signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def resolve_spec_identifier ( self , obj_name ) :
"""Find reference name based on spec identifier
Spec identifiers are used in parameter and return type definitions , but
should be a user - friendly version instead . Use docfx ` ` references ` `
lookup mapping for resolution .
If the spec identifier referen... | ref = self . references . get ( obj_name )
if ref is None :
return obj_name
resolved = ref . get ( "fullName" , obj_name )
spec = ref . get ( "spec.csharp" , [ ] )
parts = [ ]
for part in spec :
if part . get ( "name" ) == "<" :
parts . append ( "{" )
elif part . get ( "name" ) == ">" :
part... |
def create_csv ( filename , csv_data , mode = "w" ) :
"""Create a CSV file with the given data and store it in the
file with the given name .
: param filename : name of the file to store the data in
: pram csv _ data : the data to be stored in the file
: param mode : the mode in which we have to open the fi... | with open ( filename , mode ) as f :
csv_data . replace ( "_" , r"\_" )
f . write ( csv_data ) |
def get_es_action_item ( data_item , action_settings , es_type , id_field = None ) :
'''This method will return an item formated and ready to append
to the action list''' | action_item = dict . copy ( action_settings )
if id_field is not None :
id_val = first ( list ( get_dict_key ( data_item , id_field ) ) )
if id_val is not None :
action_item [ '_id' ] = id_val
elif data_item . get ( 'id' ) :
if data_item [ 'id' ] . startswith ( "%s/" % action_settings [ '_index' ] )... |
def decode ( self , value ) :
"""The decoder for this schema .
Tries each decoder in order of the types specified for this schema .""" | # Use the default value unless the field accepts None types
has_null_encoder = bool ( encode_decode_null in self . _decoders )
if value is None and self . _default is not None and not has_null_encoder :
value = self . _default
for decoder in self . _decoders :
try :
return decoder ( value )
except V... |
def predict ( self , quadruplets ) :
"""Predicts the ordering between sample distances in input quadruplets .
For each quadruplet , returns 1 if the quadruplet is in the right order (
first pair is more similar than second pair ) , and - 1 if not .
Parameters
quadruplets : array - like , shape = ( n _ quadr... | check_is_fitted ( self , 'transformer_' )
quadruplets = check_input ( quadruplets , type_of_inputs = 'tuples' , preprocessor = self . preprocessor_ , estimator = self , tuple_size = self . _tuple_size )
return np . sign ( self . decision_function ( quadruplets ) ) |
def run_func ( self , func_path , * func_args , ** kwargs ) :
"""Run a function in Matlab and return the result .
Parameters
func _ path : str
Name of function to run or a path to an m - file .
func _ args : object , optional
Function args to send to the function .
nargout : int , optional
Desired num... | if not self . started :
raise ValueError ( 'Session not started, use start()' )
nargout = kwargs . pop ( 'nargout' , 1 )
func_args += tuple ( item for pair in zip ( kwargs . keys ( ) , kwargs . values ( ) ) for item in pair )
dname = os . path . dirname ( func_path )
fname = os . path . basename ( func_path )
func_... |
def delete_user_contact_list ( self , id , contact_list_id , ** data ) :
"""DELETE / users / : id / contact _ lists / : contact _ list _ id /
Deletes the contact list . Returns ` ` { " deleted " : true } ` ` .""" | return self . delete ( "/users/{0}/contact_lists/{0}/" . format ( id , contact_list_id ) , data = data ) |
def verify ( self , obj ) :
"""Verify that the object conforms to this verifier ' s schema
Args :
obj ( object ) : A python object to verify
Returns :
bytes or byterray : The decoded byte buffer
Raises :
ValidationError : If there is a problem verifying the object , a
ValidationError is thrown with at... | if self . encoding == 'none' and not isinstance ( obj , ( bytes , bytearray ) ) :
raise ValidationError ( 'Byte object was not either bytes or a bytearray' , type = obj . __class__ . __name__ )
elif self . encoding == 'base64' :
try :
data = base64 . b64decode ( obj )
return data
except Type... |
def validate_uncle ( cls , block : BaseBlock , uncle : BaseBlock , uncle_parent : BaseBlock ) -> None :
"""Validate the given uncle in the context of the given block .""" | if uncle . block_number >= block . number :
raise ValidationError ( "Uncle number ({0}) is higher than block number ({1})" . format ( uncle . block_number , block . number ) )
if uncle . block_number != uncle_parent . block_number + 1 :
raise ValidationError ( "Uncle number ({0}) is not one above ancestor's num... |
def change_sample ( self , old_samp_name , new_samp_name , new_site_name = None , new_er_data = None , new_pmag_data = None , replace_data = False ) :
"""Find actual data objects for sample and site .
Then call Sample class change method to update sample name and data . .""" | sample = self . find_by_name ( old_samp_name , self . samples )
if not sample :
print ( '-W- {} is not a currently existing sample, so it cannot be updated' . format ( old_samp_name ) )
return False
if new_site_name :
new_site = self . find_by_name ( new_site_name , self . sites )
if not new_site :
... |
def vn ( x ) :
"""value or none , returns none if x is an empty list""" | if x == [ ] :
return None
if isinstance ( x , list ) :
return '|' . join ( x )
if isinstance ( x , datetime ) :
return x . isoformat ( )
return x |
def read_command ( self ) :
"""Read a command from the user line by line .
Returns a code object suitable for execution .""" | reader = self . reader
line = yield from reader . readline ( )
if line == b'' : # lost connection
raise ConnectionResetError ( )
try : # skip the newline to make CommandCompiler work as advertised
codeobj = self . attempt_compile ( line . rstrip ( b'\n' ) )
except SyntaxError :
yield from self . send_except... |
def remove_sites ( self , indices ) :
"""Delete sites with at indices .
