signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def compute_index ( self , axis , data_object , compute_diff = True ) :
"""Computes the index after a number of rows have been removed .
Note : In order for this to be used properly , the indexes must not be
changed before you compute this .
Args :
axis : The axis to extract the index from .
data _ object... | def pandas_index_extraction ( df , axis ) :
if not axis :
return df . index
else :
try :
return df . columns
except AttributeError :
return pandas . Index ( [ ] )
index_obj = self . index if not axis else self . columns
old_blocks = self . data if compute_diff els... |
def nameop_put_collision ( cls , collisions , nameop ) :
"""Record a nameop as collided with another nameop in this block .""" | # these are supposed to have been put here by nameop _ set _ collided
history_id_key = nameop . get ( '__collided_history_id_key__' , None )
history_id = nameop . get ( '__collided_history_id__' , None )
try :
assert cls . nameop_is_collided ( nameop ) , "Nameop not collided"
assert history_id_key is not None ,... |
def rm_docs ( self ) :
"""Remove converted docs .""" | for filename in self . created :
if os . path . exists ( filename ) :
os . unlink ( filename ) |
def parse_args ( self , argv ) :
"""parse arguments / options
: param argv : argument list to parse , usually ` ` sys . argv [ 1 : ] ` `
: type argv : list
: returns : parsed arguments
: rtype : : py : class : ` argparse . Namespace `""" | desc = 'Report on AWS service limits and usage via boto3, optionally ' 'warn about any services with usage nearing or exceeding their' ' limits. For further help, see ' '<http://awslimitchecker.readthedocs.org/>'
# # # # # # IMPORTANT license notice # # # # #
# Pursuant to Sections 5 ( b ) and 13 of the GNU Affero Gene... |
def camel_case ( string ) :
"""Converts a string to camel case . For example : :
camel _ case ( ' one _ two _ three ' ) - > ' oneTwoThree '""" | if not string :
return string
parts = snake_case ( string ) . split ( '_' )
rv = ''
while parts :
part = parts . pop ( 0 )
rv += part or '_'
if part :
break
return rv + '' . join ( x . title ( ) for x in parts ) |
def over ( self , window ) :
"""Add a window clause to be applied to downstream analytic expressions""" | return GroupedTableExpr ( self . table , self . by , having = self . _having , order_by = self . _order_by , window = window , ) |
def add_empty_dataset ( self , value = 1 ) :
"""Create an empty data set . Empty means : all elements have the same
value .
Parameters
value : float , optional
which value to assign all element parameters . Default is one .""" | subdata = np . ones ( self . grid . nr_of_elements ) * value
pid = self . add_data ( subdata )
return pid |
def on_focusout ( self , event , a ) :
"""function that gets called whenever anywhere except entry is clicked""" | if event . widget . get ( ) == '' :
event . widget . insert ( 0 , default_text [ a ] )
event . widget . config ( fg = 'grey' ) |
def _primary_input ( self , index ) :
'''Primary input for the zkproof''' | primary_input = z . ZcashByteData ( )
primary_input += self . tx_joinsplits [ index ] . anchor
primary_input += self . tx_joinsplits [ index ] . nullifiers
primary_input += self . tx_joinsplits [ index ] . commitments
primary_input += self . tx_joinsplits [ index ] . vpub_old
primary_input += self . tx_joinsplits [ ind... |
def choose_labels ( alternatives ) :
"""Prompt the user select several labels from the provided alternatives .
At least one label must be selected .
: param list alternatives : Sequence of options that are available to select from
: return : Several selected labels""" | if not alternatives :
raise ValueError
if not isinstance ( alternatives , list ) :
raise TypeError
choice_map = OrderedDict ( ( '{}' . format ( i ) , value ) for i , value in enumerate ( alternatives , 1 ) )
# prepend a termination option
input_terminator = '0'
choice_map . update ( { input_terminator : '<done>... |
def get_dedicated_package ( self , ha_enabled = False ) :
"""Retrieves the dedicated firewall package .
: param bool ha _ enabled : True if HA is to be enabled on the firewall
False for No HA
: returns : A dictionary containing the dedicated virtual server firewall
package""" | fwl_filter = 'Hardware Firewall (Dedicated)'
ha_fwl_filter = 'Hardware Firewall (High Availability)'
_filter = utils . NestedDict ( { } )
if ha_enabled :
_filter [ 'items' ] [ 'description' ] = utils . query_filter ( ha_fwl_filter )
else :
_filter [ 'items' ] [ 'description' ] = utils . query_filter ( fwl_filte... |
def addAccount ( self , username , domain , password , avatars = None , protocol = u'email' , disabled = 0 , internal = False , verified = True ) :
"""Create a user account , add it to this LoginBase , and return it .
This method must be called within a transaction in my store .
@ param username : the user ' s ... | # unicode ( None ) = = u ' None ' , kids .
if username is not None :
username = unicode ( username )
if domain is not None :
domain = unicode ( domain )
if password is not None :
password = unicode ( password )
if self . accountByAddress ( username , domain ) is not None :
raise DuplicateUser ( username... |
def create_account_invitation ( self , account_id , body , ** kwargs ) : # noqa : E501
"""Create a user invitation . # noqa : E501
An endpoint for inviting a new or an existing user to join the account . * * Example usage : * * ` curl - X POST https : / / api . us - east - 1 . mbedcloud . com / v3 / accouns / { a... | kwargs [ '_return_http_data_only' ] = True
if kwargs . get ( 'asynchronous' ) :
return self . create_account_invitation_with_http_info ( account_id , body , ** kwargs )
# noqa : E501
else :
( data ) = self . create_account_invitation_with_http_info ( account_id , body , ** kwargs )
# noqa : E501
ret... |
def remove_credentials ( self , credIDs ) :
"""Removes a credential ID from the database""" | for credID in credIDs :
cur = self . conn . cursor ( )
cur . execute ( "DELETE FROM users WHERE id=?" , [ credID ] )
cur . close ( ) |
def getfile ( self , project_id , file_path , ref ) :
"""Allows you to receive information about file in repository like name , size , content .
