signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def min_heapify ( arr , start , simulation , iteration ) :
"""Min heapify helper for min _ heap _ sort""" | # Offset last _ parent by the start ( last _ parent calculated as if start index was 0)
# All array accesses need to be offset by start
end = len ( arr ) - 1
last_parent = ( end - start - 1 ) // 2
# Iterate from last parent to first
for parent in range ( last_parent , - 1 , - 1 ) :
current_parent = parent
# Ite... |
def _viz_prototype ( self , vis_fn ) :
'''Outputs a function which will log the arguments to Visdom in an appropriate way .
Args :
vis _ fn : A function , such as self . vis . image''' | def _viz_logger ( * args , ** kwargs ) :
self . win = vis_fn ( * args , win = self . win , env = self . env , opts = self . opts , ** kwargs )
return _viz_logger |
def send_email ( self , ** kwargs ) :
"""Sends an email using Mandrill ' s API . Returns a
Requests : class : ` Response ` object .
At a minimum kwargs must contain the keys to , from _ email , and text .
Everything passed as kwargs except for the keywords ' key ' , ' async ' ,
and ' ip _ pool ' will be sen... | endpoint = self . messages_endpoint
data = { 'async' : kwargs . pop ( 'async' , False ) , 'ip_pool' : kwargs . pop ( 'ip_pool' , '' ) , 'key' : kwargs . pop ( 'key' , self . api_key ) , }
if not data . get ( 'key' , None ) :
raise ValueError ( 'No Mandrill API key has been configured' )
# Sending a template through... |
def update_bundle ( self , href = None , name = None , notify_url = None , version = None , external_id = None ) :
"""Update a bundle . Note that only the ' name ' and ' notify _ url ' can
be update .
' href ' the relative href to the bundle . May not be None .
' name ' the name of the bundle . May be None . ... | # Argument error checking .
assert href is not None
assert version is None or isinstance ( version , int )
# Prepare the data we ' re going to include in our bundle update .
data = None
fields = { }
if name is not None :
fields [ 'name' ] = name
if notify_url is not None :
fields [ 'notify_url' ] = notify_url
i... |
def _validate_format ( req ) :
'''Validate jsonrpc compliance of a jsonrpc - dict .
req - the request as a jsonrpc - dict
raises SLOJSONRPCError on validation error''' | # check for all required keys
for key in SLOJSONRPC . _min_keys :
if not key in req :
logging . debug ( 'JSONRPC: Fmt Error: Need key "%s"' % key )
raise SLOJSONRPCError ( - 32600 )
# check all keys if allowed
for key in req . keys ( ) :
if not key in SLOJSONRPC . _allowed_keys :
logging... |
def ephemeral ( cls ) :
"""Creates a new ephemeral key constructed using a raw 32 - byte string from urandom .
Ephemeral keys are used once for each encryption task and are then discarded ;
they are not intended for long - term or repeat use .""" | private_key = nacl . public . PrivateKey ( os . urandom ( 32 ) )
return cls ( private_key . public_key , private_key ) |
def require_paragraph ( self ) :
"""Create a new paragraph unless the currently - active container
is already a paragraph .""" | if self . _containers and _is_paragraph ( self . _containers [ - 1 ] ) :
return False
else :
self . start_paragraph ( )
return True |
def ifadd ( self , iff , addr ) :
"""Add an interface ' iff ' with provided address into routing table .
Ex : ifadd ( ' eth0 ' , ' 2001 : bd8 : cafe : 1 : : 1/64 ' ) will add following entry into # noqa : E501
Scapy6 internal routing table :
Destination Next Hop iface Def src @ Metric
2001 : bd8 : cafe : 1 ... | addr , plen = ( addr . split ( "/" ) + [ "128" ] ) [ : 2 ]
addr = in6_ptop ( addr )
plen = int ( plen )
naddr = inet_pton ( socket . AF_INET6 , addr )
nmask = in6_cidr2mask ( plen )
prefix = inet_ntop ( socket . AF_INET6 , in6_and ( nmask , naddr ) )
self . invalidate_cache ( )
self . routes . append ( ( prefix , plen ... |
def src_paths_changed ( self ) :
"""See base class docstring .""" | # Get the diff dictionary
diff_dict = self . _git_diff ( )
# Return the changed file paths ( dict keys )
# in alphabetical order
return sorted ( diff_dict . keys ( ) , key = lambda x : x . lower ( ) ) |
def reader ( self ) :
from ambry . orm . exc import NotFoundError
from fs . errors import ResourceNotFoundError
"""The reader for the datafile""" | try :
return self . datafile . reader
except ResourceNotFoundError :
raise NotFoundError ( "Failed to find partition file, '{}' " . format ( self . datafile . path ) ) |
def constraints_stmt ( stmt , env = None ) :
"""Since a statement may define new names or return an expression ,
the constraints that result are in a
ConstrainedEnv mapping names to types , with constraints , and maybe
having a return type ( which is a constrained type )""" | env = env or { }
if isinstance ( stmt , ast . FunctionDef ) :
arg_env = fn_env ( stmt . args )
body_env = extended_env ( env , arg_env )
constraints = [ ]
return_type = None
# TODO : should be fresh and constrained ?
for body_stmt in stmt . body :
cs = constraints_stmt ( body_stmt , env ... |
def add_doc_to_update ( self , action , update_spec , action_buffer_index ) :
"""Prepare document for update based on Elasticsearch response .
Set flag if document needs to be retrieved from Elasticsearch""" | doc = { "_index" : action [ "_index" ] , "_type" : action [ "_type" ] , "_id" : action [ "_id" ] , }
# If get _ from _ ES = = True - > get document ' s source from Elasticsearch
get_from_ES = self . should_get_id ( action )
self . doc_to_update . append ( ( doc , update_spec , action_buffer_index , get_from_ES ) ) |
def split ( X , Y , question ) :
"""Partitions a dataset .
