key):
"""Show item's image"""
data = self.model.get_data()
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plt.imshow(data[key])
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def add(self, isoel, col1, col2, channel_width,
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Each list item resembles one isoelastic line stored
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def request(self, url, method = u"get", data = None, headers = None, **kwargs):
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public method for doing the live request
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def _authorization_headers_valid(self, token_type, token):
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Type of token to access resources.
token (str)
Server Token or OAuth 2.0 Access Token.
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def order_verification(self, institute, case, user, link, variant):
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def dump(self, itemkey, filename=None, path=None):
"""
Dump a file attachment to disk, with optional filename and path
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def is_compatible(self, obj):
"""Check if characters can be combined into a textline
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def env():
"""Verify PCI variables and construct exported variables"""
if cij.ssh.env():
cij.err("cij.pci.env: invalid SSH environment")
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pci = cij.env_to_dict(PREFIX, REQUIRED)
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def create_node(self, config_file=None, seed=None, tags=None):
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Parameters
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config_file : pycbc.workflow.core.File
A ``pycbc.workflow.core.File`` for inference configuration file
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def fasta_files_equal(seq_file1, seq_file2):
"""Check equality of a FASTA file to another FASTA file
Args:
seq_file1: Path to a FASTA file
seq_file2: Path to another FASTA file
Returns:
bool: If the sequences are the same
"""
# Load already set representative sequence
... | [
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def get_temp_filename(suffix=None):
""" return a string in the form of temp_X, where X is a large integer """
file = tempfile.mkstemp(suffix=suffix or "", prefix="temp_", dir=os.getcwd()) # or "" for Python 2 compatibility
os.close(file[0])
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def openssh_tunnel(lport, rport, server, remoteip='127.0.0.1', keyfile=None, password=None, timeout=60):
"""Create an ssh tunnel using command-line ssh that connects port lport
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def pre_fork(self, process_manager):
'''
Pre-fork we need to create the zmq router device
'''
salt.transport.mixins.auth.AESReqServerMixin.pre_fork(self, process_manager)
if USE_LOAD_BALANCER:
self.socket_queue = multiprocessing.Queue()
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def gen_filter(name, op, value, is_or=False):
"""Generates a single filter expression for ``filter[]``."""
if op not in OPERATORS:
raise ValueError('Unknown operator {}'.format(op))
result = u'{} {} {}'.format(name, op, escape_filter(value))
if is_or:
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def get_entity_from_dimensions(dimensions, text):
"""
Infer the underlying entity of a unit (e.g. "volume" for "m^3").
Just based on the unit's dimensionality if the classifier is disabled.
"""
new_dimensions = [{'base': l.NAMES[i['base']].entity.name,
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def from_dict(data, ctx):
"""
Instantiate a new AccountSummary from a dict (generally from loading a
JSON response). The data used to instantiate the AccountSummary is a
shallow copy of the dict passed in, with any complex child types
instantiated appropriately.
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def overlap(self, other):
"""
Returns True if both ranges share any points.
>>> intrange(1, 10).overlap(intrange(5, 15))
True
>>> intrange(1, 5).overlap(intrange(5, 10))
False
This is the same as the ``&&`` operator for two ranges in PostgreSQL.
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def maybe_base_expanded_node_name(self, node_name):
"""Expand the base name if there are node names nested under the node.
For example, if there are two nodes in the graph, "a" and "a/read", then
calling this function on "a" will give "a/(a)", a form that points at
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def _get_groups(self):
"""
Returns an _LDAPUserGroups object, which can determine group
membership.
"""
if self._groups is None:
self._groups = _LDAPUserGroups(self)
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def register_warning_code(code, exception_type, domain='core'):
"""Register a new warning code"""
Logger._warning_code_to_exception[code] = (exception_type, domain)
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def filedet(name, fobj=None, suffix=None):
"""
Detect file type by filename.
:param name: file name
:param fobj: file object
:param suffix: file suffix like ``py``, ``.py``
:return: file type full name, such as ``python``, ``bash``
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name = name or (fobj and fobj.name) or suffix
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def basis_comparison_report(bs1, bs2, uncontract_general=False):
'''
Compares two basis set dictionaries and prints a report about their differences
'''
all_bs1 = list(bs1['elements'].keys())
if uncontract_general:
bs1 = manip.uncontract_general(bs1)
bs2 = manip.uncontract_general(... | [
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def convert_to_cluster_template(self, plugin_name, hadoop_version,
template_name, filecontent):
"""Convert to cluster template
Create Cluster Template directly, avoiding Cluster Template
mechanism.
"""
resp = self.api.post('/plugins/%s/%s/conv... | [
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def is_empty(self):
"""
Test interval emptiness.
:return: True if interval is empty, False otherwise.
"""
return (
self._lower > self._upper or
(self._lower == self._upper and (self._left == OPEN or self._right == OPEN))
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def json(self, **kwargs):
"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
"""
if not self.encoding and len(self.content) > 3:
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def get_type_name(self):
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Returns the type name of the PKCS7 structure
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"""
nid = _lib.OBJ_obj2nid(self._pkcs7.type)
string_type = _lib.OBJ_nid2sn(nid)
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def add_file(self, path, parent=None, tree=TreeType.SOURCE_ROOT, target_name=None, force=True, file_options=FileOptions()):
"""
Adds a file to the project, taking care of the type of the file and creating additional structures depending on
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def ToDeltas(self):
"""Convert the sequence to the sequence of differences between points.