Note that file content is Base64 encoded .
: param project _ id : project _ id
: param file _ path : Full path to file . Ex . lib / class . rb
: param ref : The na... | data = { 'file_path' : file_path , 'ref' : ref }
request = requests . get ( '{0}/{1}/repository/files' . format ( self . projects_url , project_id ) , headers = self . headers , data = data , verify = self . verify_ssl , auth = self . auth , timeout = self . timeout )
if request . status_code == 200 :
return reques... |
def get_system_info ( self , x = 255 , y = 255 ) :
"""Discover the integrity and resource availability of a whole
SpiNNaker system .
This command performs : py : meth : ` . get _ chip _ info ` on all working chips in
the system returning an enhanced : py : class : ` dict `
( : py : class : ` . SystemInfo ` ... | # A quick way of getting a list of working chips
p2p_tables = self . get_p2p_routing_table ( x , y )
# Calculate the extent of the system
max_x = max ( x_ for ( x_ , y_ ) , r in iteritems ( p2p_tables ) if r != consts . P2PTableEntry . none )
max_y = max ( y_ for ( x_ , y_ ) , r in iteritems ( p2p_tables ) if r != cons... |
def solar_azimuth ( self , dateandtime , latitude , longitude ) :
"""Calculate the azimuth angle of the sun .
: param dateandtime : The date and time for which to calculate
the angle .
: type dateandtime : : class : ` ~ datetime . datetime `
: param latitude : Latitude - Northern latitudes should be positiv... | if latitude > 89.8 :
latitude = 89.8
if latitude < - 89.8 :
latitude = - 89.8
if dateandtime . tzinfo is None :
zone = 0
utc_datetime = dateandtime
else :
zone = - dateandtime . utcoffset ( ) . total_seconds ( ) / 3600.0
utc_datetime = dateandtime . astimezone ( pytz . utc )
timenow = ( utc_date... |
def ParseBookmarkRow ( self , parser_mediator , query , row , ** unused_kwargs ) :
"""Parses a bookmark row .
Args :
parser _ mediator ( ParserMediator ) : mediates interactions between parsers
and other components , such as storage and dfvfs .
query ( str ) : query that created the row .
row ( sqlite3 . ... | query_hash = hash ( query )
rev_host = self . _GetRowValue ( query_hash , row , 'rev_host' )
bookmark_type = self . _GetRowValue ( query_hash , row , 'type' )
event_data = FirefoxPlacesBookmarkEventData ( )
event_data . host = rev_host or 'N/A'
event_data . offset = self . _GetRowValue ( query_hash , row , 'id' )
event... |
def pack_args_by_32 ( holder , maxlen , arg , typ , context , placeholder , dynamic_offset_counter = None , datamem_start = None , zero_pad_i = None , pos = None ) :
"""Copy necessary variables to pre - allocated memory section .
: param holder : Complete holder for all args
: param maxlen : Total length in byt... | if isinstance ( typ , BaseType ) :
if isinstance ( arg , LLLnode ) :
value = unwrap_location ( arg )
else :
value = parse_expr ( arg , context )
value = base_type_conversion ( value , value . typ , typ , pos )
holder . append ( LLLnode . from_list ( [ 'mstore' , placeholder , value ]... |
def escape_attr ( s ) :
'''escape the given string such that it can be placed in an XML attribute , like :
< foo bar = ' $ value ' >
Args :
s ( str ) : the string to escape .
Returns :
str : the escaped string .''' | esc = xml . sax . saxutils . quoteattr ( s )
esc = esc . encode ( 'ascii' , 'xmlcharrefreplace' ) . decode ( 'ascii' )
esc = RESTRICTED_CHARS . sub ( '' , esc )
return esc |
def create ( self , typ , data , return_response = False ) :
"""Create new type
Valid arguments :
skip : number of records to skip
limit : number of records to limit request to""" | res = self . _request ( typ , method = 'POST' , data = data )
if res . status_code != 201 :
try :
data = res . json ( )
self . _throw ( res , data )
except ValueError as e :
if not isinstance ( e , InvalidRequestException ) :
self . _throw ( res , { } )
else :
... |
def add_output_arg ( self , out ) :
"""Add an output as an argument""" | self . add_arg ( out . _dax_repr ( ) )
self . _add_output ( out ) |
def firstPass ( ASTs , verbose ) :
'''Return a dictionary of function definition nodes , a dictionary of
imported object names and a dictionary of imported module names . All three
dictionaries use source file paths as keys .''' | fdefs = dict ( )
cdefs = dict ( )
imp_obj_strs = dict ( )
imp_mods = dict ( )
for ( root , path ) in ASTs :
fdefs [ path ] = [ ]
fdefs [ path ] . append ( formatBodyNode ( root , path ) )
imp_obj_strs [ path ] = [ ]
imp_mods [ path ] = [ ]
cdefs [ path ] = [ ]
for ( node , stack ) in traversal (... |
def _build_prior ( self , unconstrained_tensor , constrained_tensor ) :
"""Build a tensorflow representation of the prior density .
The log Jacobian is included .""" | if not misc . is_tensor ( unconstrained_tensor ) :
raise GPflowError ( "Unconstrained input must be a tensor." )
if not misc . is_tensor ( constrained_tensor ) :
raise GPflowError ( "Constrained input must be a tensor." )
prior_name = 'prior'
if self . prior is None :
return tf . constant ( 0.0 , settings .... |
def update_file ( self , path ) :
'''Updates the file watcher and calls the appropriate method for results
@ return : False if we need to keep trying the connection''' | try : # grab the file
result , stat = self . zoo_client . get ( path , watch = self . watch_file )
except ZookeeperError :
self . set_valid ( False )
self . call_error ( self . INVALID_GET )
return False
if self . pointer :
if result is not None and len ( result ) > 0 :
self . pointed_at_exp... |
def is_valid ( self , instance ) :
'''Perform validation for * instance * and stores serialized data ,
indexes and errors into local cache .
