signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def get_bank ( self ) :
"""Gets the ` ` Bank ` ` at this node .
return : ( osid . assessment . Bank ) - the bank represented by this
node
* compliance : mandatory - - This method must be implemented . *""" | if self . _lookup_session is None :
mgr = get_provider_manager ( 'ASSESSMENT' , runtime = self . _runtime , proxy = self . _proxy )
self . _lookup_session = mgr . get_bank_lookup_session ( proxy = getattr ( self , "_proxy" , None ) )
return self . _lookup_session . get_bank ( Id ( self . _my_map [ 'id' ] ) ) |
def get_entries ( self ) :
"""Return a list of the entries ( messages ) that would be part of the
current " view " ; that is , all of the ones from this . po file matching the
current query or msg _ filter .""" | if self . query : # Scenario # 1 : terms matching a search query
rx = re . compile ( re . escape ( self . query ) , re . IGNORECASE )
def concat_entry ( e ) :
return ( six . text_type ( e . msgstr ) + six . text_type ( e . msgid ) + six . text_type ( e . msgctxt ) + six . text_type ( e . comment ) + u''... |
def canOrder ( self , commit : Commit ) -> Tuple [ bool , Optional [ str ] ] :
"""Return whether the specified commitRequest can be returned to the node .
Decision criteria :
- If have got just n - f Commit requests then return request to node
- If less than n - f of commit requests then probably don ' t have... | quorum = self . quorums . commit . value
if not self . commits . hasQuorum ( commit , quorum ) :
return False , "no quorum ({}): {} commits where f is {}" . format ( quorum , commit , self . f )
key = ( commit . viewNo , commit . ppSeqNo )
if self . has_already_ordered ( * key ) :
return False , "already ordere... |
def _port_action_vxlan ( self , port , segment , func ) :
"""Verify configuration and then process event .""" | # If the segment is None , just log a warning message and return .
if segment is None :
self . _log_missing_segment ( )
return
device_id = port . get ( 'device_id' )
mcast_group = segment . get ( api . PHYSICAL_NETWORK )
host_id = port . get ( bc . portbindings . HOST_ID )
vni = segment . get ( api . SEGMENTATI... |
def get_children_to_delete ( self ) :
"""Return all children that are not referenced
: returns : list or : class : ` Reftrack `
: rtype : list
: raises : None""" | refobjinter = self . get_refobjinter ( )
children = self . get_all_children ( )
todelete = [ ]
for c in children :
if c . status ( ) is None : # if child is not in scene we do not have to delete it
continue
rby = refobjinter . referenced_by ( c . get_refobj ( ) )
if rby is None : # child is not part... |
def undefine ( self ) :
"""Undefine the Template .
Python equivalent of the CLIPS undeftemplate command .
The object becomes unusable after this method has been called .""" | if lib . EnvUndeftemplate ( self . _env , self . _tpl ) != 1 :
raise CLIPSError ( self . _env ) |
def owner_type ( self , value ) :
"""Set ` ` owner _ type ` ` to the given value .
In addition :
* Update the internal type of the ` ` owner ` ` field .
* Update the value of the ` ` owner ` ` field if a value is already set .""" | self . _owner_type = value
if value == 'User' :
self . _fields [ 'owner' ] = entity_fields . OneToOneField ( User )
if hasattr ( self , 'owner' ) : # pylint : disable = no - member
self . owner = User ( self . _server_config , id = self . owner . id if isinstance ( self . owner , Entity ) else self . ow... |
def create ( self , build_sid ) :
"""Create a new DeploymentInstance
: param unicode build _ sid : The build _ sid
: returns : Newly created DeploymentInstance
: rtype : twilio . rest . serverless . v1 . service . environment . deployment . DeploymentInstance""" | data = values . of ( { 'BuildSid' : build_sid , } )
payload = self . _version . create ( 'POST' , self . _uri , data = data , )
return DeploymentInstance ( self . _version , payload , service_sid = self . _solution [ 'service_sid' ] , environment_sid = self . _solution [ 'environment_sid' ] , ) |
def set_vads_payment_config ( self ) :
"""vads _ payment _ config can be set only after object saving .
A custom payment config can be set once PaymentRequest saved
( adding elements to the m2m relationship ) . As a consequence
we set vads _ payment _ config just before sending data elements
to payzen .""" | self . vads_payment_config = tools . get_vads_payment_config ( self . payment_config , self . custom_payment_config . all ( ) ) |
def restore ( name = None , ** kwargs ) :
'''Make sure that the system contains the packages and repos from a
frozen state .
Read the list of packages and repositories from the freeze file ,
and compare it with the current list of packages and repos . If
there is any difference , all the missing packages ar... | if not status ( name ) :
raise CommandExecutionError ( 'Frozen state not found.' )
frozen_pkgs = { }
frozen_repos = { }
for name , content in zip ( _paths ( name ) , ( frozen_pkgs , frozen_repos ) ) :
with fopen ( name ) as fp :
content . update ( json . load ( fp ) )
# The ordering of removing or addin... |
def open_only ( f ) :
"decorator" | @ functools . wraps ( f )
def f2 ( self , * args , ** kwargs ) :
if self . closed :
raise NotSupportedError ( 'connection is closed' )
return f ( self , * args , ** kwargs )
return f2 |
def implied_vol ( self , value , precision = 1.0e-5 , iters = 100 ) :
"""Get implied vol at the specified price using an iterative approach .