The value of each point v[i] is replaced by v[i+1] - v[i], except for the
last point which is dropped.
"""
if len(self.data) < 2:
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def _offset(value):
"""Parse timezone to offset in seconds.
Args:
value: A timezone in the '+0000' format. An integer would also work.
Returns:
The timezone offset from GMT in seconds as an integer.
"""
o = int(value)
if o == 0:
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def value_loss_given_predictions(value_prediction,
rewards,
reward_mask,
gamma=0.99):
"""Computes the value loss given the prediction of the value function.
Args:
value_prediction: np.ndarray of shape (B, T+1, 1)... | [
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def update(self):
"""
Update this `~photutils.isophote.EllipseSample` instance.
This method calls the
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the values that match the current ``geometry`` attribute, and
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def map_azure_exceptions(key=None, exc_pass=()):
"""Map Azure-specific exceptions to the simplekv-API."""
from azure.common import AzureMissingResourceHttpError, AzureHttpError,\
AzureException
try:
yield
except AzureMissingResourceHttpError as ex:
if ex.__class__.__name__ not in... | [
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def get_otp(hsm, args):
""" Get OTP from YubiKey. """
if args.no_otp:
return None
if hsm.version.have_unlock():
if args.stdin:
otp = sys.stdin.readline()
while otp and otp[-1] == '\n':
otp = otp[:-1]
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otp = raw_input('Enter adm... | [
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def netloc(self):
"""Network location including host and port"""
if self.port:
return '%s:%d' % (self.host, self.port)
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def create_default_file(cls, data=None, mode=None):
"""Create a config file and override data if specified."""
filepath = cls.get_default_filepath()
if not filepath:
return False
filename = os.path.basename(filepath)
config = read_file(get_data_path(), filename)
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def iconcat(a, b):
"Same as a += b, for a and b sequences."
if not hasattr(a, '__getitem__'):
msg = "'%s' object can't be concatenated" % type(a).__name__
raise TypeError(msg)
a += b
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def _fix_reindent(self, result):
"""Fix a badly indented line.
This is done by adding or removing from its initial indent only.
"""
num_indent_spaces = int(result['info'].split()[1])
line_index = result['line'] - 1
target = self.source[line_index]
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def save_task_info(self, res, mem_gb=0):
"""
:param self: an object with attributes .hdf5, .argnames, .sent
:parent res: a :class:`Result` object
:param mem_gb: memory consumption at the saving time (optional)
"""
mon = res.mon
name = mon.operation[6:] # strip 'total '
if self.hdf5:
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def get_choices(self):
"""stub"""
# ideally would return a displayText object in text ... except for legacy
# use cases like OEA, it expects a text string.
choices = []
# for current_choice in self.my_osid_object.object_map['choices']:
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def _calculate_price_by_slippage(self, action: str, price: float) -> float:
"""
计算考虑滑点之后的价格
:param action: 交易动作， 支持 ['buy', 'sell']
:param price: 原始交易价格
:return: 考虑滑点后的交易价格
"""
if action == "buy":
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if action ==... | [
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def loggers(self):
"""Return all the loggers that should be activated"""
ret = []
if self.logger_name:
if isinstance(self.logger_name, logging.Logger):
ret.append((self.logger_name.name, self.logger_name))
else:
ret.append((self.logger_name... | [
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def iscm_md_update_dict(self, keypath, data):
"""
Update a metadata dictionary entry
"""
current = self.metadata
for k in string.split(keypath, "."):
if not current.has_key(k):
current[k] = {}
current = current[k]
current.update(dat... | [
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... | 31.3 | 5.1 |
def download(sid, credentials=None, subjects_path=None, overwrite=False, release='HCP_1200',
database='hcp-openaccess', file_list=None):
'''
download(sid) downloads the data for subject with the given subject id. By default, the subject
will be placed in the first HCP subject directory in the... | [
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... | 60.266667 | 30.233333 |
def prepare_notebook_context(request, notebook_context):
"""Fill in notebook context with default values."""
if not notebook_context:
notebook_context = {}
# Override notebook Jinja templates
if "extra_template_paths" not in notebook_context:
notebook_context["extra_template_paths"] = ... | [
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... | 46.804878 | 34.341463 |
def git_checkout(git_branch=None, locale_root=None):
"""
Checkouts branch to last commit
:param git_branch: branch to checkout
:param locale_root: locale folder path
:return: tuple stdout, stderr of completed command
"""
if git_branch is None:
git_branch = settings.GIT_BRANCH
if ... | [
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def neurite_root_section_ids(self):
'''Get the section IDs of the intitial neurite sections'''
sec = self.sections
return [i for i, ss in enumerate(sec)
if ss.pid > -1 and (sec[ss.pid].ntype == POINT_TYPE.SOMA and
ss.ntype != POINT_TYPE.SOMA)] | [
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"."... | 52.333333 | 18.333333 |
def recalculate_checksums(self, flags=0):
"""
(Re)calculates the checksum for any IPv4/ICMP/ICMPv6/TCP/UDP checksum present in the given packet.
Individual checksum calculations may be disabled via the appropriate flag.
Typically this function should be invoked on a modified packet befor... | [
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")... | 51.785714 | 28.357143 |
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