text stringlengths 89 104k | code_tokens list | avg_line_len float64 7.91 980 | score float64 0 630 |
|---|---|---|---|
def surface_ras_shift(self):
"""Freesurfer uses two coordinate systems: one for volumes ("RAS") and
one for surfaces ("tkReg", "tkRAS", and "Surface RAS").
To get from surface to volume coordinates, add this numbers.
To get from volume to surface coordinates, substract this numbers.
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def AppendToFile(filename, contents, eol_style=EOL_STYLE_NATIVE, encoding=None, binary=False):
'''
Appends content to a local file.
:param unicode filename:
:param unicode contents:
:type eol_style: EOL_STYLE_XXX constant
:param eol_style:
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def to_dict(self):
"""
Convert this VirtualIP to a dict representation for passing
to the API.
"""
if self.id:
return {"id": self.id}
return {"type": self.type, "ipVersion": self.ip_version} | [
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async def on_raw_329(self, message):
""" Channel creation time. """
target, channel, timestamp = message.params
if not self.in_channel(channel):
return
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def auth_proxy(self, method):
"""Authentication proxy for API requests.
This is required because the API objects are naive of ``HelpScout``,
so they would otherwise be unauthenticated.
Args:
method (callable): A method call that should be authenticated. It
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def reset(self):
"""Reset the value to the default"""
if self.resetable:
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def middleware(self, *args, **kwargs):
"""
A decorator that can be used to implement a Middleware plugin to
all of the Blueprints that belongs to this specific Blueprint Group.
In case of nested Blueprint Groups, the same middleware is applied
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def store_file(self, filename, file_content, content_type):
"""
Store a small file in an Upload Area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:param str filename: The name the file will have in the Upload Area
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def delete_saml_provider(name, region=None, key=None, keyid=None, profile=None):
'''
Delete SAML provider
CLI Example:
.. code-block:: bash
salt myminion boto_iam.delete_saml_provider my_saml_provider_name
'''
conn = _get_conn(region=region, key=key, keyid=keyid, profile=profile)
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def list(gandi, state, id, limit, datacenter):
"""List virtual machines."""
options = {
'items_per_page': limit,
}
if state:
options['state'] = state
if datacenter:
options['datacenter_id'] = gandi.datacenter.usable_id(datacenter)
output_keys = ['hostname', 'state']
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def reduce_filename(f):
r'''
Expects something like /tmp/tmpAjry4Gdsbench/test.weights.e5.XXX.YYY.pb
Where XXX is a variation on the model size for example
And where YYY is a const related to the training dataset
'''
f = os.path.basename(f).split('.')
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def _processSegmentUpdates(self, activeColumns):
"""
Go through the list of accumulated segment updates and process them
as follows:
if the segment update is too old, remove the update
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def dict_of_sets_add(dictionary, key, value):
# type: (DictUpperBound, Any, Any) -> None
"""Add value to a set in a dictionary by key
Args:
dictionary (DictUpperBound): Dictionary to which to add values
key (Any): Key within dictionary
value (Any): Value to add to set in dictionary
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def _query_iterator(self, result, chunksize, columns, coerce_float=True,
parse_dates=None):
"""Return generator through chunked result set."""
while True:
data = result.fetchmany(chunksize)
if not data:
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def get_vlan_from_query_reply(self, reply, vsiid, mac):
"""Parse the query reply from VDP daemon to get the VLAN value. """
hints_ret, fail_reason = self.check_hints(reply)
if not hints_ret:
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def to_lal_type_str(pytype):
"""Convert the input python type to a LAL type string
Examples
--------
To convert a python type:
>>> from gwpy.utils.lal import to_lal_type_str
>>> to_lal_type_str(float)
'REAL8'
To convert a `numpy.dtype`:
>>> import numpy
>>> to_lal_type_str(nu... | [
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def irecarray_to_py(a):
"""Slow conversion of a recarray into a list of records with python types.
Get the field names from :attr:`a.dtype.names`.
:Returns: iterator so that one can handle big input arrays
"""
pytypes = [pyify(typestr) for name,typestr in a.dtype.descr]
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def set_params(self, params):
"""Sets multiple GO-PCA Server parameters using a dictionary.
Parameters
----------
params: dict
Dictionary containing the parameter values.
