signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def fix_config ( self , options ) :
"""Fixes the options , if necessary . I . e . , it adds all required elements to the dictionary .
: param options : the options to fix
: type options : dict
: return : the ( potentially ) fixed options
: rtype : dict""" | options = super ( Console , self ) . fix_config ( options )
opt = "prefix"
if opt not in options :
options [ opt ] = ""
if opt not in self . help :
self . help [ opt ] = "The prefix for the output (string)."
return options |
def rotate ( self , vecs ) :
"""Rotate input vector ( s ) by the rotation matrix . `
Args :
vecs ( np . ndarray ) : Input vector ( s ) with dtype = np . float32.
The shape can be a single vector ( D , ) or several vectors ( N , D )
Returns :
np . ndarray : Rotated vectors with the same shape and dtype to ... | assert vecs . dtype == np . float32
assert vecs . ndim in [ 1 , 2 ]
if vecs . ndim == 2 :
return vecs @ self . R
elif vecs . ndim == 1 :
return ( vecs . reshape ( 1 , - 1 ) @ self . R ) . reshape ( - 1 ) |
def get_invitation ( self , invitation_id , ** kwargs ) : # noqa : E501
"""Details of a user invitation . # noqa : E501
An endpoint for retrieving the details of an active user invitation sent for a new or an existing user to join the account . * * Example usage : * * ` curl https : / / api . us - east - 1 . mbed... | kwargs [ '_return_http_data_only' ] = True
if kwargs . get ( 'asynchronous' ) :
return self . get_invitation_with_http_info ( invitation_id , ** kwargs )
# noqa : E501
else :
( data ) = self . get_invitation_with_http_info ( invitation_id , ** kwargs )
# noqa : E501
return data |
def _determine_colorspace ( self , colorspace = None , ** kwargs ) :
"""Determine the colorspace from the supplied inputs .
Parameters
colorspace : str , optional
Either ' rgb ' or ' gray ' .""" | if colorspace is None : # Must infer the colorspace from the image dimensions .
if len ( self . shape ) < 3 : # A single channel image is grayscale .
self . _colorspace = opj2 . CLRSPC_GRAY
elif self . shape [ 2 ] == 1 or self . shape [ 2 ] == 2 : # A single channel image or an image with two channels i... |
def create_css ( self , fileid = None ) :
"""Generate the final CSS string""" | if fileid :
rules = self . _rules . get ( fileid ) or [ ]
else :
rules = self . rules
compress = self . _scss_opts . get ( 'compress' , True )
if compress :
sc , sp , tb , nl = False , '' , '' , ''
else :
sc , sp , tb , nl = True , ' ' , ' ' , '\n'
scope = set ( )
return self . _create_css ( rules , sc... |
def _rollback ( self , where ) :
"""Truncate the output buffer at offset I { where } , and remove any
compression table entries that pointed beyond the truncation
point .
@ param where : the offset
@ type where : int""" | self . output . seek ( where )
self . output . truncate ( )
keys_to_delete = [ ]
for k , v in self . compress . iteritems ( ) :
if v >= where :
keys_to_delete . append ( k )
for k in keys_to_delete :
del self . compress [ k ] |
def _check_remote_option ( self , option ) :
"""Test the status of remote negotiated Telnet options .""" | if not self . telnet_opt_dict . has_key ( option ) :
self . telnet_opt_dict [ option ] = TelnetOption ( )
return self . telnet_opt_dict [ option ] . remote_option |
def members_data_for_in ( self , leaderboard_name , members ) :
'''Retrieve the optional member data for a given list of members in the named leaderboard .
@ param leaderboard _ name [ String ] Name of the leaderboard .
@ param members [ Array ] Member names .
@ return Array of strings of optional member data... | return self . redis_connection . hmget ( self . _member_data_key ( leaderboard_name ) , members ) |
def run_from_argv ( self , argv ) :
"""Set the default Gherkin test runner for its options to be parsed .""" | self . test_runner = test_runner_class
super ( Command , self ) . run_from_argv ( argv ) |
def previous_unwrittable_on_col ( view , coords ) :
"""Return position of the previous ( in column ) letter that is unwrittable""" | x , y = coords
miny = - 1
for offset in range ( y - 1 , miny , - 1 ) :
letter = view [ x , offset ]
if letter not in REWRITABLE_LETTERS :
return offset
return None |
def join ( strings : Optional [ Sequence [ str ] ] , separator : str = "" ) -> str :
"""Join strings in a given sequence .
Return an empty string if it is None or empty , otherwise join all items together
separated by separator if provided .""" | return separator . join ( s for s in strings if s ) if strings else "" |
def tokenize ( self , string ) :
'''Yield tokens from the input string or throw ConfigParseError''' | pos = 0
while pos < len ( string ) :
m = SKIP_RE . match ( string , pos = pos )
if m :
skip_lines = m . group ( 0 ) . split ( '\n' )
if len ( skip_lines ) > 1 :
self . row += len ( skip_lines ) - 1
self . column = 1 + len ( skip_lines [ - 1 ] )
else :
... |
def escape ( x , lb = False ) :
"""Ensure a string does not contain HTML - reserved characters ( including
double quotes )
Optionally also insert a linebreak if the string is too long""" | # Insert a linebreak ? Roughly around the middle of the string ,
if lb :
l = len ( x )
if l >= 10 :
l >>= 1
# middle of the string
s1 = x . find ( ' ' , l )
# first ws to the right
s2 = x . rfind ( ' ' , 0 , l )
# first ws to the left
if s2 > 0 :
... |
def getbfs ( coords , gbasis ) :
"""Convenience function for both wavefunction and density based on PyQuante Ints . py .""" | sym2powerlist = { 'S' : [ ( 0 , 0 , 0 ) ] , 'P' : [ ( 1 , 0 , 0 ) , ( 0 , 1 , 0 ) , ( 0 , 0 , 1 ) ] , 'D' : [ ( 2 , 0 , 0 ) , ( 0 , 2 , 0 ) , ( 0 , 0 , 2 ) , ( 1 , 1 , 0 ) , ( 0 , 1 , 1 ) , ( 1 , 0 , 1 ) ] , 'F' : [ ( 3 , 0 , 0 ) , ( 2 , 1 , 0 ) , ( 2 , 0 , 1 ) , ( 1 , 2 , 0 ) , ( 1 , 1 , 1 ) , ( 1 , 0 , 2 ) , ( 0 , 3 ... |
def getVoxelsScalar ( self , vmin = None , vmax = None ) :
"""Return voxel content as a ` ` numpy . array ` ` .
