signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def orientality ( obj , sun ) :
"""Returns if an object is oriental or
occidental to the sun .""" | dist = angle . distance ( sun . lon , obj . lon )
return OCCIDENTAL if dist < 180 else ORIENTAL |
def substitute_minor_for_major ( progression , substitute_index , ignore_suffix = False ) :
"""Substitute minor chords for its major equivalent .
' m ' and ' m7 ' suffixes recognized , and [ ' II ' , ' III ' , ' VI ' ] if there is no
suffix .
Examples :
> > > substitute _ minor _ for _ major ( [ ' VI ' ] , ... | ( roman , acc , suff ) = parse_string ( progression [ substitute_index ] )
res = [ ]
# Minor to major substitution
if suff == 'm' or suff == 'm7' or suff == '' and roman in [ 'II' , 'III' , 'VI' ] or ignore_suffix :
n = skip ( roman , 2 )
a = interval_diff ( roman , n , 3 ) + acc
if suff == 'm' or ignore_su... |
def groupby_field ( records , field_name , skip_none = True ) :
"""Given a list of objects , group them into a dictionary by
the unique values of a given field name .""" | return apply_groupby ( records , lambda obj : getattr ( obj , field_name ) , skip_none = skip_none ) |
def get_policies_from_git ( self ) :
"""Retrieve policies from the Git repo . Returns a dictionary containing all the roles and policies
Returns :
: obj : ` dict ` of ` str ` : ` dict `""" | fldr = mkdtemp ( )
try :
url = 'https://{token}:x-oauth-basic@{server}/{repo}' . format ( ** { 'token' : self . dbconfig . get ( 'git_auth_token' , self . ns ) , 'server' : self . dbconfig . get ( 'git_server' , self . ns ) , 'repo' : self . dbconfig . get ( 'git_repo' , self . ns ) } )
policies = { 'GLOBAL' : ... |
def _fix_genotypes_object ( self , genotypes , variant_info ) :
"""Fixes a genotypes object ( variant name , multi - allelic value .""" | # Checking the name ( if there were duplications )
if self . has_index and variant_info . name != genotypes . variant . name :
if not variant_info . name . startswith ( genotypes . variant . name ) :
raise ValueError ( "Index file not synced with IMPUTE2 file" )
genotypes . variant . name = variant_info... |
def discard_saved_state ( self , f_remove_file ) :
"""Forcibly resets the machine to " Powered Off " state if it is
currently in the " Saved " state ( previously created by : py : func : ` save _ state ` ) .
Next time the machine is powered up , a clean boot will occur .
This operation is equivalent to resett... | if not isinstance ( f_remove_file , bool ) :
raise TypeError ( "f_remove_file can only be an instance of type bool" )
self . _call ( "discardSavedState" , in_p = [ f_remove_file ] ) |
def get_min_distance ( element ) :
"""Gets the minimum sampling distance of the x - and y - coordinates
in a grid .""" | try :
from scipy . spatial . distance import pdist
return pdist ( element . array ( [ 0 , 1 ] ) ) . min ( )
except :
return _get_min_distance_numpy ( element ) |
def apply_tile_groups ( self , tile_groups ) :
"""Increase mana , xp , money , anvils and scrolls based on tile groups .""" | self_increase_types = ( 'r' , 'g' , 'b' , 'y' , 'x' , 'm' , 'h' , 'c' )
attack_types = ( 's' , '*' )
total_attack = 0
for tile_group in tile_groups :
group_type = None
type_count = 0
type_multiplier = 1
for tile in tile_group : # try to get the group type
if not group_type : # try to set the gro... |
def get_related_node ( self , node , relation ) :
"""Looks for an edge from node to some other node , such that the edge
is annotated with the given relation . If there exists such an edge ,
returns the name of the node it points to . Otherwise , returns None .""" | G = self . G
for edge in G . edges ( node ) :
to = edge [ 1 ]
to_relation = G . edges [ node , to ] [ 'relation' ]
if to_relation == relation :
return to
return None |
def get_ntlm2_response ( password , server_challenge , client_challenge ) :
"""Generate the Unicode MD4 hash for the password associated with these credentials .""" | md5 = hashlib . new ( 'md5' )
md5 . update ( server_challenge + client_challenge )
ntlm2_session_hash = md5 . digest ( ) [ : 8 ]
ntlm_hash = PasswordAuthentication . ntowfv1 ( password . encode ( 'utf-16le' ) )
response = PasswordAuthentication . _encrypt_des_block ( ntlm_hash [ : 7 ] , ntlm2_session_hash )
response +=... |
def nic_add ( self , container , nic ) :
"""Hot plug a nic into a container
: param container : container ID
: param nic : {
' type ' : nic _ type # one of default , bridge , zerotier , macvlan , passthrough , vlan , or vxlan ( note , vlan and vxlan only supported by ovs )
' id ' : id # depends on the type ... | args = { 'container' : container , 'nic' : nic }
self . _nic_add . check ( args )
return self . _client . json ( 'corex.nic-add' , args ) |
def read_moc_fits_hdu ( moc , hdu , include_meta = False ) :
"""Read data from a FITS table HDU into a MOC .""" | if include_meta :
header = hdu . header
if 'MOCTYPE' in header :
moc . type = header [ 'MOCTYPE' ]
if 'MOCID' in header :
moc . id = header [ 'MOCID' ]
if 'ORIGIN' in header :
moc . origin = header [ 'ORIGIN' ]
if 'EXTNAME' in header :
moc . name = header [ 'EXTNAME' ... |
def rouge ( hypotheses , references ) :
"""Calculates average rouge scores for a list of hypotheses and
references""" | # Filter out hyps that are of 0 length
# hyps _ and _ refs = zip ( hypotheses , references )
# hyps _ and _ refs = [ _ for _ in hyps _ and _ refs if len ( _ [ 0 ] ) > 0]
# hypotheses , references = zip ( * hyps _ and _ refs )
# Calculate ROUGE - 1 F1 , precision , recall scores
rouge_1 = [ rouge_n ( [ hyp ] , [ ref ] ,... |
def ic45 ( msg ) :
"""Icing .