There is no closed - form inverse of BSM - value as a function of sigma ,
so start at an anchoring volatility level from Brenner & Subrahmanyam
(1988 ) and work iterati... | vol = np . sqrt ( 2.0 * np . pi / self . T ) * ( value / self . S0 )
for _ in itertools . repeat ( None , iters ) : # Faster than range
opt = BSM ( S0 = self . S0 , K = self . K , T = self . T , r = self . r , sigma = vol , kind = self . kind , )
diff = value - opt . value ( )
if abs ( diff ) < precision :
... |
def copy ( self ) :
"""Returns a copy of Filter .""" | other = ConcurrentMeanStdFilter ( self . shape )
other . sync ( self )
return other |
def _set_redistribute_isis ( self , v , load = False ) :
"""Setter method for redistribute _ isis , mapped from YANG variable / routing _ system / router / router _ bgp / address _ family / ipv6 / ipv6 _ unicast / default _ vrf / af _ ipv6 _ uc _ and _ vrf _ cmds _ call _ point _ holder / redistribute / redistribut... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = redistribute_isis . redistribute_isis , is_container = 'container' , presence = True , yang_name = "redistribute-isis" , rest_name = "isis" , parent = self , path_helper = self . _path_helper , extmethods = self . _extmethods... |
def kegg_mapping_and_metadata_parallelize ( self , sc , kegg_organism_code , custom_gene_mapping = None , outdir = None , set_as_representative = False , force_rerun = False ) :
"""Map all genes in the model to KEGG IDs using the KEGG service .
Steps :
1 . Download all metadata and sequence files in the sequenc... | # First map all of the organism ' s KEGG genes to UniProt
kegg_to_uniprot = ssbio . databases . kegg . map_kegg_all_genes ( organism_code = kegg_organism_code , target_db = 'uniprot' )
# Parallelize the genes list
genes_rdd = sc . parallelize ( self . genes )
# Write a sub - function to carry out the bulk of the origin... |
def get ( self , repi , mag ) :
""": param repi : an array of epicentral distances in the range self . repi
: param mag : a magnitude in the range self . mags
: returns : an array of equivalent distances""" | mag_idx = numpy . abs ( mag - self . mags ) . argmin ( )
dists = [ ]
for dist in repi :
repi_idx = numpy . abs ( dist - self . repi ) . argmin ( )
dists . append ( self . reqv [ repi_idx , mag_idx ] )
return numpy . array ( dists ) |
def connected_components ( G ) :
"""Compute the connected components of a graph .
The connected components of a graph G , which is represented by a
symmetric sparse matrix , are labeled with the integers 0,1 , . . ( K - 1 ) where
K is the number of components .
Parameters
G : symmetric matrix , preferably... | G = asgraph ( G )
N = G . shape [ 0 ]
components = np . empty ( N , G . indptr . dtype )
fn = amg_core . connected_components
fn ( N , G . indptr , G . indices , components )
return components |
def subscribe ( self , client , channel_name ) :
"""Register a new client to receive messages on a channel .""" | if channel_name not in self . channels :
self . channels [ channel_name ] = channel = Channel ( channel_name )
channel . start ( )
self . channels [ channel_name ] . subscribe ( client ) |
def send ( self , ws , seq ) :
"""Sends heartbeat message to Discord
Attributes :
ws : Websocket connection to discord
seq : Sequence number of heartbeat""" | payload = { 'op' : 1 , 'd' : seq }
payload = json . dumps ( payload )
logger . debug ( "Sending heartbeat with payload {}" . format ( payload ) )
ws . send ( payload )
return |
def find ( query ) :
"""Search by Name , SMILES , InChI , InChIKey , etc . Returns first 100 Compounds""" | assert type ( query ) == str or type ( query ) == str , 'query not a string object'
searchurl = 'http://www.chemspider.com/Search.asmx/SimpleSearch?query=%s&token=%s' % ( urlquote ( query ) , TOKEN )
response = urlopen ( searchurl )
tree = ET . parse ( response )
elem = tree . getroot ( )
csid_tags = elem . getiterator... |
def shape ( self ) :
"""Raster shape .""" | if self . _shape is None :
self . _populate_from_rasterio_object ( read_image = False )
return self . _shape |
def listeners_iter ( self ) :
"""Return an iterator over the mapping of event = > listeners bound .
The listener list ( s ) returned should * * not * * be mutated .
NOTE ( harlowja ) : Each listener in the yielded ( event , listeners )
tuple is an instance of the : py : class : ` ~ . Listener ` type , which
... | topics = set ( six . iterkeys ( self . _topics ) )
while topics :
event_type = topics . pop ( )
try :
yield event_type , self . _topics [ event_type ]
except KeyError :
pass |
def transformToNative ( obj ) :
"""Turn obj . value into a datetime . timedelta .""" | if obj . isNative :
return obj
obj . isNative = True
obj . value = obj . value
if obj . value == '' :
return obj
else :
deltalist = stringToDurations ( obj . value )
# When can DURATION have multiple durations ? For now :
if len ( deltalist ) == 1 :
obj . value = deltalist [ 0 ]
retu... |
def add ( self , cmd ) :
'''Add a new command ( waypoint ) at the end of the command list .
. . note : :
Commands are sent to the vehicle only after you call : : py : func : ` upload ( ) < Vehicle . commands . upload > ` .
: param Command cmd : The command to be added .''' | self . wait_ready ( )
self . _vehicle . _handler . fix_targets ( cmd )
self . _vehicle . _wploader . add ( cmd , comment = 'Added by DroneKit' )
self . _vehicle . _wpts_dirty = True |
def get_observer_look ( self , utc_time , lon , lat , alt ) :
"""Calculate observers look angle to a satellite .
