positive stringlengths 100 30.3k | anchor stringlengths 1 15k |
|---|---|
def curate(community):
"""Index page with uploader and list of existing depositions.
:param community_id: ID of the community to curate.
"""
if request.method == 'POST':
action = request.json.get('action')
recid = request.json.get('recid')
# 'recid' is mandatory
if not ... | Index page with uploader and list of existing depositions.
:param community_id: ID of the community to curate. |
def completions(self, symbol, attribute, recursive = False):
"""Finds all possible symbol completions of the given symbol that belong
to this module and its dependencies.
:arg symbol: the code symbol that needs to be completed.
:arg attribute: one of ['dependencies', 'publics', 'members... | Finds all possible symbol completions of the given symbol that belong
to this module and its dependencies.
:arg symbol: the code symbol that needs to be completed.
:arg attribute: one of ['dependencies', 'publics', 'members',
'types', 'executables'] for specifying which collections t... |
def do_rm(self, params):
"""
\x1b[1mNAME\x1b[0m
rm - Remove the znode
\x1b[1mSYNOPSIS\x1b[0m
rm <path> [path] [path] ... [path]
\x1b[1mEXAMPLES\x1b[0m
> rm /foo
> rm /foo /bar
"""
for path in params.paths:
try:
self.client_context.de... | \x1b[1mNAME\x1b[0m
rm - Remove the znode
\x1b[1mSYNOPSIS\x1b[0m
rm <path> [path] [path] ... [path]
\x1b[1mEXAMPLES\x1b[0m
> rm /foo
> rm /foo /bar |
def do_watch(self, *args):
""" Watch Dynamo tables consumed capacity """
tables = []
if not self.engine.cached_descriptions:
self.engine.describe_all()
all_tables = list(self.engine.cached_descriptions)
for arg in args:
candidates = set((t for t in all_tab... | Watch Dynamo tables consumed capacity |
def children_rest_names(self):
""" Gets the list of all possible children ReST names.
Returns:
list: list containing all possible rest names as string
Example:
>>> entity = NUEntity()
>>> entity.children_rest_names
["foo",... | Gets the list of all possible children ReST names.
Returns:
list: list containing all possible rest names as string
Example:
>>> entity = NUEntity()
>>> entity.children_rest_names
["foo", "bar"] |
def update(self,**kwargs):
"""
Updates the values for a QuantFigure
The key-values are automatically assigned to the correct
section of the QuantFigure
"""
if 'columns' in kwargs:
self._d=ta._ohlc_dict(self.df,columns=kwargs.pop('columns',None))
schema=self._get_schema()
annotations=kwargs.pop('anno... | Updates the values for a QuantFigure
The key-values are automatically assigned to the correct
section of the QuantFigure |
def get_kbs_info(kbtype="", searchkbname=""):
"""A convenience method.
:param kbtype: type of kb -- get only kb's of this type
:param searchkbname: get only kb's where this sting appears in the name
"""
# query + order by
query = models.KnwKB.query.order_by(
models.KnwKB.name)
# fil... | A convenience method.
:param kbtype: type of kb -- get only kb's of this type
:param searchkbname: get only kb's where this sting appears in the name |
def pytype_to_ctype(t):
""" Python -> pythonic type binding. """
if isinstance(t, List):
return 'pythonic::types::list<{0}>'.format(
pytype_to_ctype(t.__args__[0])
)
elif isinstance(t, Set):
return 'pythonic::types::set<{0}>'.format(
pytype_to_ctype(t.__args__... | Python -> pythonic type binding. |
def utc_datetime_and_leap_second(self):
"""Convert to a Python ``datetime`` in UTC, plus a leap second value.
Convert this time to a `datetime`_ object and a leap second::
dt, leap_second = t.utc_datetime_and_leap_second()
If the third-party `pytz`_ package is available, then its
... | Convert to a Python ``datetime`` in UTC, plus a leap second value.
Convert this time to a `datetime`_ object and a leap second::
dt, leap_second = t.utc_datetime_and_leap_second()
If the third-party `pytz`_ package is available, then its
``utc`` timezone will be used as the timezo... |
def get_raw_token(self, header):
"""
Extracts an unvalidated JSON web token from the given "Authorization"
header value.
"""
parts = header.split()
if len(parts) == 0:
# Empty AUTHORIZATION header sent
return None
if parts[0] not in AUTH_... | Extracts an unvalidated JSON web token from the given "Authorization"
header value. |
def ipop_range(self, start=0, stop=-1, callback=None, withscores=True):
'''pop a range from the :class:`OrderedMixin`'''
backend = self.backend
res = backend.structure(self).ipop_range(start, stop,
withscores=withscores)
if not callba... | pop a range from the :class:`OrderedMixin` |
def _periodically_flush_profile_events(self):
"""Drivers run this as a thread to flush profile data in the
background."""