Args :
msg ( String ) : 28 bytes hexadecimal message string
Returns :
int : Icing level . 0 = NIL , 1 = Light , 2 = Moderate , 3 = Severe""" | d = hex2bin ( data ( msg ) )
if d [ 9 ] == '0' :
return None
ic = bin2int ( d [ 10 : 12 ] )
return ic |
def import_process_element ( process_elements_dict , process_element ) :
"""Adds attributes of BPMN process element to appropriate field process _ attributes .
Diagram inner representation contains following process attributes :
- id - assumed to be required in XML file , even thought BPMN 2.0 schema doesn ' t ... | process_id = process_element . getAttribute ( consts . Consts . id )
process_element_attributes = { consts . Consts . id : process_element . getAttribute ( consts . Consts . id ) , consts . Consts . name : process_element . getAttribute ( consts . Consts . name ) if process_element . hasAttribute ( consts . Consts . na... |
def focusPrev ( self , event ) :
"""Set focus to previous item in sequence""" | try :
event . widget . tk_focusPrev ( ) . focus_set ( )
except TypeError : # see tkinter equivalent code for tk _ focusPrev to see
# commented original version
name = event . widget . tk . call ( 'tk_focusPrev' , event . widget . _w )
event . widget . _nametowidget ( str ( name ) ) . focus_set ( ) |
def prefer_master ( nodes : List [ DiscoveredNode ] ) -> Optional [ DiscoveredNode ] :
"""Select the master if available , otherwise fall back to a replica .""" | return max ( nodes , key = attrgetter ( "state" ) ) |
def match_sr ( self , svc_ref , cid = None ) : # type : ( ServiceReference , Optional [ Tuple [ str , str ] ] ) - > bool
"""Checks if this export registration matches the given service reference
: param svc _ ref : A service reference
: param cid : A container ID
: return : True if the service matches this ex... | with self . __lock :
our_sr = self . get_reference ( )
if our_sr is None :
return False
sr_compare = our_sr == svc_ref
if cid is None :
return sr_compare
our_cid = self . get_export_container_id ( )
if our_cid is None :
return False
return sr_compare and our_cid == ci... |
def dot_product ( t1 , t2 , keep_dims = False , name = None , reduction_dim = None ) :
"""Computes the dot product of t1 and t2.
Args :
t1 : A rank 2 tensor .
t2 : A tensor that is the same size as t1.
keep _ dims : If true , reduction does not change the rank of the input .
name : Optional name for this ... | with tf . name_scope ( name , 'dot' , [ t1 , t2 ] ) as scope :
t1 = tf . convert_to_tensor ( t1 , name = 't1' )
t2 = tf . convert_to_tensor ( t2 , name = 't2' )
mul = tf . multiply ( t1 , t2 )
if not reduction_dim :
reduction_dim = _last_index ( mul , 1 )
return tf . reduce_sum ( mul , reduc... |
def dtypes_summary ( df ) :
"""Takes in a dataframe and returns a dataframe with
information on the data - types present in each column .
Parameters :
df - DataFrame
Dataframe to summarize""" | output_df = pd . DataFrame ( [ ] )
row_count = df . shape [ 0 ]
row_indexes = [ 'rows_numerical' , 'rows_string' , 'rows_date_time' , 'category_count' , 'largest_category' , 'rows_na' , 'rows_total' ]
for colname in df :
data = df [ colname ]
# data is the pandas series associated with this column
# number ... |
def find_rdataset ( self , rdclass , rdtype , covers = dns . rdatatype . NONE , create = False ) :
"""Find an rdataset matching the specified properties in the
current node .
@ param rdclass : The class of the rdataset
@ type rdclass : int
@ param rdtype : The type of the rdataset
@ type rdtype : int
@ ... | for rds in self . rdatasets :
if rds . match ( rdclass , rdtype , covers ) :
return rds
if not create :
raise KeyError
rds = dns . rdataset . Rdataset ( rdclass , rdtype )
self . rdatasets . append ( rds )
return rds |
def search_artists_by_name ( self , artist_name : str , limit : int = 5 ) -> List [ NameExternalIDPair ] :
"""Returns zero or more artist name - external ID pairs that match the specified artist name .
Arguments :
artist _ name ( str ) : The artist name to search in the Spotify API .
limit ( int ) : The maxim... | response : requests . Response = requests . get ( self . _API_URL_TEMPLATE . format ( "search" ) , params = { "q" : artist_name , "type" : "artist" , "limit" : limit } , headers = { "Authorization" : "Bearer {}" . format ( self . _token . access_token ) } )
# TODO : handle API rate limiting
response . raise_for_status ... |
def match ( self , source_obj_features , target_obj_features ) :
"""Matches features between two graspable objects based on a full distance matrix .