For each row in the dataset , check if it matches the question . If
so , add it to ' true rows ' , otherwise , add it to ' false rows ' .""" | true_X , false_X = [ ] , [ ]
true_Y , false_Y = [ ] , [ ]
for x , y in zip ( X , Y ) :
if question . match ( x ) :
true_X . append ( x )
true_Y . append ( y )
else :
false_X . append ( x )
false_Y . append ( y )
return ( np . array ( true_X ) , np . array ( false_X ) , np . array... |
def viz_json ( net , dendro = True , links = False ) :
'''make the dictionary for the clustergram . js visualization''' | from . import calc_clust
import numpy as np
all_dist = calc_clust . group_cutoffs ( )
for inst_rc in net . dat [ 'nodes' ] :
inst_keys = net . dat [ 'node_info' ] [ inst_rc ]
all_cats = [ x for x in inst_keys if 'cat-' in x ]
for i in range ( len ( net . dat [ 'nodes' ] [ inst_rc ] ) ) :
inst_dict =... |
def autodiscover ( path = None , plugin_prefix = 'intake_' ) :
"""Scan for Intake plugin packages and return a dict of plugins .
This function searches path ( or sys . path ) for packages with names that
start with plugin _ prefix . Those modules will be imported and scanned for
subclasses of intake . source ... | plugins = { }
for importer , name , ispkg in pkgutil . iter_modules ( path = path ) :
if name . startswith ( plugin_prefix ) :
t = time . time ( )
new_plugins = load_plugins_from_module ( name )
for plugin_name , plugin in new_plugins . items ( ) :
if plugin_name in plugins :
... |
def readMangleFile ( infile , lon , lat , index = None ) :
"""DEPRECATED : 2018-05-04
Mangle must be set up on your system .
The index argument is a temporary file naming convention to avoid file conflicts .
Coordinates must be given in the native coordinate system of the Mangle file .""" | msg = "'mask.readMangleFile': ADW 2018-05-05"
DeprecationWarning ( msg )
if index is None :
index = np . random . randint ( 0 , 1.e10 )
coordinate_file = 'temp_coordinate_%010i.dat' % ( index )
maglim_file = 'temp_maglim_%010i.dat' % ( index )
writer = open ( coordinate_file , 'w' )
for ii in range ( 0 , len ( lon ... |
def update ( self ) :
"""Update this range""" | if not self . _track_changes :
return True
# there ' s nothing to update
data = self . to_api_data ( restrict_keys = self . _track_changes )
response = self . session . patch ( self . build_url ( '' ) , data = data )
if not response :
return False
data = response . json ( )
for field in self . _track_changes :
... |
def download_url ( url , dir_name = '.' , save_name = None , store_directory = None , messages = True , suffix = '' ) :
"""Download a file from a url and save it to disk .""" | if sys . version_info >= ( 3 , 0 ) :
from urllib . parse import quote
from urllib . request import urlopen
from urllib . error import HTTPError , URLError
else :
from urllib2 import quote
from urllib2 import urlopen
from urllib2 import URLError as HTTPError
i = url . rfind ( '/' )
file = url [ i... |
def __setup_tool_config ( self , conf ) :
"""Setups toolbox object and authorization mechanism based
on supplied toolbox _ path .""" | tool_config_files = conf . get ( "tool_config_files" , None )
if not tool_config_files : # For compatibity with Galaxy , allow tool _ config _ file
# option name .
tool_config_files = conf . get ( "tool_config_file" , None )
toolbox = None
if tool_config_files :
toolbox = ToolBox ( tool_config_files )
else :
... |
def get_value_len ( value ) :
'''Get length of ` ` value ` ` . If ` ` value ` ` ( eg , iterator ) has no len ( ) , convert it to list first .
return both length and converted value .''' | try :
Nvalue = len ( value )
except TypeError : # convert iterator / generator to list
value = list ( value )
Nvalue = len ( value )
return Nvalue , value |
def zip ( * args , ** kwargs ) :
"""Returns a list of tuples , where the i - th tuple contains the i - th element
from each of the argument sequences or iterables ( or default if too short ) .""" | args = [ list ( iterable ) for iterable in args ]
n = max ( map ( len , args ) )
v = kwargs . get ( "default" , None )
return _zip ( * [ i + [ v ] * ( n - len ( i ) ) for i in args ] ) |
def flatten_list ( lobj ) :
"""Recursively flattens a list .
: param lobj : List to flatten
: type lobj : list
: rtype : list
For example :
> > > import pmisc
> > > pmisc . flatten _ list ( [ 1 , [ 2 , 3 , [ 4 , 5 , 6 ] ] , 7 ] )
[1 , 2 , 3 , 4 , 5 , 6 , 7]""" | ret = [ ]
for item in lobj :
if isinstance ( item , list ) :
for sub_item in flatten_list ( item ) :
ret . append ( sub_item )
else :
ret . append ( item )
return ret |
def get_prep_value ( self , value ) :
"""Perform preliminary non - db specific value checks and conversions .""" | if value :
if not isinstance ( value , PhoneNumber ) :
value = to_python ( value )
if value . is_valid ( ) :
format_string = getattr ( settings , "PHONENUMBER_DB_FORMAT" , "E164" )
fmt = PhoneNumber . format_map [ format_string ]
value = value . format_as ( fmt )
else :
... |
def colored ( cls , color , message ) :
"""Small function to wrap a string around a color
Args :
color ( str ) : name of the color to wrap the string with , must be one
of the class properties
message ( str ) : String to wrap with the color
Returns :
str : the colored string""" | return getattr ( cls , color . upper ( ) ) + message + cls . DEFAULT |
def run_optimization ( self ) :
"""Run the optimization , call run _ one _ step with suitable placeholders .
Returns :
True if certificate is found
False otherwise""" | penalty_val = self . params [ 'init_penalty' ]
# Don ' t use smoothing initially - very inaccurate for large dimension
self . smooth_on = False
smooth_val = 0
learning_rate_val = self . params [ 'init_learning_rate' ]
self . current_outer_step = 1
while self . current_outer_step <= self . params [ 'outer_num_steps' ] :... |
def _publish_response ( self , slug , message ) :
"""Publish a response message for a device
Args :
slug ( string ) : The device slug that we are publishing on behalf of
message ( dict ) : A set of key value pairs that are used to create the message
that is sent .""" | resp_topic = self . topics . gateway_topic ( slug , 'data/response' )
self . _logger . debug ( "Publishing response message: (topic=%s) (message=%s)" , resp_topic , message )
self . client . publish ( resp_topic , message ) |
def measure_fps ( self , window = 1 , callback = '%1.1f FPS' ) :
"""Measure the current FPS
Sets the update window , connects the draw event to update _ fps
and sets the callback function .
