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dbarsam/python-vsgen | vsgen/util/entrypoints.py | entrypoint | def entrypoint(section, option):
"""
Returns the the entry point object given a section, option pair.
:param str section: The section name in the entry point collection
:param str option: The option name in the entry point collection
:return: The entry point object if available.
"""
try:
... | python | def entrypoint(section, option):
"""
Returns the the entry point object given a section, option pair.
:param str section: The section name in the entry point collection
:param str option: The option name in the entry point collection
:return: The entry point object if available.
"""
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go-macaroon-bakery/py-macaroon-bakery | macaroonbakery/checkers/_declared.py | infer_declared | def infer_declared(ms, namespace=None):
'''Retrieves any declared information from the given macaroons and returns
it as a key-value map.
Information is declared with a first party caveat as created by
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If there are two caveats that declare the same key with different values,
th... | python | def infer_declared(ms, namespace=None):
'''Retrieves any declared information from the given macaroons and returns
it as a key-value map.
Information is declared with a first party caveat as created by
declared_caveat.
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go-macaroon-bakery/py-macaroon-bakery | macaroonbakery/checkers/_declared.py | infer_declared_from_conditions | def infer_declared_from_conditions(conds, namespace=None):
''' like infer_declared except that it is passed a set of first party
caveat conditions as a list of string rather than a set of macaroons.
'''
conflicts = []
# If we can't resolve that standard namespace, then we'll look for
# just bare... | python | def infer_declared_from_conditions(conds, namespace=None):
''' like infer_declared except that it is passed a set of first party
caveat conditions as a list of string rather than a set of macaroons.
'''
conflicts = []
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useblocks/groundwork | groundwork/patterns/gw_base_pattern.py | GwBasePattern._pre_activate_injection | def _pre_activate_injection(self):
"""
Injects functions before the activation routine of child classes gets called
"""
# Let's be sure that this plugins class is registered and available on application level under
# application.plugins.classes. This allows to reuse this class fo... | python | def _pre_activate_injection(self):
"""
Injects functions before the activation routine of child classes gets called
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useblocks/groundwork | groundwork/patterns/gw_base_pattern.py | SignalsPlugin.register | def register(self, signal, description):
"""
Registers a new signal.
Only registered signals are allowed to be send.
:param signal: Unique name of the signal
:param description: Description of the reason or use case, why this signal is needed.
Used fo... | python | def register(self, signal, description):
"""
Registers a new signal.
Only registered signals are allowed to be send.
:param signal: Unique name of the signal
:param description: Description of the reason or use case, why this signal is needed.
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useblocks/groundwork | groundwork/patterns/gw_base_pattern.py | SignalsPlugin.get | def get(self, signal=None):
"""
Returns a single signal or a dictionary of signals for this plugin.
"""
return self.__app.signals.get(signal, self._plugin) | python | def get(self, signal=None):
"""
Returns a single signal or a dictionary of signals for this plugin.
"""
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useblocks/groundwork | groundwork/patterns/gw_base_pattern.py | SignalsPlugin.get_receiver | def get_receiver(self, receiver=None):
"""
Returns a single receiver or a dictionary of receivers for this plugin.
"""
return self.__app.signals.get_receiver(receiver, self._plugin) | python | def get_receiver(self, receiver=None):
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Returns a single receiver or a dictionary of receivers for this plugin.
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ets-labs/python-domain-models | domain_models/views.py | ContextViewMetaClass.validate | def validate(mcs, bases, attributes):
"""Check attributes."""
if bases[0] is object:
return None
mcs.check_model_cls(attributes)
mcs.check_include_exclude(attributes)
mcs.check_properties(attributes) | python | def validate(mcs, bases, attributes):
"""Check attributes."""
if bases[0] is object:
return None
mcs.check_model_cls(attributes)
mcs.check_include_exclude(attributes)
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ets-labs/python-domain-models | domain_models/views.py | ContextViewMetaClass.get_properties | def get_properties(attributes):
"""Return tuple of names of defined properties.
:type attributes: dict
:rtype: list
"""
return [key for key, value in six.iteritems(attributes)
if isinstance(value, property)] | python | def get_properties(attributes):
"""Return tuple of names of defined properties.
:type attributes: dict
:rtype: list
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ets-labs/python-domain-models | domain_models/views.py | ContextViewMetaClass.check_properties | def check_properties(mcs, attributes):
"""Check whether intersections exist.
:type attributes: dict
"""
include, exclude = mcs.get_prepared_include_exclude(attributes)
properties = mcs.get_properties(attributes)
intersections = list(
set(properties).intersect... | python | def check_properties(mcs, attributes):
"""Check whether intersections exist.