Args :
indices : Sequence of indices of sites to delete .""" | self . _sites = [ self . _sites [ i ] for i in range ( len ( self . _sites ) ) if i not in indices ] |
def _get_variable_names ( arr ) :
"""Return the variable names of an array""" | if VARIABLELABEL in arr . dims :
return arr . coords [ VARIABLELABEL ] . tolist ( )
else :
return arr . name |
def get_class_field ( cls , field_name ) :
"""Add management of dynamic fields : if a normal field cannot be retrieved ,
check if it can be a dynamic field and in this case , create a copy with
the given name and associate it to the model .""" | try :
field = super ( ModelWithDynamicFieldMixin , cls ) . get_class_field ( field_name )
except AttributeError : # the " has _ field " returned True but getattr raised . . . we have a DynamicField
dynamic_field = cls . _get_dynamic_field_for ( field_name )
field = cls . _add_dynamic_field_to_model ( dynami... |
def hsts_header ( self ) :
"""Returns the proper HSTS policy .""" | hsts_policy = 'max-age={0}' . format ( self . hsts_age )
if self . hsts_include_subdomains :
hsts_policy += '; includeSubDomains'
return hsts_policy |
def random_sample ( self , num_samples , df = None , replace = False , weights = None , random_state = 100 , axis = 'row' ) :
'''Return random sample of matrix .''' | if df is None :
df = self . dat_to_df ( )
if axis == 'row' :
axis = 0
if axis == 'col' :
axis = 1
df = self . export_df ( )
df = df . sample ( n = num_samples , replace = replace , weights = weights , random_state = random_state , axis = axis )
self . load_df ( df ) |
def auto_key ( ) :
"""This method attempts to auto - generate a unique cryptographic key based on the hardware ID .
It should * NOT * be used in production , or to replace a proper key , but it can help get will
running in local and test environments more easily .""" | import uuid
import time
import random
import hashlib
node = uuid . getnode ( )
h = hashlib . md5 ( )
h . update ( str ( "%s" % node ) . encode ( 'utf-8' ) )
key1 = h . hexdigest ( )
time . sleep ( random . uniform ( 0 , 0.5 ) )
node = uuid . getnode ( )
h = hashlib . md5 ( )
h . update ( str ( "%s" % node ) . encode ( ... |
def filter ( self ) :
"""Called when parallelize is False .
This function will generate the file names in a directory tree by walking the tree either top - down or
bottom - up . For each directory in the tree rooted at directory top ( including top itself ) , it yields a 3 - tuple
( dirpath , dirnames , filen... | self . _printer ( 'Standard Walk' )
count = Counter ( length = 3 )
for directory in self . directory :
self . _printer ( 'Searching ' + directory )
for root , directories , files in os . walk ( directory , topdown = self . topdown ) :
root = root [ len ( str ( directory ) ) + 1 : ]
self . _print... |
def archive_basename ( filename ) :
'''returns the basename ( name without extension ) of a recognized archive file''' | for archive in archive_formats :
if filename . endswith ( archive_formats [ archive ] [ 'suffix' ] ) :
return filename . rstrip ( '.' + archive_formats [ archive ] [ 'suffix' ] )
return False |
def _ParseStringOption ( cls , options , argument_name , default_value = None ) :
"""Parses a string command line argument .
Args :
options ( argparse . Namespace ) : parser options .
argument _ name ( str ) : name of the command line argument .
default _ value ( Optional [ str ] ) : default value of the co... | argument_value = getattr ( options , argument_name , None )
if argument_value is None :
return default_value
if isinstance ( argument_value , py2to3 . BYTES_TYPE ) :
encoding = sys . stdin . encoding
# Note that sys . stdin . encoding can be None .
if not encoding :
encoding = locale . getprefer... |
def rsdl_rn ( self , AX , Y ) :
"""Compute primal residual normalisation term .""" | # The primal residual normalisation term is
# max ( | | A x ^ ( k ) | | _ 2 , | | B y ^ ( k ) | | _ 2 ) and B = - ( I I I . . . ) ^ T .
# The scaling by sqrt ( Nb ) of the l2 norm of Y accounts for the
# block replication introduced by multiplication by B
return max ( ( np . linalg . norm ( AX ) , np . sqrt ( self . Nb... |
def get_protocol_from_name ( name ) :
"""Returns the protocol class for the protocol with the given name .
: type name : str
: param name : The name of the protocol .
: rtype : Protocol
: return : The protocol class .""" | cls = protocol_map . get ( name )
if not cls :
raise ValueError ( 'Unsupported protocol "%s".' % name )
return cls |
def checks ( similarities , verbose = False ) :
"""Check that a matrix is a proper similarity matrix and bring
appropriate changes if applicable .
Parameters
similarities : array of shape ( n _ samples , n _ samples )
A matrix of pairwise similarities between ( sub ) - samples of the data - set .
verbose ... | if similarities . size == 0 :
raise ValueError ( "\nERROR: Cluster_Ensembles: checks: the similarities " "matrix provided as input happens to be empty.\n" )
elif np . where ( np . isnan ( similarities ) ) [ 0 ] . size != 0 :
raise ValueError ( "\nERROR: Cluster_Ensembles: checks: input similarities " "matrix co... |
def pool_revert ( self , pool_id , version_id ) :
"""Function to revert a specific pool ( Requires login ) ( UNTESTED ) .
Parameters :
pool _ id ( int ) : Where pool _ id is the pool id .
version _ id ( int ) :""" | return self . _get ( 'pools/{0}/revert.json' . format ( pool_id ) , { 'version_id' : version_id } , method = 'PUT' , auth = True ) |
def load_model_from_path ( model_path , meta = False , ** overrides ) :
"""Load a model from a data directory path . Creates Language class with
pipeline from meta . json and then calls from _ disk ( ) with path .""" | from . tokenizer_loader import TokenizerLoader
if not meta :
meta = get_model_meta ( model_path )
tokenizer_loader = TokenizerLoader ( meta = meta , ** overrides )
tokenizers = meta . get ( 'tokenizers' , [ ] )
disable = overrides . get ( 'disable' , [ ] )
if tokenizers is True :
tokenizers = TokenizerLoader . ... |
def set_title ( self , title : str , url : str = None ) -> None :
"""Sets the title of the embed .