Parameters
window : float
The time - window ( in seconds ) to calculate FPS . Default 1.0.
callback : function | s... | # Connect update _ fps function to draw
self . events . draw . disconnect ( self . _update_fps )
if callback :
if isinstance ( callback , string_types ) :
callback_str = callback
# because callback gets overwritten
def callback ( x ) :
print ( callback_str % x )
self . _fps_w... |
def close ( self ) :
"""Closes the handle opened by open ( ) .
The remapped function is WinDivertClose : :
BOOL WinDivertClose (
_ _ in HANDLE handle
For more info on the C call visit : http : / / reqrypt . org / windivert - doc . html # divert _ close""" | if not self . is_open :
raise RuntimeError ( "WinDivert handle is not open." )
windivert_dll . WinDivertClose ( self . _handle )
self . _handle = None |
def load_collection_from_stream ( resource , stream , content_type ) :
"""Creates a new collection for the registered resource and calls
` load _ into _ collection _ from _ stream ` with it .""" | coll = create_staging_collection ( resource )
load_into_collection_from_stream ( coll , stream , content_type )
return coll |
def delete ( self ) :
"""Extend to the delete the session from storage""" | self . clear ( )
if os . path . isfile ( self . _filename ) :
os . unlink ( self . _filename )
else :
LOGGER . debug ( 'Session file did not exist: %s' , self . _filename ) |
def write_to_textfile ( path , registry ) :
"""Write metrics to the given path .
This is intended for use with the Node exporter textfile collector .
The path must end in . prom for the textfile collector to process it .""" | tmppath = '%s.%s.%s' % ( path , os . getpid ( ) , threading . current_thread ( ) . ident )
with open ( tmppath , 'wb' ) as f :
f . write ( generate_latest ( registry ) )
# rename ( 2 ) is atomic .
os . rename ( tmppath , path ) |
def write_headers ( self , observations , sys_header ) :
"""Writes the header part of the astrom file so that only the source
data has to be filled in .""" | if self . _header_written :
raise AstromFormatError ( "Astrom file already has headers." )
self . _write_observation_list ( observations )
self . _write_observation_headers ( observations )
self . _write_sys_header ( sys_header )
self . _write_source_header ( )
self . _header_written = True |
def _set_red_profile_ecn ( self , v , load = False ) :
"""Setter method for red _ profile _ ecn , mapped from YANG variable / qos / ecn / red _ profile / red _ profile _ ecn ( container )
If this variable is read - only ( config : false ) in the
source YANG file , then _ set _ red _ profile _ ecn is considered ... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = red_profile_ecn . red_profile_ecn , is_container = 'container' , presence = False , yang_name = "red-profile-ecn" , rest_name = "ecn" , parent = self , path_helper = self . _path_helper , extmethods = self . _extmethods , reg... |
def get_token ( self , user_id ) :
"""Get user token
Checks if a custom token implementation is registered and uses that .
Otherwise falls back to default token implementation . Returns a string
token on success .
: param user _ id : int , user id
: return : str""" | if not self . jwt_implementation :
return self . default_token_implementation ( user_id )
try :
implementation = import_string ( self . jwt_implementation )
except ImportError :
msg = 'Failed to import custom JWT implementation. '
msg += 'Check that configured module exists [{}]'
raise x . Configura... |
def semantic_similarity ( go_id1 , go_id2 , godag , branch_dist = None ) :
'''Finds the semantic similarity ( inverse of the semantic distance )
between two GO terms .''' | dist = semantic_distance ( go_id1 , go_id2 , godag , branch_dist )
if dist is not None :
return 1.0 / float ( dist ) |
def getReffs ( self , level = 1 , subreference = None ) -> CtsReferenceSet :
"""Reference available at a given level
: param level : Depth required . If not set , should retrieve first encountered level ( 1 based ) . 0 retrieves inside
a range
: param subreference : Subreference ( optional )
: returns : Lis... | level += self . depth
if not subreference :
subreference = self . reference
return self . textObject . getValidReff ( level , reference = subreference ) |
def visualize_model ( onnx_model , open_browser = True , dest = "index.html" ) :
"""Creates a graph visualization of an ONNX protobuf model .
It creates a SVG graph with * d3 . js * and stores it into a file .
: param model : ONNX model ( protobuf object )
: param open _ browser : opens the browser
: param ... | graph = onnx_model . graph
model_info = "Model produced by: " + onnx_model . producer_name + " version(" + onnx_model . producer_version + ")"
html_str = """
<!doctype html>
<meta charset="utf-8">
<title>ONNX Visualization</title>
<script src="https://d3js.org/d3.v3.min.js"></script>
<link rel="styl... |
def weather ( searchterm ) :
"""Get the weather for a place given by searchterm
Returns a title and a list of forecasts .
The title describes the location for the forecast ( i . e . " Portland , ME USA " )
The list of forecasts is a list of dictionaries in slack attachment fields
format ( see https : / / ap... | unit = "si" if os . environ . get ( "WEATHER_CELSIUS" ) else "us"
geo = requests . get ( "https://api.mapbox.com/geocoding/v5/mapbox.places/{}.json?limit=1&access_token={}" . format ( quote ( searchterm . encode ( "utf8" ) ) , MAPBOX_API_TOKEN ) ) . json ( )
citystate = geo [ "features" ] [ 0 ] [ "place_name" ]
lon , l... |
def to_array ( self , itaper , normalization = '4pi' , csphase = 1 ) :
"""Return the spherical harmonic coefficients of taper i as a numpy
array .