# Note(rkn): This is run on a background thread in the driver. It uses
# the raylet client. This should be ok because it doesn't read
# from the raylet client... | Drivers run this as a thread to flush profile data in the
background. |
def ReplaceIxes(self, path, old_prefix, old_suffix, new_prefix, new_suffix):
"""
Replace old_prefix with new_prefix and old_suffix with new_suffix.
env - Environment used to interpolate variables.
path - the path that will be modified.
old_prefix - construction variable for the ... | Replace old_prefix with new_prefix and old_suffix with new_suffix.
env - Environment used to interpolate variables.
path - the path that will be modified.
old_prefix - construction variable for the old prefix.
old_suffix - construction variable for the old suffix.
new_prefix - c... |
def subcmd_list_parser(subcmd):
""" list subcommand """
subcmd.add_argument(
'--broker',
action='store',
dest='broker',
help=u'Route to the Ansible Service Broker'
)
subcmd.add_argument(
'--secure',
action='store_true',
dest='verify',
help=... | list subcommand |
def _glslify(r):
"""Transform a string or a n-tuple to a valid GLSL expression."""
if isinstance(r, string_types):
return r
else:
assert 2 <= len(r) <= 4
return 'vec{}({})'.format(len(r), ', '.join(map(str, r))) | Transform a string or a n-tuple to a valid GLSL expression. |
def wait_for_window_map_state(self, window, state):
"""
Wait for a window to have a specific map state.
State possibilities:
IsUnmapped - window is not displayed.
IsViewable - window is mapped and shown (though may be
clipped by windows on top of it)
... | Wait for a window to have a specific map state.
State possibilities:
IsUnmapped - window is not displayed.
IsViewable - window is mapped and shown (though may be
clipped by windows on top of it)
IsUnviewable - window is mapped but a parent window is unmapped.
... |
def absolute_abundance(coverage, total_bases):
"""
absolute abundance = (number of bases mapped to genome / total number of bases in sample) * 100
"""
absolute = {}
for genome in coverage:
absolute[genome] = []
index = 0
for calc in coverage[genome]:
bases = calc[0]
total = total_bases[index]
absolu... | absolute abundance = (number of bases mapped to genome / total number of bases in sample) * 100 |
def add_value(self, field_name: str, value: object = None, json_path: str = None,
json_path_extraction: str = None, keep_empty: bool = False) -> None:
"""
Add a value to knowledge graph.
Input can either be a value or a json_path. If the input is json_path, the helper function ... | Add a value to knowledge graph.
Input can either be a value or a json_path. If the input is json_path, the helper function _add_doc_value is
called.
If the input is a value, then it is handled
Args:
field_name: str, the field name in the knowledge graph
value: th... |
def meff_SO(self, **kwargs):
'''
Returns the split-off hole effective mass
calculated from Eg_Gamma(T), Delta_SO, Ep and F.
Interpolation of Eg_Gamma(T), Delta_SO, Ep and luttinger1, and
then calculation of meff_SO is recommended for alloys.
'''
Eg = self... | Returns the split-off hole effective mass
calculated from Eg_Gamma(T), Delta_SO, Ep and F.
Interpolation of Eg_Gamma(T), Delta_SO, Ep and luttinger1, and
then calculation of meff_SO is recommended for alloys. |
def parse_config(filename):
"""
Parses a versionupgrade configuration file. Example:
tag v{VERSION}
branch v{VERSION}
message Prepare {VERSION} release
upgrade setup.py: version = '{VERSION}'
upgrade __init__.py:__version__ = '{VERSION}'
sub docs/changelog/v{VERSION}.md:# v{VER... | Parses a versionupgrade configuration file. Example:
tag v{VERSION}
branch v{VERSION}
message Prepare {VERSION} release
upgrade setup.py: version = '{VERSION}'
upgrade __init__.py:__version__ = '{VERSION}'
sub docs/changelog/v{VERSION}.md:# v{VERSION} (unreleased):# v{VERSION} ({DA... |
def getObjectives(self):
"""
Get all the objectives declared.
"""
objectives = lock_and_call(
lambda: self._impl.getObjectives(),
self._lock
)
return EntityMap(objectives, Objective) | Get all the objectives declared. |
def convert_ages_to_calendar_year(self, er_ages_rec):
"""
convert all age units to calendar year
Parameters
----------
er_ages_rec : Dict type object containing preferbly at least keys
'age', 'age_unit', and either 'age_range_high', 'age_range_low'
or 'ag... | convert all age units to calendar year
Parameters
----------
er_ages_rec : Dict type object containing preferbly at least keys
'age', 'age_unit', and either 'age_range_high', 'age_range_low'
or 'age_sigma'
Returns
-------
er_ages_rec : Same dict ... |
def id_pseudopath(self):
"""
Looks like a path, but with ids stuck in when available
"""
try:
pseudopath = Fields(str(self.value[auto_id_field]))
except (TypeError, AttributeError, KeyError): # This may not be all the interesting exceptions
pseudopath = se... | Looks like a path, but with ids stuck in when available |
def plot_two_columns(self, reset_xlimits=False, reset_ylimits=False):
"""Simple line plot for two selected columns."""
self.clear_plot()
if self.tab is None: # No table data to plot
return
plt_kw = {
'lw': self.settings.get('linewidth', 1),
'ls': se... | Simple line plot for two selected columns. |
def _build(self):
"""Returns a tuple containing observation and target one-hot tensors."""
q = tf.FIFOQueue(
self._queue_capacity, [self._dtype, self._dtype],
shapes=[[self._num_steps, self._batch_size, self._vocab_size]]*2)
obs, target = tf.py_func(self._get_batch, [], [tf.int32, tf.int32])... | Returns a tuple containing observation and target one-hot tensors. |
def set_length_and_maybe_checksums(self, record, payload_offset=None):
'''Set the content length and possibly the checksums.'''
if self._params.digests:
record.compute_checksum(payload_offset)
else:
record.set_content_length() | Set the content length and possibly the checksums. |
def create(self):
"""POST /datastores: Create a new item."""