Parameters
title : str
Title of the embed .
url : str or None , optional
URL hyperlink of the title .""" | self . title = title
self . url = url |
def install_exception_handler ( handler ) :
"""Installs an exception handler .
Args :
handler : ExceptionHandler , the exception handler to install .
Raises :
TypeError : Raised when the handler was not of the correct type .
All installed exception handlers will be called if main ( ) exits via
an abnorm... | if not isinstance ( handler , ExceptionHandler ) :
raise TypeError ( 'handler of type %s does not inherit from ExceptionHandler' % type ( handler ) )
EXCEPTION_HANDLERS . append ( handler ) |
def add_entity ( self , domain , ** kwargs ) :
'''Add a new Entity to tracking .''' | # Set the entity ' s mapping func if one was specified
map_func = kwargs . get ( 'map_func' , None )
if map_func is not None and not callable ( kwargs [ 'map_func' ] ) :
if self . entity_mapper is None :
raise ValueError ( "Mapping function '%s' specified for Entity " "'%s', but no entity mapper was passed ... |
def jcrop_css ( css_url = None ) :
"""Load jcrop css file .
: param css _ url : The custom CSS URL .""" | if css_url is None :
if current_app . config [ 'AVATARS_SERVE_LOCAL' ] :
css_url = url_for ( 'avatars.static' , filename = 'jcrop/css/jquery.Jcrop.min.css' )
else :
css_url = 'https://cdn.jsdelivr.net/npm/jcrop-0.9.12@0.9.12/css/jquery.Jcrop.min.css'
return Markup ( '<link rel="stylesheet" href=... |
def update ( self , force = False ) :
"""Fetch new posts from the server .
Arguments :
force ( bool ) : Force a thread update , even if thread has 404 ' d .
Returns :
int : How many new posts have been fetched .""" | # The thread has already 404 ' ed , this function shouldn ' t do anything anymore .
if self . is_404 and not force :
return 0
if self . _last_modified :
headers = { 'If-Modified-Since' : self . _last_modified }
else :
headers = None
# random connection errors , just return 0 and try again later
try :
re... |
def reset_index ( self , ** kwargs ) :
"""Removes all levels from index and sets a default level _ 0 index .
Returns :
A new QueryCompiler with updated data and reset index .""" | drop = kwargs . get ( "drop" , False )
new_index = pandas . RangeIndex ( len ( self . index ) )
if not drop :
if isinstance ( self . index , pandas . MultiIndex ) : # TODO ( devin - petersohn ) ensure partitioning is properly aligned
new_column_names = pandas . Index ( self . index . names )
new_col... |
def get_page_numbers ( current_page , num_pages ) :
"""Default callable for page listing .
Produce a Digg - style pagination .""" | if current_page <= 2 :
start_page = 1
else :
start_page = current_page - 2
if num_pages <= 4 :
end_page = num_pages
else :
end_page = start_page + 4
if end_page > num_pages :
end_page = num_pages
pages = [ ]
if current_page != 1 :
pages . append ( 'first' )
pages . append ( 'previous... |
def do_operation ( database , keys , table , operation , latencies_ms ) :
"""Does a single operation and records latency .""" | key = random . choice ( keys )
start = timeit . default_timer ( )
if operation == 'read' :
read ( database , table , key )
elif operation == 'update' :
update ( database , table , key )
else :
raise ValueError ( 'Unknown operation: %s' % operation )
end = timeit . default_timer ( )
latencies_ms [ operation ... |
def build_full_toctree ( builder , docname , prune , collapse ) :
"""Return a single toctree starting from docname containing all
sub - document doctrees .""" | env = builder . env
doctree = env . get_doctree ( env . config . master_doc )
toctrees = [ ]
for toctreenode in doctree . traverse ( addnodes . toctree ) :
toctree = env . resolve_toctree ( docname , builder , toctreenode , collapse = collapse , prune = prune , )
toctrees . append ( toctree )
if not toctrees :
... |
def json_success_response ( data , response ) :
"""Formats the response of a successful token request as JSON .
Also adds default headers and status code .""" | response . body = json . dumps ( data )
response . status_code = 200
response . add_header ( "Content-Type" , "application/json" )
response . add_header ( "Cache-Control" , "no-store" )
response . add_header ( "Pragma" , "no-cache" ) |
def get_all_reserved_instances ( self , reserved_instances_id = None , filters = None ) :
"""Describes Reserved Instance offerings that are available for purchase .
: type reserved _ instance _ ids : list
: param reserved _ instance _ ids : A list of the reserved instance ids that
will be returned . If not pr... | params = { }
if reserved_instances_id :
self . build_list_params ( params , reserved_instances_id , 'ReservedInstancesId' )
if filters :
self . build_filter_params ( params , filters )
return self . get_list ( 'DescribeReservedInstances' , params , [ ( 'item' , ReservedInstance ) ] , verb = 'POST' ) |
def _update_pwm ( self ) :
"""Update the pwm values of the driver regarding the current state .""" | if self . _is_on :
values = self . _get_pwm_values ( )
else :
values = [ 0 ] * len ( self . _driver . pins )
self . _driver . set_pwm ( values ) |
def get_network ( network_id , summary = False , include_data = 'N' , scenario_ids = None , template_id = None , ** kwargs ) :
"""Return a whole network as a dictionary .
network _ id : ID of the network to retrieve
include _ data : ' Y ' or ' N ' . Indicate whether scenario data is to be returned .