Parameters
source _ obj _ features : : obj : ` BagOfFeatures `
bag of the source objects features
target _ obj _ features : : obj : ` BagOfFeatures `
bag of ... | if not isinstance ( source_obj_features , f . BagOfFeatures ) :
raise ValueError ( 'Must supply source bag of object features' )
if not isinstance ( target_obj_features , f . BagOfFeatures ) :
raise ValueError ( 'Must supply target bag of object features' )
# source feature descriptors and keypoints
source_desc... |
def fits_recarray_to_dict ( table ) :
"""Convert a FITS recarray to a python dictionary .""" | cols = { }
for icol , col in enumerate ( table . columns . names ) :
col_data = table . data [ col ]
if type ( col_data [ 0 ] ) == np . float32 :
cols [ col ] = np . array ( col_data , dtype = float )
elif type ( col_data [ 0 ] ) == np . float64 :
cols [ col ] = np . array ( col_data , dtype... |
def list_kinesis_applications ( region , filter_by_kwargs ) :
"""List all the kinesis applications along with the shards for each stream""" | conn = boto . kinesis . connect_to_region ( region )
streams = conn . list_streams ( ) [ 'StreamNames' ]
kinesis_streams = { }
for stream_name in streams :
shard_ids = [ ]
shards = conn . describe_stream ( stream_name ) [ 'StreamDescription' ] [ 'Shards' ]
for shard in shards :
shard_ids . append ( ... |
def _set_counts_state ( self , v , load = False ) :
"""Setter method for counts _ state , mapped from YANG variable / counts _ state ( container )
If this variable is read - only ( config : false ) in the
source YANG file , then _ set _ counts _ state is considered as a private
method . Backends looking to po... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = counts_state . counts_state , is_container = 'container' , presence = False , yang_name = "counts-state" , rest_name = "counts-state" , parent = self , path_helper = self . _path_helper , extmethods = self . _extmethods , reg... |
def get_model_class ( klass , api = None , use_request_api = True ) :
"""Generates the Model Class based on the klass
loads automatically the corresponding json schema file form schemes folder
: param klass : json schema filename
: param use _ request _ api : if True autoinitializes request class if api is No... | if api is None and use_request_api :
api = APIClient ( )
_type = klass
if isinstance ( klass , dict ) :
_type = klass [ 'type' ]
schema = loaders . load_schema_raw ( _type )
model_cls = model_factory ( schema , base_class = RemoteResource )
model_cls . __api__ = api
return model_cls |
def checkIsMember ( self , CorpNum ) :
"""회원가입여부 확인
args
CorpNum : 회원 사업자번호
return
회원가입여부 True / False
raise
PopbillException""" | if CorpNum == None or CorpNum == '' :
raise PopbillException ( - 99999999 , "사업자번호가 입력되지 않았습니다." )
return self . _httpget ( '/Join?CorpNum=' + CorpNum + '&LID=' + self . __linkID , None , None ) |
def websafe_dither ( self ) :
"""Return the two websafe colors nearest to this one .
Returns :
A tuple of two grapefruit . Color instances which are the two
web safe colors closest this one .
> > > c = Color . from _ rgb ( 1.0 , 0.45 , 0.0)
> > > c1 , c2 = c . websafe _ dither ( )
> > > c1
Color ( 1.0... | return ( Color ( rgb_to_websafe ( * self . __rgb ) , 'rgb' , self . __a , self . __wref ) , Color ( rgb_to_websafe ( alt = True , * self . __rgb ) , 'rgb' , self . __a , self . __wref ) ) |
def parse_query ( self , query ) :
"""Creates a tinydb Query ( ) object from the query dict
: param query : object containing the dictionary representation of the
query
: return : composite Query ( )""" | logger . debug ( u'query to parse2: {}' . format ( query ) )
# this should find all records
if query == { } or query is None :
return Query ( ) . _id != u'-1'
# noqa
q = None
# find the final result of the generator
for c in self . parse_condition ( query ) :
if q is None :
q = c
else :
q = ... |
def stack_nll ( shape , components , ylims , weights = None ) :
"""Combine the log - likelihoods from a number of components .
Parameters
shape : tuple
The shape of the return array
components : ` ~ fermipy . castro . CastroData _ Base `
The components to be stacked
weights : array - like
Returns
no... | n_bins = shape [ 0 ]
n_vals = shape [ 1 ]
if weights is None :
weights = np . ones ( ( len ( components ) ) )
norm_vals = np . zeros ( shape )
nll_vals = np . zeros ( shape )
nll_offsets = np . zeros ( ( n_bins ) )
for i in range ( n_bins ) :
log_min = np . log10 ( ylims [ 0 ] )
log_max = np . log10 ( ylims... |
def main ( ) :
"""process the main task""" | args = get_args ( )
args . start = date_parser . parse ( args . start )
args . end = date_parser . parse ( args . end )
args . step = timedelta ( args . step )
config = Config ( args . config )
times = [ args . start + i * args . step for i in range ( int ( ( args . end - args . start ) / args . step ) ) ]
for i , time... |
def entropy_of_contacts ( records , normalize = False ) :
"""The entropy of the user ' s contacts .
Parameters
normalize : boolean , default is False
Returns a normalized entropy between 0 and 1.""" | counter = Counter ( r . correspondent_id for r in records )
raw_entropy = entropy ( counter . values ( ) )
n = len ( counter )
if normalize and n > 1 :
return raw_entropy / math . log ( n )
else :
return raw_entropy |
def get_command_from_module ( command_module , remote_connection : environ . RemoteConnection ) :
"""Returns the execution command to use for the specified module , which may
be different depending upon remote connection
: param command _ module :
: param remote _ connection :
: return :""" | use_remote = ( remote_connection . active and hasattr ( command_module , 'execute_remote' ) )
return ( command_module . execute_remote if use_remote else command_module . execute ) |
def AuthorizeUser ( self , user , subject ) :
"""Allow given user access to a given subject .""" | user_set = self . authorized_users . setdefault ( subject , set ( ) )
user_set . add ( user ) |
def aug_sysargv ( cmdstr ) :
"""DEBUG FUNC modify argv to look like you ran a command""" | import shlex
argv = shlex . split ( cmdstr )
sys . argv . extend ( argv ) |
def filter_out_empty_lists ( input_list ) :
"""Function to remove all empty lists from a given list of lists .
Args :
input _ list ( List ) : A list possibly containing empty lists alongside other items .
Returns :
List : A list containing only non - empty items from the input list .
Examples :
> > > fi... | filtered_list = [ element for element in input_list if element ]
return filtered_list |
def Spearman ( poly , dist , sample = 10000 , retall = False , ** kws ) :
"""Calculate Spearman ' s rank - order correlation coefficient .
Args :
poly ( Poly ) :
Polynomial of interest .
dist ( Dist ) :
Defines the space where correlation is taken .
sample ( int ) :
Number of samples used in estimatio... | samples = dist . sample ( sample , ** kws )
poly = polynomials . flatten ( poly )
Y = poly ( * samples )
if retall :
return spearmanr ( Y . T )
return spearmanr ( Y . T ) [ 0 ] |
def extend ( self , clauses , weights = None ) :
"""Add several clauses to WCNF formula . The clauses should be given in
the form of list . For every clause in the list , method
: meth : ` append ` is invoked .