Returns
-------
None
"""
for k,v in params.iteritems():
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def _rightleft(self, direction):
"""Provides curses horizontal padding"""
if direction == "left" and self.padding != 0:
self.padding -= 1
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def find_revision_number(self, revision=None):
"""Find the local revision number of the given revision."""
# Make sure the local repository exists.
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def __annotate_sequence_with_quality(seq, q_line_parts):
"""Extract meta data from pre-tokenized maf q-line and populate sequence.
q -- quality information about an aligned base in a species. Two fields after
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def doFeedback(self, item_id, use_comment_template, buyer_id, comment, comment_type, op):
"""http://allegro.pl/webapi/documentation.php/show/id,42"""
return self.__ask__('doFeedback',
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def _construct_module(info, target):
"""Build a module from templates and user supplied information"""
for path in paths:
real_path = os.path.abspath(os.path.join(target, path.format(**info)))
log("Making directory '%s'" % real_path)
os.makedirs(real_path)
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def match_tweet(self, tweet, user_stream):
"""
Check if a tweet matches the defined criteria
:param tweet: The tweet in question
:type tweet: :class:`~responsebot.models.Tweet`
:return: True if matched, False otherwise
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def _get_alpha(self, C, vs30, pga_rock):
"""
Returns the alpha, the linearised functional relationship between the
site amplification and the PGA on rock. Equation 31.
"""
alpha = np.zeros(len(pga_rock))
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def google_maps_geoloc_link(data):
"""
Get a link to google maps pointing on this IP's geolocation.
Args:
data (str/tuple): IP address or (latitude, longitude).
Returns:
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def report_view(self, request, key, period):
"""
Processes the reporting action.
"""
if not self.has_change_permission(request, None):
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def score(self, query, normalized=True, synonimizer=None, return_suffix_scores=False):
"""
Matches the string against the GAST using
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def delete(self, path, data={}):
'''Perform DELETE Request'''
if len(data) != 0:
parameter_string = ''
for k,v in data.items():
parameter_string += '{}={}'.format(k,v)
parameter_string += '&'
path += '?' + parameter_string
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def _find_matcher(self, alias):
""" Finds a matcher based on the given alias or raises an error if no
matcher could be found.
"""
matcher = lookup(alias)
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def detect(self, G):
"""Detect a single core-periphery pair.
Parameters
----------
G : NetworkX graph object
Examples
--------
>>> import networkx as nx
>>> import cpalgorithm as cpa
>>> G = nx.karate_club_graph() # load the karate club network.
>>> lrc = cp.LowRankCore()
>>> lrc.detect(G)
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def makeLys(segID, N, CA, C, O, geo):
'''Creates a Lysine residue'''
##R-Group
CA_CB_length=geo.CA_CB_length
C_CA_CB_angle=geo.C_CA_CB_angle
N_C_CA_CB_diangle=geo.N_C_CA_CB_diangle
CB_CG_length=geo.CB_CG_length
CA_CB_CG_angle=geo.CA_CB_CG_angle
N_CA_CB_CG_diangle=geo.N_CA_CB_CG_diangle
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def move_item_into_viewport(self, item):
"""Causes the `item` to be moved into the viewport
The zoom factor and the position of the viewport are updated to move the `item` into the viewport. If `item`
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:param Sta... | [
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def create(self, name, serviceId, timezone, description, enabled):
"""
Create a connector for the organization in the Watson IoT Platform.
The connector must reference the target service that the Watson IoT Platform will store the IoT data in.
Parameters:
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def get_id(date=None, project: str = 'sip',
instance_id: int = None) -> str:
"""Get a SBI Identifier.
Args:
date (str or datetime.datetime, optional): UTC date of the SBI
project (str, optional ): Project Name
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def is_group_valid(self, groupID):
"""
Check if this group ID is valid.
"""
cur = self.conn.cursor()
cur.execute('SELECT * FROM groups WHERE id=? LIMIT 1', [groupID])
results = cur.fetchall()
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def clean_title(self, title):
"""Clean title with the use of og:site_name
in this case try to get rid of site name
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"""
# check if we have the site name in opengraph data
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def processWhileRunning(self):
"""
Run tasks until stopService is called.
"""
work = self.step()
for result, more in work:
yield result
if not self.running:
break
if more:
delay = 0.1
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def _get_aux_specs(self):
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# Drop the "core" specifications, which are handled separately.
specs = self._specs_in.copy()
[specs.pop(core) for core in self._CORE_SPEC_NAMES]
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def evaluate(ref_intervals_hier, ref_labels_hier,
est_intervals_hier, est_labels_hier, **kwargs):
'''Compute all hierarchical structure metrics for the given reference and
estimated annotations.