# url('datastores')
content = request.environ['wsgi.input'].read(int(request.environ['CONTENT_LENGTH']))
content = content.decode('utf8')
content = simplejson.loads(content)
new = DataStore(content['name'],
... | POST /datastores: Create a new item. |
def get_cdr(self, start=0, count=-1, **kwargs):
"""Request range of CDR messages"""
sha = encode_to_sha("{:d},{:d}".format(start, count))
return self._queue_msg({'cmd': cmd.CMD_MESSAGE_CDR,
'sha': sha}, **kwargs) | Request range of CDR messages |
def send(self, **extra):
"""
Sends email batch.
:return: Information about sent emails.
:rtype: `list`
"""
emails = self.as_dict(**extra)
responses = [self._manager._send_batch(*batch) for batch in chunks(emails, self.MAX_SIZE)]
return sum(responses, []) | Sends email batch.
:return: Information about sent emails.
:rtype: `list` |
async def start_child():
"""
Start the child process that will look for changes in modules.
"""
logger.info('Started to watch for code changes')
loop = asyncio.get_event_loop()
watcher = aionotify.Watcher()
flags = (
aionotify.Flags.MODIFY |
aionotify.Flags.DELETE |
... | Start the child process that will look for changes in modules. |
def plot_expected_repeat_purchases(
model,
title="Expected Number of Repeat Purchases per Customer",
xlabel="Time Since First Purchase",
ax=None,
label=None,
**kwargs
):
"""
Plot expected repeat purchases on calibration period .
Parameters
----------
model: lifetimes model
... | Plot expected repeat purchases on calibration period .
Parameters
----------
model: lifetimes model
A fitted lifetimes model.
max_frequency: int, optional
The maximum frequency to plot.
title: str, optional
Figure title
xlabel: str, optional
Figure xlabel
ax:... |
def request_location(cls, text, *,
resize=None, single_use=None, selective=None):
"""
Creates a new button that will request
the user's location upon being clicked.
``resize``, ``single_use`` and ``selective`` are documented in `text`.
"""
return... | Creates a new button that will request
the user's location upon being clicked.
``resize``, ``single_use`` and ``selective`` are documented in `text`. |
def centroid_distance(item_a, time_a, item_b, time_b, max_value):
"""
Euclidean distance between the centroids of item_a and item_b.
Args:
item_a: STObject from the first set in ObjectMatcher
time_a: Time integer being evaluated
item_b: STObject from the second set in ObjectMatcher
... | Euclidean distance between the centroids of item_a and item_b.
Args:
item_a: STObject from the first set in ObjectMatcher
time_a: Time integer being evaluated
item_b: STObject from the second set in ObjectMatcher
time_b: Time integer being evaluated
max_value: Maximum distan... |
def checks(self):
'''Return the list of all check methods.'''
condition = lambda a: a.startswith('check_')
return (getattr(self, a) for a in dir(self) if condition(a)) | Return the list of all check methods. |
def add(self, node):
"""Add Node, replace existing node if node with node_id is present."""
if not isinstance(node, Node):
raise TypeError()
for i, j in enumerate(self.__nodes):
if j.node_id == node.node_id:
self.__nodes[i] = node
return
... | Add Node, replace existing node if node with node_id is present. |
def move_back_boxed_texts(self):
"""
The only intended use for this function is to patch a problem seen in
at least one PLoS article (journal.pgen.0020002). This will move any
<boxed-text> elements over to the receiving element, which is probably
the main body.
"""
... | The only intended use for this function is to patch a problem seen in
at least one PLoS article (journal.pgen.0020002). This will move any
<boxed-text> elements over to the receiving element, which is probably
the main body. |
def is_refreshable_url(self, request):
"""Takes a request and returns whether it triggers a refresh examination
:arg HttpRequest request:
:returns: boolean
"""
# Do not attempt to refresh the session if the OIDC backend is not used
backend_session = request.session.get... | Takes a request and returns whether it triggers a refresh examination
:arg HttpRequest request:
:returns: boolean |
def add_or_update(self, app_id):
'''
Add or update the category.