http : / / celestrak . com / columns / v02n02/
utc _ time : Observation time ( datetime object )
lon : Longitude of observer position on ground in degrees east
lat : Latitude of observer position... | utc_time = dt2np ( utc_time )
( pos_x , pos_y , pos_z ) , ( vel_x , vel_y , vel_z ) = self . get_position ( utc_time , normalize = False )
( opos_x , opos_y , opos_z ) , ( ovel_x , ovel_y , ovel_z ) = astronomy . observer_position ( utc_time , lon , lat , alt )
lon = np . deg2rad ( lon )
lat = np . deg2rad ( lat )
thet... |
def add_paths_to_os ( self , key = None , update = None ) :
'''Add the paths in tree environ into the os environ
This code goes through the tree environ and checks
for existence in the os environ , then adds them
Parameters :
key ( str ) :
The section name to check against / add
update ( bool ) :
If T... | if key is not None :
allpaths = key if isinstance ( key , list ) else [ key ]
else :
allpaths = [ k for k in self . environ . keys ( ) if 'default' not in k ]
for key in allpaths :
paths = self . get_paths ( key )
self . check_paths ( paths , update = update ) |
def _get_decimal128 ( data , position , dummy0 , dummy1 , dummy2 ) :
"""Decode a BSON decimal128 to bson . decimal128 . Decimal128.""" | end = position + 16
return Decimal128 . from_bid ( data [ position : end ] ) , end |
def fast_cov ( x , y = None , destination = None ) :
"""calculate the covariance matrix for the columns of x ( MxN ) , or optionally , the covariance matrix between the
columns of x and and the columns of y ( MxP ) . ( In the language of statistics , the columns are variables , the rows
are observations ) .
A... | validate_inputs ( x , y , destination )
if y is None :
y = x
if destination is None :
destination = numpy . zeros ( ( x . shape [ 1 ] , y . shape [ 1 ] ) )
mean_x = numpy . mean ( x , axis = 0 )
mean_y = numpy . mean ( y , axis = 0 )
mean_centered_x = ( x - mean_x ) . astype ( destination . dtype )
mean_centere... |
def neighbor ( pos , tune_params ) :
"""return a random neighbor of pos""" | size = len ( pos )
pos_out = [ ]
# random mutation
# expected value is set that values all dimensions attempt to get mutated
for i in range ( size ) :
key = list ( tune_params . keys ( ) ) [ i ]
values = tune_params [ key ]
if random . random ( ) < 0.2 : # replace with random value
new_value = rando... |
def _read_file ( path ) :
'''Reads and returns the contents of a text file''' | try :
with salt . utils . files . flopen ( path , 'rb' ) as contents :
return [ salt . utils . stringutils . to_str ( line ) for line in contents . readlines ( ) ]
except ( OSError , IOError ) :
return '' |
def _set_l2_spf6_timer ( self , v , load = False ) :
"""Setter method for l2 _ spf6 _ timer , mapped from YANG variable / isis _ state / router _ isis _ config / l2 _ spf6 _ timer ( container )
If this variable is read - only ( config : false ) in the
source YANG file , then _ set _ l2 _ spf6 _ timer is conside... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = l2_spf6_timer . l2_spf6_timer , is_container = 'container' , presence = False , yang_name = "l2-spf6-timer" , rest_name = "l2-spf6-timer" , parent = self , path_helper = self . _path_helper , extmethods = self . _extmethods ,... |
def addcommenttocommit ( self , project_id , author , sha , path , line , note ) :
"""Adds an inline comment to a specific commit
: param project _ id : project id
: param author : The author info as returned by create mergerequest
: param sha : The name of a repository branch or tag or if not given the defau... | data = { 'author' : author , 'note' : note , 'path' : path , 'line' : line , 'line_type' : 'new' }
request = requests . post ( '{0}/{1}/repository/commits/{2}/comments' . format ( self . projects_url , project_id , sha ) , headers = self . headers , data = data , verify = self . verify_ssl )
if request . status_code ==... |
def merge ( self , * args ) :
"""Merge multiple dictionary objects into one .
: param variadic args : Multiple dictionary items
: return dict""" | values = [ ]
for entry in args :
values = values + list ( entry . items ( ) )
return dict ( values ) |
def get_hash ( name , password = None ) :
'''Returns the hash of a certificate in the keychain .
name
The name of the certificate ( which you can get from keychain . get _ friendly _ name ) or the
location of a p12 file .
password
The password that is used in the certificate . Only required if your passin... | if '.p12' in name [ - 4 : ] :
cmd = 'openssl pkcs12 -in {0} -passin pass:{1} -passout pass:{1}' . format ( name , password )
else :
cmd = 'security find-certificate -c "{0}" -m -p' . format ( name )
out = __salt__ [ 'cmd.run' ] ( cmd )
matches = re . search ( '-----BEGIN CERTIFICATE-----(.*)-----END CERTIFICATE... |
def delete_persistent_volume ( self , name , ** kwargs ) : # noqa : E501
"""delete _ persistent _ volume # noqa : E501
delete a PersistentVolume # noqa : E501
This method makes a synchronous HTTP request by default . To make an
asynchronous HTTP request , please pass async _ req = True
> > > thread = api . ... | kwargs [ '_return_http_data_only' ] = True
if kwargs . get ( 'async_req' ) :
return self . delete_persistent_volume_with_http_info ( name , ** kwargs )
# noqa : E501
else :
( data ) = self . delete_persistent_volume_with_http_info ( name , ** kwargs )
# noqa : E501
return data |
def get_object ( self , binding_name , cls ) :
"""Get a reference to a remote object using CORBA""" | return self . _state . get_object ( self , binding_name , cls ) |
def remove_redistribution ( self , protocol ) :
"""Removes a protocol redistribution to OSPF
Args :
protocol ( str ) : protocol to redistribute
route _ map _ name ( str ) : route - map to be used to
filter the protocols
Returns :
bool : True if the command completes successfully
Exception :
ValueErr... | protocols = [ 'bgp' , 'rip' , 'static' , 'connected' ]
if protocol not in protocols :
raise ValueError ( 'redistributed protocol must be' 'bgp, connected, rip or static' )
cmd = 'no redistribute {}' . format ( protocol )
return self . configure_ospf ( cmd ) |
def _fix ( self , fmt = 'i' ) :
"""Read pre - or suffix of line at current position with given
format ` fmt ` ( default ' i ' ) .""" | fmt = self . endian + fmt
fix = self . read ( struct . calcsize ( fmt ) )
if fix :
return struct . unpack ( fmt , fix ) [ 0 ]
else :
raise EOFError |
async def _load ( self , data , check = True ) :
"""Looking for proxies in the passed data .