The clauses can be hard or soft depending on the ` ` weights ` `
argument . If no weights are set... | if weights : # clauses are soft
for i , cl in enumerate ( clauses ) :
self . append ( cl , weight = weights [ i ] )
else : # clauses are hard
for cl in clauses :
self . append ( cl ) |
def get_incremental_uncovered_lines ( abs_path : str , base_commit : str , actual_commit : Optional [ str ] ) -> List [ Tuple [ int , str , str ] ] :
"""Uses git diff and the annotation files created by
` pytest - - cov - report annotate ` to find touched but uncovered lines in the
given file .
Args :
abs _... | # Deleted files don ' t have any lines that need to be covered .
if not os . path . isfile ( abs_path ) :
return [ ]
unified_diff_lines_str = shell_tools . output_of ( 'git' , 'diff' , '--unified=0' , base_commit , actual_commit , '--' , abs_path )
unified_diff_lines = [ e for e in unified_diff_lines_str . split ( ... |
def send ( self , message ) :
"""Make a Twilio SendGrid v3 API request with the request body generated by
the Mail object
: param message : The Twilio SendGrid v3 API request body generated by the Mail
object
: type message : Mail""" | if isinstance ( message , dict ) :
response = self . client . mail . send . post ( request_body = message )
else :
response = self . client . mail . send . post ( request_body = message . get ( ) )
return response |
def nonrepeats ( inlist ) :
"""Returns items that are NOT duplicated in the first dim of the passed list .
Usage : nonrepeats ( inlist )""" | nonrepeats = [ ]
for i in range ( len ( inlist ) ) :
if inlist . count ( inlist [ i ] ) == 1 :
nonrepeats . append ( inlist [ i ] )
return nonrepeats |
def close ( self ) :
"""Close the connection and all associated cursors . This will implicitly
roll back any uncommitted operations .""" | for c in self . cursors :
c . close ( )
self . cursors = [ ]
self . impl = None |
def check_format ( format , subtype = None , endian = None ) :
"""Check if the combination of format / subtype / endian is valid .
Examples
> > > import soundfile as sf
> > > sf . check _ format ( ' WAV ' , ' PCM _ 24 ' )
True
> > > sf . check _ format ( ' FLAC ' , ' VORBIS ' )
False""" | try :
return bool ( _format_int ( format , subtype , endian ) )
except ( ValueError , TypeError ) :
return False |
def create_releasenotes ( project_dir = os . curdir , bugtracker_url = '' ) :
"""Creates the release notes file , if not in a package .
Args :
project _ dir ( str ) : Path to the git repo of the project .
bugtracker _ url ( str ) : Url to the bug tracker for the issues .
Returns :
None
Raises :
Runtim... | pkg_info_file = os . path . join ( project_dir , 'PKG-INFO' )
if os . path . exists ( pkg_info_file ) :
return
with open ( 'RELEASE_NOTES' , 'wb' ) as releasenotes_fd :
releasenotes_fd . write ( get_releasenotes ( project_dir = project_dir , bugtracker_url = bugtracker_url , ) . encode ( 'utf-8' ) + b'\n' ) |
def sortrows ( a , i = 0 , index_out = False , recurse = True ) :
"""Sorts array " a " by columns i
Parameters
a : np . ndarray
array to be sorted
i : int ( optional )
column to be sorted by , taken as 0 by default
index _ out : bool ( optional )
return the index I such that a ( I ) = sortrows ( a , i... | I = np . argsort ( a [ : , i ] )
a = a [ I , : ]
# We recursively call sortrows to make sure it is sorted best by every
# column
if recurse & ( len ( a [ 0 ] ) > i + 1 ) :
for b in np . unique ( a [ : , i ] ) :
ids = a [ : , i ] == b
colids = range ( i ) + range ( i + 1 , len ( a [ 0 ] ) )
a... |
def call ( self ) :
"""Make the API call again and fetch fresh data .""" | data = self . _downloader . download ( )
# Only try to pass errors arg if supported
if sys . version >= "2.7" :
data = data . decode ( "utf-8" , errors = "ignore" )
else :
data = data . decode ( "utf-8" )
self . update ( json . loads ( data ) )
self . _fetched = True |
def calculate_total ( d : dict ) -> int :
"""Function to compute the total of all values in the specified dictionary .
Args :
d ( dict ) : dictionary with values to be summed .
Returns :
int : the sum of all values in the dictionary .
Examples :
> > > calculate _ total ( { ' a ' : 100 , ' b ' : 200 , ' ... | total = sum ( d . values ( ) )
return total |
def _check_for_legal_children ( self , name , elt , mustqualify = 1 ) :
'''Check if all children of this node are elements or whitespace - only
text nodes .''' | inheader = name == "Header"
for n in _children ( elt ) :
t = n . nodeType
if t == _Node . COMMENT_NODE :
continue
if t != _Node . ELEMENT_NODE :
if t == _Node . TEXT_NODE and n . nodeValue . strip ( ) == "" :
continue
raise ParseException ( "Non-element child in " + name ... |
def _single_resource_json_response ( resource , depth = 0 ) :
"""Return the JSON representation of * resource * .
: param resource : : class : ` sandman . model . Model ` to render
: type resource : : class : ` sandman . model . Model `
: rtype : : class : ` flask . Response `""" | links = resource . links ( )
response = jsonify ( ** resource . as_dict ( depth ) )
response . headers [ 'Link' ] = ''
for link in links :
response . headers [ 'Link' ] += '<{}>; rel="{}",' . format ( link [ 'uri' ] , link [ 'rel' ] )
response . headers [ 'Link' ] = response . headers [ 'Link' ] [ : - 1 ]
return re... |
def time_delta_pusher ( please_stop , appender , queue , interval ) :
"""appender - THE FUNCTION THAT ACCEPTS A STRING
queue - FILLED WITH LOG ENTRIES { " template " : template , " params " : params } TO WRITE
interval - timedelta
USE IN A THREAD TO BATCH LOGS BY TIME INTERVAL""" | next_run = time ( ) + interval
while not please_stop :
profiler = Thread . current ( ) . cprofiler
profiler . disable ( )
( Till ( till = next_run ) | please_stop ) . wait ( )
profiler . enable ( )
next_run = time ( ) + interval
logs = queue . pop_all ( )
if not logs :
continue
l... |
def get_instance ( self , payload ) :
"""Build an instance of NewKeyInstance
: param dict payload : Payload response from the API
: returns : twilio . rest . api . v2010 . account . new _ key . NewKeyInstance
: rtype : twilio . rest . api . v2010 . account . new _ key . NewKeyInstance""" | return NewKeyInstance ( self . _version , payload , account_sid = self . _solution [ 'account_sid' ] , ) |
def autodiscover ( cls , module_paths : List [ str ] , subclass : 'Container' = None ) -> None :
"""Load all modules automatically and find bases and eggs .