:type attributes: dict
"""
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properties = mcs.get_properties(attributes)
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SandstoneHPC/sandstone-ide | sandstone/lib/filesystem/filewatcher.py | FilesystemEventHandler.on_deleted | def on_deleted(self, event):
"""
Event Handler when a file is deleted
"""
key = 'filesystem:file_deleted'
data = {
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'is_directory': event.is_directory,
'dirpath': os.path.dirname(event.src_path)
}
bms... | python | def on_deleted(self, event):
"""
Event Handler when a file is deleted
"""
key = 'filesystem:file_deleted'
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'is_directory': event.is_directory,
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go-macaroon-bakery/py-macaroon-bakery | macaroonbakery/httpbakery/agent/_agent.py | read_auth_info | def read_auth_info(agent_file_content):
'''Loads agent authentication information from the
specified content string, as read from an agents file.
The returned information is suitable for passing as an argument
to the AgentInteractor constructor.
@param agent_file_content The agent file content (str)... | python | def read_auth_info(agent_file_content):
'''Loads agent authentication information from the
specified content string, as read from an agents file.
The returned information is suitable for passing as an argument
to the AgentInteractor constructor.
@param agent_file_content The agent file content (str)... | [
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go-macaroon-bakery/py-macaroon-bakery | macaroonbakery/httpbakery/agent/_agent.py | AgentInteractor.interact | def interact(self, client, location, interaction_required_err):
'''Implement Interactor.interact by obtaining obtaining
a macaroon from the discharger, discharging it with the
local private key using the discharged macaroon as
a discharge token'''
p = interaction_required_err.int... | python | def interact(self, client, location, interaction_required_err):
'''Implement Interactor.interact by obtaining obtaining
a macaroon from the discharger, discharging it with the
local private key using the discharged macaroon as
a discharge token'''
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go-macaroon-bakery/py-macaroon-bakery | macaroonbakery/httpbakery/agent/_agent.py | AgentInteractor.legacy_interact | def legacy_interact(self, client, location, visit_url):
'''Implement LegacyInteractor.legacy_interact by obtaining
the discharge macaroon using the client's private key
'''
agent = self._find_agent(location)
# Shallow-copy the client so that we don't unexpectedly side-effect
... | python | def legacy_interact(self, client, location, visit_url):
'''Implement LegacyInteractor.legacy_interact by obtaining
the discharge macaroon using the client's private key
'''
agent = self._find_agent(location)
# Shallow-copy the client so that we don't unexpectedly side-effect
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go-macaroon-bakery/py-macaroon-bakery | macaroonbakery/checkers/_time.py | expiry_time | def expiry_time(ns, cavs):
''' Returns the minimum time of any time-before caveats found
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The ns parameter is
:param ns: used to determine the standard namespace prefix - if
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... | python | def expiry_time(ns, cavs):
''' Returns the minimum time of any time-before caveats found
in the given list or None if no such caveats were found.
The ns parameter is
:param ns: used to determine the standard namespace prefix - if
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Phyks/libbmc | libbmc/tools.py | replace_all | def replace_all(text, replace_dict):
"""
Replace multiple strings in a text.
.. note::
Replacements are made successively, without any warranty on the order \
in which they are made.
:param text: Text to replace in.
:param replace_dict: Dictionary mapping strings to replace with ... | python | def replace_all(text, replace_dict):
"""
Replace multiple strings in a text.
.. note::
Replacements are made successively, without any warranty on the order \
in which they are made.
:param text: Text to replace in.
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Phyks/libbmc | libbmc/tools.py | map_or_apply | def map_or_apply(function, param):
"""
Map the function on ``param``, or apply it, depending whether ``param`` \
is a list or an item.
:param function: The function to apply.
:param param: The parameter to feed the function with (list or item).
:returns: The computed value or ``None``.
... | python | def map_or_apply(function, param):
"""
Map the function on ``param``, or apply it, depending whether ``param`` \
is a list or an item.
:param function: The function to apply.
:param param: The parameter to feed the function with (list or item).
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Phyks/libbmc | libbmc/tools.py | batch | def batch(iterable, size):
"""
Get items from a sequence a batch at a time.
.. note:
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https://code.activestate.com/recipes/303279-getting-items-in-batches/.
.. note:
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"""
Get items from a sequence a batch at a time.
.. note:
Adapted from
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Phyks/libbmc | libbmc/tools.py | slugify | def slugify(value):
"""
Normalizes string, converts to lowercase, removes non-alpha characters,
and converts spaces to hyphens to have nice filenames.