: param float vmin : rescale scalar content to match ` vmin ` and ` vmax ` range .
: param float vmax : rescale scalar content to match ` vmin ` and ` vmax ` range .""" | nx , ny , nz = self . image . GetDimensions ( )
voxdata = np . zeros ( [ nx , ny , nz ] )
lsx = range ( nx )
lsy = range ( ny )
lsz = range ( nz )
renorm = vmin is not None and vmax is not None
for i in lsx :
for j in lsy :
for k in lsz :
s = self . image . GetScalarComponentAsFloat ( i , j , k ... |
def set_state_data ( cls , entity , data ) :
"""Sets the state data for the given entity to the given data .
This also works for unmanaged entities .""" | attr_names = get_domain_class_attribute_names ( type ( entity ) )
nested_items = [ ]
for attr , new_attr_value in iteritems_ ( data ) :
if not attr . entity_attr in attr_names :
raise ValueError ( 'Can not set attribute "%s" for entity ' '"%s".' % ( attr . entity_attr , entity ) )
if '.' in attr . entit... |
def reverseCommit ( self ) :
"""Re - insert the previously removed character ( s ) .""" | # Get the text cursor for the current document .
tc = self . qteWidget . textCursor ( )
# Mark the previously inserted text and remove it .
tc . setPosition ( self . cursorPos0 , QtGui . QTextCursor . MoveAnchor )
tc . setPosition ( self . cursorPos1 , QtGui . QTextCursor . KeepAnchor )
tc . removeSelectedText ( )
tc .... |
def gracefulShutdown ( self ) :
"""Start shutting down""" | if not self . bf . perspective :
log . msg ( "No active connection, shutting down NOW" )
reactor . stop ( )
return
log . msg ( "Telling the master we want to shutdown after any running builds are finished" )
d = self . bf . perspective . callRemote ( "shutdown" )
def _shutdownfailed ( err ) :
if err . c... |
def _pick_inserted_ops_moment_indices ( operations : Sequence [ ops . Operation ] , start : int = 0 , frontier : Dict [ ops . Qid , int ] = None ) -> Tuple [ Sequence [ int ] , Dict [ ops . Qid , int ] ] :
"""Greedily assigns operations to moments .
Args :
operations : The operations to assign to moments .
st... | if frontier is None :
frontier = defaultdict ( lambda : 0 )
moment_indices = [ ]
for op in operations :
op_start = max ( start , max ( frontier [ q ] for q in op . qubits ) )
moment_indices . append ( op_start )
for q in op . qubits :
frontier [ q ] = max ( frontier [ q ] , op_start + 1 )
return... |
def stochastic_from_dist ( name , logp , random = None , logp_partial_gradients = { } , dtype = np . float , mv = False ) :
"""Return a Stochastic subclass made from a particular distribution .
: Parameters :
name : string
The name of the new class .
logp : function
The log - probability function .
rand... | ( args , defaults ) = utils . get_signature ( logp )
parent_names = args [ 1 : ]
try :
parents_default = dict ( zip ( args [ - len ( defaults ) : ] , defaults ) )
except TypeError : # No parents at all .
parents_default = { }
name = capitalize ( name )
# Build docstring from distribution
parents_str = ''
if par... |
def _summarize_inputs ( samples , out_dir ) :
"""Summarize inputs for MultiQC reporting in display .""" | logger . info ( "summarize target information" )
if samples [ 0 ] . get ( "analysis" , "" ) . lower ( ) in [ "variant" , "variant2" ] :
metrics_dir = utils . safe_makedir ( os . path . join ( out_dir , "report" , "metrics" ) )
samples = _merge_target_information ( samples , metrics_dir )
logger . info ( "summar... |
def post_authentication ( self , user , request , sid , ** kwargs ) :
"""Things that are done after a successful authentication .
: param user :
: param request :
: param sid :
: param kwargs :
: return : A dictionary with ' response _ args '""" | response_info = { }
# Do the authorization
try :
permission = self . endpoint_context . authz ( user , client_id = request [ 'client_id' ] )
except ToOld as err :
return self . error_response ( response_info , 'access_denied' , 'Authentication to old {}' . format ( err . args ) )
except Exception as err :
r... |
def _set_priv ( self , v , load = False ) :
"""Setter method for priv , mapped from YANG variable / rbridge _ id / snmp _ server / user / priv ( enumeration )
If this variable is read - only ( config : false ) in the
source YANG file , then _ set _ priv is considered as a private
method . Backends looking to ... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = RestrictedClassType ( base_type = unicode , restriction_type = "dict_key" , restriction_arg = { u'AES128' : { 'value' : 2 } , u'DES' : { 'value' : 0 } , u'nopriv' : { 'value' : 1 } } , ) , default = unicode ( "nopriv" ) , is_... |
def _MergeMessage ( node , source , destination , replace_message , replace_repeated ) :
"""Merge all fields specified by a sub - tree from source to destination .""" | source_descriptor = source . DESCRIPTOR
for name in node :
child = node [ name ]
field = source_descriptor . fields_by_name [ name ]
if field is None :
raise ValueError ( 'Error: Can\'t find field {0} in message {1}.' . format ( name , source_descriptor . full_name ) )
if child : # Sub - paths a... |
def output_size ( self ) :
"""Returns the module output size .""" | if callable ( self . _output_size ) :
self . _output_size = self . _output_size ( )
return self . _output_size |
def atlas_peer_refresh_zonefile_inventory ( my_hostport , peer_hostport , byte_offset , timeout = None , peer_table = None , con = None , path = None , local_inv = None ) :
"""Refresh a peer ' s zonefile recent inventory vector entries ,
by removing every bit after byte _ offset and re - synchronizing them .