Usage
coeffs = x . to _ array ( itaper , [ normalization , csphase ] )
Returns
coeffs : ndarray , shape ( 2 , lwin + 1 , lwin + 11)
3 - D numpy ndarray of th... | if type ( normalization ) != str :
raise ValueError ( 'normalization must be a string. ' + 'Input type was {:s}' . format ( str ( type ( normalization ) ) ) )
if normalization . lower ( ) not in ( '4pi' , 'ortho' , 'schmidt' ) :
raise ValueError ( "normalization must be '4pi', 'ortho' " + "or 'schmidt'. Provide... |
def _select_next_server ( self ) :
"""Looks up in the server pool for an available server
and attempts to connect .""" | # Continue trying to connect until there is an available server
# or bail in case there are no more available servers .
while True :
if len ( self . _server_pool ) == 0 :
self . _current_server = None
raise ErrNoServers
now = time . time ( )
s = self . _server_pool . pop ( 0 )
if self . ... |
def inspect ( self , nids = None , wslice = None , ** kwargs ) :
"""Inspect the tasks ( SCF iterations , Structural relaxation . . . ) and
produces matplotlib plots .
Args :
nids : List of node identifiers .
wslice : Slice object used to select works .
kwargs : keyword arguments passed to ` task . inspect... | figs = [ ]
for task in self . select_tasks ( nids = nids , wslice = wslice ) :
if hasattr ( task , "inspect" ) :
fig = task . inspect ( ** kwargs )
if fig is None :
cprint ( "Cannot inspect Task %s" % task , color = "blue" )
else :
figs . append ( fig )
else :
... |
def addEdgeToGraph ( parentNodeName , childNodeName , graphFileHandle , colour = "black" , length = "10" , weight = "1" , dir = "none" , label = "" , style = "" ) :
"""Links two nodes in the graph together .""" | graphFileHandle . write ( 'edge[color=%s,len=%s,weight=%s,dir=%s,label="%s",style=%s];\n' % ( colour , length , weight , dir , label , style ) )
graphFileHandle . write ( "%s -- %s;\n" % ( parentNodeName , childNodeName ) ) |
def get_sessionmaker ( sqlalchemy_url , engine = None ) :
"""Create session with database to work in""" | if engine is None :
engine = create_engine ( sqlalchemy_url )
return sessionmaker ( bind = engine ) |
def count ( self ) :
"""Returns the number of bits set to True in the bit string .
Usage :
assert BitString ( ' 00110 ' ) . count ( ) = = 2
Arguments : None
Return :
An int , the number of bits with value 1.""" | result = 0
bits = self . _bits
while bits :
result += bits % 2
bits >>= 1
return result |
def split_adhoc_filters_into_base_filters ( fd ) :
"""Mutates form data to restructure the adhoc filters in the form of the four base
filters , ` where ` , ` having ` , ` filters ` , and ` having _ filters ` which represent
free form where sql , free form having sql , structured where clauses and structured
h... | adhoc_filters = fd . get ( 'adhoc_filters' )
if isinstance ( adhoc_filters , list ) :
simple_where_filters = [ ]
simple_having_filters = [ ]
sql_where_filters = [ ]
sql_having_filters = [ ]
for adhoc_filter in adhoc_filters :
expression_type = adhoc_filter . get ( 'expressionType' )
... |
async def addNodes ( self , nodedefs ) :
'''Quickly add / modify a list of nodes from node definition tuples .
This API is the simplest / fastest way to add nodes , set node props ,
and add tags to nodes remotely .
Args :
nodedefs ( list ) : A list of node definition tuples . See below .
A node definition... | async with await self . snap ( ) as snap :
snap . strict = False
async for node in snap . addNodes ( nodedefs ) :
yield node |
def limits ( self , x1 , x2 , y1 , y2 ) :
"""Set the coordinate boundaries of plot""" | import math
self . x1 = x1
self . x2 = x2
self . y1 = y1
self . y2 = y2
self . xscale = ( self . cx2 - self . cx1 ) / ( self . x2 - self . x1 )
self . yscale = ( self . cy2 - self . cy1 ) / ( self . y2 - self . y1 )
ra1 = self . x1
ra2 = self . x2
dec1 = self . y1
dec2 = self . y2
( sx1 , sy2 ) = self . p2c ( ( ra1 , d... |
def template ( page = None , layout = None , ** kwargs ) :
"""Decorator to change the view template and layout .
It works on both View class and view methods
on class
only $ layout is applied , everything else will be passed to the kwargs
Using as first argument , it will be the layout .
: first arg or $ ... | pkey = "_template_extends__"
def decorator ( f ) :
if inspect . isclass ( f ) :
layout_ = layout or page
extends = kwargs . pop ( "extends" , None )
if extends and hasattr ( extends , pkey ) :
items = getattr ( extends , pkey ) . items ( )
if "layout" in items :
... |
def monthly ( usaf , year , field = 'GHI (W/m^2)' ) :
"""monthly insolation""" | m = [ ]
lastm = 1
usafdata = Data ( usaf , year )
t = 0
for r in usafdata :
r [ 'GHI (W/m^2)' ] = r [ 'Glo Mod (Wh/m^2)' ]
r [ 'DHI (W/m^2)' ] = r [ 'Dif Mod (Wh/m^2)' ]
r [ 'DNI (W/m^2)' ] = r [ 'Dir Mod (Wh/m^2)' ]
if r [ 'datetime' ] . month != lastm :
m . append ( t / 1000. )
t = 0
... |
def remove_setting ( self , section , name , save = False ) :
'''remove a setting from the global config''' | configfile = get_configfile ( )
return _remove_setting ( section , name , configfile , save ) |
def angular_power_spectrum ( self ) :
"""Returns the angular power spectrum for the set of coefficients .
That is , we compute
c _ n = sum cnm * conj ( cnm )
m = - n
Returns :
power _ spectrum ( numpy . array , dtype = double ) spectrum as a function of n .""" | # Added this routine as a result of my discussions with Ajinkya Nene
# https : / / github . com / anene
list_of_modes = self . _reshape_m_vecs ( )
Nmodes = len ( list_of_modes )
angular_power = np . zeros ( Nmodes , dtype = np . double )
for n in range ( 0 , Nmodes ) :
mode = np . array ( list_of_modes [ n ] , dtyp... |
def load ( yaml_string , schema = None , label = u"<unicode string>" ) :
"""Parse the first YAML document in a string
and produce corresponding YAML object .""" | return generic_load ( yaml_string , schema = schema , label = label ) |
def time_from_hhmmssmmm ( string , decimal_separator = "." ) :
"""Parse the given ` ` HH : MM : SS . mmm ` ` string and return a time value .