Transform the passed data from [ raw string | file - like object | list ]
to set { ( host , port ) , . . . } : { ( ' 192.168.0.1 ' , ' 80 ' ) , }""" | log . debug ( 'Load proxies from the raw data' )
if isinstance ( data , io . TextIOWrapper ) :
data = data . read ( )
if isinstance ( data , str ) :
data = IPPortPatternLine . findall ( data )
proxies = set ( data )
for proxy in proxies :
await self . _handle ( proxy , check = check )
await self . _on_check... |
def nguHanh ( tenHanh ) :
"""Args :
tenHanh ( string ) : Tên Hành trong ngũ hành , Kim hoặc K , Moc hoặc M ,
Thuy hoặc T , Hoa hoặc H , Tho hoặc O
Returns :
Dictionary : ID của Hành , tên đầy đủ của Hành , số Cục của Hành
Raises :
Exception : Description""" | if tenHanh in [ "Kim" , "K" ] :
return { "id" : 1 , "tenHanh" : "Kim" , "cuc" : 4 , "tenCuc" : "Kim tứ Cục" , "css" : "hanhKim" }
elif tenHanh == "Moc" or tenHanh == "M" :
return { "id" : 2 , "tenHanh" : "Mộc" , "cuc" : 3 , "tenCuc" : "Mộc tam Cục" , "css" : "hanhMoc" }
elif tenHanh == "Thuy" or tenHanh == "T" ... |
def inner_products ( self , vec ) :
"""Get the inner product of a vector with every embedding .
: param ( np . array ) vector : the query vector
: return ( list [ tuple [ str , float ] ] ) : a map of embeddings to inner products""" | products = self . array . dot ( vec )
return self . _word_to_score ( np . arange ( len ( products ) ) , products ) |
def constructor ( self , random , args ) :
"""Return a candidate solution for an ant colony optimization .""" | self . _use_ants = True
candidate = [ ]
while len ( candidate ) < len ( self . components ) : # Find feasible components
feasible_components = [ ]
if len ( candidate ) == 0 :
feasible_components = self . components
else :
remaining_capacity = self . capacity - sum ( [ c . element for c in ca... |
def _transform_data ( self , X ) :
"""Binarize the data for each column separately .""" | if self . _binarizers == [ ] :
raise NotFittedError ( )
if self . binarize is not None :
X = binarize ( X , threshold = self . binarize )
if len ( self . _binarizers ) != X . shape [ 1 ] :
raise ValueError ( "Expected input with %d features, got %d instead" % ( len ( self . _binarizers ) , X . shape [ 1 ] )... |
def pack ( self ) :
"Pack and save file" | pack_name = self . args . prefix + op . basename ( self . path )
pack_path = op . join ( self . args . output or self . basedir , pack_name )
self . out ( "Packing: %s" % self . path )
self . out ( "Output: %s" % pack_path )
if self . args . format :
ext = self . get_ext ( self . path )
self . parsers [ ext ] =... |
def InitPrivateKey ( self ) :
"""Makes sure this client has a private key set .
It first tries to load an RSA key from the certificate .
If no certificate is found , or it is invalid , we make a new random RSA key ,
and store it as our certificate .
Returns :
An RSA key - either from the certificate or a ... | if self . private_key :
try :
self . common_name = rdf_client . ClientURN . FromPrivateKey ( self . private_key )
logging . info ( "Starting client %s" , self . common_name )
return self . private_key
except type_info . TypeValueError :
pass
# We either have an invalid key or no ... |
def relabel ( self , i ) :
'''API : relabel ( self , i )
Description :
Used by max _ flow _ preflowpush ( ) method for relabelling node i .
Input :
i : Node that is being relabelled .
Post :
' distance ' attribute of node i is updated .''' | min_distance = 2 * len ( self . get_node_list ( ) ) + 1
for j in self . get_neighbors ( i ) :
if ( self . get_node_attr ( j , 'distance' ) < min_distance and ( self . get_edge_attr ( i , j , 'flow' ) < self . get_edge_attr ( i , j , 'capacity' ) ) ) :
min_distance = self . get_node_attr ( j , 'distance' )
f... |
def infer_transportation_mode ( self , clf , min_time ) :
"""In - place transportation mode inferring of segments
Returns :
This track""" | for segment in self . segments :
segment . infer_transportation_mode ( clf , min_time )
return self |
def files ( self ) :
"""Files in torrent .
List of namedtuples ( filepath , size ) .
: rtype : list [ TorrentFile ]""" | files = [ ]
info = self . _struct . get ( 'info' )
if not info :
return files
if 'files' in info :
base = info [ 'name' ]
for f in info [ 'files' ] :
files . append ( TorrentFile ( join ( base , * f [ 'path' ] ) , f [ 'length' ] ) )
else :
files . append ( TorrentFile ( info [ 'name' ] , info [ ... |
def get_service_account_token ( request , service_account = 'default' ) :
"""Get the OAuth 2.0 access token for a service account .