Th... | if timeout is None :
timeout = atlas_inv_timeout ( )
if local_inv is None : # get local zonefile inv
inv_len = atlasdb_zonefile_inv_length ( con = con , path = path )
local_inv = atlas_make_zonefile_inventory ( 0 , inv_len , con = con , path = path )
maxlen = len ( local_inv )
with AtlasPeerTableLocked ( pe... |
def visualize_explanation ( explanation , label = None ) :
"""Given the output of the explain ( ) endpoint , produces a terminal visual that plots response strength over a sequence""" | if not sys . version_info [ : 2 ] >= ( 3 , 5 ) :
raise IndicoError ( "Python >= 3.5+ is required for explanation visualization" )
try :
from colr import Colr as C
except ImportError :
raise IndicoError ( "Package colr >= 0.8.1 is required for explanation visualization." )
cursor = 0
text = explanation [ 'te... |
def _with_retries ( self , pool , fn ) :
"""Performs the passed function with retries against the given pool .
: param pool : the connection pool to use
: type pool : Pool
: param fn : the function to pass a transport
: type fn : function""" | skip_nodes = [ ]
def _skip_bad_nodes ( transport ) :
return transport . _node not in skip_nodes
retry_count = self . retries - 1
first_try = True
current_try = 0
while True :
try :
with pool . transaction ( _filter = _skip_bad_nodes , yield_resource = True ) as resource :
transport = resourc... |
def prepend_name_scope ( name , import_scope ) :
"""Prepends name scope to a name .""" | # Based on tensorflow / python / framework / ops . py implementation .
if import_scope :
try :
str_to_replace = r"([\^]|loc:@|^)(.*)"
return re . sub ( str_to_replace , r"\1" + import_scope + r"/\2" , tf . compat . as_str_any ( name ) )
except TypeError as e : # If the name is not of a type we c... |
def get_element_id ( self , complete_name ) :
"""Get the TocElement element id - number of the element with the
supplied name .""" | [ group , name ] = complete_name . split ( '.' )
element = self . get_element ( group , name )
if element :
return element . ident
else :
logger . warning ( 'Unable to find variable [%s]' , complete_name )
return None |
def edit_message_text ( self , chat_id : Union [ int , str ] , message_id : int , text : str , parse_mode : str = "" , disable_web_page_preview : bool = None , reply_markup : "pyrogram.InlineKeyboardMarkup" = None ) -> "pyrogram.Message" :
"""Use this method to edit text messages .
Args :
chat _ id ( ` ` int ` ... | style = self . html if parse_mode . lower ( ) == "html" else self . markdown
r = self . send ( functions . messages . EditMessage ( peer = self . resolve_peer ( chat_id ) , id = message_id , no_webpage = disable_web_page_preview or None , reply_markup = reply_markup . write ( ) if reply_markup else None , ** style . pa... |
def website_verificable ( self , website ) :
"""True if the website is LetsEncrypt verificable : it should have the verification app
on the / . well - known path""" | required_app = [ self . LETSENCRYPT_VERIFY_APP_NAME , '/.well-known' ]
for app in website [ 'website_apps' ] :
if app == required_app :
return True
return False |
def show_health_monitor ( self , health_monitor , ** _params ) :
"""Fetches information of a certain load balancer health monitor .""" | return self . get ( self . health_monitor_path % ( health_monitor ) , params = _params ) |
def get_identifier ( self ) :
"""For methods this is the return type , the name and the ( non - pretty )
argument descriptor . For fields it is simply the name .
The return - type of methods is attached to the identifier when
it is a bridge method , which can technically allow two methods
with the same name... | ident = self . get_name ( )
if self . is_method :
args = "," . join ( self . get_arg_type_descriptors ( ) )
if self . is_bridge ( ) :
ident = "%s(%s):%s" % ( ident , args , self . get_descriptor ( ) )
else :
ident = "%s(%s)" % ( ident , args )
return ident |
def next_frame_glow_shapes ( ) :
"""Hparams for qualitative and quantitative results on shapes dataset .""" | hparams = next_frame_glow_bair_quant ( )
hparams . video_num_input_frames = 1
hparams . video_num_target_frames = 2
hparams . num_train_frames = 2
hparams . num_cond_latents = 1
hparams . coupling = "additive"
hparams . coupling_width = 512
hparams . latent_encoder_depth = 10
hparams . latent_skip = False
hparams . lea... |
def validate ( self , options ) :
"""Validate the options or exit ( )""" | if not options . port :
self . parser . error ( "'port' is required" )
if options . port == options . monitor_port :
self . parser . error ( "'port' and 'monitor-port' must not be the same." )
if options . buffer_size <= 0 :
self . parser . error ( "'buffer_size' must be > 0." )
try :
codecs . getencode... |
def stop_transmit ( self , fd ) :
"""Stop yielding writeability events for ` fd ` .