'''
logger.info('Collect info: user-{0}, uid-{1}'.format(self.userinfo.uid, app_id))
MCollect.add_or_update(self.userinfo.uid, app_id)
out_dic = {'success': True}
return json.dump(out_dic, self) | Add or update the category. |
def makeMany2ManyRelatedManager(formodel, name_relmodel, name_formodel):
'''formodel is the model which the manager .'''
class _Many2ManyRelatedManager(Many2ManyRelatedManager):
pass
_Many2ManyRelatedManager.formodel = formodel
_Many2ManyRelatedManager.name_relmodel = name_relmodel
... | formodel is the model which the manager . |
def next(self, n=1):
"""Move up by `n` steps in the Hilbert space::
>>> hs = LocalSpace('tls', basis=('g', 'e'))
>>> ascii(BasisKet('g', hs=hs).next())
'|e>^(tls)'
>>> ascii(BasisKet(0, hs=hs).next())
'|e>^(tls)'
We can also go multiple step... | Move up by `n` steps in the Hilbert space::
>>> hs = LocalSpace('tls', basis=('g', 'e'))
>>> ascii(BasisKet('g', hs=hs).next())
'|e>^(tls)'
>>> ascii(BasisKet(0, hs=hs).next())
'|e>^(tls)'
We can also go multiple steps:
>>> hs = LocalS... |
def load_data(self, filename, ext):
"""Load data from filename"""
from spyder_kernels.utils.iofuncs import iofunctions
from spyder_kernels.utils.misc import fix_reference_name
glbs = self._mglobals()
load_func = iofunctions.load_funcs[ext]
data, error_message = load_fun... | Load data from filename |
def post(self, request, hook_id):
"""
Process Telegram webhook.
1. Serialize Telegram message
2. Get an enabled Telegram bot
3. Create :class:`Update <permabots.models.telegram_api.Update>`
5. Delay processing to a task
6. Response provid... | Process Telegram webhook.
1. Serialize Telegram message
2. Get an enabled Telegram bot
3. Create :class:`Update <permabots.models.telegram_api.Update>`
5. Delay processing to a task
6. Response provider |
def index_template_exists(name, hosts=None, profile=None):
'''
Return a boolean indicating whether given index template exists
name
Index template name
CLI example::
salt myminion elasticsearch.index_template_exists testindex_templ
'''
es = _get_instance(hosts, profile)
tr... | Return a boolean indicating whether given index template exists
name
Index template name
CLI example::
salt myminion elasticsearch.index_template_exists testindex_templ |
def get_verbatim(key, **kwargs):
'''
Gets a verbatim occurrence record without any interpretation
:param key: [int] A GBIF occurrence key
:return: A dictionary, of results
Usage::
from pygbif import occurrences
occurrences.get_verbatim(key = 1258202889)
occurrences.get_ve... | Gets a verbatim occurrence record without any interpretation
:param key: [int] A GBIF occurrence key
:return: A dictionary, of results
Usage::
from pygbif import occurrences
occurrences.get_verbatim(key = 1258202889)
occurrences.get_verbatim(key = 1227768771)
occurrences.... |
def Compile(self, filter_implemention):
"""Returns the data_store filter implementation from the attribute."""
return self.operator_method(self.attribute_obj, filter_implemention,
*self.args) | Returns the data_store filter implementation from the attribute. |
def dataset(self):
"""A Tablib Dataset containing the row."""
data = tablib.Dataset()
data.headers = self.keys()
row = _reduce_datetimes(self.values())
data.append(row)
return data | A Tablib Dataset containing the row. |
def add_0x(string):
"""Add 0x to string at start.
"""
if isinstance(string, bytes):
string = string.decode('utf-8')
return '0x' + str(string) | Add 0x to string at start. |
def add_to_cart(item_id):
""" Cart with Product """
cart = Cart(session['cart'])
if cart.change_item(item_id, 'add'):
session['cart'] = cart.to_dict()
return list_products() | Cart with Product |
def build_headers(self):
'''
Return the list of headers as two-tuples
'''
if not 'Content-Type' in self.headers:
content_type = self.content_type
if self.encoding != DEFAULT_ENCODING:
content_type += '; charset=%s' % self.encoding
self.... | Return the list of headers as two-tuples |
def sort_members(tup, names):
"""Return two pairs of members, scalar and tuple members.
The scalars will be sorted s.t. the unbound members are at the top.
"""
scalars, tuples = partition(lambda x: not is_tuple_node(tup.member[x].value), names)
unbound, bound = partition(lambda x: tup.member[x].value.is_unbo... | Return two pairs of members, scalar and tuple members.
The scalars will be sorted s.t. the unbound members are at the top. |
def pool_build(name, **kwargs):
'''
Build a defined libvirt storage pool.
:param name: libvirt storage pool name
:param connection: libvirt connection URI, overriding defaults
:param username: username to connect with, overriding defaults
:param password: password to connect with, overriding de... | Build a defined libvirt storage pool.
:param name: libvirt storage pool name
:param connection: libvirt connection URI, overriding defaults
:param username: username to connect with, overriding defaults
:param password: password to connect with, overriding defaults
.. versionadded:: 2019.2.0
... |
def create_stack(StackName=None, TemplateBody=None, TemplateURL=None, Parameters=None, DisableRollback=None, TimeoutInMinutes=None, NotificationARNs=None, Capabilities=None, ResourceTypes=None, RoleARN=None, OnFailure=None, StackPolicyBody=None, StackPolicyURL=None, Tags=None, ClientRequestToken=None):
"""
Crea... | Creates a stack as specified in the template. After the call completes successfully, the stack creation starts. You can check the status of the stack via the DescribeStacks API.