From Django's "django/template/defaultfilters.py".
>>> slugify("El pingüino Wenceslao hizo kilómetros bajo exhaustiva lluvia y frío, añoraba a su q... | python | def slugify(value):
"""
Normalizes string, converts to lowercase, removes non-alpha characters,
and converts spaces to hyphens to have nice filenames.
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>>> slugify("El pingüino Wenceslao hizo kilómetros bajo exhaustiva lluvia y frío, añoraba a su q... | [
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Phyks/libbmc | libbmc/citations/repositories/arxiv.py | get_plaintext_citations | def get_plaintext_citations(arxiv_id):
"""
Get the citations of a given preprint, in plain text.
.. note::
Bulk download of sources from arXiv is not permitted by their API. \
You should have a look at http://arxiv.org/help/bulk_data_s3.
:param arxiv_id: The arXiv id (e.g. ``1... | python | def get_plaintext_citations(arxiv_id):
"""
Get the citations of a given preprint, in plain text.
.. note::
Bulk download of sources from arXiv is not permitted by their API. \
You should have a look at http://arxiv.org/help/bulk_data_s3.
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Phyks/libbmc | libbmc/citations/repositories/arxiv.py | get_cited_dois | def get_cited_dois(arxiv_id):
"""
Get the DOIs of the papers cited in a .bbl file.
.. note::
Bulk download of sources from arXiv is not permitted by their API. \
You should have a look at http://arxiv.org/help/bulk_data_s3.
:param arxiv_id: The arXiv id (e.g. ``1401.2910`` or ... | python | def get_cited_dois(arxiv_id):
"""
Get the DOIs of the papers cited in a .bbl file.
.. note::
Bulk download of sources from arXiv is not permitted by their API. \
You should have a look at http://arxiv.org/help/bulk_data_s3.
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eonpatapon/contrail-api-cli | contrail_api_cli/main.py | get_subcommand_kwargs | def get_subcommand_kwargs(mgr, name, namespace):
"""Get subcommand options from global parsed
arguments.
"""
subcmd = mgr.get(name)
subcmd_kwargs = {}
for opt in list(subcmd.args.values()) + list(subcmd.options.values()):
if hasattr(namespace, opt.dest):
subcmd_kwargs[opt.des... | python | def get_subcommand_kwargs(mgr, name, namespace):
"""Get subcommand options from global parsed
arguments.
"""
subcmd = mgr.get(name)
subcmd_kwargs = {}
for opt in list(subcmd.args.values()) + list(subcmd.options.values()):
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Phyks/libbmc | libbmc/citations/plaintext.py | get_plaintext_citations | def get_plaintext_citations(file):
"""
Parse a plaintext file to get a clean list of plaintext citations. The \
file should have one citation per line.
:param file: Either the path to the plaintext file or the content of a \
plaintext file.
:returns: A list of cleaned plaintext... | python | def get_plaintext_citations(file):
"""
Parse a plaintext file to get a clean list of plaintext citations. The \
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:param file: Either the path to the plaintext file or the content of a \
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Phyks/libbmc | libbmc/citations/plaintext.py | get_cited_dois | def get_cited_dois(file):
"""
Get the DOIs of the papers cited in a plaintext file. The file should \
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.. note::
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"""
Get the DOIs of the papers cited in a plaintext file. The file should \
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Phyks/libbmc | libbmc/isbn.py | is_valid | def is_valid(isbn_id):
"""
Check that a given string is a valid ISBN.
:param isbn_id: the isbn to be checked.
:returns: boolean indicating whether the isbn is valid or not.
>>> is_valid("978-3-16-148410-0")
True
>>> is_valid("9783161484100")
True
>>> is_valid("9783161484100aa")
... | python | def is_valid(isbn_id):
"""
Check that a given string is a valid ISBN.
:param isbn_id: the isbn to be checked.
:returns: boolean indicating whether the isbn is valid or not.
>>> is_valid("978-3-16-148410-0")
True
>>> is_valid("9783161484100")
True
>>> is_valid("9783161484100aa")
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Phyks/libbmc | libbmc/isbn.py | extract_from_text | def extract_from_text(text):
"""
Extract ISBNs from a text.
:param text: Some text.
:returns: A list of canonical ISBNs found in the text.
>>> extract_from_text("978-3-16-148410-0 9783161484100 9783161484100aa abcd 0136091814 0136091812 9780136091817 123456789X")
['9783161484100', '97831614841... | python | def extract_from_text(text):
"""
Extract ISBNs from a text.
:param text: Some text.