This has ... | log . debug ( "getting network %s" % network_id )
user_id = kwargs . get ( 'user_id' )
network_id = int ( network_id )
try :
log . debug ( "Querying Network %s" , network_id )
net_i = db . DBSession . query ( Network ) . filter ( Network . id == network_id ) . options ( noload ( 'scenarios' ) ) . options ( nolo... |
def response_body_to_dict ( http_requests_response , content_type , xml_root_element_name = None , is_list = False ) :
"""Convert a XML or JSON response in a Python dict
: param http _ requests _ response : ' Requests ( lib ) ' response
: param content _ type : Expected content - type header value ( Accept head... | logger . info ( "Converting response body from API (XML or JSON) to Python dict" )
if HEADER_REPRESENTATION_JSON == content_type :
try :
return http_requests_response . json ( )
except Exception , e :
logger . error ( "Error parsing the response to JSON. Exception:" + str ( e ) )
raise e... |
def scaleBy ( self , value , origin = None , width = False , height = False ) :
"""* * width * * indicates if the glyph ' s width should be scaled .
* * height * * indicates if the glyph ' s height should be scaled .
The origin must not be specified when scaling the width or height .""" | value = normalizers . normalizeTransformationScale ( value )
if origin is None :
origin = ( 0 , 0 )
origin = normalizers . normalizeCoordinateTuple ( origin )
if origin != ( 0 , 0 ) and ( width or height ) :
raise FontPartsError ( ( "The origin must not be set when " "scaling the width or height." ) )
super ( B... |
def user ( self , email : str ) -> models . User :
"""Fetch a user from the database .""" | return self . User . query . filter_by ( email = email ) . first ( ) |
def alert ( text = '' , title = '' , button = OK_TEXT , root = None , timeout = None ) :
"""Displays a simple message box with text and a single OK button . Returns the text of the button clicked on .""" | assert TKINTER_IMPORT_SUCCEEDED , 'Tkinter is required for pymsgbox'
return _buttonbox ( msg = text , title = title , choices = [ str ( button ) ] , root = root , timeout = timeout ) |
def del_group ( self ) :
"""Delete current group .""" | idx = self . tabs . currentIndex ( )
self . tabs . removeTab ( idx )
self . apply ( ) |
def _start_monitoring ( self ) :
"""Internal method that monitors the directory for changes""" | # Grab all the timestamp info
before = self . _file_timestamp_info ( self . path )
while True :
gevent . sleep ( 1 )
after = self . _file_timestamp_info ( self . path )
added = [ fname for fname in after . keys ( ) if fname not in before . keys ( ) ]
removed = [ fname for fname in before . keys ( ) if f... |
def extract ( fileobj , keywords , comment_tags , options ) :
"""Extracts translation messages from underscore template files .
This method does also extract django templates . If a template does not
contain any django translation tags we always fallback to underscore extraction .
This is a plugin to Babel , ... | encoding = options . get ( 'encoding' , 'utf-8' )
original_position = fileobj . tell ( )
text = fileobj . read ( ) . decode ( encoding )
if django . VERSION [ : 2 ] >= ( 1 , 9 ) :
tokens = Lexer ( text ) . tokenize ( )
else :
tokens = Lexer ( text , None ) . tokenize ( )
vars = [ token . token_type != TOKEN_TEX... |
def _ssh_forward_accept ( ssh_session , timeout_ms ) :
"""Waiting for an incoming connection from a reverse forwarded port . Note
that this results in a kernel block until a connection is received .""" | ssh_channel = c_ssh_forward_accept ( c_void_p ( ssh_session ) , c_int ( timeout_ms ) )
if ssh_channel is None :
raise SshTimeoutException ( )
return ssh_channel |
def uninstall ( ) :
"""Uninstall data and resource locations""" | _check_root ( )
response = _ask ( "This will delete all data of your HFOS installations! Type" "YES to continue:" , default = "N" , show_hint = False )
if response == 'YES' :
shutil . rmtree ( '/var/lib/hfos' )
shutil . rmtree ( '/var/cache/hfos' ) |
def _normalize ( val ) :
'''Fix Salt ' s yaml - ification of on / off , and otherwise normalize the on / off
values to be used in writing the options file''' | if isinstance ( val , bool ) :
return 'on' if val else 'off'
return six . text_type ( val ) . lower ( ) |
def what_task ( self , token_id , presented_pronunciation , index , phonemes , phonemes_probability , warn = True , default = True ) :
"""Provide the prediction of the what task .
This function is used to predict the probability of a given phoneme being reported at a given index
for a given token .
: param to... | if phonemes_probability is not None and not 0. < phonemes_probability < 1. and warn :
logging . warning ( 'Setting a probability of [{}] to phonemes [{}] for token [{}].\n ' 'Using probabilities of 0.0 or 1.0 ' 'may lead to likelihoods of -Infinity' . format ( phonemes_probability , phonemes , token_id ) )
default_... |
def amplify_gmfs ( imts , vs30s , gmfs ) :
"""Amplify the ground shaking depending on the vs30s""" | n = len ( vs30s )
out = [ amplify_ground_shaking ( im . period , vs30s [ i ] , gmfs [ m * n + i ] ) for m , im in enumerate ( imts ) for i in range ( n ) ]
return numpy . array ( out ) |
def call_member ( obj , f , * args , ** kwargs ) :
"""Calls the specified method , property or attribute of the given object
Parameters
obj : object
The object that will be used
f : str or function
Name of or reference to method , property or attribute
failfast : bool
If True , will raise an exception... | # get function name
if not isinstance ( f , str ) :
fname = f . __func__ . __name__
else :
fname = f
# get the method ref
method = getattr ( obj , fname )
# handle cases
if inspect . ismethod ( method ) :
return method ( * args , ** kwargs )
# attribute or property
return method |
def unzip ( self , remotepath , subpath = '/' , start = 0 , limit = 1000 ) :
'''Usage : unzip < remotepath > [ < subpath > [ < start > [ < limit > ] ] ]''' | rpath = get_pcs_path ( remotepath )
return self . __panapi_unzip_file ( rpath , subpath , start , limit ) ; |
def list ( self , pattern = '*' ) :
"""Returns a list of resource descriptors that match the filters .