Return ` ` True ` ` if the instance is ready to be saved to database .''' | dbdata = instance . dbdata
data = dbdata [ 'cleaned_data' ] = { }
errors = dbdata [ 'errors' ] = { }
# Loop over scalar fields first
for field , value in instance . fieldvalue_pairs ( ) :
name = field . attname
try :
svalue = field . set_get_value ( instance , value )
except Exception as e :
... |
def modpath_last ( module , entry_point ) :
"""Provides the raw _ _ path _ _ . Incompatible with PEP 302 - based import
hooks and incompatible with zip _ safe packages .
Deprecated . Will be removed by calmjs - 4.0.""" | module_paths = modpath_all ( module , entry_point )
if len ( module_paths ) > 1 :
logger . info ( "module '%s' has multiple paths, default selecting '%s' as base." , module . __name__ , module_paths [ - 1 ] , )
return module_paths [ - 1 : ] |
def read ( self , length = None ) :
"""Fill bytes and read some number of bytes
( up to length if specified )
< = length bytes may be read if reached the end of input
if at buffer boundary , will attempt to read again until
specified length is read""" | all_buffs = [ ]
while length is None or length > 0 :
self . _fillbuff ( )
if self . empty ( ) :
break
buff = self . buff . read ( length )
all_buffs . append ( buff )
if length :
length -= len ( buff )
return b'' . join ( all_buffs ) |
def from_dict ( data , ctx ) :
"""Instantiate a new AccountChangesState from a dict ( generally from
loading a JSON response ) . The data used to instantiate the
AccountChangesState is a shallow copy of the dict passed in , with any
complex child types instantiated appropriately .""" | data = data . copy ( )
if data . get ( 'unrealizedPL' ) is not None :
data [ 'unrealizedPL' ] = ctx . convert_decimal_number ( data . get ( 'unrealizedPL' ) )
if data . get ( 'NAV' ) is not None :
data [ 'NAV' ] = ctx . convert_decimal_number ( data . get ( 'NAV' ) )
if data . get ( 'marginUsed' ) is not None :... |
def main ( ) :
"""Entrypoint for compare _ layers""" | parser = argparse . ArgumentParser ( description = 'Tool for testing caffe to mxnet conversion layer by layer' )
parser . add_argument ( '--image_url' , type = str , default = 'https://github.com/dmlc/web-data/raw/master/mxnet/doc/' 'tutorials/python/predict_image/cat.jpg' , help = 'input image to test inference, can b... |
def is_superset_of ( self , other , soft_combinator = False ) :
"""Return True iff this selector matches the same elements as ` other ` ,
and perhaps others .
That is , ` ` . foo ` ` is a superset of ` ` . foo . bar ` ` , because the latter is
more specific .
Set ` soft _ combinator ` true to ignore the spe... | # Combinators must match , OR be compatible - - space is a superset of > ,
# ~ is a superset of +
if soft_combinator and self . combinator == ' ' :
combinator_superset = True
else :
combinator_superset = ( self . combinator == other . combinator or ( self . combinator == ' ' and other . combinator == '>' ) or (... |
def delete_max ( self ) :
"""Delete the right - most value from a tree .""" | # Attempt to rotate left - leaning reds to the right .
if self . left . red :
self = self . rotate_right ( )
# Base case : If there are no selfs greater than this self , then this is
# the self to delete .
if self . right is NULL :
return NULL , self . value
# Acquire more reds if necessary to continue the trav... |
def RedirectDemo ( handler , t ) :
"""Demonstration of redirecting to another number .""" | # t . say ( " One moment please . " )
t . redirect ( SIP_PHONE )
json = t . RenderJson ( )
logging . info ( "RedirectDemo json: %s" % json )
handler . response . out . write ( json ) |
def predict_log_partial_hazard ( self , X ) :
r"""This is equivalent to R ' s linear . predictors .
Returns the log of the partial hazard for the individuals , partial since the
baseline hazard is not included . Equal to : math : ` ( x - \ bar { x } ) ' \ beta `
Parameters
X : numpy array or DataFrame
a (... | if isinstance ( X , pd . DataFrame ) :
order = self . hazards_ . index
X = X [ order ]
check_for_numeric_dtypes_or_raise ( X )
X = X . astype ( float )
index = _get_index ( X )
X = normalize ( X , self . _norm_mean . values , 1 )
return pd . DataFrame ( np . dot ( X , self . hazards_ ) , index = index ) |
def chunk_by ( fn : Callable [ [ T ] , object ] ) :
"""> > > from Redy . Collections import Traversal , Flow
> > > lst : Iterable [ int ] = [ 0 , 1 , 2 , 3 , 4 , 5 , 6]
> > > x = Flow ( lst ) [ Traversal . chunk _ by ( lambda x : x / / 3 ) ]
> > > assert list ( x . unbox ) = = [ [ 0 , 1 , 2 ] , [ 3 , 4 , 5 ] ... | def inner ( seq : ActualIterable [ T ] ) -> ActualIterable [ ActualIterable [ T ] ] :
seq = iter ( seq )
try :
head = next ( seq )
except StopIteration :
return iter ( seq )
current_status = fn ( head )
group = [ head ]
for each in seq :
status = fn ( each )
if st... |
def on ( self , event , handler = None , namespace = None ) :
"""Register an event handler .
: param event : The event name . It can be any string . The event names
` ` ' connect ' ` ` , ` ` ' message ' ` ` and ` ` ' disconnect ' ` ` are
reserved and should not be used .
: param handler : The function that ... | namespace = namespace or '/'
def set_handler ( handler ) :
if namespace not in self . handlers :
self . handlers [ namespace ] = { }
self . handlers [ namespace ] [ event ] = handler
return handler
if handler is None :
return set_handler
set_handler ( handler ) |
def _validate_inputs ( self , inputdict ) :
"""Validate input links .""" | # Check inputdict
try :
parameters = inputdict . pop ( self . get_linkname ( 'parameters' ) )
except KeyError :
raise InputValidationError ( "No parameters specified for this " "calculation" )
if not isinstance ( parameters , RipsDistanceMatrixParameters ) :
raise InputValidationError ( "parameters not of t... |
def on_close ( self , stats , previous_stats ) :
"""Print the extended JSON report to reporter ' s output .