Redundant calls to : meth : ` stop _ transmit ` are silently ignored , this may
change in future .""" | self . _wfds . pop ( fd , None )
self . _update ( fd ) |
def _get_user ( self , username ) :
"""Custom helper method to retrieve a user ' s data from Redis .""" | data = self . client . get ( self . _key ( username ) )
if data is None :
return None
return json . loads ( data . decode ( ) ) |
def get_extensions ( extstr ) :
"""Return zero or greater Annotation Extensions , given a line of text .""" | # Extension examples :
# has _ direct _ input ( UniProtKB : P37840 ) , occurs _ in ( GO : 0005576)
# part _ of ( UBERON : 0006618 ) , part _ of ( UBERON : 0002302)
# occurs _ in ( CL : 0000988 ) | occurs _ in ( CL : 0001021)
if not extstr :
return None
exts = [ ]
for ext_lst in extstr . split ( '|' ) :
grp = [ ... |
def block_specification_to_number ( block : BlockSpecification , web3 : Web3 ) -> BlockNumber :
"""Converts a block specification to an actual block number""" | if isinstance ( block , str ) :
msg = f"string block specification can't contain {block}"
assert block in ( 'latest' , 'pending' ) , msg
number = web3 . eth . getBlock ( block ) [ 'number' ]
elif isinstance ( block , T_BlockHash ) :
number = web3 . eth . getBlock ( block ) [ 'number' ]
elif isinstance (... |
def is_koish ( board , c ) :
'Check if c is surrounded on all sides by 1 color , and return that color' | if board [ c ] != EMPTY :
return None
neighbors = { board [ n ] for n in NEIGHBORS [ c ] }
if len ( neighbors ) == 1 and EMPTY not in neighbors :
return list ( neighbors ) [ 0 ]
else :
return None |
def connect_sqs ( aws_access_key_id = None , aws_secret_access_key = None , ** kwargs ) :
""": type aws _ access _ key _ id : string
: param aws _ access _ key _ id : Your AWS Access Key ID
: type aws _ secret _ access _ key : string
: param aws _ secret _ access _ key : Your AWS Secret Access Key
: rtype :... | from boto . sqs . connection import SQSConnection
return SQSConnection ( aws_access_key_id , aws_secret_access_key , ** kwargs ) |
def vq_discrete_bottleneck ( x , hparams ) :
"""Simple vector quantized discrete bottleneck .""" | tf . logging . info ( "Using EMA with beta = {}" . format ( hparams . beta ) )
bottleneck_size = 2 ** hparams . bottleneck_bits
x_shape = common_layers . shape_list ( x )
x = tf . reshape ( x , [ - 1 , hparams . hidden_size ] )
x_means_hot , e_loss = vq_nearest_neighbor ( x , hparams )
means , ema_means , ema_count = (... |
from typing import List
def even_length_sorted ( strings : List [ str ] ) -> List [ str ] :
"""A function that receives a list of strings as input ,
removes strings with odd length from it ,
and returns the altered list sorted in ascending order .
The input list always contains strings and could include dupli... | # Sorting alphabetically
strings . sort ( )
# Removing odd length strings and sorting by length
even_length_strings = sorted ( [ s for s in strings if len ( s ) % 2 == 0 ] , key = len )
return even_length_strings |
def check_for_insufficient_eth ( self , transaction_name : str , transaction_executed : bool , required_gas : int , block_identifier : BlockSpecification , ) :
"""After estimate gas failure checks if our address has enough balance .
If the account did not have enough ETH balance to execute the ,
transaction the... | if transaction_executed :
return
our_address = to_checksum_address ( self . address )
balance = self . web3 . eth . getBalance ( our_address , block_identifier )
required_balance = required_gas * self . gas_price ( )
if balance < required_balance :
msg = f'Failed to execute {transaction_name} due to insufficien... |
def _f_lcs ( llcs , m , n ) :
"""Computes the LCS - based F - measure score
Source : http : / / research . microsoft . com / en - us / um / people / cyl / download / papers /
rouge - working - note - v1.3.1 . pdf
: param llcs : Length of LCS
: param m : number of words in reference summary
: param n : num... | r_lcs = llcs / m
p_lcs = llcs / n
beta = p_lcs / r_lcs
num = ( 1 + ( beta ** 2 ) ) * r_lcs * p_lcs
denom = r_lcs + ( ( beta ** 2 ) * p_lcs )
return num / denom |
def applyFilters ( self , endpoint ) :
"""Apply filter functions to an endpoint until one of them
returns non - None .""" | for filter_function in self . filter_functions :
e = filter_function ( endpoint )
if e is not None : # Once one of the filters has returned an
# endpoint , do not apply any more .
return e
return None |
def from_rdmol ( rdmol , assign_descriptor = True ) :
"""Convert RDMol to molecule""" | mol = Compound ( )
conf = rdmol . GetConformer ( )
Chem . Kekulize ( rdmol )
for atom in rdmol . GetAtoms ( ) :
key = atom . GetIdx ( )
a = Atom ( atom . GetSymbol ( ) )
a . coords = conf . GetAtomPosition ( key )
mol . add_atom ( key , a )
for bond in rdmol . GetBonds ( ) :
u = bond . GetBeginAtomI... |
def import_syscal_bin ( self , filename , ** kwargs ) :
"""Syscal import
timestep : int or : class : ` datetime . datetime `
if provided use this value to set the ' timestep ' column of the
produced dataframe . Default : 0""" | timestep = kwargs . get ( 'timestep' , None )
if 'timestep' in kwargs :
del ( kwargs [ 'timestep' ] )
self . logger . info ( 'IRIS Syscal Pro bin import' )
with LogDataChanges ( self , filter_action = 'import' ) :
data , electrodes , topography = reda_syscal . import_bin ( filename , ** kwargs )
if timestep... |
def on_message ( self , unused_channel , basic_deliver , properties , body ) :
"""Invoked by pika when a message is delivered from RabbitMQ . The
channel is passed for your convenience . The basic _ deliver object that
is passed in carries the exchange , routing key , delivery tag and
a redelivered flag for t... | logger . info ( 'Received message' , delivery_tag = basic_deliver . delivery_tag , app_id = properties . app_id , msg = body , )
self . acknowledge_message ( basic_deliver . delivery_tag ) |
def _url_to ( self , page ) :
"""Get the url of a page""" | anchor = ""
if "#" in page :
page , anchor = page . split ( "#" )
anchor = "#" + anchor
meta = self . _get_page_meta ( page )
return meta . get ( "url" ) |
def get_new_user_credentials ( self ) :
"""Gets new credentials
: return : New user credentials file upon user prompt""" | # OAuth2.0 authorization flow
flow = client . flow_from_clientsecrets ( self . app_secrets , self . scope )
flow . user_agent = self . app_name
return tools . run_flow ( flow , self . store ) |
def _handle_socket ( self , event : int , fd : int , multi : Any , data : bytes ) -> None :
"""Called by libcurl when it wants to change the file descriptors
it cares about .""" | event_map = { pycurl . POLL_NONE : ioloop . IOLoop . NONE , pycurl . POLL_IN : ioloop . IOLoop . READ , pycurl . POLL_OUT : ioloop . IOLoop . WRITE , pycurl . POLL_INOUT : ioloop . IOLoop . READ | ioloop . IOLoop . WRITE , }
if event == pycurl . POLL_REMOVE :
if fd in self . _fds :
self . io_loop . remove_h... |
def memory ( self , name , mem = 0 , swap = 0 ) :
"""Set / Get memory cgroup specification / limitation
the call to this method will always GET the current set values for both mem and swap .