Args :
pattern : An optional pattern to further filter the descriptors . This can
include Unix shell - style wildcards . E . g . ` ` " aws * " ` ` , ` ` " * cluster * " ` ` .
Returns :
A list of Resource... | if self . _descriptors is None :
self . _descriptors = self . _client . list_resource_descriptors ( filter_string = self . _filter_string )
return [ resource for resource in self . _descriptors if fnmatch . fnmatch ( resource . type , pattern ) ] |
def get_cluster_assignment ( self ) :
"""Fetch the cluster layout in form of assignment from zookeeper""" | plan = self . get_cluster_plan ( )
assignment = { }
for elem in plan [ 'partitions' ] :
assignment [ ( elem [ 'topic' ] , elem [ 'partition' ] ) ] = elem [ 'replicas' ]
return assignment |
def copy ( self , * args , ** kwargs ) :
'''Returns a copy of the current data object
: param flag : if an argument is provided , this returns an updated copy of current object ( ie . equivalent to obj . copy ( ) ; obj . update ( flag ) ) , optimising the memory (
: keyword True deep : deep copies the object ( ... | deep = kwargs . get ( 'deep' , True )
if len ( args ) > 0 :
return self . updated_copy ( * args )
else :
return copy . deepcopy ( self ) if deep else copy . copy ( self ) |
def _euler_to_q ( self , euler ) :
"""Create q array from euler angles
: param euler : array [ roll , pitch , yaw ] in rad
: returns : array q which represents a quaternion [ w , x , y , z ]""" | assert ( len ( euler ) == 3 )
phi = euler [ 0 ]
theta = euler [ 1 ]
psi = euler [ 2 ]
c_phi_2 = np . cos ( phi / 2 )
s_phi_2 = np . sin ( phi / 2 )
c_theta_2 = np . cos ( theta / 2 )
s_theta_2 = np . sin ( theta / 2 )
c_psi_2 = np . cos ( psi / 2 )
s_psi_2 = np . sin ( psi / 2 )
q = np . zeros ( 4 )
q [ 0 ] = ( c_phi_2... |
def __script ( self , mode , filestem ) :
"""Makes the script file to be run by yap .""" | scriptPath = '%s/%s' % ( self . tmpdir , Aleph . SCRIPT )
script = open ( scriptPath , 'w' )
# Permit the owner to execute and read this script
os . chmod ( scriptPath , S_IREAD | S_IEXEC )
cat = lambda x : script . write ( x + '\n' )
cat ( ":- initialization(run_aleph)." )
cat ( "run_aleph :- " )
cat ( "consult(aleph)... |
def _validate_id_types ( self ) :
'''Check that the ID types are integers for Rosetta , SEQRES , and UniParc sequences and 6 - character PDB IDs for the ATOM sequences .''' | for sequences in [ self . uniparc_sequences , self . fasta_sequences , self . seqres_sequences , self . rosetta_sequences ] :
for chain_id , sequence in sequences . iteritems ( ) :
sequence_id_types = set ( map ( type , sequence . ids ( ) ) )
if sequence_id_types :
assert ( len ( sequenc... |
def elcm_request ( irmc_info , method , path , ** kwargs ) :
"""send an eLCM request to the server
: param irmc _ info : dict of iRMC params to access the server node
' irmc _ address ' : host ,
' irmc _ username ' : user _ id ,
' irmc _ password ' : password ,
' irmc _ port ' : 80 or 443 , default is 443... | host = irmc_info [ 'irmc_address' ]
port = irmc_info . get ( 'irmc_port' , 443 )
auth_method = irmc_info . get ( 'irmc_auth_method' , 'basic' )
userid = irmc_info [ 'irmc_username' ]
password = irmc_info [ 'irmc_password' ]
client_timeout = irmc_info . get ( 'irmc_client_timeout' , 60 )
# Request headers , params , and... |
def add_patchs_to_build_without_pkg_config ( self , lib_dir , include_dir ) :
"""Add patches to remove pkg - config command and rpm . pc part .
Replace with given library _ path : lib _ dir and include _ path : include _ dir
without rpm . pc file .""" | additional_patches = [ { 'src' : r"pkgconfig\('--libs-only-L'\)" , 'dest' : "['{0}']" . format ( lib_dir ) , } , # Considering - libs - only - l and - libs - only - L
# https : / / github . com / rpm - software - management / rpm / pull / 327
{ 'src' : r"pkgconfig\('--libs(-only-l)?'\)" , 'dest' : "['rpm', 'rpmio']" , ... |
def _fixPermissions ( tool , workDir ) :
"""Deprecated .
Fix permission of a mounted Docker directory by reusing the tool to change
ownership . Docker natively runs as a root inside the container , and files
written to the mounted directory are implicitly owned by root .
: param list baseDockerCall : Docker... | if os . geteuid ( ) == 0 : # we ' re running as root so this chown is redundant
return
baseDockerCall = [ 'docker' , 'run' , '--log-driver=none' , '-v' , os . path . abspath ( workDir ) + ':/data' , '--rm' , '--entrypoint=chown' ]
stat = os . stat ( workDir )
command = baseDockerCall + [ tool ] + [ '-R' , '{}:{}' .... |
def nvmlEventSetCreate ( ) :
r"""* Create an empty set of events .
* Event set should be freed by \ ref nvmlEventSetFree
* For Fermi & tm ; or newer fully supported devices .
* @ param set Reference in which to return the event handle
* @ return
* - \ ref NVML _ SUCCESS if the event has been set
* - \ r... | fn = _nvmlGetFunctionPointer ( "nvmlEventSetCreate" )
eventSet = c_nvmlEventSet_t ( )
ret = fn ( byref ( eventSet ) )
_nvmlCheckReturn ( ret )
return eventSet |
def rename_attribute ( self , attribute : str , new_name : str ) -> None :
"""Renames an attribute .