Examples
--------
A toy example with two two-layer annotations
>>> ref_i = [[[0, 30], ... | [
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def set_attrs(self, **attrs):
"""Set the given attributes on *all* commands in collection."""
commands = tuple(self.values())
for name, value in attrs.items():
for command in commands:
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def to_hex(x):
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Converts input to the hex string
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def write_collection_from_tmpfile(self, collection_id, tmpfi, parent_sha, auth_info, commit_msg=''):
"""Given a collection_id, temporary filename of content, branch and auth_info
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return self.write_doc_from_tmpfile(collection_id,
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def my_psd(x,NFFT=2**10,Fs=1):
"""
A local version of NumPy's PSD function that returns the plot arrays.
A mlab.psd wrapper function that returns two ndarrays;
makes no attempt to auto plot anything.
Parameters
----------
x : ndarray input signal
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def send_message(self, message, room_id, **kwargs):
"""
Send a message to a given room
"""
return SendMessage(settings=self.settings, **kwargs).call(
message=message,
room_id=room_id,
**kwargs
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def add_subgroups(self, subgroups):
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Add a list of SubGroupDefinition objects to this composite.
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def containerFor(self, entry):
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Returns a container for the inputed entry widget.
:param entry | <XOrbQueryEntryWidget>
:return <XOrbQueryContainer> || None
"""
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index = self._compoundStack.index(entry)
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def class_name(self):
"""str: class name of the key or None if not available."""
if not self._registry_key and self._registry:
self._GetKeyFromRegistry()
if not self._registry_key:
return None
return self._registry_key.class_name | [
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def _transform_col(self, x, i):
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def get_subdomain_ops_at_txid(txid, proxy=None, hostport=None):
"""
Get the list of subdomain operations added by a txid
Returns the list of operations ([{...}]) on success
Returns {'error': ...} on failure
"""
assert proxy or hostport, 'Need proxy or hostport'
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def debug(message, *args, **kwargs):
"""
debug output goes to stderr so you can still redirect the stdout to a file
or another program. Controlled by the JUT_DEBUG environment variable being
present
"""
if 'end' in kwargs:
end = kwargs['end']
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def process_hv_plots(widgets, plots):
"""
Temporary fix to patch HoloViews plot comms
"""
bokeh_plots = []
for plot in plots:
if hasattr(plot, '_update_callbacks'):
for subplot in plot.traverse(lambda x: x):
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def xml(self, url, method='get', params=None, data=None):
"""
请求并返回xml
:type url: str
:param url: API
:type method: str
:param method: HTTP METHOD
:type params: dict
:param params: query
:type data: dict
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def get_next_types(self, n=None):
"""Gets the next set of ``Types`` in this list.
The specified amount must be less than or equal to the return
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arg: n (cardinal): the number of ``Type`` elements requested
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def cg(output,
show,
verbose,
classname,
methodname,
descriptor,
accessflag,
no_isolated,
apk):
"""
Create a call graph and export it into a graph format.
classnames are found in the type "Lfoo/bar/bla;".
Example:
\b
$ androguard cg ... | [
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def process_event(event_filter, callback, timeout_callback, timeout, args,
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"""
Start to watch one event.
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def dirsWavFeatureExtraction(dirNames, mt_win, mt_step, st_win, st_step, compute_beat=False):
'''
Same as dirWavFeatureExtraction, but instead of a single dir it
takes a list of paths as input and returns a list of feature matrices.
EXAMPLE:
[features, classNames] =
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def user_parse(data):
"""Parse information from the provider."""
yield 'id', data.get('uuid')
yield 'username', data.get('username')
yield 'last_name', data.get('display_name')
links = data.get('links', {})
yield 'picture', links.get('avatar', {}).get('href')
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def _jobresult(self, jobid, json=True, headers=None):
"""Poll the async job result.
To be run via in a Thread, the result is put within
the result list which is a hack.
"""
failures = 0
total_time = self.job_timeout or 2**30
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def reduced_formula(self):
"""
Returns a reduced formula string with appended charge.
"""
reduced_formula = super().reduced_formula
charge = self._charge / self.get_reduced_composition_and_factor()[1]
if charge > 0:
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def addCity(self, fileName):
"""Add a JSON file and read the users.