:returns: A list of canonical ISBNs found in the text.
>>> extract_from_text("978-3-16-148410-0 9783161484100 9783161484100aa abcd 0136091814 0136091812 9780136091817 123456789X")
['9783161484100', '97831614841... | [
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Phyks/libbmc | libbmc/isbn.py | get_bibtex | def get_bibtex(isbn_identifier):
"""
Get a BibTeX string for the given ISBN.
:param isbn_identifier: ISBN to fetch BibTeX entry for.
:returns: A BibTeX string or ``None`` if could not fetch it.
>>> get_bibtex('9783161484100')
'@book{9783161484100,\\n title = {Berkeley, Oakland: Albany, Eme... | python | def get_bibtex(isbn_identifier):
"""
Get a BibTeX string for the given ISBN.
:param isbn_identifier: ISBN to fetch BibTeX entry for.
:returns: A BibTeX string or ``None`` if could not fetch it.
>>> get_bibtex('9783161484100')
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eonpatapon/contrail-api-cli | contrail_api_cli/parser.py | CommandParser.used_options | def used_options(self):
"""Return options already used in the
command line
rtype: command.Option generator
"""
for option_str in filter(lambda c: c.startswith('-'), self.words):
for option in list(self.cmd.options.values()):
if option_str in option.op... | python | def used_options(self):
"""Return options already used in the
command line
rtype: command.Option generator
"""
for option_str in filter(lambda c: c.startswith('-'), self.words):
for option in list(self.cmd.options.values()):
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eonpatapon/contrail-api-cli | contrail_api_cli/parser.py | CommandParser.available_options | def available_options(self):
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rtype: command.Option generator
"""
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rtype: command.Option generator
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rtype: command.Arg generator
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crm416/semantic | semantic/solver.py | MathService._preprocess | def _preprocess(inp):
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inp = re.sub(r'to the (.*) power', r'to \g<1>', inp)
inp = re.sub(r'to the (.*?)(\b)', r'to \g<1>\g<2>', inp)
inp = re.sub(r'log of', r'log', inp)
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inp = re.sub(r'to the (.*) power', r'to \g<1>', inp)
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go-macaroon-bakery/py-macaroon-bakery | macaroonbakery/checkers/_caveat.py | declared_caveat | def declared_caveat(key, value):
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'''Returns a "declared" caveat asserting that the given key is
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go-macaroon-bakery/py-macaroon-bakery | macaroonbakery/checkers/_caveat.py | _operation_caveat | def _operation_caveat(cond, ops):
''' Helper for allow_caveat and deny_caveat.
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'''
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return _first_party(con... | python | def _operation_caveat(cond, ops):
''' Helper for allow_caveat and deny_caveat.
It checks that all operation names are valid before creating the caveat.
'''
for op in ops:
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@param s string or bytes
@return bytes
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go-macaroon-bakery/py-macaroon-bakery | macaroonbakery/_utils/__init__.py | raw_urlsafe_b64encode | def raw_urlsafe_b64encode(b):
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@return bytes decoded
'''
b = to_bytes(b)
b = base64.urlsafe_b64encode(b)
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'''Base64 encode using URL-safe encoding with padding removed.
@param b bytes to decode
@return bytes decoded
'''
b = to_bytes(b)
b = base64.urlsafe_b64encode(b)
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go-macaroon-bakery/py-macaroon-bakery | macaroonbakery/_utils/__init__.py | cookie | def cookie(
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@param name The cookie name {str}
@param value The cookie value {str}
@param url The URL path of the cookie {str}
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url,
name,
value,
expires=None):
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@param name The cookie name {str}
@param value The cookie value {str}
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swevm/scaleio-py | scaleiopy/im.py | Im._login | def _login(self):
"""
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"""
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"""
LOGIN CAN ONLY BE DONE BY POSTING TO A HTTP FORM.