Args :
request ( google . auth . transport . Request ) : A callable used to make
HTTP requests .
service _ account ( str ) : The string ' default ' or a service account email
... | token_json = get ( request , 'instance/service-accounts/{0}/token' . format ( service_account ) )
token_expiry = _helpers . utcnow ( ) + datetime . timedelta ( seconds = token_json [ 'expires_in' ] )
return token_json [ 'access_token' ] , token_expiry |
def get_scratch_path ( self , local_file ) :
"""Construct and return a path in the scratch area from a local file .""" | ( local_dirname , local_basename ) = self . split_local_path ( local_file )
return self . construct_scratch_path ( local_dirname , local_basename ) |
def _process_slice ( self , arg ) :
"""process the input slice for use calling the C code""" | start = arg . start
stop = arg . stop
step = arg . step
nrows = self . _info [ 'nrows' ]
if step is None :
step = 1
if start is None :
start = 0
if stop is None :
stop = nrows
if start < 0 :
start = nrows + start
if start < 0 :
raise IndexError ( "Index out of bounds" )
if stop < 0 :
sto... |
def mappability ( args ) :
"""% prog mappability reference . fasta
Generate 50mer mappability for reference genome . Commands are based on gem
mapper . See instructions :
< https : / / github . com / xuefzhao / Reference . Mappability >""" | p = OptionParser ( mappability . __doc__ )
p . add_option ( "--mer" , default = 50 , type = "int" , help = "User mer size" )
p . set_cpus ( )
opts , args = p . parse_args ( args )
if len ( args ) != 1 :
sys . exit ( not p . print_help ( ) )
ref , = args
K = opts . mer
pf = ref . rsplit ( "." , 1 ) [ 0 ]
mm = MakeMa... |
def parse_pseudo_lang ( self , sel , m , has_selector ) :
"""Parse pseudo language .""" | values = m . group ( 'values' )
patterns = [ ]
for token in RE_VALUES . finditer ( values ) :
if token . group ( 'split' ) :
continue
value = token . group ( 'value' )
if value . startswith ( ( '"' , "'" ) ) :
parts = css_unescape ( value [ 1 : - 1 ] , True ) . split ( '-' )
else :
... |
def get_fws ( value ) :
"""FWS = 1 * WSP
This isn ' t the RFC definition . We ' re using fws to represent tokens where
folding can be done , but when we are parsing the * un * folding has already
been done so we don ' t need to watch out for CRLF .""" | newvalue = value . lstrip ( )
fws = WhiteSpaceTerminal ( value [ : len ( value ) - len ( newvalue ) ] , 'fws' )
return fws , newvalue |
def partition_ordered ( sequence , key = None ) :
"""Partition ordered sequence by key .
Sequence is expected to already be ordered .
Parameters
sequence : iterable data .
key : partition key function
Yields
iterable tuple ( s ) of partition key , data list pairs .
Examples
1 . By object attributes ... | yield from ( ( k , list ( g ) ) for k , g in groupby ( sequence , key = key ) ) |
def auto_delete_cohort ( instance , ** kwargs ) :
"Deletes and auto - created cohort named after the instance ." | cohorts = Cohort . objects . filter ( autocreated = True )
if isinstance ( instance , Project ) :
cohorts = cohorts . filter ( project = instance )
elif isinstance ( instance , Batch ) :
cohorts = cohorts . filter ( batch = instance )
else :
return
count = cohorts . count ( )
cohorts . delete ( )
log . info... |
def main ( args_list = None ) :
"""Script which loads variants and annotates them with overlapping genes
and predicted coding effects .
Example usage :
varcode
- - vcf mutect . vcf - - vcf strelka . vcf - - maf tcga _ brca . maf - - variant chr1 498584 C G - - json - variants more _ variants . json""" | print_version_info ( )
if args_list is None :
args_list = sys . argv [ 1 : ]
args = arg_parser . parse_args ( args_list )
variants = variant_collection_from_args ( args )
effects = variants . effects ( )
if args . only_coding :
effects = effects . drop_silent_and_noncoding ( )
if args . one_per_variant :
va... |
def angleOfView ( XY , shape = None , a = None , f = None , D = None , center = None ) :
'''Another vignetting equation from :
M . Koentges , M . Siebert , and D . Hinken , " Quantitative analysis of PV - modules by electroluminescence images for quality control "
2009
f - - > Focal length
D - - > Diameter ... | if a is None :
assert f is not None and D is not None
# https : / / en . wikipedia . org / wiki / Angular _ aperture
a = 2 * np . arctan2 ( D / 2 , f )
x , y = XY
try :
c0 , c1 = center
except :
s0 , s1 = shape
c0 , c1 = s0 / 2 , s1 / 2
rx = ( x - c0 ) ** 2
ry = ( y - c1 ) ** 2
return 1 / ( 1 + ... |
def filter ( self , * args , ** kwargs ) :
"""See : py : meth : ` nornir . core . inventory . Inventory . filter `
Returns :
: obj : ` Nornir ` : A new object with same configuration as ` ` self ` ` but filtered inventory .""" | b = Nornir ( ** self . __dict__ )
b . inventory = self . inventory . filter ( * args , ** kwargs )
return b |
def var_explained ( y_true , y_pred ) :
"""Fraction of variance explained .""" | var_resid = K . var ( y_true - y_pred )
var_y_true = K . var ( y_true )
return 1 - var_resid / var_y_true |
def results_class_wise_metrics ( self ) :
"""Class - wise metrics
Returns
dict
results in a dictionary format""" | results = { }
for scene_id , scene_label in enumerate ( self . scene_label_list ) :
if scene_label not in results :
results [ scene_label ] = { }
results [ scene_label ] [ 'count' ] = { }
results [ scene_label ] [ 'count' ] [ 'Ncorr' ] = self . scene_wise [ scene_label ] [ 'Ncorr' ]
results [ sc... |
def Increment ( self , delta , fields = None ) :
"""Increments counter value by a given delta .""" | if delta < 0 :
raise ValueError ( "Counter increment should not be < 0 (received: %d)" % delta )
self . _metric_values [ _FieldsToKey ( fields ) ] = self . Get ( fields = fields ) + delta |
def ph2full ( ptrans , htrans ) :
"""Convert a p - state transition matrix and h - state matrices to the full transation matrix
The full transmat hase N = n _ pstates * n _ hstates states""" | n_pstates = len ( ptrans )
n_hstates = len ( htrans [ 0 , 0 ] )
N = n_pstates * n_hstates
trans = np . zeros ( ( N , N ) )
for pidx in range ( n_pstates ) :
for hidx in range ( n_hstates ) :
trans [ pidx * n_hstates + hidx ] = ( ptrans [ pidx , : , np . newaxis ] * htrans [ pidx , : , hidx ] ) . flatten ( )... |
def _install_toolplus ( args ) :
"""Install additional tools we cannot distribute , updating local manifest .""" | manifest_dir = os . path . join ( _get_data_dir ( ) , "manifest" )
toolplus_manifest = os . path . join ( manifest_dir , "toolplus-packages.yaml" )
system_config = os . path . join ( _get_data_dir ( ) , "galaxy" , "bcbio_system.yaml" )
# Handle toolplus installs inside Docker container
if not os . path . exists ( syste... |
def wasModified ( self ) :
"""Check to see if this module has been modified on disk since the last
time it was cached .