Use only if is _ mapping ( ) returns true .
If the attribute does not exist , this will do nothing .
Args :
attribute : The ( old ) name of the attribute to rename .
new _ name : The new name to rename it ... | for key_node , _ in self . yaml_node . value :
if key_node . value == attribute :
key_node . value = new_name
break |
def mtx_refl ( nv , reps = 1 ) :
"""Generate block - diagonal reflection matrix about nv .
reps must be > = 1 and indicates the number of times the reflection
matrix should be repeated along the block diagonal . Typically this
will be the number of atoms in a geometry .
. . todo : : Complete mtx _ refl docs... | # Imports
import numpy as np
from scipy import linalg as spla
from . . const import PRM
# Ensure | nv | is large enough for confident directionality
if spla . norm ( nv ) < PRM . ZERO_VEC_TOL :
raise ValueError ( "Norm of 'nv' is too small." )
# # end if
# Ensure nv is a normalized np . float64 3 - vector
nv = make... |
def cube ( f ) :
"""Read a full cube from a file
Takes an open segy file ( created with segyio . open ) or a file name .
If the file is a prestack file , the cube returned has the dimensions
` ` ( fast , slow , offset , sample ) ` ` . If it is post - stack ( only the one
offset ) , the dimensions are normal... | if not isinstance ( f , segyio . SegyFile ) :
with segyio . open ( f ) as fl :
return cube ( fl )
ilsort = f . sorting == segyio . TraceSortingFormat . INLINE_SORTING
fast = f . ilines if ilsort else f . xlines
slow = f . xlines if ilsort else f . ilines
fast , slow , offs = len ( fast ) , len ( slow ) , le... |
def get_method_descriptor ( self , class_name , method_name , descriptor ) :
"""Return the specific method
: param class _ name : the class name of the method
: type class _ name : string
: param method _ name : the name of the method
: type method _ name : string
: param descriptor : the descriptor of th... | key = class_name + method_name + descriptor
if self . __cache_methods is None :
self . __cache_methods = { }
for i in self . get_classes ( ) :
for j in i . get_methods ( ) :
self . __cache_methods [ j . get_class_name ( ) + j . get_name ( ) + j . get_descriptor ( ) ] = j
return self . __cach... |
def unstar ( self ) :
"""Un - star this gist .
: returns : bool - - True if successful , False otherwise""" | url = self . _build_url ( 'star' , base_url = self . _api )
return self . _boolean ( self . _delete ( url ) , 204 , 404 ) |
def sometimesish ( fn ) :
"""Has a 50/50 chance of calling a function""" | def wrapped ( * args , ** kwargs ) :
if random . randint ( 1 , 2 ) == 1 :
return fn ( * args , ** kwargs )
return wrapped |
def load_nouns ( self , file ) :
"""Load dict from file for random words .
: param str file : filename""" | with open ( os . path . join ( main_dir , file + '.dat' ) , 'r' ) as f :
self . nouns = json . load ( f ) |
def _kmp_search_first ( self , pInput_sequence , pPattern ) :
"""use KMP algorithm to search the first occurrence in the input _ sequence of the pattern . both arguments are integer arrays . return the position of the occurence if found ; otherwise , - 1.""" | input_sequence , pattern = pInput_sequence , [ len ( bin ( e ) ) for e in pPattern ]
n , m = len ( input_sequence ) , len ( pattern )
d = p = 0
next = self . _kmp_construct_next ( pattern )
while d < n and p < m :
p = next [ len ( bin ( input_sequence [ d ] ) ) ] [ p ]
d += 1
if p == m :
return d - p
else :... |
def _normalize ( self , address ) :
"""Normalize prefixes , suffixes and other to make matching original to returned easier .""" | normalized_address = [ ]
if self . logger :
self . logger . debug ( "Normalizing Address: {0}" . format ( address ) )
for token in address . split ( ) :
if token . upper ( ) in self . parser . suffixes . keys ( ) :
normalized_address . append ( self . parser . suffixes [ token . upper ( ) ] . lower ( ) ... |
def create_rot2d ( angle ) :
"""Create 2D rotation matrix""" | ca = math . cos ( angle )
sa = math . sin ( angle )
return np . array ( [ [ ca , - sa ] , [ sa , ca ] ] ) |
def _get_pgtiou ( pgt ) :
"""Returns a PgtIOU object given a pgt .
The PgtIOU ( tgt ) is set by the CAS server in a different request
that has completed before this call , however , it may not be found in
the database by this calling thread , hence the attempt to get the
ticket is retried for up to 5 second... | pgtIou = None
retries_left = 5
if not settings . CAS_PGT_FETCH_WAIT :
retries_left = 1
while not pgtIou and retries_left :
try :
return PgtIOU . objects . get ( tgt = pgt )
except PgtIOU . DoesNotExist :
if settings . CAS_PGT_FETCH_WAIT :
time . sleep ( 1 )
retries_left -... |
def watermark_text ( image , text , corner = 2 ) :
'''Adds a text watermark to an instance of a PIL Image .
The text will be sized so that the height of the text is
roughly 1/20th the height of the base image . The text will
be white with a thin black outline .
Args :
image : An instance of a PIL Image . ... | # Load Font
FONT_PATH = ''
if resource_exists ( __name__ , 'resources/fonts/SourceSansPro-Regular.ttf' ) :
FONT_PATH = resource_filename ( __name__ , 'resources/fonts/SourceSansPro-Regular.ttf' )
padding = 5
was_P = image . mode == 'P'
was_L = image . mode == 'L'
# Fix PIL palette issue by converting palette images... |
def _resolve_number_of_copies ( self , items ) :
"""For the given objects generate as many copies as the desired number
of stickers .
: param items : list of objects whose stickers are going to be previewed .