: param string string : the string to be parsed
: param string decimal _ separator : the decimal separator to be used
: rtype : : class : ` ~ aeneas . exacttiming . Tim... | if decimal_separator == "," :
pattern = HHMMSS_MMM_PATTERN_COMMA
else :
pattern = HHMMSS_MMM_PATTERN
v_length = TimeValue ( "0.000" )
try :
match = pattern . search ( string )
if match is not None :
v_h = int ( match . group ( 1 ) )
v_m = int ( match . group ( 2 ) )
v_s = int ( m... |
def pack_nibbles ( nibbles ) :
"""pack nibbles to binary
: param nibbles : a nibbles sequence . may have a terminator""" | if nibbles [ - 1 ] == NIBBLE_TERMINATOR :
flags = 2
nibbles = nibbles [ : - 1 ]
else :
flags = 0
oddlen = len ( nibbles ) % 2
flags |= oddlen
# set lowest bit if odd number of nibbles
if oddlen :
nibbles = [ flags ] + nibbles
else :
nibbles = [ flags , 0 ] + nibbles
o = b''
for i in range ( 0 , len ... |
def close ( self ) -> Awaitable [ None ] :
"""Close all ongoing DNS calls .""" | for ev in self . _throttle_dns_events . values ( ) :
ev . cancel ( )
return super ( ) . close ( ) |
def errors ( self ) :
"""Computes and returns the error and standard deviation of the
filter at this time step .
Returns
error : np . array size 1xorder + 1
std : np . array size 1xorder + 1""" | n = self . n
dt = self . dt
order = self . _order
sigma = self . sigma
error = np . zeros ( order + 1 )
std = np . zeros ( order + 1 )
if n == 0 :
return ( error , std )
if order == 0 :
error [ 0 ] = sigma / sqrt ( n )
std [ 0 ] = sigma / sqrt ( n )
elif order == 1 :
if n > 1 :
error [ 0 ] = sig... |
def cloud_init ( names , host = None , quiet = False , ** kwargs ) :
'''Wrapper for using lxc . init in saltcloud compatibility mode
names
Name of the containers , supports a single name or a comma delimited
list of names .
host
Minion to start the container on . Required .
path
path to the container ... | if quiet :
log . warning ( "'quiet' argument is being deprecated. Please migrate to --quiet" )
return __salt__ [ 'lxc.init' ] ( names = names , host = host , saltcloud_mode = True , quiet = quiet , ** kwargs ) |
def centers_of_labels ( labels ) :
'''Return the i , j coordinates of the centers of a labels matrix
The result returned is an 2 x n numpy array where n is the number
of the label minus one , result [ 0 , x ] is the i coordinate of the center
and result [ x , 1 ] is the j coordinate of the center .
You can ... | max_labels = np . max ( labels )
if max_labels == 0 :
return np . zeros ( ( 2 , 0 ) , int )
result = scind . center_of_mass ( np . ones ( labels . shape ) , labels , np . arange ( max_labels ) + 1 )
result = np . array ( result )
if result . ndim == 1 :
result . shape = ( 2 , 1 )
return result
return result... |
def do_training ( num_epoch , optimizer , kvstore , learning_rate , model_prefix , decay ) :
"""Perform CapsNet training""" | summary_writer = SummaryWriter ( args . tblog_dir )
lr_scheduler = SimpleLRScheduler ( learning_rate )
optimizer_params = { 'lr_scheduler' : lr_scheduler }
module . init_params ( )
module . init_optimizer ( kvstore = kvstore , optimizer = optimizer , optimizer_params = optimizer_params )
n_epoch = 0
while True :
if... |
def log_to_console ( status = True , level = None ) :
"""Log events to the console .
Args :
status ( bool , Optional , Default = True )
whether logging to console should be turned on ( True ) or off ( False )
level ( string , Optional , Default = None ) :
level of logging ; whichever level is chosen all h... | if status :
if level is not None :
logger . setLevel ( level )
console_handler = logging . StreamHandler ( )
# create formatter
formatter = logging . Formatter ( '%(levelname)s-%(name)s: %(message)s' )
# add formatter to handler
console_handler . setFormatter ( formatter )
logger . a... |
def _process_changes ( self , newRev , branch ) :
"""Read changes since last change .
- Read list of commit hashes .
- Extract details from each commit .
- Add changes to database .""" | # initial run , don ' t parse all history
if not self . lastRev :
return
rebuild = False
if newRev in self . lastRev . values ( ) :
if self . buildPushesWithNoCommits :
existingRev = self . lastRev . get ( branch )
if existingRev is None : # This branch was completely unknown , rebuild
... |
def get_config_env_key ( k : str ) -> str :
"""Returns a scrubbed environment variable key , PULUMI _ CONFIG _ < k > , that can be used for
setting explicit varaibles . This is unlike PULUMI _ CONFIG which is just a JSON - serialized bag .""" | env_key = ''
for c in k :
if c == '_' or 'A' <= c <= 'Z' or '0' <= c <= '9' :
env_key += c
elif 'a' <= c <= 'z' :
env_key += c . upper ( )
else :
env_key += '_'
return 'PULUMI_CONFIG_%s' % env_key |
def _execute_model ( self , feed_dict , out_dict ) :
"""Executes model .
: param feed _ dict : Input dictionary mapping nodes to input data .
: param out _ dict : Output dictionary mapping names to nodes .
: return : Dictionary mapping names to input data .""" | network_out = self . sess . run ( list ( out_dict . values ( ) ) , feed_dict = feed_dict )
run_out = dict ( zip ( list ( out_dict . keys ( ) ) , network_out ) )
return run_out |
def fourier_ratios ( phase_shifted_coeffs ) :
r"""Returns the : math : ` R _ { j1 } ` and : math : ` \ phi _ { j1 } ` values for the given
phase - shifted coefficients .