A COOKIE IS THEN USED FOR INTERACTING WITH THE API
"""
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swevm/scaleio-py | scaleiopy/im.py | Im._do_get | def _do_get(self, uri, **kwargs):
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Convinient method for GET requests
Returns http request status value from a POST request
"""
#TODO:
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scaleioapi_get_head... | python | def _do_get(self, uri, **kwargs):
"""
Convinient method for GET requests
Returns http request status value from a POST request
"""
#TODO:
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swevm/scaleio-py | scaleiopy/im.py | Im.uploadFileToIM | def uploadFileToIM (self, directory, filename, title):
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Parameters as they look in the form for uploading packages to IM
"""
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parameters = {'data-filename-placement':'inside',
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"""
Parameters as they look in the form for uploading packages to IM
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ph4r05/monero-serialize | monero_serialize/xmrrpc.py | dump_varint_t | async def dump_varint_t(writer, type_or, pv):
"""
Binary dump of the integer of given type
:param writer:
:param type_or:
:param pv:
:return:
"""
width = int_mark_to_size(type_or)
n = (pv << 2) | type_or
buffer = _UINT_BUFFER
for _ in range(width):
buffer[0] = n & 0... | python | async def dump_varint_t(writer, type_or, pv):
"""
Binary dump of the integer of given type
:param writer:
:param type_or:
:param pv:
:return:
"""
width = int_mark_to_size(type_or)
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ph4r05/monero-serialize | monero_serialize/xmrrpc.py | dump_varint | async def dump_varint(writer, val):
"""
Binary dump of the variable size integer
:param writer:
:param val:
:return:
"""
if val <= 63:
return await dump_varint_t(writer, PortableRawSizeMark.BYTE, val)
elif val <= 16383:
return await dump_varint_t(writer, PortableRawSizeM... | python | async def dump_varint(writer, val):
"""
Binary dump of the variable size integer
:param writer:
:param val:
:return:
"""
if val <= 63:
return await dump_varint_t(writer, PortableRawSizeMark.BYTE, val)
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ph4r05/monero-serialize | monero_serialize/xmrrpc.py | load_varint | async def load_varint(reader):
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result = buffer[0]
shift = 8
fo... | python | async def load_varint(reader):
"""
Binary load of variable size integer serialized by dump_varint
:param reader:
:return:
"""
buffer = _UINT_BUFFER
await reader.areadinto(buffer)
width = int_mark_to_size(buffer[0] & PortableRawSizeMark.MASK)
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ph4r05/monero-serialize | monero_serialize/xmrrpc.py | dump_string | async def dump_string(writer, val):
"""
Binary string dump
:param writer:
:param val:
:return:
"""
await dump_varint(writer, len(val))
await writer.awrite(val) | python | async def dump_string(writer, val):
"""
Binary string dump
:param writer:
:param val:
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"""
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ph4r05/monero-serialize | monero_serialize/xmrrpc.py | load_string | async def load_string(reader):
"""
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"""
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fvalue = bytearray(ivalue)
await reader.areadinto(fvalue)
return bytes(fvalue) | python | async def load_string(reader):
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ph4r05/monero-serialize | monero_serialize/xmrrpc.py | dump_blob | async def dump_blob(writer, elem, elem_type, params=None):
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:param elem_type:
:param params:
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:param elem_type:
:param params:
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ph4r05/monero-serialize | monero_serialize/xmrrpc.py | Blobber.container_load | async def container_load(self, container_type, params=None, container=None, obj=None):
"""
Loads container of elements from the reader. Supports the container ref.
Returns loaded container.
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"""
Loads container of elements from the reader. Supports the container ref.
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jenisys/parse_type | bin/make_localpi.py | make_index_for | def make_index_for(package, index_dir, verbose=True):
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dbarsam/python-vsgen | vsgen/util/config.py | VSGConfigParser._convert_to_list | def _convert_to_list(self, value, delimiters):
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dbarsam/python-vsgen | vsgen/util/config.py | VSGConfigParser.getlist | def getlist(self, section, option, raw=False, vars=None, fallback=[], delimiters=','):
"""
A convenience method which coerces the option in the specified section to a list of strings.
"""
v = self.get(section, option, raw=raw, vars=vars, fallback=fallback)
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A convenience method which coerces the option in the specified section to a list of strings.
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dbarsam/python-vsgen | vsgen/util/config.py | VSGConfigParser.getfile | def getfile(self, section, option, raw=False, vars=None, fallback="", validate=False):
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A convenience method which coerces the option in the specified section to a file.
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dbarsam/python-vsgen | vsgen/util/config.py | VSGConfigParser.getdir | def getdir(self, section, option, raw=False, vars=None, fallback="", validate=False):
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dbarsam/python-vsgen | vsgen/util/config.py | VSGConfigParser.getdirs | def getdirs(self, section, option, raw=False, vars=None, fallback=[]):
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useblocks/groundwork | groundwork/patterns/gw_documents_pattern.py | DocumentsListPlugin.register | def register(self, name, content, description=None):
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useblocks/groundwork | groundwork/patterns/gw_documents_pattern.py | DocumentsListApplication.unregister | def unregister(self, document):
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Unregisters an existing document, so that this document is no longer available.
This function is mainly used during plugin deactivation.