See also: AWS API Documentation
:example: response = client.create_stack(
StackName='string',
TemplateBody=... |
def maybe_convert_platform(values):
""" try to do platform conversion, allow ndarray or list here """
if isinstance(values, (list, tuple)):
values = construct_1d_object_array_from_listlike(list(values))
if getattr(values, 'dtype', None) == np.object_:
if hasattr(values, '_values'):
... | try to do platform conversion, allow ndarray or list here |
def cli(env, volume_id, replicant_id, immediate):
"""Failover a block volume to the given replicant volume."""
block_storage_manager = SoftLayer.BlockStorageManager(env.client)
success = block_storage_manager.failover_to_replicant(
volume_id,
replicant_id,
immediate
)
if su... | Failover a block volume to the given replicant volume. |
def on_exception(func):
"""
Run a function when a handler thows an exception. It's return value is
returned to AWS.
Usage::
>>> # to create a reusable decorator
>>> @on_exception
... def handle_errors(exception):
... print(exception)
... return {'statusC... | Run a function when a handler thows an exception. It's return value is
returned to AWS.
Usage::
>>> # to create a reusable decorator
>>> @on_exception
... def handle_errors(exception):
... print(exception)
... return {'statusCode': 500, 'body': 'uh oh'}
... |
def saveh5(self, h5file, qpi_slice=None, series_slice=None,
time_interval=None, count=None, max_count=None):
"""Save the data set as an hdf5 file (qpimage.QPSeries format)
Parameters
----------
h5file: str, pathlib.Path, or h5py.Group
Where to store the series... | Save the data set as an hdf5 file (qpimage.QPSeries format)
Parameters
----------
h5file: str, pathlib.Path, or h5py.Group
Where to store the series data
qpi_slice: tuple of (slice, slice)
If not None, only store a slice of each QPImage
in `h5file`. A... |
def addmul_number_dicts(series):
'''Multiply dictionaries by a numeric values and add them together.
:parameter series: a tuple of two elements tuples. Each serie is of the form::
(weight,dictionary)
where ``weight`` is a number and ``dictionary`` is a dictionary with
numeric values.
:parameter s... | Multiply dictionaries by a numeric values and add them together.
:parameter series: a tuple of two elements tuples. Each serie is of the form::
(weight,dictionary)
where ``weight`` is a number and ``dictionary`` is a dictionary with
numeric values.
:parameter skip: optional list of field names to ski... |
def init_from_fcnxs(ctx, fcnxs_symbol, fcnxs_args_from, fcnxs_auxs_from):
""" use zero initialization for better convergence, because it tends to oputut 0,
and the label 0 stands for background, which may occupy most size of one image.
"""
fcnxs_args = fcnxs_args_from.copy()
fcnxs_auxs = fcnxs_auxs_... | use zero initialization for better convergence, because it tends to oputut 0,
and the label 0 stands for background, which may occupy most size of one image. |
def _sighash_prep(self, index, script):
'''
SproutTx, int, byte-like -> SproutTx
Sighashes suck
Performs the sighash setup described here:
https://en.bitcoin.it/wiki/OP_CHECKSIG#How_it_works
https://bitcoin.stackexchange.com/questions/3374/how-to-redeem-a-basic-tx
... | SproutTx, int, byte-like -> SproutTx
Sighashes suck
Performs the sighash setup described here:
https://en.bitcoin.it/wiki/OP_CHECKSIG#How_it_works
https://bitcoin.stackexchange.com/questions/3374/how-to-redeem-a-basic-tx
We save on complexity by refusing to support OP_CODESEPARAT... |
def sd_journal_send(**kwargs):
"""
Send a message to the journald log.
@param kwargs: Mapping between field names to values, both as bytes.
@raise IOError: If the operation failed.
"""
# The function uses printf formatting, so we need to quote
# percentages.
fields = [
_ffi.new... | Send a message to the journald log.
@param kwargs: Mapping between field names to values, both as bytes.
@raise IOError: If the operation failed. |
def show(self, item, variant):
"""
Show a variant.
:param item: Item object or id
:param variant: Variant object or id
:return:
"""
url = self._build_url(self.endpoint.show(item, variant))
return self._get(url) | Show a variant.
:param item: Item object or id
:param variant: Variant object or id
:return: |
def unfinished_objects(self):
'''
Leaves only versions of those objects that has some version with
`_end == None` or with `_end > right cutoff`.
'''
mask = self._end_isnull
if self._rbound is not None:
mask = mask | (self._end > self._rbound)
oids = se... | Leaves only versions of those objects that has some version with
`_end == None` or with `_end > right cutoff`. |
async def get_next_opponent(self):
""" Get the opponent of the potential next match. See :func:`get_next_match`
|methcoro|
Raises:
APIException
"""
next_match = await self.get_next_match()
if next_match is not None:
opponent_id = next_match.play... | Get the opponent of the potential next match. See :func:`get_next_match`
|methcoro|
Raises:
APIException |
def copyToLocal(self, paths, dst, check_crc=False):
''' Copy files that match the file source pattern
to the local name. Source is kept. When copying multiple,
files, the destination must be a directory.