If mem is not zero , the memory will set the memory limit to the given value , and swap to the given value ( even 0)
: ... | args = { 'name' : name , 'mem' : mem , 'swap' : swap , }
self . _memory_spec . check ( args )
return self . _client . json ( 'cgroup.memory.spec' , args ) |
def colorbrewer2_url ( self ) :
"""URL that can be used to view the color map at colorbrewer2 . org .""" | url = 'http://colorbrewer2.org/index.html?type={0}&scheme={1}&n={2}'
return url . format ( self . type . lower ( ) , self . name , self . number ) |
def parse_relation ( obj : dict ) -> BioCRelation :
"""Deserialize a dict obj to a BioCRelation object""" | rel = BioCRelation ( )
rel . id = obj [ 'id' ]
rel . infons = obj [ 'infons' ]
for node in obj [ 'nodes' ] :
rel . add_node ( BioCNode ( node [ 'refid' ] , node [ 'role' ] ) )
return rel |
def _handle_status ( self , key , value ) :
"""Parse a status code from the attached GnuPG process .
: raises : : exc : ` ~ exceptions . ValueError ` if the status message is unknown .""" | if key in ( "DELETE_PROBLEM" , "KEY_CONSIDERED" ) :
self . status = self . problem_reason . get ( value , "Unknown error: %r" % value )
else :
raise ValueError ( "Unknown status message: %r" % key ) |
def breslauer_corrections ( seq , pars_error ) :
'''Sum corrections for Breslauer ' 84 method .
: param seq : sequence for which to calculate corrections .
: type seq : str
: param pars _ error : dictionary of error corrections
: type pars _ error : dict
: returns : Corrected delta _ H and delta _ S param... | deltas_corr = [ 0 , 0 ]
contains_gc = 'G' in str ( seq ) or 'C' in str ( seq )
only_at = str ( seq ) . count ( 'A' ) + str ( seq ) . count ( 'T' ) == len ( seq )
symmetric = seq == seq . reverse_complement ( )
terminal_t = str ( seq ) [ 0 ] == 'T' + str ( seq ) [ - 1 ] == 'T'
for i , delta in enumerate ( [ 'delta_h' , ... |
def angle_to_cartesian ( lon , lat ) :
"""Convert spherical coordinates to cartesian unit vectors .""" | theta = np . array ( np . pi / 2. - lat )
return np . vstack ( ( np . sin ( theta ) * np . cos ( lon ) , np . sin ( theta ) * np . sin ( lon ) , np . cos ( theta ) ) ) . T |
def read_data ( self , chan = None , begtime = None , endtime = None , begsam = None , endsam = None , s_freq = None ) :
"""Read the data and creates a ChanTime instance
Parameters
chan : list of strings
names of the channels to read
begtime : int or datedelta or datetime or list
start of the data to read... | data = ChanTime ( )
data . start_time = self . header [ 'start_time' ]
data . s_freq = s_freq = s_freq if s_freq else self . header [ 's_freq' ]
if chan is None :
chan = self . header [ 'chan_name' ]
if not ( isinstance ( chan , list ) or isinstance ( chan , tuple ) ) :
raise TypeError ( 'Parameter "chan" shoul... |
def gen_cannon_grad_spec ( choose , coeffs , pivots ) :
"""Generate Cannon gradient spectra
Parameters
labels : default values for [ teff , logg , feh , cfe , nfe , afe , ak ]
choose : val of cfe or nfe , whatever you ' re varying
low : lowest val of cfe or nfe , whatever you ' re varying
high : highest v... | base_labels = [ 4800 , 2.5 , 0.03 , 0.10 , - 0.17 , - 0.17 , 0 , - 0.16 , - 0.13 , - 0.15 , 0.13 , 0.08 , 0.17 , - 0.062 ]
label_names = np . array ( [ 'TEFF' , 'LOGG' , 'AK' , 'Al' , 'Ca' , 'C' , 'Fe' , 'Mg' , 'Mn' , 'Ni' , 'N' , 'O' , 'Si' , 'Ti' ] )
label_atnum = np . array ( [ 0 , 1 , - 1 , 13 , 20 , 6 , 26 , 12 , ... |
def _parse_for_element_meta_data ( self , meta_data ) :
"""Load meta data for state elements
The meta data of the state meta data file also contains the meta data for state elements ( data ports ,
outcomes , etc ) . This method parses the loaded meta data for each state element model . The meta data of the
el... | # print ( " _ parse meta data " , meta _ data )
for data_port_m in self . input_data_ports :
self . _copy_element_meta_data_from_meta_file_data ( meta_data , data_port_m , "input_data_port" , data_port_m . data_port . data_port_id )
for data_port_m in self . output_data_ports :
self . _copy_element_meta_data_fr... |
def close ( self ) :
"""Closes the lvm and vg _ t handle . Usually you would never need to use this method
unless you are doing operations using the ctypes function wrappers in conversion . py
* Raises : *
* HandleError""" | if self . handle :
cl = lvm_vg_close ( self . handle )
if cl != 0 :
raise HandleError ( "Failed to close VG handle after init check." )
self . __vgh = None
self . lvm . close ( ) |
def set_type ( spec , obj_type ) :
"""Updates type integer in the cerate UO specification .
Type has to already have generations flags set correctly .
Generation field is set accordingly .