: param dict stats : Metrics for the current pylint run
: param dict previous _ stats : Metrics for the previous pylint run""" | reports = { 'messages' : self . _messages , 'stats' : stats , 'previous' : previous_stats , }
print ( json . dumps ( reports , cls = JSONSetEncoder , indent = 4 ) , file = self . out ) |
def present ( name , clients = None , hosts = None , options = None , exports = '/etc/exports' ) :
'''Ensure that the named export is present with the given options
name
The export path to configure
clients
A list of hosts and the options applied to them .
This option may not be used in combination with
... | path = name
ret = { 'name' : name , 'changes' : { } , 'result' : None , 'comment' : '' }
if not clients :
if not hosts :
ret [ 'result' ] = False
ret [ 'comment' ] = 'Either \'clients\' or \'hosts\' must be defined'
return ret
# options being None is handled by add _ export ( )
clien... |
def destroy ( name , call = None ) :
'''Destroy a node .
CLI Example :
. . code - block : : bash
salt - cloud - - destroy mymachine''' | if call == 'function' :
raise SaltCloudSystemExit ( 'The destroy action must be called with -d, --destroy, ' '-a or --action.' )
__utils__ [ 'cloud.fire_event' ] ( 'event' , 'destroying instance' , 'salt/cloud/{0}/destroying' . format ( name ) , args = { 'name' : name } , sock_dir = __opts__ [ 'sock_dir' ] , transp... |
def plot_predict ( self , h = 5 , past_values = 20 , intervals = True , ** kwargs ) :
"""Makes forecast with the estimated model
Parameters
h : int ( default : 5)
How many steps ahead would you like to forecast ?
past _ values : int ( default : 20)
How many past observations to show on the forecast graph ... | import matplotlib . pyplot as plt
import seaborn as sns
figsize = kwargs . get ( 'figsize' , ( 10 , 7 ) )
nsims = kwargs . get ( 'nsims' , 200 )
if self . latent_variables . estimated is False :
raise Exception ( "No latent variables estimated!" )
else : # Retrieve data , dates and ( transformed ) latent variables
... |
def read ( self , len = 1024 , buffer = None ) :
"""Read data from connection
Read up to len bytes and return them .
Arguments :
len - - maximum number of bytes to read
Return value :
string containing read bytes""" | try :
return self . _wrap_socket_library_call ( lambda : SSL_read ( self . _ssl . value , len , buffer ) , ERR_READ_TIMEOUT )
except openssl_error ( ) as err :
if err . ssl_error == SSL_ERROR_SYSCALL and err . result == - 1 :
raise_ssl_error ( ERR_PORT_UNREACHABLE , err )
raise |
def get_frame_list ( ) :
"""Create the list of frames""" | # TODO : use this function in IPS below ( less code duplication )
frame_info_list = [ ]
frame_list = [ ]
frame = inspect . currentframe ( )
while frame is not None :
frame_list . append ( frame )
info = inspect . getframeinfo ( frame )
frame_info_list . append ( info )
frame = frame . f_back
frame_info_... |
def getQueryEngineDescriptionResponse ( self , queryEngine , vendorSpecific = None , ** kwargs ) :
"""CNRead . getQueryEngineDescription ( session , queryEngine ) →
QueryEngineDescription https : / / releases . dataone . org / online / api -
documentation - v2.0.1 / apis / CN _ APIs . html # CNRead . getQueryEn... | return self . GET ( [ 'query' , queryEngine ] , query = kwargs , headers = vendorSpecific ) |
def Validate ( self , win ) :
"""Returns True if Value in digits , False otherwise""" | val = self . GetWindow ( ) . GetValue ( )
for x in val :
if x not in string . digits :
return False
return True |
def send_notification ( self , method , params ) :
"""Send a notification""" | msg = self . _encoder . create_notification ( method , params )
self . _send_message ( msg ) |
def cut_edges ( image , numPix ) :
"""cuts out the edges of a 2d image and returns re - sized image to numPix
center is well defined for odd pixel sizes .
: param image : 2d numpy array
: param numPix : square size of cut out image
: return : cutout image with size numPix""" | nx , ny = image . shape
if nx < numPix or ny < numPix :
print ( 'WARNING: image can not be resized, in routine cut_edges.' )
return image
if nx % 2 == 0 or ny % 2 == 0 or numPix % 2 == 0 : # pass
print ( "WARNING: image or cutout side are even number. This routine only works for odd numbers %s %s %s" % ( nx... |
def save_var ( self , key , value , ** kwargs ) :
'Save one variable to the database .' | # Check whether Highwall ' s variables table exists
self . __check_or_create_vars_table ( )
column_type = get_column_type ( value )
tmp = quote ( self . __vars_table_tmp )
self . execute ( u'DROP TABLE IF EXISTS %s' % tmp , commit = False )
# This is vulnerable to injection
self . execute ( u'CREATE TABLE %s (`value` %... |
def _iter_channels ( framefile ) :
"""Yields the name and type of each channel in a GWF file TOC
* * Requires : * * | LDAStools . frameCPP | _
Parameters
framefile : ` str ` , ` LDAStools . frameCPP . IFrameFStream `
path of GWF file , or open file stream , to read""" | from LDAStools import frameCPP
if not isinstance ( framefile , frameCPP . IFrameFStream ) :
framefile = open_gwf ( framefile , 'r' )
toc = framefile . GetTOC ( )
for typename in ( 'Sim' , 'Proc' , 'ADC' ) :
typen = typename . lower ( )
for name in getattr ( toc , 'Get{0}' . format ( typename ) ) ( ) :
... |
def plot_places ( self ) :
'''Plot places ( in the parameter space ) of all the generated artifacts
and the artifacts accepted to the domain .''' | from matplotlib import pyplot as plt
fig , ax = plt . subplots ( )
title = "Agent places, artifacts and env artifacts ({} env artifacts)" . format ( len ( self . artifacts ) )
x = [ ]
y = [ ]
for a in self . get_agents ( ) :
args = a . arg_history
x = x + [ e [ 0 ] for e in args ]
y = y + [ e [ 1 ] for e in... |
def moving_average_smooth ( t , y , dy , span = None , cv = True , t_out = None , span_out = None , period = None ) :
"""Perform a moving - average smooth of the data
Parameters
t , y , dy : array _ like
time , value , and error in value of the input data
span : array _ like
the integer spans of the data ... | prep = _prep_smooth ( t , y , dy , span , t_out , span_out , period )
t , y , dy , span , t_out , span_out , indices = prep
w = 1. / ( dy ** 2 )
w , yw = windowed_sum ( [ w , y * w ] , t = t , span = span , subtract_mid = cv , indices = indices , period = period )
if t_out is None or span_out is not None :
return y... |
def base64_bytes ( x ) :
"""Turn base64 into bytes""" | if six . PY2 :
return base64 . decodestring ( x )
return base64 . decodebytes ( bytes_encode ( x ) ) |
def get_all_attributes ( klass_or_instance ) :
"""Get all attribute members ( attribute , property style method ) .""" | pairs = list ( )
for attr , value in inspect . getmembers ( klass_or_instance , lambda x : not inspect . isroutine ( x ) ) :
if not ( attr . startswith ( "__" ) or attr . endswith ( "__" ) ) :
pairs . append ( ( attr , value ) )
return pairs |
def score ( self , eval_instances , verbosity = 0 ) :
'''Return scores ( negative log likelihoods ) assigned to each testing
instance in ` eval _ instances ` .