:param fileName: path to the JSON file. This file has to have a list of
users, called users.
:type fileName: str.
"""
with open(fileName) as data_file:
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def _as_label(self, index_or_label):
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return index_or_label
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def snip_line(line, max_width, split_at):
"""Shorten a line to a maximum length."""
if len(line) < max_width:
return line
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def release(self, force=False):
"""Release an exclusive lock on this integration task.
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"""
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def list_firewall_rules(self, retrieve_all=True, **_params):
"""Fetches a list of all firewall rules for a project."""
# Pass filters in "params" argument to do_request
return self.list('firewall_rules', self.firewall_rules_path,
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def find_datasets(self, dataset_name=None, **kwargs):
"""Finds and returns all datasets from the database which matches the requirement.
In some case, the data in a dataset can be stored separately for better management.
Parameters
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dataset_name : str
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def process(self, request, item):
"""Process a PayPal direct payment."""
warn_untested()
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wpp = PayPalWPP(request)
params = self.cleaned_data
params['creditcardtype'] = self.fields['acct'].card_type
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def is_device_virtual(self):
"""Returns if the device is physical or virtual. """
for ip in self.obj_dict:
drvr_obj = self.obj_dict.get(ip).get('drvr_obj')
ret = drvr_obj.is_device_virtual()
# No way to pin a device as of now, so return the first
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def update(old_template=None, old_version=None, new_template=None, new_version=None,
enter_parameters=False):
"""Updates the temple project to the latest template
Proceeeds in the following steps:
1. Ensure we are inside the project repository
2. Obtain the latest version of the package tem... | [
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def total_surface_energy(self):
"""
Total surface energy of the Wulff shape.
Returns:
(float) sum(surface_energy_hkl * area_hkl)
"""
tot_surface_energy = 0
for hkl in self.miller_energy_dict.keys():
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def case(institute_id, case_name):
"""Return a variant."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
if case_obj is None:
return abort(404)
return Response(json_util.dumps(case_obj), mimetype='application/json') | [
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def deprecated_arg_names(arg_mapping):
"""
Decorator which marks a functions keyword arguments as deprecated. It will
result in a warning being emitted when the deprecated keyword argument is
used, and the function being called with the new argument.
Parameters
----------
arg_mapping : dict... | [
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def iter_entry_points(cls, target):
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def is_topk(self, topk=10, reverse=False):
"""
Create an SArray indicating which elements are in the top k.
Entries are '1' if the corresponding element in the current SArray is a
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def runserver(ctx, conf, port, foreground):
"""Run the fnExchange server"""
config = read_config(conf)
debug = config['conf'].get('debug', False)
click.echo('Debug mode {0}.'.format('on' if debug else 'off'))
port = port or config['conf']['server']['port']
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def get_segmentation(recording, annotations, internal_id=None):
"""
Parameters
----------
recording :
A HandwrittenData object
annotations : list of strings
internal_id : string
An identifier for the dataset, e.g. 'user1/200922-947-111.ink'.
Returns
-------
tuple : s... | [
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def _freq_parser(self, freq):
"""Parse timedelta.
Valid keywords "days", "day", "d", "hours", "hour", "h",
"minutes", "minute", "min", "m", "seconds", "second", "sec", "s",
"weeks", "week", "w",
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freq = freq.lower().strip()
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def fix_repeat_dt(dt_list, offset_s=0.001):
"""Add some small offset to remove duplicate times
Needed for xarray interp, which expects monotonically increasing times
"""
idx = (np.diff(dt_list) == timedelta(0))
while np.any(idx):
dt_list[idx.nonzero()[0] + 1] += timedelta(seconds=offset_s)
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def frombinary(path, ext='bin', conf='conf.json', dtype=None, shape=None, skip=0, index=None, labels=None, engine=None, credentials=None):
"""
Load series data from flat binary files.
Parameters
----------
path : string URI or local filesystem path
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def write(self, obj, value, merge=False):
"""
Returns
object: full copy of new obj
"""
full = deepcopy(obj)
frag = full
parts, last = self.parts[:-1], self.parts[-1]
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def use(self, url, name='mytable'):
'''Changes the data provider
>>> yql.use('http://myserver.com/mytables.xml')
'''
self.yql_table_url = url
self.yql_table_name = name
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def default_index(func):
"""Decorator assuring the wrapped method may only run if we are the default
repository index. This is as we rely on git commands that operate
on that index only. """
@wraps(func)
def check_default_index(self, *args, **kwargs):
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def min(self):
"""Minimum value."""
if self._prop.fmin is None:
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def execute(api):
"""Executes operation.