: param spec :
: param obj _ type :
: return :""" | if spec is None :
raise ValueError ( 'Spec cannot be None' )
if TemplateFields . generation not in spec :
spec [ TemplateFields . generation ] = { }
spec [ TemplateFields . generation ] [ TemplateFields . commkey ] = Gen . CLIENT if ( obj_type & ( int ( 1 ) << TemplateFields . FLAG_COMM_GEN ) ) > 0 else Gen . L... |
def generate_molecule_object_dict ( source , format , values ) :
"""Generate a dictionary that represents a Squonk MoleculeObject when
written as JSON
: param source : Molecules in molfile or smiles format
: param format : The format of the molecule . Either ' mol ' or ' smiles '
: param values : Optional d... | m = { "uuid" : str ( uuid . uuid4 ( ) ) , "source" : source , "format" : format }
if values :
m [ "values" ] = values
return m |
def is_square_product ( val : int ) -> bool :
"""This function determines if a given number can be obtained as the product of two squares .
Args :
val ( int ) : Input number .
Returns :
bool : Returns True if the given number can be expressed as the product of squares of two numbers . Otherwise , False .
... | for i in range ( 2 , val + 1 ) :
if i * i > val :
break
for j in range ( 2 , val + 1 ) :
if i * i * j * j == val :
return True
return False |
def match_regex ( self , regex : Pattern , required : bool = False , meaning : str = "" ) -> str :
"""Parse input based on a regular expression .
Args :
regex : Compiled regular expression object .
required : Should the exception be raised on unexpected input ?
meaning : Meaning of ` regex ` ( for use in er... | mo = regex . match ( self . input , self . offset )
if mo :
self . offset = mo . end ( )
return mo . group ( )
if required :
raise UnexpectedInput ( self , meaning ) |
def add_tab ( self , tab , title = '' , icon = None ) :
"""Adds a tab to main tab widget .
: param tab : Widget to add as a new tab of the main tab widget .
: param title : Tab title
: param icon : Tab icon""" | if icon :
tab . _icon = icon
if not hasattr ( tab , 'clones' ) :
tab . clones = [ ]
if not hasattr ( tab , 'original' ) :
tab . original = None
if icon :
self . main_tab_widget . addTab ( tab , icon , title )
else :
self . main_tab_widget . addTab ( tab , title )
self . main_tab_widget . setCurrentI... |
def add_isohybrid ( self , part_entry = 1 , mbr_id = None , part_offset = 0 , geometry_sectors = 32 , geometry_heads = 64 , part_type = 0x17 , mac = False ) : # type : ( int , Optional [ int ] , int , int , int , int , bool ) - > None
'''Make an ISO a ' hybrid ' , which means that it can be booted either from a
C... | if not self . _initialized :
raise pycdlibexception . PyCdlibInvalidInput ( 'This object is not yet initialized; call either open() or new() to create an ISO' )
if self . eltorito_boot_catalog is None :
raise pycdlibexception . PyCdlibInvalidInput ( 'The ISO must have an El Torito Boot Record to add isohybrid s... |
def get_response ( self , request , parent , * args , ** kwargs ) :
"""Render this collected content to a response .
: param request : the request
: param parent : the parent collection
: param args :
: param kwargs :
: return :""" | context = { 'page' : self , }
try :
return TemplateResponse ( request , self . get_layout_template_name ( ) , context )
except AttributeError :
raise AttributeError ( "You need to define " "`get_layout_template_name()` on your `%s` model, " "or override `get_response()`" % type ( self ) . __name__ ) |
def save_spec ( spec , filename ) :
"""Save a protobuf model specification to file .
Parameters
spec : Model _ pb
Protobuf representation of the model
filename : str
File path where the spec gets saved .
Examples
. . sourcecode : : python
> > > coremltools . utils . save _ spec ( spec , ' HousePrice... | name , ext = _os . path . splitext ( filename )
if not ext :
filename = "%s.mlmodel" % filename
else :
if ext != '.mlmodel' :
raise Exception ( "Extension must be .mlmodel (not %s)" % ext )
with open ( filename , 'wb' ) as f :
s = spec . SerializeToString ( )
f . write ( s ) |
def truncate ( hmac_result , length = 6 ) :
"""Perform the truncating .""" | assert ( len ( hmac_result ) == 20 )
offset = ord ( hmac_result [ 19 ] ) & 0xf
bin_code = ( ord ( hmac_result [ offset ] ) & 0x7f ) << 24 | ( ord ( hmac_result [ offset + 1 ] ) & 0xff ) << 16 | ( ord ( hmac_result [ offset + 2 ] ) & 0xff ) << 8 | ( ord ( hmac_result [ offset + 3 ] ) & 0xff )
return bin_code % ( 10 ** l... |
def phred_13_to_18 ( self , new_path = None , in_place = True ) :
"""Illumina - 1.3 format conversion to Illumina - 1.8 format via BioPython .""" | # New file #
if new_path is None :
new_fastq = self . __class__ ( new_temp_path ( suffix = self . extension ) )
else :
new_fastq = self . __class__ ( new_path )
# Do it #
self . format = 'fastq-illumina'
new_fastq . open ( 'w' )
new_fastq . handle . writelines ( seq . format ( 'fastq-sanger' ) for seq in self )... |
def RIBSystemRouteLimitExceeded_RIBRouteLimit ( self , ** kwargs ) :
"""Auto Generated Code""" | config = ET . Element ( "config" )
RIBSystemRouteLimitExceeded = ET . SubElement ( config , "RIBSystemRouteLimitExceeded" , xmlns = "http://brocade.com/ns/brocade-notification-stream" )
RIBRouteLimit = ET . SubElement ( RIBSystemRouteLimitExceeded , "RIBRouteLimit" )
RIBRouteLimit . text = kwargs . pop ( 'RIBRouteLimit... |
def have_all_block_data ( self ) :
"""Have we received all block data ?""" | if not ( self . num_blocks_received == self . num_blocks_requested ) :
log . debug ( "num blocks received = %s, num requested = %s" % ( self . num_blocks_received , self . num_blocks_requested ) )
return False
return True |
def execute_sparql_query ( query , prefix = None , endpoint = 'https://query.wikidata.org/sparql' , user_agent = config [ 'USER_AGENT_DEFAULT' ] , as_dataframe = False ) :
"""Static method which can be used to execute any SPARQL query
: param prefix : The URI prefixes required for an endpoint , default is the Wik... | if not endpoint :
endpoint = 'https://query.wikidata.org/sparql'
if prefix :
query = prefix + '\n' + query
params = { 'query' : '#Tool: PBB_core fastrun\n' + query , 'format' : 'json' }
headers = { 'Accept' : 'application/sparql-results+json' , 'User-Agent' : user_agent }
response = requests . get ( endpoint , ... |
def _extract_dot15d4address ( pkt , source = True ) :
"""This function extracts the source / destination address of a 6LoWPAN
from its upper Dot15d4Data ( 802.15.4 data ) layer .