: param eval _ instances : The data to use to evaluate the model .
Instances should have at least the ` input ` and ` output ` fields
populated . ` ... | if hasattr ( self , '_using_default_combined' ) and self . _using_default_combined :
raise NotImplementedError
self . _using_default_separate = True
return self . predict_and_score ( eval_instances , verbosity = verbosity ) [ 1 ] |
def get_name ( model_id ) :
"""Get the name for a model .
: returns str : The model ' s name . If the id has no associated name , then " id = { ID } ( no name ) " is returned .""" | name = _names . get ( model_id )
if name is None :
name = 'id = %s (no name)' % str ( model_id )
return name |
def getReadNoise ( self , exten ) :
"""Method for returning the readnoise of a detector ( in counts ) .
Returns
readnoise : float
The readnoise of the detector in * * units of counts / electrons * * .""" | rn = self . _image [ exten ] . _rdnoise
if self . proc_unit == 'native' :
rn = self . _rdnoise / self . getGain ( exten )
return rn |
def to_array ( self ) :
"""Serializes this PhotoSize to a dictionary .
: return : dictionary representation of this object .
: rtype : dict""" | array = super ( PhotoSize , self ) . to_array ( )
array [ 'file_id' ] = u ( self . file_id )
# py2 : type unicode , py3 : type str
array [ 'width' ] = int ( self . width )
# type int
array [ 'height' ] = int ( self . height )
# type int
if self . file_size is not None :
array [ 'file_size' ] = int ( self . file_siz... |
def update_selection_sm_prior ( self ) :
"""State machine prior update of tree selection""" | if self . _do_selection_update :
return
self . _do_selection_update = True
tree_selection , selected_model_list , sm_selection , sm_selected_model_list = self . get_selections ( )
if tree_selection is not None : # self . _ logger . info ( " SM SELECTION IS : { 2 } \ n { 0 } , \ n { 1 } " . format ( selected _ model... |
def add_latlonalt ( self , lat , lon , altitude , terrain_alt = False ) :
'''add a point via latitude / longitude / altitude''' | if terrain_alt :
frame = mavutil . mavlink . MAV_FRAME_GLOBAL_TERRAIN_ALT
else :
frame = mavutil . mavlink . MAV_FRAME_GLOBAL_RELATIVE_ALT
p = mavutil . mavlink . MAVLink_mission_item_message ( self . target_system , self . target_component , 0 , frame , mavutil . mavlink . MAV_CMD_NAV_WAYPOINT , 0 , 0 , 0 , 0 ... |
async def unmount ( self , device ) :
"""Unmount a Device if mounted .
: param device : device object , block device path or mount path
: returns : whether the device is unmounted""" | device = self . _find_device ( device )
if not self . is_handleable ( device ) or not device . is_filesystem :
self . _log . warn ( _ ( 'not unmounting {0}: unhandled device' , device ) )
return False
if not device . is_mounted :
self . _log . info ( _ ( 'not unmounting {0}: not mounted' , device ) )
re... |
def set_exception ( self , exc_info ) :
"""This method allows you to set an exception in the future without requring
that exception to be raised from the futures worker . This method can be
called on an unbound future .
: param exc _ info : Either an exception info tuple or an exception value .
In the latte... | if not isinstance ( exc_info , tuple ) :
if not isinstance ( exc_info , BaseException ) :
raise TypeError ( 'expected BaseException instance' )
try : # TODO : Filld the traceback so it appears as if the exception
# was actually raised by the caller ? ( Not sure if possible )
raise exc_info
... |
def make_output_layers ( self ) :
"""Extract the ordering of output layers .""" | self . output_layers = [ ]
# import pytest ; pytest . set _ trace ( )
if hasattr ( self . model , 'output_layers' ) : # find corresponding output layers in CoreML model
# assume output layers are not shared
# Helper function to recursively extract output layers
# even if the model has a layer which is a nested model
... |
def reset_permission_factories ( self ) :
"""Remove cached permission factories .""" | for key in ( 'read' , 'create' , 'update' , 'delete' ) :
full_key = '{0}_permission_factory' . format ( key )
if full_key in self . __dict__ :
del self . __dict__ [ full_key ] |
def obo ( self ) :
"""str : the ` Relationship ` serialized in an ` ` [ Typedef ] ` ` stanza .