Args:
api: The base API object
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A response body object
"""
try:
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except Exception as exception:
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def read_sensor(self, device_id, sensor_uri):
"""Return sensor value based on sensor_uri."""
url = MINUT_DEVICES_URL + "/{device_id}/{sensor_uri}".format(
device_id=device_id, sensor_uri=sensor_uri)
res = self._request(url, request_type='GET', data={'limit': 1})
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def connect(
host="localhost",
port=1113,
discovery_host=None,
discovery_port=2113,
username=None,
password=None,
loop=None,
name=None,
selector=select_random,
) -> Client:
""" Create a new client.
Examples:
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def main( argv ):
"""main program loop"""
global output_dir
try:
opts, args = getopt.getopt( sys.argv[1:], \
"ht:o:p:", \
["help", "title=", "output=", "prefix="] )
except getopt.GetoptError:
usage()
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def replace(
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default=_void,
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):
"""Creates a customized copy of the Parameter."""
if name is _void:
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def Get(self,key):
"""Get alert by providing name, ID, or other unique key.
If key is not unique and finds multiple matches only the first
will be returned
"""
for alert in self.alerts:
if alert.id == key: return(alert)
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def to_json(self):
"""
:return: str
"""
json_dict = self.to_json_basic()
json_dict['day'] = self._day
json_dict['mon'] = self._mon
json_dict['year'] = self._year
return json.dumps(json_dict) | [
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def singularize(plural):
"""Convert plural word to its singular form.
Args:
plural: A word in its plural form.
Returns:
The word in its singular form.
"""
if plural in UNCOUNTABLES:
return plural
for i in IRREGULAR:
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def _get_general_coverage(data, itype):
"""Retrieve coverage information from new shared SV bins.
"""
work_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
return [{"bam": work_bam, "file": tz.get_in(["depth", "bins", "target"], data),
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def _connect(self):
"""
Connect to the EC2 cloud provider.
:return: :py:class:`boto.ec2.connection.EC2Connection`
:raises: Generic exception on error
"""
# check for existing connection
if self._ec2_connection:
return self._ec2_connection
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"_ec2host... | 37.784314 | 16.921569 |
def rename(self, old, new):
"""Rename the old schema/identifier to the new schema/identifier and
update references.
If the new schema/identifier is already present, that is an error.
If the schema/identifier key is absent, we only debug log and return,
assuming it's a temp table... | [
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",... | 37.933333 | 20.833333 |
def send_capabilties_request(self, vehicle, name, m):
'''An alias for send_capabilities_request.
The word "capabilities" was misspelled in previous versions of this code. This is simply
an alias to send_capabilities_request using the legacy name.
'''
return self.send_capabilitie... | [
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def get_collection(self, session, query, api_key):
"""
Fetch a collection of resources of a specified type.
:param session: SQLAlchemy session
:param query: Dict of query args
:param api_type: The type of the model
"""
model = self._fetch_model(api_key)
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def parse_args():
'''Parse command line arguments'''
parser = argparse.ArgumentParser(
description='Morphology feature plotter',
epilog='Note: Makes plots of various features and superimposes\
input distributions. Plots are saved to PDF file.',
formatter_class=argparse.ArgumentDe... | [
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def _gccalc(lon, lat, azimuth, maxdist=None):
"""
Original javascript on http://williams.best.vwh.net/gccalc.htm
Translated into python by Thomas Lecocq
This function is a black box, because trigonometry is difficult
"""
glat1 = lat * np.pi / 180.
glon1 = lon * np.pi / 180.
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"1.852243... | 27.681818 | 18.439394 |
def stop(self):
'''
Stop the fuzzing session
'''
self.logger.info('Stopping client fuzzer')
self._target_control_thread.stop()
self.target.signal_mutated()
super(ClientFuzzer, self).stop() | [
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def handle_fobj(backend, f, **kwargs):
"""
Handle a file-like object.
Called by `get()` when provided a file-like. This function will prefer the
backend's `handle_fobj()` if one is provided. Otherwise, it will write the
data to a temporary file and call `handle_path()`.
"""
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... | 35.71875 | 19.65625 |
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