: type items : list
: returns : list containing n copies of each object in the items list
: rtype... | copied_items = [ ]
for obj in items :
for copy in range ( self . get_copies_count ( ) ) :
copied_items . append ( obj )
return copied_items |
def find_sinks ( obj ) :
"""Returns a dictionary of sink methods found on this object ,
keyed on method name . Sink methods are identified by
( self , context ) arguments on this object . For example :
def f ( self , context ) :
is a sink method , but
def f ( self , ctx ) :
is not .""" | SINK_ARGSPEC = [ 'self' , 'context' ]
return { n : m for n , m in inspect . getmembers ( obj , inspect . ismethod ) if inspect . getargspec ( m ) [ 0 ] == SINK_ARGSPEC } |
def from_json ( self , json ) :
"""Create resource out of JSON data .
: param json : JSON dict .
: return : Resource with a type defined by the given JSON data .""" | res_type = json [ 'sys' ] [ 'type' ]
if ResourceType . Array . value == res_type :
return self . create_array ( json )
elif ResourceType . Entry . value == res_type :
return self . create_entry ( json )
elif ResourceType . Asset . value == res_type :
return ResourceFactory . create_asset ( json )
elif Resou... |
def valueFromString ( self , value , context = None ) :
"""Re - implements the orb . Column . valueFromString method to
lookup a reference object based on the given value .
: param value : < str >
: param context : < orb . Context > | | None
: return : < orb . Model > | | None""" | model = self . referenceModel ( )
return model ( value , context = context ) |
def density ( self ) :
"""The percent of non - ` ` fill _ value ` ` points , as decimal .
Examples
> > > s = SparseArray ( [ 0 , 0 , 1 , 1 , 1 ] , fill _ value = 0)
> > > s . density
0.6""" | r = float ( self . sp_index . npoints ) / float ( self . sp_index . length )
return r |
def aggregate ( self , aggregates = None , drilldowns = None , cuts = None , order = None , page = None , page_size = None , page_max = None ) :
"""Main aggregation function . This is used to compute a given set of
aggregates , grouped by a given set of drilldown dimensions ( i . e .
dividers ) . The query can ... | def prep ( cuts , drilldowns = False , aggregates = False , columns = None ) :
q = select ( columns )
bindings = [ ]
cuts , q , bindings = Cuts ( self ) . apply ( q , bindings , cuts )
attributes = None
if drilldowns is not False :
attributes , q , bindings = Drilldowns ( self ) . apply ( q ... |
def resolve_symbol ( self , symbol , bCaseSensitive = False ) :
"""Resolves a debugging symbol ' s address .
@ type symbol : str
@ param symbol : Name of the symbol to resolve .
@ type bCaseSensitive : bool
@ param bCaseSensitive : C { True } for case sensitive matches ,
C { False } for case insensitive .... | if bCaseSensitive :
for ( SymbolName , SymbolAddress , SymbolSize ) in self . iter_symbols ( ) :
if symbol == SymbolName :
return SymbolAddress
for ( SymbolName , SymbolAddress , SymbolSize ) in self . iter_symbols ( ) :
try :
SymbolName = win32 . UnDecorateSymbolName ( S... |
def of ( cls , value ) :
"""Given either a dictionary or a ` ConfigSource ` object , return
a ` ConfigSource ` object . This lets a function accept either type
of object as an argument .""" | if isinstance ( value , ConfigSource ) :
return value
elif isinstance ( value , dict ) :
return ConfigSource ( value )
else :
raise TypeError ( u'source value must be a dict' ) |
def dedup ( args ) :
"""% prog dedup scaffolds . fasta
Remove redundant contigs with CD - HIT . This is run prior to
assembly . sspace . embed ( ) .""" | from jcvi . formats . fasta import gaps
from jcvi . apps . cdhit import deduplicate , ids
p = OptionParser ( dedup . __doc__ )
p . set_align ( pctid = GoodPct )
p . set_mingap ( default = 10 )
opts , args = p . parse_args ( args )
if len ( args ) != 1 :
sys . exit ( not p . print_help ( ) )
scaffolds , = args
minga... |
def convolve_sep3 ( data , hx , hy , hz , res_g = None , sub_blocks = ( 1 , 1 , 1 ) , tmp_g = None ) :
"""convolves 3d data with kernel h = outer ( hx , hy , hz )
boundary conditions are clamping to edge .
data , hx , hy . . . . are either np array or a gpu buffer ( OCLArray )""" | if isinstance ( data , np . ndarray ) :
data = np . ascontiguousarray ( data )
if sub_blocks == ( 1 , 1 , 1 ) or sub_blocks is None :
return _convolve_sep3_numpy ( data , hx , hy , hz )
else : # cut the image into tile and operate on every of them
N_sub = [ int ( np . ceil ( 1. * n / s ) ) f... |
def get ( dataset , ** kwargs ) :
"""Return dataframe of requested dataset from Quandl .
: param dataset : str or list , depending on single dataset usage or multiset usage
Dataset codes are available on the Quandl website
: param str api _ key : Downloads are limited to 50 unless api _ key is specified
: p... | _convert_params_to_v3 ( kwargs )
data_format = kwargs . pop ( 'returns' , 'pandas' )
ApiKeyUtil . init_api_key_from_args ( kwargs )
# Check whether dataset is given as a string
# ( for a single dataset ) or an array ( for a multiset call )
# Unicode String
if isinstance ( dataset , string_types ) :
dataset_args = _... |
def _get_variable_from_filepath ( self ) :
"""Determine the file variable from the filepath .
Returns
str
Best guess of variable name from the filepath""" | try :
return self . regexp_capture_variable . search ( self . filepath ) . group ( 1 )
except AttributeError :
self . _raise_cannot_determine_variable_from_filepath_error ( ) |
def connect_iam ( 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 . iam import IAMConnection
return IAMConnection ( aws_access_key_id , aws_secret_access_key , ** kwargs ) |
def decode ( self , data ) :
"""Parses the file , creating a CWRFile from it .