@ return : True if it has been modified , False if not .""" | self . filePath . restat ( )
mtime = self . filePath . getmtime ( )
if mtime >= self . lastModified :
return True
else :
return False |
def from_string ( string ) :
"""Reads a string representation to a Cssr object .
Args :
string ( str ) : A string representation of a CSSR .
Returns :
Cssr object .""" | lines = string . split ( "\n" )
toks = lines [ 0 ] . split ( )
lengths = [ float ( i ) for i in toks ]
toks = lines [ 1 ] . split ( )
angles = [ float ( i ) for i in toks [ 0 : 3 ] ]
latt = Lattice . from_lengths_and_angles ( lengths , angles )
sp = [ ]
coords = [ ]
for l in lines [ 4 : ] :
m = re . match ( r"\d+\s... |
def debug ( self ) :
"""Return debug setting""" | debug = False
if os . path . isfile ( os . path . join ( self . tcex . args . tc_temp_path , 'DEBUG' ) ) :
debug = True
return debug |
def get_owner_asset_ids ( self , address ) :
"""Get the list of assets owned by an address owner .
: param address : ethereum account address , hex str
: return :""" | block_filter = self . _get_event_filter ( owner = address )
log_items = block_filter . get_all_entries ( max_tries = 5 )
did_list = [ ]
for log_i in log_items :
did_list . append ( id_to_did ( log_i . args [ '_did' ] ) )
return did_list |
def set_server ( self , pos , key , value ) :
"""Set the key to the value for the pos ( position in the list ) .""" | self . _ports_list [ pos ] [ key ] = value |
def execute ( self , context , goals ) :
"""Executes the supplied goals and their dependencies against the given context .
: param context : The pants run context .
: param list goals : A list of ` ` Goal ` ` objects representing the command line goals explicitly
requested .
: returns int : An exit code of ... | try :
self . attempt ( context , goals )
return 0
except TaskError as e :
message = str ( e )
if message :
print ( '\nFAILURE: {0}\n' . format ( message ) )
else :
print ( '\nFAILURE\n' )
return e . exit_code |
def push ( self , value ) :
"""SNEAK value TO FRONT OF THE QUEUE""" | if self . closed and not self . allow_add_after_close :
Log . error ( "Do not push to closed queue" )
with self . lock :
self . _wait_for_queue_space ( )
if not self . closed :
self . queue . appendleft ( value )
return self |
def update_package_versions ( self , batch_request , feed_id ) :
"""UpdatePackageVersions .
[ Preview API ] Update several packages from a single feed in a single request . The updates to the packages do not happen atomically .
: param : class : ` < NuGetPackagesBatchRequest > < azure . devops . v5_0 . nuget . ... | route_values = { }
if feed_id is not None :
route_values [ 'feedId' ] = self . _serialize . url ( 'feed_id' , feed_id , 'str' )
content = self . _serialize . body ( batch_request , 'NuGetPackagesBatchRequest' )
self . _send ( http_method = 'POST' , location_id = '00c58ea7-d55f-49de-b59f-983533ae11dc' , version = '5... |
def view_500 ( request , url = None ) :
"""it returns a 500 http response""" | res = render_to_response ( "500.html" , context_instance = RequestContext ( request ) )
res . status_code = 500
return res |
def select ( self , Class , set = None , recursive = True , ignore = True , node = None ) :
"""See : meth : ` AbstractElement . select `""" | if self . include :
return self . subdoc . data [ 0 ] . select ( Class , set , recursive , ignore , node )
# pass it on to the text node of the subdoc
else :
return iter ( [ ] ) |
def network_profile_name_list ( self , obj ) :
"""Get AP profile names .""" | profile_list = pointer ( WLAN_PROFILE_INFO_LIST ( ) )
self . _wlan_get_profile_list ( self . _handle , byref ( obj [ 'guid' ] ) , byref ( profile_list ) )
profiles = cast ( profile_list . contents . ProfileInfo , POINTER ( WLAN_PROFILE_INFO ) )
profile_name_list = [ ]
for i in range ( profile_list . contents . dwNumber... |
def yosys_area_delay ( library , abc_cmd = None , block = None ) :
"""Synthesize with Yosys and return estimate of area and delay .
: param library : stdcell library file to target in liberty format
: param abc _ cmd : string of commands for yosys to pass to abc for synthesis
: param block : pyrtl block to an... | if abc_cmd is None :
abc_cmd = 'strash;scorr;ifraig;retime;dch,-f;map;print_stats;'
else : # first , replace whitespace with commas as per yosys requirements
re . sub ( r"\s+" , ',' , abc_cmd )
# then append with " print _ stats " to generate the area and delay info
abc_cmd = '%s;print_stats;' % abc_cmd... |
def installed ( name , features = None , recurse = False , restart = False , source = None , exclude = None ) :
'''Install the windows feature . To install a single feature , use the ` ` name ` `
parameter . To install multiple features , use the ` ` features ` ` parameter .