:param document: Name of the document
"""
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useblocks/groundwork | groundwork/patterns/gw_documents_pattern.py | DocumentsListApplication.get | def get(self, document=None, plugin=None):
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:param plugin: Plugin object, under which the document was registered
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useblocks/groundwork | groundwork/pluginmanager.py | PluginManager.initialise_by_names | def initialise_by_names(self, plugins=None):
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useblocks/groundwork | groundwork/pluginmanager.py | PluginManager.get | def get(self, name=None):
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useblocks/groundwork | groundwork/pluginmanager.py | PluginManager.is_active | def is_active(self, name):
"""
Returns True if plugin exists and is active.
If plugin does not exist, it returns None
:param name: plugin name
:return: boolean or None
"""
if name in self._plugins.keys():
return self._plugins["name"].active
re... | python | def is_active(self, name):
"""
Returns True if plugin exists and is active.
If plugin does not exist, it returns None
:param name: plugin name
:return: boolean or None
"""
if name in self._plugins.keys():
return self._plugins["name"].active
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useblocks/groundwork | groundwork/pluginmanager.py | PluginClassManager.register | def register(self, classes=[]):
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useblocks/groundwork | groundwork/pluginmanager.py | PluginClassManager.get | def get(self, name=None):
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:param name: Name of a plugin
:return: None, single plugin or dictionary of plugins
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dbarsam/python-vsgen | vsgen/solution.py | VSGSolution.write | def write(self):
"""
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retu... | python | def write(self):
"""
Writes the ``.sln`` file to disk.
"""
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atarashansky/self-assembling-manifold | SAM.py | SAM.load_annotations | def load_annotations(self, aname, sep=','):
"""Loads cell annotations.
Loads the cell annoations specified by the 'aname' path.
Parameters
----------
aname - string
The path to the annotations file. First column should be cell IDs
and second column shoul... | python | def load_annotations(self, aname, sep=','):
"""Loads cell annotations.
Loads the cell annoations specified by the 'aname' path.
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aname - string
The path to the annotations file. First column should be cell IDs
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atarashansky/self-assembling-manifold | SAM.py | SAM.dispersion_ranking_NN | def dispersion_ranking_NN(self, nnm, num_norm_avg=50):
"""Computes the spatial dispersion factors for each gene.
Parameters
----------
nnm - scipy.sparse, float
Square cell-to-cell nearest-neighbor matrix.
num_norm_avg - int, optional, default 50
The top... | python | def dispersion_ranking_NN(self, nnm, num_norm_avg=50):
"""Computes the spatial dispersion factors for each gene.
Parameters
----------
nnm - scipy.sparse, float
Square cell-to-cell nearest-neighbor matrix.
num_norm_avg - int, optional, default 50
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atarashansky/self-assembling-manifold | SAM.py | SAM.plot_correlated_groups | def plot_correlated_groups(self, group=None, n_genes=5, **kwargs):
"""Plots orthogonal expression patterns.
In the default mode, plots orthogonal gene expression patterns. A
specific correlated group of genes can be specified to plot gene
expression patterns within that group.
... | python | def plot_correlated_groups(self, group=None, n_genes=5, **kwargs):
"""Plots orthogonal expression patterns.
In the default mode, plots orthogonal gene expression patterns. A
specific correlated group of genes can be specified to plot gene
expression patterns within that group.
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atarashansky/self-assembling-manifold | SAM.py | SAM.plot_correlated_genes | def plot_correlated_genes(
self,
name,
n_genes=5,
number_of_features=1000,
**kwargs):
"""Plots gene expression patterns correlated with the input gene.
Parameters
----------
name - string
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self,
name,
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number_of_features=1000,
**kwargs):
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name - string
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atarashansky/self-assembling-manifold | SAM.py | SAM.run_tsne | def run_tsne(self, X=None, metric='correlation', **kwargs):
"""Wrapper for sklearn's t-SNE implementation.
See sklearn for the t-SNE documentation. All arguments are the same
with the exception that 'metric' is set to 'precomputed' by default,
implying that this function expects a dista... | python | def run_tsne(self, X=None, metric='correlation', **kwargs):
"""Wrapper for sklearn's t-SNE implementation.
See sklearn for the t-SNE documentation. All arguments are the same
with the exception that 'metric' is set to 'precomputed' by default,
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atarashansky/self-assembling-manifold | SAM.py | SAM.run_umap | def run_umap(self, X=None, metric=None, **kwargs):
"""Wrapper for umap-learn.
See https://github.com/lmcinnes/umap sklearn for the documentation
and source code.