params :
- source : if True , the address is the source one . Otherwise , it is the
destination .
returns : the packed & proces... | underlayer = pkt . underlayer
while underlayer is not None and not isinstance ( underlayer , Dot15d4Data ) : # noqa : E501
underlayer = underlayer . underlayer
if type ( underlayer ) == Dot15d4Data :
addr = underlayer . src_addr if source else underlayer . dest_addr
if underlayer . underlayer . fcf_destaddr... |
def estimateabundance ( self ) :
"""Estimate the abundance of taxonomic groups""" | logging . info ( 'Estimating abundance of taxonomic groups' )
# Create and start threads
for i in range ( self . cpus ) : # Send the threads to the appropriate destination function
threads = Thread ( target = self . estimate , args = ( ) )
# Set the daemon to true - something to do with thread management
th... |
def resize_pty ( self , width = 80 , height = 24 , width_pixels = 0 , height_pixels = 0 ) :
"""Resize the pseudo - terminal . This can be used to change the width and
height of the terminal emulation created in a previous ` get _ pty ` call .
: param int width : new width ( in characters ) of the terminal scree... | m = Message ( )
m . add_byte ( cMSG_CHANNEL_REQUEST )
m . add_int ( self . remote_chanid )
m . add_string ( "window-change" )
m . add_boolean ( False )
m . add_int ( width )
m . add_int ( height )
m . add_int ( width_pixels )
m . add_int ( height_pixels )
self . transport . _send_user_message ( m ) |
def run ( ) :
"""Run the workbench server""" | # Load the configuration file relative to this script location
config_path = os . path . join ( os . path . dirname ( os . path . realpath ( __file__ ) ) , 'config.ini' )
workbench_conf = ConfigParser . ConfigParser ( )
config_ini = workbench_conf . read ( config_path )
if not config_ini :
print 'Could not locate c... |
def open ( self ) :
"""Open a connection to an IOS - XR device .
Connects to the device using SSH and drops into XML mode .""" | try :
self . device = ConnectHandler ( device_type = 'cisco_xr' , ip = self . hostname , port = self . port , username = self . username , password = self . password , ** self . netmiko_kwargs )
self . device . timeout = self . timeout
self . _xml_agent_alive = True
# successfully open thus alive
except... |
def get_form ( self , request , obj = None , ** kwargs ) :
"""Returns a Form class for use in the admin add view . This is used by
add _ view and change _ view .""" | parent_id = request . GET . get ( 'parent_id' , None )
if not parent_id :
parent_id = request . POST . get ( 'parent_id' , None )
if parent_id :
return AddFolderPopupForm
else :
folder_form = super ( FolderAdmin , self ) . get_form ( request , obj = None , ** kwargs )
def folder_form_clean ( form_obj ) ... |
def read_struct ( fstream ) :
"""Read a likwid struct from the text stream .
Args :
fstream : Likwid ' s filestream .
Returns ( dict ( str : str ) ) :
A dict containing all likwid ' s struct info as key / value pairs .""" | line = fstream . readline ( ) . strip ( )
fragments = line . split ( "," )
fragments = [ x for x in fragments if x is not None ]
partition = dict ( )
if not len ( fragments ) >= 3 :
return None
partition [ "struct" ] = fragments [ 0 ]
partition [ "info" ] = fragments [ 1 ]
partition [ "num_lines" ] = fragments [ 2 ... |
def get_client_alg_keys ( client ) :
"""Takes a client and returns the set of keys associated with it .
Returns a list of keys .""" | if client . jwt_alg == 'RS256' :
keys = [ ]
for rsakey in RSAKey . objects . all ( ) :
keys . append ( jwk_RSAKey ( key = importKey ( rsakey . key ) , kid = rsakey . kid ) )
if not keys :
raise Exception ( 'You must add at least one RSA Key.' )
elif client . jwt_alg == 'HS256' :
keys = [... |
def safeprint ( message , write_to_stderr = False , newline = True ) :
"""Wrapper around click . echo used to encapsulate its functionality .
Also protects against EPIPE during click . echo calls , as this can happen
normally in piped commands when the consumer closes before the producer .""" | try :
click . echo ( message , nl = newline , err = write_to_stderr )
except IOError as err :
if err . errno is errno . EPIPE :
pass
else :
raise |
def getAppExt ( self , loops = float ( 'inf' ) ) :
"""getAppExt ( loops = float ( ' inf ' ) )
Application extention . This part specifies the amount of loops .
If loops is 0 or inf , it goes on infinitely .""" | if loops == 0 or loops == float ( 'inf' ) :
loops = 2 ** 16 - 1
# bb = " " application extension should not be used
# ( the extension interprets zero loops
# to mean an infinite number of loops )
# Mmm , does not seem to work
if True :
bb = "\x21\xFF\x0B"
# application extension
bb += "N... |
def create_message_buffer ( size , type ) :
"""Create a message buffer""" | rtn = wrapper . nn_allocmsg ( size , type )
if rtn is None :
raise NanoMsgAPIError ( )
return rtn |
def keyPressEvent ( self , event ) :
"""Handles the key press event . When the user hits F5 , the current
code edit will be executed within the console ' s scope .