: param module _ paths : List of paths that should be discovered
: param subclass : Optional Container subclass that should be used""" | def find_base ( bases : set , implementation : Type ) :
found = { b for b in bases if issubclass ( implementation , b ) }
if not found :
raise ConfigurationError ( "No base defined for %r" % implementation )
elif len ( found ) > 1 :
raise ConfigurationError ( "More than one base found for %r... |
def _memory_profile ( with_gc = False ) :
"""Helper for memory debugging . Mostly just a namespace where I experiment with
guppy and heapy .
References :
http : / / stackoverflow . com / questions / 2629680 / deciding - between - subprocess - multiprocessing - and - thread - in - python
Reset Numpy Memory :... | import utool as ut
if with_gc :
garbage_collect ( )
import guppy
hp = guppy . hpy ( )
print ( '[hpy] Waiting for heap output...' )
heap_output = hp . heap ( )
print ( heap_output )
print ( '[hpy] total heap size: ' + ut . byte_str2 ( heap_output . size ) )
ut . util_resources . memstats ( ) |
def get_properties ( obj ) :
"""Get values of all properties in specified object and returns them as a map .
: param obj : an object to get properties from .
: return : a map , containing the names of the object ' s properties and their values .""" | properties = { }
for property_name in dir ( obj ) :
property = getattr ( obj , property_name )
if PropertyReflector . _is_property ( property , property_name ) :
properties [ property_name ] = property
return properties |
def get_source_by_name ( self , name ) :
"""Return a single source in the ROI with the given name . The
input name string can match any of the strings in the names
property of the source object . Case and whitespace are
ignored when matching name strings . If no sources are found
or multiple sources then an... | srcs = self . get_sources_by_name ( name )
if len ( srcs ) == 1 :
return srcs [ 0 ]
elif len ( srcs ) == 0 :
raise Exception ( 'No source matching name: ' + name )
elif len ( srcs ) > 1 :
raise Exception ( 'Multiple sources matching name: ' + name ) |
def send_complete ( self ) :
"""Verify if connection should be closed based on amount of data that was sent .""" | self . active = True
if self . should_finish ( ) :
self . _detach ( )
# Avoid race condition when waiting for write callback and session getting closed in between
if not self . _finished :
self . safe_finish ( )
else :
if self . session :
self . session . flush ( ) |
def peer_retrieve ( key , relation_name = 'cluster' ) :
"""Retrieve a named key from peer relation ` relation _ name ` .""" | cluster_rels = relation_ids ( relation_name )
if len ( cluster_rels ) > 0 :
cluster_rid = cluster_rels [ 0 ]
return relation_get ( attribute = key , rid = cluster_rid , unit = local_unit ( ) )
else :
raise ValueError ( 'Unable to detect' 'peer relation {}' . format ( relation_name ) ) |
def load_module ( self , module , module_uri = None ) :
"""load _ module
Attempts to load module by name , if it is not available ,
loads it by url""" | # Check to see that module isn ' t availble in python path
try :
import_module ( module )
except ImportError , e :
if module_uri is None :
raise e
else :
return module
if not CACHE_DOWNLOADS :
module_name = self . _unique_module_name ( module )
else :
module_name = self . _sanitize_module_na... |
def add_lifecycle_set_storage_class_rule ( self , storage_class , ** kw ) :
"""Add a " delete " rule to lifestyle rules configured for this bucket .
See https : / / cloud . google . com / storage / docs / lifecycle and
https : / / cloud . google . com / storage / docs / json _ api / v1 / buckets
. . literalin... | rules = list ( self . lifecycle_rules )
rules . append ( LifecycleRuleSetStorageClass ( storage_class , ** kw ) )
self . lifecycle_rules = rules |
def update ( self , permission ) :
"""In - place update of permissions .""" | self . needs . update ( permission . needs )
self . excludes . update ( permission . excludes ) |
def reset ( self ) :
"""Reset the statistics data for this object .""" | self . _count = 0
self . _exception_count = 0
self . _stat_start_time = None
self . _time_sum = float ( 0 )
self . _time_min = float ( 'inf' )
self . _time_max = float ( 0 )
self . _server_time_sum = float ( 0 )
self . _server_time_min = float ( 'inf' )
self . _server_time_max = float ( 0 )
self . _server_time_stored =... |
def _readData ( self , id3 , data ) :
"""Raises ID3JunkFrameError ; Returns leftover data""" | for reader in self . _framespec :
if len ( data ) or reader . handle_nodata :
try :
value , data = reader . read ( id3 , self , data )
except SpecError as e :
raise ID3JunkFrameError ( e )
else :
raise ID3JunkFrameError ( "no data left" )
self . _setattr ( rea... |
def find_resource_ids ( self ) :
"""Given a resource path and API Id , find resource Id .""" | all_resources = self . client . get_resources ( restApiId = self . api_id )
parent_id = None
resource_id = None
for resource in all_resources [ 'items' ] :
if resource [ 'path' ] == "/" :
parent_id = resource [ 'id' ]
if resource [ 'path' ] == self . trigger_settings [ 'resource' ] :
resource_id... |
def set_page_artid ( self , page_start = None , page_end = None , artid = None ) :
"""Add artid , start , end pages to publication info of a reference .