:param paths: Paths to copy
:type paths: list of strings
:param d... | Copy files that match the file source pattern
to the local name. Source is kept. When copying multiple,
files, the destination must be a directory.
:param paths: Paths to copy
:type paths: list of strings
:param dst: Destination path
:type dst: string
:param ch... |
def hessian(self, coordinates):
"""Compute the force-field Hessian for the given coordinates.
Argument:
| ``coordinates`` -- A numpy array with the Cartesian atom
coordinates, with shape (N,3).
Returns:
| ``hessian`` -- A numpy arr... | Compute the force-field Hessian for the given coordinates.
Argument:
| ``coordinates`` -- A numpy array with the Cartesian atom
coordinates, with shape (N,3).
Returns:
| ``hessian`` -- A numpy array with the Hessian, with shape (3*N,
... |
def update_frame(self, key, ranges=None, element=None):
"""
Update the internal state of the Plot to represent the given
key tuple (where integers represent frames). Returns this
state.
"""
reused = isinstance(self.hmap, DynamicMap) and self.overlaid
if not reused... | Update the internal state of the Plot to represent the given
key tuple (where integers represent frames). Returns this
state. |
def ReadFromFile(self, artifacts_reader, filename):
"""Reads artifact definitions into the registry from a file.
Args:
artifacts_reader (ArtifactsReader): an artifacts reader.
filename (str): name of the file to read from.
"""
for artifact_definition in artifacts_reader.ReadFile(filename):
... | Reads artifact definitions into the registry from a file.
Args:
artifacts_reader (ArtifactsReader): an artifacts reader.
filename (str): name of the file to read from. |
def optimize(self):
"""Optimize certain stacked wildcard patterns."""
subpattern = None
if (self.content is not None and
len(self.content) == 1 and len(self.content[0]) == 1):
subpattern = self.content[0][0]
if self.min == 1 and self.max == 1:
if self.... | Optimize certain stacked wildcard patterns. |
def stop(self):
"""
Stop tracing. Reinstalls the :ref:`hunter.Tracer.previous` tracer.
"""
if self._handler is not None:
sys.settrace(self._previous)
self._handler = self._previous = None
if self.threading_support is None or self.threading_support:
... | Stop tracing. Reinstalls the :ref:`hunter.Tracer.previous` tracer. |
def stable_u_range_dict(self, chempot_range, ref_delu, no_doped=True,
no_clean=False, delu_dict={}, miller_index=(),
dmu_at_0=False, return_se_dict=False):
"""
Creates a dictionary where each entry is a key pointing to a
chemical potential ... | Creates a dictionary where each entry is a key pointing to a
chemical potential range where the surface of that entry is stable.
Does so by enumerating through all possible solutions (intersect)
for surface energies of a specific facet.
Args:
chempot_range ([max_chempot, min... |
def delete_account_metadata(self, prefix=None):
"""
Removes all metadata matching the specified prefix from the account.
By default, the standard account metadata prefix ('X-Account-Meta-') is
prepended to the header name if it isn't present. For non-standard
headers, you must i... | Removes all metadata matching the specified prefix from the account.
By default, the standard account metadata prefix ('X-Account-Meta-') is
prepended to the header name if it isn't present. For non-standard
headers, you must include a non-None prefix, such as an empty string. |
def write(self, data):
"""
write data on the OUT endpoint associated to the HID interface
"""
for _ in range(64 - len(data)):
data.append(0)
#logging.debug("send: %s", data)
self.device.write(bytearray([0]) + data)
return | write data on the OUT endpoint associated to the HID interface |
def strip_textpad(text):
"""
Attempt to intelligently strip excess whitespace from the output of a
curses textpad.
"""
if text is None:
return text
# Trivial case where the textbox is only one line long.
if '\n' not in text:
return text.r... | Attempt to intelligently strip excess whitespace from the output of a
curses textpad. |
def user_tickets_assigned(self, user_id, external_id=None, **kwargs):
"https://developer.zendesk.com/rest_api/docs/core/tickets#allowed-for"
api_path = "/api/v2/users/{user_id}/tickets/assigned.json"
api_path = api_path.format(user_id=user_id)
api_query = {}
if "query" in kwargs.... | https://developer.zendesk.com/rest_api/docs/core/tickets#allowed-for |
def memoryview_safe(x):
"""Make array safe to run in a Cython memoryview-based kernel. These
kernels typically break down with the error ``ValueError: buffer source
array is read-only`` when running in dask distributed.
See Also
--------
https://github.com/dask/distributed/issues/1978
https... | Make array safe to run in a Cython memoryview-based kernel. These
kernels typically break down with the error ``ValueError: buffer source
array is read-only`` when running in dask distributed.
See Also
--------
https://github.com/dask/distributed/issues/1978
https://github.com/cggh/scikit-allel... |
def whoami(self,
note=None,
loglevel=logging.DEBUG):
"""Returns the current user by executing "whoami".