. . math : :
R _ { j1 } = A _ j / A _ 1
. . math : :
\ phi _ { j1 } = \ phi _ j - j \ phi _ 1
* * Parameters * *
phase _ shifted _ c... | n_coeff = phase_shifted_coeffs . size
# n _ coeff = 2 * degree + 1 = > degree = ( n _ coeff - 1 ) / 2
degree = ( n_coeff - 1 ) / 2
amplitudes = phase_shifted_coeffs [ 1 : : 2 ]
phases = phase_shifted_coeffs [ 2 : : 2 ]
# there are degree - 1 amplitude ratios , and degree - 1 phase deltas ,
# so altogether there are 2 *... |
def reset_time_estimate ( self , ** kwargs ) :
"""Resets estimated time for the object to 0 seconds .
Args :
* * kwargs : Extra options to send to the server ( e . g . sudo )
Raises :
GitlabAuthenticationError : If authentication is not correct
GitlabTimeTrackingError : If the time tracking update cannot ... | path = '%s/%s/reset_time_estimate' % ( self . manager . path , self . get_id ( ) )
return self . manager . gitlab . http_post ( path , ** kwargs ) |
def get_worker ( self , * queues ) :
"""Returns an RQ worker instance for the given queue names , e . g . : :
configured _ worker = rq . get _ worker ( )
default _ worker = rq . get _ worker ( ' default ' )
default _ low _ worker = rq . get _ worker ( ' default ' , ' low ' )
: param \\ * queues : Names of q... | if not queues :
queues = self . queues
queues = [ self . get_queue ( name ) for name in queues ]
worker_cls = import_attribute ( self . worker_class )
worker = worker_cls ( queues , connection = self . connection , job_class = self . job_class , queue_class = self . queue_class , )
for exception_handler in self . _... |
def reverseComplement ( seq ) :
'''Helper function for generating reverse - complements''' | revComp = ''
complement = { 'A' : 'T' , 'C' : 'G' , 'G' : 'C' , 'T' : 'A' , 'N' : 'N' , '$' : '$' }
for c in reversed ( seq ) :
revComp += complement [ c ]
return revComp |
def get_layout_settings ( self ) :
"""Return the layout state for this splitter and its children .
Record the current state , including file names and current line
numbers , of the splitter panels .
Returns :
A dictionary containing keys { hexstate , sizes , splitsettings } .
hexstate : String of saveStat... | splitsettings = [ ]
for editorstack , orientation in self . iter_editorstacks ( ) :
clines = [ ]
cfname = ''
# XXX - this overrides value from the loop to always be False ?
orientation = False
if hasattr ( editorstack , 'data' ) :
clines = [ finfo . editor . get_cursor_line_number ( ) for fi... |
def session ( self ) :
"""This is a session between the consumer ( your website ) and the provider
( e . g . Twitter ) . It is * not * a session between a user of your website
and your website .
: return :""" | return self . session_class ( client_key = self . client_key , client_secret = self . client_secret , signature_method = self . signature_method , signature_type = self . signature_type , rsa_key = self . rsa_key , client_class = self . client_class , force_include_body = self . force_include_body , blueprint = self , ... |
def _broadcast_shapes ( s1 , s2 ) :
"""Given array shapes ` s1 ` and ` s2 ` , compute the shape of the array that would
result from broadcasting them together .""" | n1 = len ( s1 )
n2 = len ( s2 )
n = max ( n1 , n2 )
res = [ 1 ] * n
for i in range ( n ) :
if i >= n1 :
c1 = 1
else :
c1 = s1 [ n1 - 1 - i ]
if i >= n2 :
c2 = 1
else :
c2 = s2 [ n2 - 1 - i ]
if c1 == 1 :
rc = c2
elif c2 == 1 or c1 == c2 :
rc = c1
... |
def build_strain_specific_models ( self , save_models = False ) :
"""Using the orthologous genes matrix , create and modify the strain specific models based on if orthologous
genes exist .
Also store the sequences directly in the reference GEM - PRO protein sequence attribute for the strains .""" | if len ( self . df_orthology_matrix ) == 0 :
raise RuntimeError ( 'Empty orthology matrix' )
# Create an emptied copy of the reference GEM - PRO
for strain_gempro in tqdm ( self . strains ) :
log . debug ( '{}: building strain specific model' . format ( strain_gempro . id ) )
# For each genome , load the me... |
def _new_level ( self , depth ) :
"""Create a new level and header and connect signals
: param depth : the depth level
: type depth : int
: returns : None
: rtype : None
: raises : None""" | l = self . create_level ( depth )
h = self . create_header ( depth )
self . add_lvl_to_ui ( l , h )
l . new_root . connect ( partial ( self . set_root , depth + 1 ) )
self . _levels . append ( l ) |
def proto_value_for_feature ( example , feature_name ) :
"""Get the value of a feature from Example regardless of feature type .""" | feature = get_example_features ( example ) [ feature_name ]
if feature is None :
raise ValueError ( 'Feature {} is not on example proto.' . format ( feature_name ) )
feature_type = feature . WhichOneof ( 'kind' )
if feature_type is None :
raise ValueError ( 'Feature {} on example proto has no declared type.' . ... |
def iterdata ( fd , close_fd = True , ** opts ) :
'''Iterate through the data provided by a file like object .
Optional parameters may be used to control how the data
is deserialized .
Examples :
The following example show use of the iterdata function . : :
with open ( ' foo . csv ' , ' rb ' ) as fd :
f... | fmt = opts . get ( 'format' , 'lines' )
fopts = fmtopts . get ( fmt , { } )
# set default options for format
for opt , val in fopts . items ( ) :
opts . setdefault ( opt , val )
ncod = opts . get ( 'encoding' )
if ncod is not None :
fd = codecs . getreader ( ncod ) ( fd )
fmtr = fmtyielders . get ( fmt )
if fmt... |
def get_updates ( self , ** kwargs ) :
'''Get parameter update expressions for performing optimization .
Keyword arguments can be applied here to set any of the global
optimizer attributes .