Note :
The following guide was used :
ftp : / / ftp . geneontology . org / pub / go / www / GO . format . obo - 1_4 . shtml""" | lines = [ "[Typedef]" , "id: {}" . format ( self . obo_name ) , "name: {}" . format ( self . obo_name ) ]
if self . complementary is not None :
lines . append ( "inverse_of: {}" . format ( self . complementary ) )
if self . symmetry is not None :
lines . append ( "is_symmetric: {}" . format ( self . symmetry ) ... |
def do_visualize ( self , line ) :
"""Visualize an ontology - ie wrapper for export command""" | if not self . current :
self . _help_noontology ( )
return
line = line . split ( )
try : # from . . viz . builder import action _ visualize
from . . ontodocs . builder import action_visualize
except :
self . _print ( "This command requires the ontodocs package: `pip install ontodocs`" )
return
impor... |
def print_probabilities ( state : State , ndigits : int = 4 , file : TextIO = None ) -> None :
"""Pretty print state probabilities .
Args :
state :
ndigits : Number of digits of accuracy
file : Output stream ( Defaults to stdout )""" | prob = bk . evaluate ( state . probabilities ( ) )
for index , prob in np . ndenumerate ( prob ) :
prob = round ( prob , ndigits )
if prob == 0.0 :
continue
ket = "" . join ( [ str ( n ) for n in index ] )
print ( ket , ":" , prob , file = file ) |
def make_event ( event : Callable ) -> Callable :
"""Create an event from a method signature .""" | @ property # type : ignore
@ wraps ( event )
def actualevent ( self ) : # pylint : disable = missing - docstring
name = event . __name__ [ 3 : ]
try : # the getter post processing function
# is preserved with an underscore
getter = event ( self ) . __name__
except AttributeError :
getter... |
def iter ( self ) :
"""Extract DIAMOND records and yield C { ReadAlignments } instances .
@ return : A generator that yields C { ReadAlignments } instances .""" | # Note that self . _ reader is already initialized ( in _ _ init _ _ ) for
# the first input file . This is less clean than it could be , but it
# makes testing easier , since open ( ) is then only called once for
# each input file .
reads = iter ( self . reads )
first = True
for filename in self . filenames :
if f... |
def _compile_signature ( self , iexec , call_name ) :
"""Compiles the signature for the specified executable and returns
as a dictionary .""" | if iexec is not None :
summary = iexec . summary
if isinstance ( iexec , Function ) :
summary = iexec . returns + "| " + iexec . summary
elif isinstance ( iexec , Subroutine ) and len ( iexec . modifiers ) > 0 :
summary = ", " . join ( iexec . modifiers ) + " | " + iexec . summary
elif i... |
def get_filters ( self ) :
"""Returns the result filters
: rtype : str or None""" | if self . _filters :
filters_list = self . _filters
if isinstance ( filters_list [ - 1 ] , Enum ) :
filters_list = filters_list [ : - 1 ]
return ' ' . join ( [ fs . value if isinstance ( fs , Enum ) else fs [ 1 ] for fs in filters_list ] ) . strip ( )
else :
return None |
def get_crystal_field_spin ( self , coordination : str = "oct" , spin_config : str = "high" ) :
"""Calculate the crystal field spin based on coordination and spin
configuration . Only works for transition metal species .
Args :
coordination ( str ) : Only oct and tet are supported at the moment .
spin _ con... | if coordination not in ( "oct" , "tet" ) or spin_config not in ( "high" , "low" ) :
raise ValueError ( "Invalid coordination or spin config." )
elec = self . full_electronic_structure
if len ( elec ) < 4 or elec [ - 1 ] [ 1 ] != "s" or elec [ - 2 ] [ 1 ] != "d" :
raise AttributeError ( "Invalid element {} for c... |
def _init_vocab ( self , token_generator , add_reserved_tokens = True ) :
"""Initialize vocabulary with tokens from token _ generator .""" | self . _id_to_token = { }
non_reserved_start_index = 0
if add_reserved_tokens :
self . _id_to_token . update ( enumerate ( RESERVED_TOKENS ) )
non_reserved_start_index = len ( RESERVED_TOKENS )
self . _id_to_token . update ( enumerate ( token_generator , start = non_reserved_start_index ) )
# _ token _ to _ id ... |
def stmts_from_path ( path , model , stmts ) :
"""Return source Statements corresponding to a path in a model .
Parameters
path : list [ tuple [ str , int ] ]
A list of tuples where the first element of the tuple is the
name of a rule , and the second is the associated polarity along
a path .
model : py... | path_stmts = [ ]
for path_rule , sign in path :
for rule in model . rules :
if rule . name == path_rule :
stmt = stmt_from_rule ( path_rule , model , stmts )
assert stmt is not None
path_stmts . append ( stmt )
return path_stmts |
def add_key ( pub ) :
"""Adds a new public key to be used when encrypting new data is needed""" | global _server_keys
key = rsa . PublicKey . load_pkcs1 ( pub )
_server_keys [ _compute_fingerprint ( key ) ] = key |
def graphql_mutation_from_summary ( summary ) :
"""This function returns a graphql mutation corresponding to the provided
summary .""" | # get the name of the mutation from the summary
mutation_name = summary [ 'name' ]
# print ( summary )
# the treat the " type " string as a gra
input_name = mutation_name + "Input"
input_fields = build_native_type_dictionary ( summary [ 'inputs' ] , name = input_name , respect_required = True )
# the inputs for the mut... |
def set_mrt ( self , s , mrt : str ) :
"""accepts a statement and adds a qualifer setting the mrt
modifies s in place
: param s : a WDBaseDataType statement
: param mrt : one of { ' close ' , ' broad ' , ' exact ' , ' related ' , ' narrow ' }
: return : s""" | valid_mrts_abv = self . ABV_MRT . keys ( )
valid_mrts_uri = self . ABV_MRT . values ( )
if mrt in valid_mrts_abv :
mrt_uri = self . ABV_MRT [ mrt ]
elif mrt in valid_mrts_uri :
mrt_uri = mrt
else :
raise ValueError ( "mrt must be one of {}, found {}" . format ( valid_mrts_abv , mrt ) )
mrt_qid = self . mrt_... |
def terminate ( name , call = None ) :
'''To do an immediate power off of a VM using its name . A ` ` SIGKILL ` `
is issued to the vmx process of the VM
CLI Example :
. . code - block : : bash
salt - cloud - a terminate vmname''' | if call != 'action' :
raise SaltCloudSystemExit ( 'The terminate action must be called with ' '-a or --action.' )
vm_properties = [ "name" , "summary.runtime.powerState" ]
vm_list = salt . utils . vmware . get_mors_with_properties ( _get_si ( ) , vim . VirtualMachine , vm_properties )
for vm in vm_list :
if vm ... |
def insert_child ( self , child_pid , index = - 1 ) :
"""Insert a new child into a PID concept .