"""
import umap as umap
if metric is None:
metric = self.distance
if(X is not None):
... | python | def run_umap(self, X=None, metric=None, **kwargs):
"""Wrapper for umap-learn.
See https://github.com/lmcinnes/umap sklearn for the documentation
and source code.
"""
import umap as umap
if metric is None:
metric = self.distance
if(X is not None):
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atarashansky/self-assembling-manifold | SAM.py | SAM.scatter | def scatter(self, projection=None, c=None, cmap='rainbow', linewidth=0.0,
edgecolor='k', axes=None, colorbar=True, s=10, **kwargs):
"""Display a scatter plot.
Displays a scatter plot using the SAM projection or another input
projection with or without annotations.
Param... | python | def scatter(self, projection=None, c=None, cmap='rainbow', linewidth=0.0,
edgecolor='k', axes=None, colorbar=True, s=10, **kwargs):
"""Display a scatter plot.
Displays a scatter plot using the SAM projection or another input
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atarashansky/self-assembling-manifold | SAM.py | SAM.show_gene_expression | def show_gene_expression(self, gene, avg=True, axes=None, **kwargs):
"""Display a gene's expressions.
Displays a scatter plot using the SAM projection or another input
projection with a particular gene's expressions overlaid.
Parameters
----------
gene - string
... | python | def show_gene_expression(self, gene, avg=True, axes=None, **kwargs):
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Displays a scatter plot using the SAM projection or another input
projection with a particular gene's expressions overlaid.
Parameters
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gene - string
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atarashansky/self-assembling-manifold | SAM.py | SAM.louvain_clustering | def louvain_clustering(self, X=None, res=1, method='modularity'):
"""Runs Louvain clustering using the vtraag implementation. Assumes
that 'louvain' optional dependency is installed.
Parameters
----------
res - float, optional, default 1
The resolution parameter whic... | python | def louvain_clustering(self, X=None, res=1, method='modularity'):
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res - float, optional, default 1
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atarashansky/self-assembling-manifold | SAM.py | SAM.kmeans_clustering | def kmeans_clustering(self, numc, X=None, npcs=15):
"""Performs k-means clustering.
Parameters
----------
numc - int
Number of clusters
npcs - int, optional, default 15
Number of principal components to use as inpute for k-means
clustering.
... | python | def kmeans_clustering(self, numc, X=None, npcs=15):
"""Performs k-means clustering.
Parameters
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numc - int
Number of clusters
npcs - int, optional, default 15
Number of principal components to use as inpute for k-means
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atarashansky/self-assembling-manifold | SAM.py | SAM.identify_marker_genes_rf | def identify_marker_genes_rf(self, labels=None, clusters=None,
n_genes=4000):
"""
Ranks marker genes for each cluster using a random forest
classification approach.
Parameters
----------
labels - numpy.array or str, optional, default Non... | python | def identify_marker_genes_rf(self, labels=None, clusters=None,
n_genes=4000):
"""
Ranks marker genes for each cluster using a random forest
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atarashansky/self-assembling-manifold | SAM.py | SAM.identify_marker_genes_corr | def identify_marker_genes_corr(self, labels=None, n_genes=4000):
"""
Ranking marker genes based on their respective magnitudes in the
correlation dot products with cluster-specific reference expression
profiles.
Parameters
----------
labels - numpy.array or str... | python | def identify_marker_genes_corr(self, labels=None, n_genes=4000):
"""
Ranking marker genes based on their respective magnitudes in the
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Parameters
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cocoakekeyu/cancan | cancan/ability.py | Ability.add | def add(self, action=None, subject=None, **conditions):
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Add ability are allowed using two arguments.
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the third one is the subject's conditions must be m... | python | def add(self, action=None, subject=None, **conditions):
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cocoakekeyu/cancan | cancan/ability.py | Ability.addnot | def addnot(self, action=None, subject=None, **conditions):
"""
Defines an ability which cannot be done.
"""
self.add_rule(Rule(False, action, subject, **conditions)) | python | def addnot(self, action=None, subject=None, **conditions):
"""
Defines an ability which cannot be done.