: param event | < QtCore . QKeyEvent >""" | if event . key ( ) == QtCore . Qt . Key_F5 or ( event . key ( ) == QtCore . Qt . Key_E and event . modifiers ( ) == QtCore . Qt . ControlModifier ) :
code = str ( self . _edit . toPlainText ( ) )
scope = self . viewWidget ( ) . codeScope ( )
exec code in scope , scope
else :
super ( XScriptView , self )... |
def endpointlist_post_save ( instance , * args , ** kwargs ) :
"""Used to process the lines of the endpoint list .""" | with open ( instance . upload . file . name , mode = 'rb' ) as f :
lines = f . readlines ( )
for url in lines :
if len ( url ) > 255 :
LOGGER . debug ( 'Skipping this endpoint, as it is more than 255 characters: %s' % url )
else :
if Endpoint . objects . filter ( url = url , catalog = instan... |
def from_dict ( cls , d ) :
"""Validates a dict instance and transforms it in a
: py : class : ` gemstone . core . structs . JsonRpcRequest `
instance
: param d : The dict instance
: return : A : py : class : ` gemstone . core . structs . JsonRpcRequest `
if everything goes well , or None if the validatio... | for key in ( "method" , "jsonrpc" ) :
if key not in d :
raise JsonRpcInvalidRequestError ( )
# check jsonrpc version
jsonrpc = d . get ( "jsonrpc" , None )
if jsonrpc != "2.0" :
raise JsonRpcInvalidRequestError ( )
# check method
method = d . get ( "method" , None )
if not method :
raise JsonRpcInva... |
def _extract_format_keys ( self , fmt_string ) :
"""Extract the keys of a format string
( the ' stuff ' in ' % ( stuff ) s '""" | class AccessSaver :
def __init__ ( self ) :
self . keys = [ ]
def __getitem__ ( self , key ) :
self . keys . append ( key )
a = AccessSaver ( )
fmt_string % a
return a . keys |
def execute_bytecode ( self , origin : Address , gas_price : int , gas : int , to : Address , sender : Address , value : int , data : bytes , code : bytes , code_address : Address = None , ) -> BaseComputation :
"""Execute raw bytecode in the context of the current state of
the virtual machine .""" | if origin is None :
origin = sender
# Construct a message
message = Message ( gas = gas , to = to , sender = sender , value = value , data = data , code = code , code_address = code_address , )
# Construction a tx context
transaction_context = self . state . get_transaction_context_class ( ) ( gas_price = gas_price... |
def html_page_context ( app , pagename , templatename , context , doctree ) :
'''Collect page names for the sitemap as HTML pages are built .''' | site = context [ 'SITEMAP_BASE_URL' ]
version = context [ 'version' ]
app . sitemap_links . add ( site + version + '/' + pagename + ".html" ) |
def run_calculation ( self , atoms = None , properties = [ 'energy' ] , system_changes = all_changes ) :
'''Internal calculation executor . We cannot use FileIOCalculator
directly since we need to support remote execution .
This calculator is different from others .
It prepares the directory , launches the re... | self . calc . calculate ( self , atoms , properties , system_changes )
self . write_input ( self . atoms , properties , system_changes )
if self . command is None :
raise RuntimeError ( 'Please configure Remote calculator!' )
olddir = os . getcwd ( )
errorcode = 0
try :
os . chdir ( self . directory )
outpu... |
def dispatchlist ( self , * , author = None , category = None , subcategory = None , sort = 'new' ) :
"""Find dispatches by certain criteria .
Parameters
author : str
Name of the nation authoring the dispatch .
category : str
Dispatch ' s primary category .
subcategory : str
Dispatch ' s secondary cat... | params = { 'sort' : sort }
if author :
params [ 'dispatchauthor' ] = author
# Here we do need to ensure that our categories are valid , cause
# NS just ignores the categories it doesn ' t recognise and returns
# whatever it feels like .
if category and subcategory :
if ( category not in dispatch_categories or s... |
def set_pointer0d ( subseqs ) :
"""Set _ pointer function for 0 - dimensional link sequences .""" | print ( ' . set_pointer0d' )
lines = Lines ( )
lines . add ( 1 , 'cpdef inline set_pointer0d' '(self, str name, pointerutils.PDouble value):' )
for seq in subseqs :
lines . add ( 2 , 'if name == "%s":' % seq . name )
lines . add ( 3 , 'self.%s = value.p_value' % seq . name )
return lines |
def _get_prop_infos ( self , prop ) :
"""Return the infos configured for this specific prop , merging the
different configuration level""" | info_dict = self . get_info_field ( prop )
main_infos = info_dict . get ( 'export' , { } ) . copy ( )
infos = main_infos . get ( self . config_key , { } )
main_infos [ 'label' ] = self . _get_title ( prop , main_infos , info_dict )
main_infos [ 'name' ] = prop . key
main_infos [ 'key' ] = prop . key
main_infos . update... |
def errdp ( marker , number ) :
"""Substitute a double precision number for the first occurrence of
a marker found in the current long error message .
http : / / naif . jpl . nasa . gov / pub / naif / toolkit _ docs / C / cspice / errdp _ c . html
: param marker : A substring of the error message to be replac... | marker = stypes . stringToCharP ( marker )
number = ctypes . c_double ( number )
libspice . errdp_c ( marker , number ) |
def iter_archive ( self , resource ) :
"""Returns iterator over files within archive .
* * Important Note * * : caller should read files as they are yielded .
Reading out of order is slow .
Args :
resource : path to archive or ` tfds . download . Resource ` .
Returns :
Generator yielding tuple ( path _ ... | if isinstance ( resource , six . string_types ) :
resource = resource_lib . Resource ( path = resource )
return extractor . iter_archive ( resource . path , resource . extract_method ) |
def list_upgrades ( refresh = True , ** kwargs ) :
'''Check whether or not an upgrade is available for all packages
The ` ` fromrepo ` ` , ` ` enablerepo ` ` , and ` ` disablerepo ` ` arguments are
supported , as used in pkg states , and the ` ` disableexcludes ` ` option is
also supported .
. . versionadde... | options = _get_options ( ** kwargs )
if salt . utils . data . is_true ( refresh ) :
refresh_db ( check_update = False , ** kwargs )
cmd = [ '--quiet' ]
cmd . extend ( options )
cmd . extend ( [ 'list' , 'upgrades' if _yum ( ) == 'dnf' else 'updates' ] )
out = _call_yum ( cmd , ignore_retcode = True )
if out [ 'retc... |
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