It requires a dictionary with two values :
- filename , containing the filename
- contents , containing the file contents
: param data : dictionary with the data to parse
: return : a CWRFile instance""" | file_name = self . _filename_decoder . decode ( data [ 'filename' ] )
file_data = data [ 'contents' ]
i = 0
max_size = len ( file_data )
while file_data [ i : i + 1 ] != 'H' and i < max_size :
i += 1
if i > 0 :
data [ 'contents' ] = file_data [ i : ]
transmission = self . _file_decoder . decode ( data [ 'conten... |
def add_nodes_from ( self , nodes , ** attr ) :
"""Add multiple nodes .
Parameters
nodes : iterable container
A container of nodes ( list , dict , set , etc . ) .
OR
A container of ( node , attribute dict ) tuples .
Node attributes are updated using the attribute dict .
attr : keyword arguments , opti... | additional_attribs = attr
# will be added to each node
for n in nodes :
try : # check , if n is a node _ id or a ( node _ id , attrib dict ) tuple
newnode = n not in self . succ
# is node in the graph , yet ?
except TypeError : # n is a ( node _ id , attribute dict ) tuple
node_id , ndic... |
def patch_for ( self , path ) :
"""Returns the ` ` Patch ` ` for the target path , creating it if necessary .
: param str path : The absolute module path to the target .
: return : The mapped ` ` Patch ` ` .
: rtype : Patch""" | if path not in self . _patches :
self . _patches [ path ] = Patch ( path )
return self . _patches [ path ] |
def _ExpandUsersVariablePathSegments ( cls , path_segments , path_separator , user_accounts ) :
"""Expands path segments with a users variable , e . g . % % users . homedir % % .
Args :
path _ segments ( list [ str ] ) : path segments .
path _ separator ( str ) : path segment separator .
user _ accounts ( l... | if not path_segments :
return [ ]
path_segments_lower = [ path_segment . lower ( ) for path_segment in path_segments ]
if path_segments_lower [ 0 ] in ( '%%users.homedir%%' , '%%users.userprofile%%' ) :
return cls . _ExpandUsersHomeDirectoryPathSegments ( path_segments , path_separator , user_accounts )
path_ex... |
def wind_shear ( shear : str , unit_alt : str = 'ft' , unit_wind : str = 'kt' ) -> str :
"""Format wind shear string into a spoken word string""" | unit_alt = SPOKEN_UNITS . get ( unit_alt , unit_alt )
unit_wind = SPOKEN_UNITS . get ( unit_wind , unit_wind )
return translate . wind_shear ( shear , unit_alt , unit_wind , spoken = True ) or 'Wind shear unknown' |
def download_results ( self , savedir = None , raw = True , calib = False , index = None ) :
"""Download the previously found and stored Opus obsids .
Parameters
savedir : str or pathlib . Path , optional
If the database root folder as defined by the config . ini should not be used ,
provide a different sav... | obsids = self . obsids if index is None else [ self . obsids [ index ] ]
for obsid in obsids :
pm = io . PathManager ( obsid . img_id , savedir = savedir )
pm . basepath . mkdir ( exist_ok = True )
to_download = [ ]
if raw is True :
to_download . extend ( obsid . raw_urls )
if calib is True ... |
def check_for_invalid_columns ( problems : List , table : str , df : DataFrame ) -> List :
"""Check for invalid columns in the given GTFS DataFrame .
Parameters
problems : list
A four - tuple containing
1 . A problem type ( string ) equal to ` ` ' error ' ` ` or ` ` ' warning ' ` ` ;
` ` ' error ' ` ` mea... | r = cs . GTFS_REF
valid_columns = r . loc [ r [ "table" ] == table , "column" ] . values
for col in df . columns :
if col not in valid_columns :
problems . append ( [ "warning" , f"Unrecognized column {col}" , table , [ ] ] )
return problems |
def ip_to_url ( ip_addr ) :
"""Resolve a hostname based off an IP address .
This is very limited and will
probably not return any results if it is a shared IP address or an
address with improperly setup DNS records .
. . code : : python
reusables . ip _ to _ url ( ' 93.184.216.34 ' ) # example . com
# N... | try :
return socket . gethostbyaddr ( ip_addr ) [ 0 ]
except ( socket . gaierror , socket . herror ) :
logger . exception ( "Could not resolve hostname" ) |
def _handleSelectAllAxes ( self , evt ) :
"""Called when the ' select all axes ' menu item is selected .""" | if len ( self . _axisId ) == 0 :
return
for i in range ( len ( self . _axisId ) ) :
self . _menu . Check ( self . _axisId [ i ] , True )
self . _toolbar . set_active ( self . getActiveAxes ( ) )
evt . Skip ( ) |
def reset ( name ) :
'''Force power down and restart an existing VM''' | ret = { }
client = salt . client . get_local_client ( __opts__ [ 'conf_file' ] )
data = vm_info ( name , quiet = True )
if not data :
__jid_event__ . fire_event ( { 'message' : 'Failed to find VM {0} to reset' . format ( name ) } , 'progress' )
return 'fail'
host = next ( six . iterkeys ( data ) )
try :
cmd... |
def seq_sha512 ( seq , normalize = True ) :
"""returns unicode sequence sha512 hexdigest for sequence ` seq ` .
> > > seq _ sha512 ( ' ' )
' cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e '
> > > seq _ sha512 ( ' ACGT ' )
'68a... | seq = normalize_sequence ( seq ) if normalize else seq
bseq = seq . encode ( "ascii" )
return hashlib . sha512 ( bseq ) . hexdigest ( ) |
async def enable ( ) :
"""Get the data from a * hole instance .""" | async with aiohttp . ClientSession ( ) as session :
data = Hole ( '192.168.0.215' , loop , session , api_token = API_TOKEN )
await data . enable ( ) |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.