Args :
page _ start ( Optional [ string ] ) : value for the field page _ start
page _ end ( Optional [ string ] ) : value for the field page _ end
artid ( ... | if page_end and not page_start :
raise ValueError ( 'End_page provided without start_page' )
self . _ensure_reference_field ( 'publication_info' , { } )
publication_info = self . obj [ 'reference' ] [ 'publication_info' ]
if page_start :
publication_info [ 'page_start' ] = page_start
if page_end :
publicati... |
def get_info ( cls ) :
"""Return information about backend and its availability .
: return : A BackendInfo tuple if the import worked , none otherwise .""" | mod = try_import ( cls . mod_name )
if not mod :
return None
version = getattr ( mod , '__version__' , None ) or getattr ( mod , 'version' , None )
return BackendInfo ( version or 'deprecated' , '' ) |
def api ( name , version , description = None , hostname = None , audiences = None , scopes = None , allowed_client_ids = None , canonical_name = None , auth = None , owner_domain = None , owner_name = None , package_path = None , frontend_limits = None , title = None , documentation = None , auth_level = None , issuer... | if auth_level is not None :
_logger . warn ( _AUTH_LEVEL_WARNING )
return _ApiDecorator ( name , version , description = description , hostname = hostname , audiences = audiences , scopes = scopes , allowed_client_ids = allowed_client_ids , canonical_name = canonical_name , auth = auth , owner_domain = owner_domain... |
def convert_obatoms_to_molecule ( self , atoms , residue_name = None , site_property = "ff_map" ) :
"""Convert list of openbabel atoms to MOlecule .
Args :
atoms ( [ OBAtom ] ) : list of OBAtom objects
residue _ name ( str ) : the key in self . map _ residue _ to _ mol . Usec to
restore the site properties ... | restore_site_props = True if residue_name is not None else False
if restore_site_props and not hasattr ( self , "map_residue_to_mol" ) :
self . _set_residue_map ( )
coords = [ ]
zs = [ ]
for atm in atoms :
coords . append ( list ( atm . coords ) )
zs . append ( atm . atomicnum )
mol = Molecule ( zs , coords... |
def _decode_addr_key ( self , obj_dict ) :
"""Callback function to handle the decoding of the ' Addr ' field .
Serf msgpack ' Addr ' as an IPv6 address , and the data needs to be unpack
using socket . inet _ ntop ( ) .
See : https : / / github . com / KushalP / serfclient - py / issues / 20
: param obj _ di... | key = b'Addr'
if key in obj_dict :
try : # Try to convert a packed IPv6 address .
# Note : Call raises ValueError if address is actually IPv4.
ip_addr = socket . inet_ntop ( socket . AF_INET6 , obj_dict [ key ] )
# Check if the address is an IPv4 mapped IPv6 address :
# ie . : : ffff : x... |
def batch ( iterable , n , fillvalue = None ) :
"""Batches the elements of given iterable .
Resulting iterable will yield tuples containing at most ` ` n ` ` elements
( might be less if ` ` fillvalue ` ` isn ' t specified ) .
: param n : Number of items in every batch
: param fillvalue : Value to fill the l... | ensure_iterable ( iterable )
if not isinstance ( n , Integral ) :
raise TypeError ( "invalid number of elements in a batch" )
if not ( n > 0 ) :
raise ValueError ( "number of elements in a batch must be positive" )
# since we must use ` ` izip _ longest ` `
# ( ` ` izip ` ` fails if ` ` n ` ` is greater than le... |
def _create_figure ( self ) :
"""Create Matplotlib figure and axes""" | # Good for development
if get_option ( 'close_all_figures' ) :
plt . close ( 'all' )
figure = plt . figure ( )
axs = self . facet . make_axes ( figure , self . layout . layout , self . coordinates )
# Dictionary to collect matplotlib objects that will
# be targeted for theming by the themeables
figure . _themeable ... |
def ARPLimitExceeded_originator_switch_info_switchVcsId ( self , ** kwargs ) :
"""Auto Generated Code""" | config = ET . Element ( "config" )
ARPLimitExceeded = ET . SubElement ( config , "ARPLimitExceeded" , xmlns = "http://brocade.com/ns/brocade-notification-stream" )
originator_switch_info = ET . SubElement ( ARPLimitExceeded , "originator-switch-info" )
switchVcsId = ET . SubElement ( originator_switch_info , "switchVcs... |
def process_event ( self , event , hover_focus ) :
"""Process any input event .
: param event : The event that was triggered .
: param hover _ focus : Whether to trigger focus change on mouse moves .
: returns : None if the Effect processed the event , else the original event .""" | # Check whether this Layout is read - only - i . e . has no active focus .
if self . _live_col < 0 or self . _live_widget < 0 : # Might just be that we ' ve unset the focus - so check we can ' t find a focus .
self . _find_next_widget ( 1 )
if self . _live_col < 0 or self . _live_widget < 0 :
return eve... |
def _add_to_publish_stack ( self , exchange , routing_key , message , properties ) :
"""Temporarily add the message to the stack to publish to RabbitMQ
: param str exchange : The exchange to publish to
: param str routing _ key : The routing key to publish with
: param str message : The message body
: param... | global message_stack
message_stack . append ( ( exchange , routing_key , message , properties ) ) |
def uses_na_format ( station : str ) -> bool :
"""Returns True if the station uses the North American format ,
False if the International format""" | if station [ 0 ] in NA_REGIONS :
return True
if station [ 0 ] in IN_REGIONS :
return False
if station [ : 2 ] in M_NA_REGIONS :
return True
if station [ : 2 ] in M_IN_REGIONS :
return False
raise BadStation ( "Station doesn't start with a recognized character set" ) |
def write_functions ( self ) :
'''Writes out a python function for each WDL " task " object .