Yields
updates : ( parameter , expression ) tuples
A sequence of parameter updates to be applied during optimizatio... | self . _prepare ( ** kwargs )
for param , grad in self . _differentiate ( ) :
for var , update in self . _get_updates_for ( param , grad ) : # For auxiliary variables , updates are meant to replace the
# existing variable value .
if var != param :
yield var , update
continue
... |
def putNamedChild ( self , res ) :
"""putNamedChild takes either an instance of hendrix . contrib . NamedResource
or any resource . Resource with a " namespace " attribute as a means of
allowing application level control of resource namespacing .
if a child is already found at an existing path ,
resources w... | try :
EmptyResource = resource . Resource
namespace = res . namespace
parts = namespace . strip ( '/' ) . split ( '/' )
# initialise parent and children
parent = self
children = self . children
# loop through all of the path parts except for the last one
for name in parts [ : - 1 ] :
... |
def objects_delete ( self , bucket , key ) :
"""Deletes the specified object .
Args :
bucket : the name of the bucket .
key : the key of the object within the bucket .
Raises :
Exception if there is an error performing the operation .""" | url = Api . _ENDPOINT + ( Api . _OBJECT_PATH % ( bucket , Api . _escape_key ( key ) ) )
datalab . utils . Http . request ( url , method = 'DELETE' , credentials = self . _credentials , raw_response = True ) |
def parse_cmd_arguments ( ) :
"""Parse command line arguments .""" | parser = argparse . ArgumentParser ( )
parser . add_argument ( 'file' , type = str , help = 'Filename to be staticfied' )
parser . add_argument ( '--static-endpoint' , help = 'Static endpoint which is "static" by default' )
parser . add_argument ( '--add-tags' , type = str , help = 'Additional tags to staticfy' )
parse... |
def make_vis_T ( model , objective_f , param_f = None , optimizer = None , transforms = None , relu_gradient_override = False ) :
"""Even more flexible optimization - base feature vis .
This function is the inner core of render _ vis ( ) , and can be used
when render _ vis ( ) isn ' t flexible enough . Unfortun... | # pylint : disable = unused - variable
t_image = make_t_image ( param_f )
objective_f = objectives . as_objective ( objective_f )
transform_f = make_transform_f ( transforms )
optimizer = make_optimizer ( optimizer , [ ] )
global_step = tf . train . get_or_create_global_step ( )
init_global_step = tf . variables_initia... |
def _temp_bool_prop ( propname , doc = "" , default = False ) :
"""Creates a property that uses the : class : ` _ TempBool ` class
Parameters
propname : str
The attribute name to use . The _ TempBool instance will be stored in the
` ` ' _ ' + propname ` ` attribute of the corresponding instance
doc : str ... | def getx ( self ) :
if getattr ( self , '_' + propname , None ) is not None :
return getattr ( self , '_' + propname )
else :
setattr ( self , '_' + propname , _TempBool ( default ) )
return getattr ( self , '_' + propname )
def setx ( self , value ) :
getattr ( self , propname ) . value... |
def _process_mappings ( self , limit = None ) :
"""This function imports linkage mappings of various entities
to genetic locations in cM or cR .
Entities include sequence variants , BAC ends , cDNA , ESTs , genes ,
PAC ends , RAPDs , SNPs , SSLPs , and STSs .
Status : NEEDS REVIEW
: param limit :
: retu... | LOG . info ( "Processing chromosome mappings" )
if self . test_mode :
graph = self . testgraph
else :
graph = self . graph
line_counter = 0
model = Model ( graph )
geno = Genotype ( graph )
raw = '/' . join ( ( self . rawdir , self . files [ 'mappings' ] [ 'file' ] ) )
taxon_num = '7955'
taxon_id = 'NCBITaxon:'... |
def get_regular_properties ( self , _type , * args , ** kwargs ) :
"""Make table with properties by schema _ id
: param str _ type :
: rtype : str""" | if not SchemaObjects . contains ( _type ) :
return _type
schema = SchemaObjects . get ( _type )
if schema . schema_type == SchemaTypes . DEFINITION and not kwargs . get ( 'definition' ) :
return ''
head = """.. csv-table::
:delim: |
:header: "Name", "Required", "Type", "Format", "Properties", "Descripti... |
def to_manager ( sdf , columns , index ) :
"""create and return the block manager from a dataframe of series ,
columns , index""" | # from BlockManager perspective
axes = [ ensure_index ( columns ) , ensure_index ( index ) ]
return create_block_manager_from_arrays ( [ sdf [ c ] for c in columns ] , columns , axes ) |
def fill ( self , text ) :
"""Set the text value of each matched element to ` text ` .
Example usage :
. . code : : python
# Set the text of the first element matched by the query to " Foo "
q . first . fill ( ' Foo ' )
Args :
text ( str ) : The text used to fill the element ( usually a text field or te... | def _fill ( elem ) : # pylint : disable = missing - docstring
elem . clear ( )
elem . send_keys ( text )
self . map ( _fill , u'fill({!r})' . format ( text ) ) . execute ( ) |
def write_question ( self , question ) :
"""Writes a question to the packet""" | self . write_name ( question . name )
self . write_short ( question . type )
self . write_short ( question . clazz ) |
def get_cleaned_data_for_step ( self , step ) :
"""Returns the cleaned data for a given ` step ` . Before returning the
cleaned data , the stored values are being revalidated through the
form . If the data doesn ' t validate , None will be returned .""" | if step in self . form_list :
form_obj = self . get_form ( step = step , data = self . storage . get_step_data ( step ) , files = self . storage . get_step_files ( step ) )
if form_obj . is_valid ( ) :
return form_obj . cleaned_data
return None |
def loads ( s , model = None , parser = None ) :
"""Deserialize s ( a str ) to a Python object .""" | with StringIO ( s ) as f :
return load ( f , model = model , parser = parser ) |
def encode ( self , obj ) :
"""Returns ` ` obj ` ` serialized as JSON formatted bytes .