@param note: See send()
@return: the output of "whoami"
@rtype: string
"""
shutit = self.shutit
shutit.handle_note(note)
res = self.send_and_get_output(' command whoami',... | Returns the current user by executing "whoami".
@param note: See send()
@return: the output of "whoami"
@rtype: string |
def to_rgba(color, alpha):
"""
Converts from hex|rgb to rgba
Parameters:
-----------
color : string
Color representation on hex or rgb
alpha : float
Value from 0 to 1.0 that represents the
alpha value.
Example:
... | Converts from hex|rgb to rgba
Parameters:
-----------
color : string
Color representation on hex or rgb
alpha : float
Value from 0 to 1.0 that represents the
alpha value.
Example:
to_rgba('#E1E5ED',0.6)
... |
def sum(self, default=None):
"""
Calculate the sum of all the values in the times series.
:param default: Value to return as a default should the calculation not be possible.
:return: Float representing the sum or `None`.
"""
return numpy.asscalar(numpy.sum(self.values))... | Calculate the sum of all the values in the times series.
:param default: Value to return as a default should the calculation not be possible.
:return: Float representing the sum or `None`. |
def _create_B(self,Y):
""" Creates OLS coefficient matrix
Parameters
----------
Y : np.array
The dependent variables Y
Returns
----------
The coefficient matrix B
"""
Z = self._create_Z(Y)
return np.dot(np.dot(Y,np.t... | Creates OLS coefficient matrix
Parameters
----------
Y : np.array
The dependent variables Y
Returns
----------
The coefficient matrix B |
def configure_shellwidget(self, give_focus=True):
"""Configure shellwidget after kernel is started"""
if give_focus:
self.get_control().setFocus()
# Set exit callback
self.shellwidget.set_exit_callback()
# To save history
self.shellwidget.executing.... | Configure shellwidget after kernel is started |
def _full_sub_array(data_obj, xj_path, create_dict_path):
"""Retrieves all array or dictionary elements for '*' JSON path marker.
:param dict|list data_obj: The current data object.
:param str xj_path: A json path.
:param bool create_dict_path create a dict path.
:return: tuple with two values: fir... | Retrieves all array or dictionary elements for '*' JSON path marker.
:param dict|list data_obj: The current data object.
:param str xj_path: A json path.
:param bool create_dict_path create a dict path.
:return: tuple with two values: first is a result and second
a boolean flag telling if ... |
def infer_bulk_complete_from_fs(datetimes, datetime_to_task, datetime_to_re):
"""
Efficiently determines missing datetimes by filesystem listing.
The current implementation works for the common case of a task writing
output to a ``FileSystemTarget`` whose path is built using strftime with
format li... | Efficiently determines missing datetimes by filesystem listing.
The current implementation works for the common case of a task writing
output to a ``FileSystemTarget`` whose path is built using strftime with
format like '...%Y...%m...%d...%H...', without custom ``complete()`` or
``exists()``.
(Eve... |
def _db_to_python(db_data: dict, table: LdapObjectClass, dn: str) -> LdapObject:
""" Convert a DbDate object to a LdapObject. """
fields = table.get_fields()
python_data = table({
name: field.to_python(db_data[name])
for name, field in fields.items()
if field.db_field
})
pyt... | Convert a DbDate object to a LdapObject. |
def calculate_frechet_distance(mu1, sigma1, mu2, sigma2, eps=1e-6):
"""Numpy implementation of the Frechet Distance.
The Frechet distance between two multivariate Gaussians X_1 ~ N(mu_1, C_1)
and X_2 ~ N(mu_2, C_2) is
d^2 = ||mu_1 - mu_2||^2 + Tr(C_1 + C_2 - 2*sqrt(C_1*C_2)).
St... | Numpy implementation of the Frechet Distance.
The Frechet distance between two multivariate Gaussians X_1 ~ N(mu_1, C_1)
and X_2 ~ N(mu_2, C_2) is
d^2 = ||mu_1 - mu_2||^2 + Tr(C_1 + C_2 - 2*sqrt(C_1*C_2)).
Stable version by Dougal J. Sutherland.
Params:
-- mu1: The mean ... |
def download(cls, filename, input_dir, dl_dir=None):
"""Download the resource from the storage."""
file_info = cls.parse_remote(filename)
if not dl_dir:
dl_dir = os.path.join(input_dir, file_info.container,
os.path.dirname(file_info.blob))
... | Download the resource from the storage. |
def _start_connection_setup(self):
"""Start the connection setup by refreshing the TOCs"""
logger.info('We are connected[%s], request connection setup',
self.link_uri)
self.platform.fetch_platform_informations(self._platform_info_fetched) | Start the connection setup by refreshing the TOCs |
def _create_centerline(self):
"""
Calculate the centerline of a polygon.
Densifies the border of a polygon which is then represented by a Numpy
array of points necessary for creating the Voronoi diagram. Once the
diagram is created, the ridges located within the polygon are
... | Calculate the centerline of a polygon.
Densifies the border of a polygon which is then represented by a Numpy
array of points necessary for creating the Voronoi diagram. Once the
diagram is created, the ridges located within the polygon are
joined and returned.