: return : a giant string containing the meat of the job defs .''' | # toil cannot technically start with multiple jobs , so an empty
# ' initialize _ jobs ' function is always called first to get around this
fn_section = 'def initialize_jobs(job):\n' + ' job.fileStore.logToMaster("initialize_jobs")\n'
for job in self . tasks_dictionary :
fn_section += self . write_function ( job... |
def get_assessment_results_session ( self , proxy ) :
"""Gets an ` ` AssessmentResultsSession ` ` to retrieve assessment results .
arg : proxy ( osid . proxy . Proxy ) : a proxy
return : ( osid . assessment . AssessmentResultsSession ) - an
assessment results session for this service
raise : NullArgument - ... | if not self . supports_assessment_results ( ) :
raise errors . Unimplemented ( )
# pylint : disable = no - member
return sessions . AssessmentResultsSession ( proxy = proxy , runtime = self . _runtime ) |
def _silence ( ) :
"""A context manager that silences sys . stdout and sys . stderr .""" | old_stdout = sys . stdout
old_stderr = sys . stderr
sys . stdout = _DummyFile ( )
sys . stderr = _DummyFile ( )
exception_occurred = False
try :
yield
except :
exception_occurred = True
# Go ahead and clean up so that exception handling can work normally
sys . stdout = old_stdout
sys . stderr = old_... |
def save_to_filename ( self , file_name , sep = '\n' ) :
"""Read all messages from the queue and persist them to local file .
Messages are written to the file and the ' sep ' string is written
in between messages . Messages are deleted from the queue after
being written to the file .
Returns the number of m... | fp = open ( file_name , 'wb' )
n = self . save_to_file ( fp , sep )
fp . close ( )
return n |
def add_filter ( self , component , filter_group = "pyxley-filter" ) :
"""Add a filter to the layout .""" | if getattr ( component , "name" ) != "Filter" :
raise Exception ( "Component is not an instance of Filter" )
if filter_group not in self . filters :
self . filters [ filter_group ] = [ ]
self . filters [ filter_group ] . append ( component ) |
def tile_read ( source , bounds , tilesize , ** kwargs ) :
"""Read data and mask .
Attributes
source : str or rasterio . io . DatasetReader
input file path or rasterio . io . DatasetReader object
bounds : list
Mercator tile bounds ( left , bottom , right , top )
tilesize : int
Output image size
kwar... | if isinstance ( source , DatasetReader ) :
return _tile_read ( source , bounds , tilesize , ** kwargs )
else :
with rasterio . open ( source ) as src_dst :
return _tile_read ( src_dst , bounds , tilesize , ** kwargs ) |
def user_find_by_user_string ( self , username , start = 0 , limit = 50 , include_inactive_users = False , include_active_users = True ) :
"""Fuzzy search using username and display name
: param username : Use ' . ' to find all users
: param start : OPTIONAL : The start point of the collection to return . Defau... | url = 'rest/api/2/user/search'
url += "?username={username}&includeActive={include_active}&includeInactive={include_inactive}&startAt={start}&maxResults={limit}" . format ( username = username , include_inactive = include_inactive_users , include_active = include_active_users , start = start , limit = limit )
return se... |
def send_report ( report , config ) :
"""Sends the report to IOpipe ' s collector .
: param report : The report to be sent .
: param config : The IOpipe agent configuration .""" | headers = { "Authorization" : "Bearer {}" . format ( config [ "token" ] ) }
url = "https://{host}{path}" . format ( ** config )
try :
response = session . post ( url , json = report , headers = headers , timeout = config [ "network_timeout" ] )
response . raise_for_status ( )
except Exception as e :
logger ... |
def date_0utc ( date ) :
"""Get the 0 UTC date for a date
Parameters
date : ee . Date
Returns
ee . Date""" | return ee . Date . fromYMD ( date . get ( 'year' ) , date . get ( 'month' ) , date . get ( 'day' ) ) |
def cigar_to_seq ( a , gap = '*' ) :
"""Accepts a pysam row .
cigar alignment is presented as a list of tuples ( operation , length ) . For
example , the tuple [ ( 0,3 ) , ( 1,5 ) , ( 0,2 ) ] refers to an alignment with 3
matches , 5 insertions and another 2 matches .
Op BAM Description
M 0 alignment matc... | seq , cigar = a . seq , a . cigar
start = 0
subseqs = [ ]
npadded = 0
if cigar is None :
return None , npadded
for operation , length in cigar :
end = start if operation == 2 else start + length
if operation == 0 : # match
subseq = seq [ start : end ]
elif operation == 1 : # insertion
su... |
def get_atom ( value ) :
"""atom = [ CFWS ] 1 * atext [ CFWS ]""" | atom = Atom ( )
if value and value [ 0 ] in CFWS_LEADER :
token , value = get_cfws ( value )
atom . append ( token )
if value and value [ 0 ] in ATOM_ENDS :
raise errors . HeaderParseError ( "expected atom but found '{}'" . format ( value ) )
token , value = get_atext ( value )
atom . append ( token )
if va... |
def chempot_plot_addons ( self , plt , xrange , ref_el , axes , pad = 2.4 , rect = [ - 0.047 , 0 , 0.84 , 1 ] , ylim = [ ] ) :
"""Helper function to a chempot plot look nicer .
Args :
plt ( Plot ) Plot to add things to .
xrange ( list ) : xlim parameter
ref _ el ( str ) : Element of the referenced chempot .... | # Make the figure look nice
plt . legend ( bbox_to_anchor = ( 1.01 , 1 ) , loc = 2 , borderaxespad = 0. )
axes . set_xlabel ( r"Chemical potential $\Delta\mu_{%s}$ (eV)" % ( ref_el ) )
ylim = ylim if ylim else axes . get_ylim ( )
plt . xticks ( rotation = 60 )
plt . ylim ( ylim )
xlim = axes . get_xlim ( )
plt . xlim (... |
def concatmap ( source , func , * more_sources , task_limit = None ) :
"""Apply a given function that creates a sequence from the elements of one
or several asynchronous sequences , and generate the elements of the created
sequences in order .
The function is applied as described in ` map ` , and must return ... | return concat . raw ( combine . smap . raw ( source , func , * more_sources ) , task_limit = task_limit ) |
def build ( tagname_or_element , ns_uri = None , adapter = None ) :
"""Return a : class : ` ~ xml4h . builder . Builder ` that represents an element in
a new or existing XML DOM and provides " chainable " methods focussed
specifically on adding XML content .