. . note : :
Some features require... | ret = { 'name' : name , 'result' : True , 'changes' : { } , 'comment' : '' }
# Check if features is not passed , use name . Split commas
if features is None :
features = name . split ( ',' )
# Make sure features is a list , split commas
if not isinstance ( features , list ) :
features = features . split ( ',' )... |
def binary2pb ( b , proto_id , proto_fmt_type ) :
"""Transfer binary to pb message
: param b : binary content to be transformed to pb message
: return : pb message""" | rsp = pb_map [ proto_id ]
if rsp is None :
return None
if proto_fmt_type == ProtoFMT . Json :
return json2pb ( type ( rsp ) , b . decode ( 'utf-8' ) )
elif proto_fmt_type == ProtoFMT . Protobuf :
rsp = type ( rsp ) ( )
# logger . debug ( ( proto _ id ) )
if IS_PY2 :
rsp . ParseFromString ( s... |
def add_metrics ( last_metrics : Collection [ Rank0Tensor ] , mets : Union [ Rank0Tensor , Collection [ Rank0Tensor ] ] ) :
"Return a dictionary for updating ` last _ metrics ` with ` mets ` ." | last_metrics , mets = listify ( last_metrics ) , listify ( mets )
return { 'last_metrics' : last_metrics + mets } |
def multipart_upload_lister ( bucket , key_marker = '' , upload_id_marker = '' , headers = None ) :
"""A generator function for listing multipart uploads in a bucket .""" | more_results = True
k = None
while more_results :
rs = bucket . get_all_multipart_uploads ( key_marker = key_marker , upload_id_marker = upload_id_marker , headers = headers )
for k in rs :
yield k
key_marker = rs . next_key_marker
upload_id_marker = rs . next_upload_id_marker
more_results =... |
def analyze ( self , using = None , ** kwargs ) :
"""Perform the analysis process on a text and return the tokens breakdown
of the text .
Any additional keyword arguments will be passed to
` ` Elasticsearch . indices . analyze ` ` unchanged .""" | return self . _get_connection ( using ) . indices . analyze ( index = self . _name , ** kwargs ) |
def _import_object ( self , path , look_for_cls_method ) :
"""Imports the module that contains the referenced method .
Args :
path : python path of class / function
look _ for _ cls _ method ( bool ) : If True , treat the last part of path as class method .
Returns :
Tuple . ( class object , class name , ... | last_nth = 2 if look_for_cls_method else 1
path = path . split ( '.' )
module_path = '.' . join ( path [ : - last_nth ] )
class_name = path [ - last_nth ]
module = importlib . import_module ( module_path )
if look_for_cls_method and path [ - last_nth : ] [ 0 ] == path [ - last_nth ] :
class_method = path [ - last_n... |
def _expand_variable_match ( positional_vars , named_vars , match ) :
"""Expand a matched variable with its value .
Args :
positional _ vars ( list ) : A list of positonal variables . This list will
be modified .
named _ vars ( dict ) : A dictionary of named variables .
match ( re . Match ) : A regular ex... | positional = match . group ( "positional" )
name = match . group ( "name" )
if name is not None :
try :
return six . text_type ( named_vars [ name ] )
except KeyError :
raise ValueError ( "Named variable '{}' not specified and needed by template " "`{}` at position {}" . format ( name , match . ... |
def _init_idxs_float ( self , usr_hdrs ) :
"""List of indexes whose values will be floats .""" | self . idxs_float = [ Idx for Hdr , Idx in self . hdr2idx . items ( ) if Hdr in usr_hdrs and Hdr in self . float_hdrs ] |
async def prepare_decrypter ( client , cdn_client , cdn_redirect ) :
"""Prepares a new CDN decrypter .
: param client : a TelegramClient connected to the main servers .
: param cdn _ client : a new client connected to the CDN .
: param cdn _ redirect : the redirect file object that caused this call .
: retu... | cdn_aes = AESModeCTR ( key = cdn_redirect . encryption_key , # 12 first bytes of the IV . . 4 bytes of the offset ( 0 , big endian )
iv = cdn_redirect . encryption_iv [ : 12 ] + bytes ( 4 ) )
# We assume that cdn _ redirect . cdn _ file _ hashes are ordered by offset ,
# and that there will be enough of these to retrie... |
def delete ( self , key ) :
""": param key : a string with length of [ 0 , 32]""" | if not is_string ( key ) :
raise Exception ( "Key must be string" )
if len ( key ) > 32 :
raise Exception ( "Max key length is 32" )
self . root_node = self . _delete_and_delete_storage ( self . root_node , bin_to_nibbles ( to_string ( key ) ) )
self . _update_root_hash ( ) |
def list_to_1d_numpy ( data , dtype = np . float32 , name = 'list' ) :
"""Convert data to 1 - D numpy array .""" | if is_numpy_1d_array ( data ) :
if data . dtype == dtype :
return data
else :
return data . astype ( dtype = dtype , copy = False )
elif is_1d_list ( data ) :
return np . array ( data , dtype = dtype , copy = False )
elif isinstance ( data , Series ) :
return data . values . astype ( dty... |
def _get_node_name ( self , node ) :
"""Get the name of the node - check for node . name and
node . type . declname . Not sure why the second one occurs
exactly - it happens with declaring a new struct field
with parameters""" | res = getattr ( node , "name" , None )
if res is None :
return res
if isinstance ( res , AST . TypeDecl ) :
return res . declname
return res |
def plot_predict ( self , h = 5 , past_values = 20 , intervals = True , ** kwargs ) :
"""Plots forecasts 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... | figsize = kwargs . get ( 'figsize' , ( 10 , 7 ) )
if self . latent_variables . estimated is False :
raise Exception ( "No latent variables estimated!" )
else :
import matplotlib . pyplot as plt
import seaborn as sns
# Retrieve data , dates and ( transformed ) latent variables
mu , Y = self . _model ... |
def system_monitor_sfp_alert_action ( self , ** kwargs ) :
"""Auto Generated Code""" | config = ET . Element ( "config" )
system_monitor = ET . SubElement ( config , "system-monitor" , xmlns = "urn:brocade.com:mgmt:brocade-system-monitor" )
sfp = ET . SubElement ( system_monitor , "sfp" )
alert = ET . SubElement ( sfp , "alert" )
action = ET . SubElement ( alert , "action" )
action . text = kwargs . pop ... |
def parse_config_file ( self , path : str , final : bool = True ) -> None :
"""Parses and loads the config file at the given path .