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cocoakekeyu/cancan | cancan/ability.py | Ability.can | def can(self, action, subject, **conditions):
"""
Check if the user has permission to perform a given action on an object
"""
for rule in self.relevant_rules_for_match(action, subject):
if rule.matches_conditions(action, subject, **conditions):
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"""
Check if the user has permission to perform a given action on an object
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cocoakekeyu/cancan | cancan/ability.py | Ability.relevant_rules_for_match | def relevant_rules_for_match(self, action, subject):
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matches = []
for rule in self.rules:
rule.expanded_actions = self.expand_actions(rule.actions)
if rule.is_relevant(action, subject):
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r... | python | def relevant_rules_for_match(self, action, subject):
"""retrive match action and subject"""
matches = []
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rule.expanded_actions = self.expand_actions(rule.actions)
if rule.is_relevant(action, subject):
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cocoakekeyu/cancan | cancan/ability.py | Ability.expand_actions | def expand_actions(self, actions):
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Accepts an array of actions and returns an array of actions which match
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Accepts an array of actions and returns an array of actions which match
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cocoakekeyu/cancan | cancan/ability.py | Ability.alias_action | def alias_action(self, *args, **kwargs):
"""
Alias one or more actions into another one.
self.alias_action('create', 'read', 'update', 'delete', to='crud')
"""
to = kwargs.pop('to', None)
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"""
Alias one or more actions into another one.
self.alias_action('create', 'read', 'update', 'delete', to='crud')
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suurjaak/InputScope | inputscope/db.py | fetch | def fetch(table, cols="*", where=(), group="", order=(), limit=(), **kwargs):
"""Convenience wrapper for database SELECT and fetch all."""
return select(table, cols, where, group, order, limit, **kwargs).fetchall() | python | def fetch(table, cols="*", where=(), group="", order=(), limit=(), **kwargs):
"""Convenience wrapper for database SELECT and fetch all."""
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suurjaak/InputScope | inputscope/db.py | fetchone | def fetchone(table, cols="*", where=(), group="", order=(), limit=(), **kwargs):
"""Convenience wrapper for database SELECT and fetch one."""
return select(table, cols, where, group, order, limit, **kwargs).fetchone() | python | def fetchone(table, cols="*", where=(), group="", order=(), limit=(), **kwargs):
"""Convenience wrapper for database SELECT and fetch one."""
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suurjaak/InputScope | inputscope/db.py | insert | def insert(table, values=(), **kwargs):
"""Convenience wrapper for database INSERT."""
values = dict(values, **kwargs).items()
sql, args = makeSQL("INSERT", table, values=values)
return execute(sql, args).lastrowid | python | def insert(table, values=(), **kwargs):
"""Convenience wrapper for database INSERT."""
values = dict(values, **kwargs).items()
sql, args = makeSQL("INSERT", table, values=values)
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suurjaak/InputScope | inputscope/db.py | select | def select(table, cols="*", where=(), group="", order=(), limit=(), **kwargs):
"""Convenience wrapper for database SELECT."""
where = dict(where, **kwargs).items()
sql, args = makeSQL("SELECT", table, cols, where, group, order, limit)
return execute(sql, args) | python | def select(table, cols="*", where=(), group="", order=(), limit=(), **kwargs):
"""Convenience wrapper for database SELECT."""
where = dict(where, **kwargs).items()
sql, args = makeSQL("SELECT", table, cols, where, group, order, limit)
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suurjaak/InputScope | inputscope/db.py | update | def update(table, values, where=(), **kwargs):
"""Convenience wrapper for database UPDATE."""
where = dict(where, **kwargs).items()
sql, args = makeSQL("UPDATE", table, values=values, where=where)
return execute(sql, args).rowcount | python | def update(table, values, where=(), **kwargs):
"""Convenience wrapper for database UPDATE."""
where = dict(where, **kwargs).items()
sql, args = makeSQL("UPDATE", table, values=values, where=where)
return execute(sql, args).rowcount | [
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suurjaak/InputScope | inputscope/db.py | delete | def delete(table, where=(), **kwargs):
"""Convenience wrapper for database DELETE."""
where = dict(where, **kwargs).items()
sql, args = makeSQL("DELETE", table, where=where)
return execute(sql, args).rowcount | python | def delete(table, where=(), **kwargs):
"""Convenience wrapper for database DELETE."""
where = dict(where, **kwargs).items()
sql, args = makeSQL("DELETE", table, where=where)
return execute(sql, args).rowcount | [
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suurjaak/InputScope | inputscope/db.py | make_cursor | def make_cursor(path, init_statements=(), _connectioncache={}):
"""Returns a cursor to the database, making new connection if not cached."""
connection = _connectioncache.get(path)
if not connection:
is_new = not os.path.exists(path) or not os.path.getsize(path)
try: is_new and os.maked... | python | def make_cursor(path, init_statements=(), _connectioncache={}):
"""Returns a cursor to the database, making new connection if not cached."""
connection = _connectioncache.get(path)
if not connection:
is_new = not os.path.exists(path) or not os.path.getsize(path)
try: is_new and os.maked... | [
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