Argument ' index ' can take the following values :
0,1,2 , . . . - insert child PID at the specified position
-1 - insert the child PID at the last position
None - insert child without order ( no re - ordering i... | self . _check_child_limits ( child_pid )
if index is None :
index = - 1
try :
with db . session . begin_nested ( ) :
if not isinstance ( child_pid , PersistentIdentifier ) :
child_pid = resolve_pid ( child_pid )
child_relations = self . _resolved_pid . child_relations . filter ( PIDR... |
def plotAAClusters ( sequence , propertyNames , showLines = True , showFigure = True ) :
"""Plot amino acid property cluster numbers for a sequence .
@ param sequence : An C { AARead } ( or a subclass ) instance .
@ param propertyNames : An iterable of C { str } property names ( each of which
must be a key of... | MISSING_AA_VALUE = 0
propertyClusters = clustersForSequence ( sequence , propertyNames , missingAAValue = MISSING_AA_VALUE )
if showFigure :
minCluster = 1
maxCluster = - 1
legend = [ ]
x = np . arange ( 0 , len ( sequence ) )
plot = plt . plot if showLines else plt . scatter
for index , propert... |
def opacity ( self , value ) :
"""Setter for * * self . _ _ opacity * * attribute .
: param value : Attribute value .
: type value : float""" | if value is not None :
assert type ( value ) in ( int , float ) , "'{0}' attribute: '{1}' type is not 'int' or 'float'!" . format ( "opacity" , value )
if value > 1 :
value = 1
elif value < 0 :
value = 0
self . __opacity = float ( value )
self . __set_style_sheet ( ) |
def take_percentile ( arr , percent ) :
"""take the top ` percent ` items in a list rounding up""" | size = len ( arr )
stop = min ( int ( size * percent ) , len ( arr ) )
return arr [ 0 : stop ] |
def num_listeners ( self , event = None ) :
"""Return the number of listeners for ` ` event ` ` .
Return the total number of listeners for all events on this object if
` ` event ` ` is : class : ` None ` .""" | if event is not None :
return len ( self . _listeners [ event ] )
else :
return sum ( len ( l ) for l in self . _listeners . values ( ) ) |
def create_poi_gdf ( polygon = None , amenities = None , north = None , south = None , east = None , west = None ) :
"""Parse GeoDataFrames from POI json that was returned by Overpass API .
Parameters
polygon : shapely Polygon or MultiPolygon
geographic shape to fetch the POIs within
amenities : list
List... | responses = osm_poi_download ( polygon = polygon , amenities = amenities , north = north , south = south , east = east , west = west )
# Parse coordinates from all the nodes in the response
coords = parse_nodes_coords ( responses )
# POI nodes
poi_nodes = { }
# POI ways
poi_ways = { }
# A list of POI relations
relation... |
def get_targets ( self , raw_string ) : # type : ( Optional [ Text ] ) - > Dict [ Text , Text ]
"""Extract targets from a string in ' key : value ' format .""" | targets = { }
if raw_string is not None :
for line in raw_string . splitlines ( ) :
if line :
target , directory = line . split ( ':' , 1 )
targets [ target . strip ( ) ] = directory . strip ( )
return targets |
def parse_digest_challenge ( authentication_header ) :
'''Parses the value of a ' WWW - Authenticate ' header . Returns an object with properties
corresponding to each of the recognized parameters in the header .''' | if not is_digest_challenge ( authentication_header ) :
return None
parts = parse_parts ( authentication_header [ 7 : ] , defaults = { 'algorithm' : 'MD5' , 'stale' : 'false' } )
if not _check_required_parts ( parts , _REQUIRED_DIGEST_CHALLENGE_PARTS ) :
return None
parts [ 'stale' ] = parts [ 'stale' ] . lower ... |
def send_request ( ** kwargs ) :
"""Return a data frame from a web service request to cBio portal .
Sends a web service requrest to the cBio portal with arguments given in
the dictionary data and returns a Pandas data frame on success .
More information about the service here :
http : / / www . cbioportal .... | skiprows = kwargs . pop ( 'skiprows' , None )
res = requests . get ( cbio_url , params = kwargs )
if res . status_code == 200 : # Adaptively skip rows based on number of comment lines
if skiprows == - 1 :
lines = res . text . split ( '\n' )
skiprows = 0
for line in lines :
if lin... |
def set_json ( self , config_json ) :
"""Permanently set the JSON configuration
Unable to call twice .""" | if self . configuration_dict is not None :
raise RuntimeError ( "Can only set configuration once" , self . configuration_dict )
schema = fetch_config ( 'ConfigurationSchema.json' )
validictory . validate ( config_json , schema )
config_json [ 'name' ] = self . name
config_json [ 'run_number' ] = self . run
config_j... |
def build_tree_from_alignment ( aln , moltype = DNA , best_tree = False , params = None ) :
"""Returns a tree from alignment
Will check MolType of aln object""" | if params is None :
params = { }
if moltype == DNA or moltype == RNA :
params [ '-nt' ] = True
elif moltype == PROTEIN :
params [ '-nt' ] = False
else :
raise ValueError , "FastTree does not support moltype: %s" % moltype . label
if best_tree :
params [ '-slow' ] = True
# Create mapping between abbr... |
def to_xml ( self ) :
'''Returns an XMLi representation of the shipping details .