The config file contains Python code that will be executed ( so
it is * * not safe * * to use untrusted config files ) . Anything in
the global namespace that matches a defined o... | config = { "__file__" : os . path . abspath ( path ) }
with open ( path , "rb" ) as f :
exec_in ( native_str ( f . read ( ) ) , config , config )
for name in config :
normalized = self . _normalize_name ( name )
if normalized in self . _options :
option = self . _options [ normalized ]
if op... |
def harden ( overrides = None ) :
"""Hardening decorator .
This is the main entry point for running the hardening stack . In order to
run modules of the stack you must add this decorator to charm hook ( s ) and
ensure that your charm config . yaml contains the ' harden ' option set to
one or more of the sup... | if overrides is None :
overrides = [ ]
def _harden_inner1 ( f ) : # As this has to be py2.7 compat , we can ' t use nonlocal . Use a trick
# to capture the dictionary that can then be updated .
_logged = { 'done' : False }
def _harden_inner2 ( * args , ** kwargs ) : # knock out hardening via a config var ; ... |
def cmdHISTORY ( self , params ) :
"""Display the command history""" | cnt = 0
self . writeline ( 'Command history\n' )
for line in self . history :
cnt = cnt + 1
self . writeline ( "%-5d : %s" % ( cnt , '' . join ( line ) ) ) |
def markov_network_bqm ( MN ) :
"""Construct a binary quadratic model for a markov network .
Parameters
G : NetworkX graph
A Markov Network as returned by : func : ` . markov _ network `
Returns
bqm : : obj : ` dimod . BinaryQuadraticModel `
A binary quadratic model .""" | bqm = dimod . BinaryQuadraticModel . empty ( dimod . BINARY )
# the variable potentials
for v , ddict in MN . nodes ( data = True , default = None ) :
potential = ddict . get ( 'potential' , None )
if potential is None :
continue
# for single nodes we don ' t need to worry about order
phi0 = pot... |
def _get_description ( self , element ) :
"""Returns the description of element .
: param element : The element .
: type element : hatemile . util . html . htmldomelement . HTMLDOMElement
: return : The description of element .
: rtype : str""" | description = None
if element . has_attribute ( 'title' ) :
description = element . get_attribute ( 'title' )
elif element . has_attribute ( 'aria-label' ) :
description = element . get_attribute ( 'aria-label' )
elif element . has_attribute ( 'alt' ) :
description = element . get_attribute ( 'alt' )
elif e... |
def list_role_binding_for_all_namespaces ( self , ** kwargs ) :
"""list or watch objects of kind RoleBinding
This method makes a synchronous HTTP request by default . To make an
asynchronous HTTP request , please pass async _ req = True
> > > thread = api . list _ role _ binding _ for _ all _ namespaces ( asy... | kwargs [ '_return_http_data_only' ] = True
if kwargs . get ( 'async_req' ) :
return self . list_role_binding_for_all_namespaces_with_http_info ( ** kwargs )
else :
( data ) = self . list_role_binding_for_all_namespaces_with_http_info ( ** kwargs )
return data |
def make_duplicate_request ( request ) :
"""Since werkzeug request objects are immutable , this is needed to create an
identical reuet object with immutable values so it can be retried after a
POST failure .""" | class FakeRequest ( object ) :
method = 'GET'
path = request . path
headers = request . headers
GET = request . GET
POST = request . POST
user = getattr ( request , 'user' , None )
cookies = request . cookies
is_xhr = request . is_xhr
return FakeRequest ( ) |
def topil ( self ) :
"""Returns a PIL . Image version of this Pix""" | from PIL import Image
# Leptonica manages data in words , so it implicitly does an endian
# swap . Tell Pillow about this when it reads the data .
pix = self
if sys . byteorder == 'little' :
if self . mode == 'RGB' :
raw_mode = 'XBGR'
elif self . mode == 'RGBA' :
raw_mode = 'ABGR'
elif self ... |
def _report_command ( self , cmd , procs = None ) :
"""Writes a command to both stdout and to the commands log file
( self . pipeline _ commands _ file ) .
: param str cmd : command to report
: param str | list [ str ] procs : process numbers for processes in the command""" | if isinstance ( procs , list ) :
procs = "," . join ( map ( str , procs ) )
if procs :
line = "\n> `{cmd}` ({procs})\n" . format ( cmd = str ( cmd ) , procs = procs )
else :
line = "\n> `{cmd}`\n" . format ( cmd = str ( cmd ) )
print ( line )
with open ( self . pipeline_commands_file , "a" ) as myfile :
... |
def step ( self , y , u , t , h ) :
"""This is called by solve , but can be called by the user who wants to
run through an integration with a control force .
y - state at t
u - control inputs at t
t - time
h - step size""" | k1 = h * self . func ( t , y , u )
k2 = h * self . func ( t + .5 * h , y + .5 * h * k1 , u )
k3 = h * self . func ( t + .5 * h , y + .5 * h * k2 , u )
k4 = h * self . func ( t + h , y + h * k3 , u )
return y + ( k1 + 2 * k2 + 2 * k3 + k4 ) / 6.0 |
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