Raises
~ ipfsapi . exceptions . EncodingError
Parameters
obj : str | list | dict | int
JSON serializable Python object
Returns
bytes""" | try :
result = json . dumps ( obj , sort_keys = True , indent = None , separators = ( ',' , ':' ) , ensure_ascii = False )
if isinstance ( result , six . text_type ) :
return result . encode ( "utf-8" )
else :
return result
except ( UnicodeEncodeError , TypeError ) as error :
raise excep... |
def set_portfast_type ( self , name , value = 'normal' ) :
"""Configures the portfast value for the specified interface
Args :
name ( string ) : The interface identifier to configure . The name
must be the full interface name ( eg Ethernet1 , not Et1 ) .
value ( string ) : The value to configure the portfas... | if value not in [ 'network' , 'edge' , 'normal' , None ] :
raise ValueError ( 'invalid portfast type value specified' )
cmds = [ 'spanning-tree portfast %s' % value ]
if value == 'edge' :
cmds . append ( 'spanning-tree portfast auto' )
return self . configure_interface ( name , cmds ) |
def register_tc_plugins ( self , plugin_name , plugin_class ) :
"""Loads a plugin as a dictionary and attaches needed parts to correct areas for testing
parts .
: param plugin _ name : Name of the plugins
: param plugin _ class : PluginBase
: return : Nothing""" | if plugin_name in self . registered_plugins :
raise PluginException ( "Plugin {} already registered! Duplicate " "plugins?" . format ( plugin_name ) )
self . logger . debug ( "Registering plugin %s" , plugin_name )
plugin_class . init ( bench = self . bench )
if plugin_class . get_bench_api ( ) is not None :
re... |
def combinations_with_replacement ( iterable , r ) :
"""This function acts as a replacement for the
itertools . combinations _ with _ replacement function . The original does not
replace items that come earlier in the provided iterator .""" | stk = [ [ i , ] for i in iterable ]
pop = stk . pop
while len ( stk ) > 0 :
top = pop ( )
if len ( top ) == r :
yield tuple ( top )
else :
stk . extend ( top + [ i ] for i in iterable ) |
def _extend_blocks ( extend_node , blocks , context ) :
"""Extends the dictionary ` blocks ` with * new * blocks in the parent node ( recursive )
: param extend _ node : The ` ` { % extends . . % } ` ` node object .
: type extend _ node : ExtendsNode
: param blocks : dict of all block names found in the templ... | try : # This needs a fresh parent context , or it will detection recursion in Django 1.9 + ,
# and thus skip the base template , which is already loaded .
parent = extend_node . get_parent ( _get_extend_context ( context ) )
except TemplateSyntaxError :
if _is_variable_extends ( extend_node ) : # we don ' t sup... |
def add_filter ( ds , patterns ) :
"""Add a filter or list of filters to a datasource . A filter is a simple
string , and it matches if it is contained anywhere within a line .
Args :
ds ( @ datasource component ) : The datasource to filter
patterns ( str , [ str ] ) : A string , list of strings , or set of... | if not plugins . is_datasource ( ds ) :
raise Exception ( "Filters are applicable only to datasources." )
delegate = dr . get_delegate ( ds )
if delegate . raw :
raise Exception ( "Filters aren't applicable to raw datasources." )
if not delegate . filterable :
raise Exception ( "Filters aren't applicable to... |
def initial_classification ( self , obresult , target_is_sky = False ) :
"""Classify input frames ,""" | # lists of targets and sky frames
with obresult . frames [ 0 ] . open ( ) as baseimg : # Initial checks
has_bpm_ext = 'BPM' in baseimg
self . logger . debug ( 'images have BPM extension: %s' , has_bpm_ext )
images_info = [ ]
for f in obresult . frames :
with f . open ( ) as img : # Getting some metadata fro... |
def RequestPacket ( self ) :
"""Create a ready - to - transmit authentication request packet .
Return a RADIUS packet which can be directly transmitted
to a RADIUS server .
: return : raw packet
: rtype : string""" | attr = self . _PktEncodeAttributes ( )
if self . authenticator is None :
self . authenticator = self . CreateAuthenticator ( )
if self . id is None :
self . id = self . CreateID ( )
header = struct . pack ( '!BBH16s' , self . code , self . id , ( 20 + len ( attr ) ) , self . authenticator )
return header + attr |
def check_dirs ( ) :
"""Check the directories if they exist .
: raises FileExistsError : if a file exists but is not a directory""" | dirs = [ MAIN_DIR , TEMP_DIR , DOWNLOAD_DIR , SAVESTAT_DIR ]
for directory in dirs :
if directory . exists ( ) and not directory . is_dir ( ) :
raise FileExistsError ( str ( directory . resolve ( ) ) + " cannot be used as a directory." ) |
def _install_requirements ( path ) :
"""Install a blueprint ' s requirements . txt""" | locations = [ os . path . join ( path , "_blueprint" ) , os . path . join ( path , "_base" ) , path ]
success = True
for location in locations :
try :
with open ( os . path . join ( location , "requirements.txt" ) ) :
puts ( "\nRequirements file found at {0}" . format ( os . path . join ( locati... |
def preview ( self ) :
"""Returns an HTML preview for a Scheduled Tweet .""" | if self . id :
resource = self . PREVIEW
resource = resource . format ( account_id = self . account . id , id = self . id )
response = Request ( self . account . client , 'get' , resource ) . perform ( )
return response . body [ 'data' ] |
def get_element_by_path ( tree , path_and_name , namespace ) : # type : ( _ Element , str , str ) - > typing . Union [ _ Element , None ]
"""Find sub - element of given path with given short name .""" | global xml_element_cache
namespace_map = { 'A' : namespace [ 1 : - 1 ] }
base_path , element_name = path_and_name . rsplit ( '/' , 1 )
if base_path in xml_element_cache :
base_element = xml_element_cache [ base_path ]
else :
base_xpath = ar_path_to_x_path ( base_path )
elems = tree . xpath ( base_xpath , na... |
def flushmany ( self ) :
"""Send a potentially huge number of pending signals over the message bus .
This method assumes that the number of pending signals might
be huge , so that they might not fit into memory . However ,
` SignalBus . flushmany ` is not very smart in handling concurrent
senders . It is mo... | models_to_flush = self . get_signal_models ( )
try :
return sum ( self . _flushmany_signals ( model ) for model in models_to_flush )
finally :
self . signal_session . remove ( ) |
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