: param tagname _ or _ element : a string name for ... | if adapter is None :
adapter = best_adapter
if isinstance ( tagname_or_element , basestring ) :
doc = adapter . create_document ( tagname_or_element , ns_uri = ns_uri )
element = doc . root
elif isinstance ( tagname_or_element , xml4h . nodes . Element ) :
element = tagname_or_element
else :
raise x... |
def get_unique_sample_files ( file_samples ) :
"""Filter file _ sample data frame to only keep one file per sample .
Params
file _ samples : ` pandas . DataFrame `
A data frame containing a mapping between file IDs and sample barcodes .
This type of data frame is returned by : meth : ` get _ file _ samples ... | assert isinstance ( file_samples , pd . DataFrame )
df = file_samples
# use shorter variable name
# sort data frame by file ID
df = df . sort_values ( 'file_id' )
# - some samples have multiple files with the same barcode ,
# corresponding to different aliquots
# get rid of those duplicates
logger . info ( 'Original nu... |
def quickVisual ( G , showLabel = False ) :
"""Just makes a simple _ matplotlib _ figure and displays it , with each node coloured by its type . You can add labels with _ showLabel _ . This looks a bit nicer than the one provided my _ networkx _ ' s defaults .
# Parameters
_ showLabel _ : ` optional [ bool ] ` ... | colours = "brcmykwg"
f = plt . figure ( 1 )
ax = f . add_subplot ( 1 , 1 , 1 )
ndTypes = [ ]
ndColours = [ ]
layout = nx . spring_layout ( G , k = 4 / math . sqrt ( len ( G . nodes ( ) ) ) )
for nd in G . nodes ( data = True ) :
if 'type' in nd [ 1 ] :
if nd [ 1 ] [ 'type' ] not in ndTypes :
ndT... |
def almost_equal ( self , mat2 , places = 7 ) :
"""Return True if the values in mat2 equal the values in this
matrix .""" | if not hasattr ( mat2 , "data" ) :
return False
for i in range ( 4 ) :
if not ( _float_almost_equal ( self . data [ i ] [ 0 ] , mat2 . data [ i ] [ 0 ] , places ) and _float_almost_equal ( self . data [ i ] [ 1 ] , mat2 . data [ i ] [ 1 ] , places ) and _float_almost_equal ( self . data [ i ] [ 2 ] , mat2 . dat... |
def run ( self ) :
"""Perform phantomas run""" | self . _logger . info ( "running for <{url}>" . format ( url = self . _url ) )
args = format_args ( self . _options )
self . _logger . debug ( "command: `{cmd}` / args: {args}" . format ( cmd = self . _cmd , args = args ) )
# run the process
try :
process = Popen ( args = [ self . _cmd ] + args , stdin = PIPE , std... |
def get_file_download ( self , file_id ) :
"""Get a file download object that contains temporary url settings needed to download the contents of a file .
: param file _ id : str : uuid of the file
: return : FileDownload""" | return self . _create_item_response ( self . data_service . get_file_url ( file_id ) , FileDownload ) |
def instantiate_object_id_field ( object_id_class_or_tuple = models . TextField ) :
"""Instantiates and returns a model field for FieldHistory . object _ id .
object _ id _ class _ or _ tuple may be either a Django model field class or a
tuple of ( model _ field , kwargs ) , where kwargs is a dict passed to
m... | if isinstance ( object_id_class_or_tuple , ( list , tuple ) ) :
object_id_class , object_id_kwargs = object_id_class_or_tuple
else :
object_id_class = object_id_class_or_tuple
object_id_kwargs = { }
if not issubclass ( object_id_class , models . fields . Field ) :
raise TypeError ( 'settings.%s must be ... |
def centerdistance ( image , voxelspacing = None , mask = slice ( None ) ) :
r"""Takes a simple or multi - spectral image and returns its voxel - wise center distance in
mm . A multi - spectral image must be supplied as a list or tuple of its spectra .
Optionally a binary mask can be supplied to select the voxe... | if type ( image ) == tuple or type ( image ) == list :
image = image [ 0 ]
return _extract_feature ( _extract_centerdistance , image , mask , voxelspacing = voxelspacing ) |
def multiple_devices_data_message ( self , registration_ids = None , condition = None , collapse_key = None , delay_while_idle = False , time_to_live = None , restricted_package_name = None , low_priority = False , dry_run = False , data_message = None , content_available = None , timeout = 5 , extra_notification_kwarg... | if not isinstance ( registration_ids , list ) :
raise InvalidDataError ( 'Invalid registration IDs (should be list)' )
payloads = [ ]
registration_id_chunks = self . registration_id_chunks ( registration_ids )
for registration_ids in registration_id_chunks : # appends a payload with a chunk of registration ids here... |
def double ( self ) :
"""Doubles this point .
Returns :
JacobianPoint : The point corresponding to ` 2 * self ` .""" | X1 , Y1 , Z1 = self . X , self . Y , self . Z
if Y1 == 0 :
return POINT_AT_INFINITY
S = ( 4 * X1 * Y1 ** 2 ) % self . P
M = ( 3 * X1 ** 2 + self . a * Z1 ** 4 ) % self . P
X3 = ( M ** 2 - 2 * S ) % self . P
Y3 = ( M * ( S - X3 ) - 8 * Y1 ** 4 ) % self . P
Z3 = ( 2 * Y1 * Z1 ) % self . P
return JacobianPoint ( X3 , ... |
def Softsign ( a ) :
"""Softsign op .""" | return np . divide ( a , np . add ( np . abs ( a ) , 1 ) ) , |
def get_new_client ( request_session = False ) :
"""Return a new ConciergeClient , pulling secrets from the environment .""" | from . client import ConciergeClient
client = ConciergeClient ( access_key = os . environ [ "MS_ACCESS_KEY" ] , secret_key = os . environ [ "MS_SECRET_KEY" ] , association_id = os . environ [ "MS_ASSOCIATION_ID" ] )
if request_session :
client . request_session ( )
return client |
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