Returns:
... |
def flatten(it):
""" Flattens any iterable
From:
http://stackoverflow.com/questions/11503065/python-function-to-flatten-generator-containing-another-generator
:param it: Iterator, iterator to flatten
:return: Generator, A generator of the flattened values
"""
for x in it:
if... | Flattens any iterable
From:
http://stackoverflow.com/questions/11503065/python-function-to-flatten-generator-containing-another-generator
:param it: Iterator, iterator to flatten
:return: Generator, A generator of the flattened values |
def _recurse(self, path):
'''
Get a list of all specified files
'''
files = {}
empty_dirs = []
try:
sub_paths = os.listdir(path)
except OSError as exc:
if exc.errno == errno.ENOENT:
# Path does not exist
sys.... | Get a list of all specified files |
def after_request(self, func: Callable, name: AppOrBlueprintKey=None) -> Callable:
"""Add an after request function.
This is designed to be used as a decorator. An example usage,
.. code-block:: python
@app.after_request
def func(response):
return respo... | Add an after request function.
This is designed to be used as a decorator. An example usage,
.. code-block:: python
@app.after_request
def func(response):
return response
Arguments:
func: The after request function itself.
name:... |
def _parse_config_file_impl(filename):
"""
Format for the file is:
credentials:
email: ...
api_token: ...
:param filename: The filename to parse
:return: A tuple with:
- email
- api_token
"""
api_key = None
email = ... | Format for the file is:
credentials:
email: ...
api_token: ...
:param filename: The filename to parse
:return: A tuple with:
- email
- api_token |
def shuffle(args):
"""
%prog shuffle p1.fastq p2.fastq
Shuffle pairs into interleaved format.
"""
p = OptionParser(shuffle.__doc__)
p.set_tag()
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
p1, p2 = args
pairsfastq = pairspf((p1, p2)) ... | %prog shuffle p1.fastq p2.fastq
Shuffle pairs into interleaved format. |
def process_transaction(self, transaction):
"""Add a transaction to ledger, updating the current state as needed.
Parameters
----------
transaction : zp.Transaction
The transaction to execute.
"""
asset = transaction.asset
if isinstance(asset, Future)... | Add a transaction to ledger, updating the current state as needed.
Parameters
----------
transaction : zp.Transaction
The transaction to execute. |
def installedOn(self):
"""
If this item is installed on another item, return the install
target. Otherwise return None.
"""
try:
return self.store.findUnique(_DependencyConnector,
_DependencyConnector.installee == self
... | If this item is installed on another item, return the install
target. Otherwise return None. |
def global_workflow_run(name_or_id, alias=None, input_params={}, always_retry=True, **kwargs):
"""
Invokes the /globalworkflow-xxxx/run API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Global-Workflows#API-method:-/globalworkflow-xxxx%5B/yyyy%5D/run
"""
input_param... | Invokes the /globalworkflow-xxxx/run API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Global-Workflows#API-method:-/globalworkflow-xxxx%5B/yyyy%5D/run |
def statcast_batter(start_dt=None, end_dt=None, player_id=None):
"""
Pulls statcast pitch-level data from Baseball Savant for a given batter.
ARGUMENTS
start_dt : YYYY-MM-DD : the first date for which you want a player's statcast data
end_dt : YYYY-MM-DD : the final date for which you want data
... | Pulls statcast pitch-level data from Baseball Savant for a given batter.
ARGUMENTS
start_dt : YYYY-MM-DD : the first date for which you want a player's statcast data
end_dt : YYYY-MM-DD : the final date for which you want data
player_id : INT : the player's MLBAM ID. Find this by calling pybaseball.pla... |
def main(argv=None):
'''Command line options.'''
if argv is None:
argv = sys.argv
else:
sys.argv.extend(argv)
parser = ArgumentParser()
parser.add_argument('-u', '--url', dest='url', required=True, help="base url (has to contain versions json)")
parser.add_argument('-o', '--out... | Command line options. |
def save(self, path, group=None, ifo='P1'):
"""
Save frequency series to a Numpy .npy, hdf, or text file. The first column
contains the sample frequencies, the second contains the values.
In the case of a complex frequency series saved as text, the imaginary
part is written as a ... | Save frequency series to a Numpy .npy, hdf, or text file. The first column
contains the sample frequencies, the second contains the values.
In the case of a complex frequency series saved as text, the imaginary
part is written as a third column. When using hdf format, the data is stored
... |
def forward(self,pixx,pixy):
""" Transform the input pixx,pixy positions in the input frame
to pixel positions in the output frame.
This method gets passed to the drizzle algorithm.
"""
# This matches WTRAXY results to better than 1e-4 pixels.
skyx,skyy = self.in... | Transform the input pixx,pixy positions in the input frame
to pixel positions in the output frame.
This method gets passed to the drizzle algorithm. |
def get_object(
self, object_t, object_id=None, relation=None, parent=None, **kwargs
):
"""
Actually query the Deezer API to retrieve the object
:returns: json dictionary
"""
url = self.object_url(object_t, object_id, relation, **kwargs)
response = self.sessi... | Actually query the Deezer API to retrieve the object
:returns: json dictionary |
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