@ return : Element''' | for n , v in { "recipient" : self . recipient } . items ( ) :
if is_empty_or_none ( v ) :
raise ValueError ( "'%s' attribute cannot be empty or None." % n )
doc = Document ( )
root = doc . createElement ( "shipping" )
root . appendChild ( self . recipient . to_xml ( "recipient" ) )
return root |
def fetch_internal ( item , request ) :
"""Fetches the given request by using the local Flask context .""" | # Break client dependence on Flask if internal fetches aren ' t being used .
from flask import make_response
from werkzeug . test import EnvironBuilder
# Break circular dependencies .
from dpxdt . server import app
# Attempt to create a Flask environment from a urllib2 . Request object .
environ_base = { 'REMOTE_ADDR' ... |
def from_values_indices ( cls , values , indices , populate = False , structure = None , voigt_rank = None , vsym = True , verbose = False ) :
"""Creates a tensor from values and indices , with options
for populating the remainder of the tensor .
Args :
values ( floats ) : numbers to place at indices
indice... | # auto - detect voigt notation
# TODO : refactor rank inheritance to make this easier
indices = np . array ( indices )
if voigt_rank :
shape = ( [ 3 ] * ( voigt_rank % 2 ) + [ 6 ] * ( voigt_rank // 2 ) )
else :
shape = np . ceil ( np . max ( indices + 1 , axis = 0 ) / 3. ) * 3
base = np . zeros ( shape . astype... |
def _temporary_filenames ( total ) :
"""Context manager to create temporary files and remove them after use .""" | temp_files = [ _get_temporary_filename ( 'optimage-' ) for i in range ( total ) ]
yield temp_files
for temp_file in temp_files :
try :
os . remove ( temp_file )
except OSError : # Continue in case we could not remove the file . One reason is that
# the fail was never created .
pass |
def decode ( value , strip = False ) :
"""Python 2/3 friendly decoding of output .
Args :
value ( str | unicode | bytes | None ) : The value to decode .
strip ( bool ) : If True , ` strip ( ) ` the returned string . ( Default value = False )
Returns :
str : Decoded value , if applicable .""" | if value is None :
return None
if isinstance ( value , bytes ) and not isinstance ( value , unicode ) :
value = value . decode ( "utf-8" )
if strip :
return unicode ( value ) . strip ( )
return unicode ( value ) |
def unregister_project ( self , project_node , raise_exception = False ) :
"""Unregisters given : class : ` umbra . components . factory . scriptProject . nodes . ProjectNode ` class Node from the Model .
: param project _ node : ProjectNode to unregister .
: type project _ node : ProjectNode
: param raise _ ... | if raise_exception :
if not project_node in self . list_project_nodes ( ) :
raise foundations . exceptions . ProgrammingError ( "{0} | '{1}' project 'ProjectNode' isn't registered!" . format ( self . __class__ . __name__ , project_node ) )
LOGGER . debug ( "> Unregistering '{0}' project 'ProjectNode'." . fo... |
def get_snapshot_closest_to_state_change ( self , state_change_identifier : int , ) -> Tuple [ int , Any ] :
"""Get snapshots earlier than state _ change with provided ID .""" | row = super ( ) . get_snapshot_closest_to_state_change ( state_change_identifier )
if row [ 1 ] :
last_applied_state_change_id = row [ 0 ]
snapshot_state = self . serializer . deserialize ( row [ 1 ] )
result = ( last_applied_state_change_id , snapshot_state )
else :
result = ( 0 , None )
return result |
def _is_mwtab ( string ) :
"""Test if input string is in ` mwtab ` format .
: param string : Input string .
: type string : : py : class : ` str ` or : py : class : ` bytes `
: return : Input string if in mwTab format or False otherwise .
: rtype : : py : class : ` str ` or : py : obj : ` False `""" | if isinstance ( string , str ) :
lines = string . split ( "\n" )
elif isinstance ( string , bytes ) :
lines = string . decode ( "utf-8" ) . split ( "\n" )
else :
raise TypeError ( "Expecting <class 'str'> or <class 'bytes'>, but {} was passed" . format ( type ( string ) ) )
lines = [ line for line in lines ... |
def relation_get ( attribute = None , unit = None , rid = None ) :
"""Get relation information""" | _args = [ 'relation-get' , '--format=json' ]
if rid :
_args . append ( '-r' )
_args . append ( rid )
_args . append ( attribute or '-' )
if unit :
_args . append ( unit )
try :
return json . loads ( subprocess . check_output ( _args ) . decode ( 'UTF-8' ) )
except ValueError :
return None
except Cal... |
def _rd_segment ( file_name , dir_name , pb_dir , fmt , n_sig , sig_len , byte_offset , samps_per_frame , skew , sampfrom , sampto , channels , smooth_frames , ignore_skew ) :
"""Read the digital samples from a single segment record ' s associated
dat file ( s ) .
Parameters
file _ name : list
The names of ... | # Avoid changing outer variables
byte_offset = byte_offset [ : ]
samps_per_frame = samps_per_frame [ : ]
skew = skew [ : ]
# Set defaults for empty fields
for i in range ( n_sig ) :
if byte_offset [ i ] == None :
byte_offset [ i ] = 0
if samps_per_frame [ i ] == None :
samps_per_frame [ i ] = 1
... |
def _buckets_nearly_equal ( a_dist , b_dist ) :
"""Determines whether two ` Distributions ` are nearly equal .
Args :
a _ dist ( : class : ` Distribution ` ) : an instance
b _ dist ( : class : ` Distribution ` ) : another instance
Return :
boolean : ` True ` if the two instances are approximately equal , ... | a_type , a_buckets = _detect_bucket_option ( a_dist )
b_type , b_buckets = _detect_bucket_option ( b_dist )
if a_type != b_type :
return False
elif a_type == u'linearBuckets' :
return _linear_buckets_nearly_equal ( a_buckets , b_buckets )
elif a_type == u'exponentialBuckets' :
return _exponential_buckets_ne... |
def SplitV ( a , splits , axis ) :
"""Split op with multiple split sizes .""" | return tuple ( np . split ( np . copy ( a ) , np . cumsum ( splits ) , axis = axis ) ) |
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