signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
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def sendmail_proxy ( subject , email , template , ** context ) :
"""Cast the lazy _ gettext ' ed subject to string before passing to Celery""" | sendmail . delay ( subject . value , email , template , ** context ) |
def get ( self ) :
"""Get a JSON - ready representation of this BCCSettings .
: returns : This BCCSettings , ready for use in a request body .
: rtype : dict""" | bcc_settings = { }
if self . enable is not None :
bcc_settings [ "enable" ] = self . enable
if self . email is not None :
bcc_settings [ "email" ] = self . email . get ( )
return bcc_settings |
def verifybamid_table ( self ) :
"""Create a table with all the columns from verify BAM ID""" | # create an ordered dictionary to preserve the order of columns
headers = OrderedDict ( )
# add each column and the title and description ( taken from verifyBAMID website )
headers [ 'RG' ] = { 'title' : 'Read Group' , 'description' : 'ReadGroup ID of sequenced lane.' , 'hidden' : all ( [ s [ 'RG' ] == 'ALL' for s in s... |
def calculate_positions ( positions ) :
"""Calculates position information""" | current_position = { 'data-x' : 0 , 'data-y' : 0 , 'data-z' : 0 , 'data-rotate-x' : 0 , 'data-rotate-y' : 0 , 'data-rotate-z' : 0 , 'data-scale' : 1 , }
positer = iter ( positions )
position = next ( positer )
_update_position ( current_position , position )
while True :
if 'path' in position : # Start of a new pat... |
def _wavGetInfo ( f : Union [ IO , str ] ) -> Tuple [ SndInfo , Dict [ str , Any ] ] :
"""Read the info of a wav file . taken mostly from scipy . io . wavfile
if extended : returns also fsize and bigendian""" | if isinstance ( f , ( str , bytes ) ) :
f = open ( f , 'rb' )
needsclosing = True
else :
needsclosing = False
fsize , bigendian = _wavReadRiff ( f )
fmt = ">i" if bigendian else "<i"
while ( f . tell ( ) < fsize ) :
chunk_id = f . read ( 4 )
if chunk_id == b'fmt ' :
chunksize , sampfmt , cha... |
def main ( prog_args = None ) :
"""What do you expect ?""" | if prog_args is None :
prog_args = sys . argv
parser = optparse . OptionParser ( )
parser . usage = """Usage: %[prog] [options] [<path>]"""
parser . add_option ( "-t" , "--test-program" , dest = "test_program" , default = "nose" , help = "specifies the test-program to use. Valid values" " include `nose` (or `nosete... |
def map2salm ( map , s , lmax ) :
"""Convert values of spin - weighted function on a grid to mode weights
Parameters
map : array _ like , complex , shape ( . . . , Ntheta , Nphi )
Values of the spin - weighted function on grid points of the sphere . This array may have more
than two dimensions , where initi... | import numpy as np
map = np . ascontiguousarray ( map , dtype = np . complex128 )
salm = np . empty ( map . shape [ : - 2 ] + ( N_lm ( lmax ) , ) , dtype = np . complex128 )
if map . ndim > 2 :
s = np . ascontiguousarray ( s , dtype = np . intc )
if s . ndim != map . ndim - 2 or np . product ( s . shape ) != np... |
def DeregisterDefinition ( self , artifact_definition ) :
"""Deregisters an artifact definition .
Artifact definitions are identified based on their lower case name .
Args :
artifact _ definition ( ArtifactDefinition ) : an artifact definition .
Raises :
KeyError : if an artifact definition is not set for... | artifact_definition_name = artifact_definition . name . lower ( )
if artifact_definition_name not in self . _artifact_definitions :
raise KeyError ( 'Artifact definition not set for name: {0:s}.' . format ( artifact_definition . name ) )
del self . _artifact_definitions [ artifact_definition_name ] |
def bed ( args ) :
"""% prog bed bedfile bamfiles
Convert bam files to bed .""" | p = OptionParser ( bed . __doc__ )
opts , args = p . parse_args ( args )
if len ( args ) < 2 :
sys . exit ( not p . print_help ( ) )
bedfile = args [ 0 ]
bamfiles = args [ 1 : ]
for bamfile in bamfiles :
cmd = "bamToBed -i {0}" . format ( bamfile )
sh ( cmd , outfile = bedfile , append = True ) |
def deleteUnused ( self ) :
"""Delete any old snapshots in path , if not kept .""" | ( count , size ) = ( 0 , 0 )
for ( diff , path ) in self . extraKeys . items ( ) :
if path . startswith ( "/" ) :
continue
keyName = self . _keyName ( diff . toUUID , diff . fromUUID , path )
count += 1
size += diff . size
if self . _skipDryRun ( logger , 'INFO' ) ( "Trash: %s" , diff ) :
... |
def _is_missing_tags_strict ( self ) :
"""Return whether missing _ tags is set to strict .""" | val = self . missing_tags
if val == MissingTags . strict :
return True
elif val == MissingTags . ignore :
return False
raise Exception ( "Unsupported 'missing_tags' value: %s" % repr ( val ) ) |
def set_min_level_to_save ( self , level ) :
"""Allow to change save level after creation""" | self . min_log_level_to_save = level
handler_class = logging . handlers . TimedRotatingFileHandler
self . _set_min_level ( handler_class , level ) |
def add ( self , anchor ) :
"""Add a new anchor to the repository .
This will create a new ID for the anchor and provision new storage for
it .
Returns : The storage ID for the Anchor which can be used to retrieve
the anchor later .""" | anchor_id = uuid . uuid4 ( ) . hex
anchor_path = self . _anchor_path ( anchor_id )
with anchor_path . open ( mode = 'wt' ) as f :
save_anchor ( f , anchor , self . root )
return anchor_id |
def reassign_label ( cls , destination_cluster , label ) :
"""Reassign a label from one cluster to another .
Args :
` destination _ cluster ` : id / label of the cluster to move the label to
` label ` : label to be moved from the source cluster""" | conn = Qubole . agent ( version = Cluster . api_version )
data = { "destination_cluster" : destination_cluster , "label" : label }
return conn . put ( cls . rest_entity_path + "/reassign-label" , data ) |
def acquire_lock ( self ) :
"""Acquire the global lock for the root directory associated with this context . When
a goal requires serialization , it will call this to acquire the lock .
: API : public""" | if self . options . for_global_scope ( ) . lock :
if not self . _lock . acquired :
self . _lock . acquire ( ) |
def _rm_parse_header_line ( parts , meta_data ) :
"""parse a repeatmasker alignment header line and place the extracted meta - data
into the provided dictionary . An example header line is : :
239 29.42 1.92 0.97 chr1 11 17 ( 41 ) C XX # YY ( 74 ) 104 1 m _ b1s502i1 4
If the alignment is to the consensus , th... | meta_data [ ALIG_SCORE_KEY ] = parts [ 0 ]
meta_data [ PCENT_SUBS_KEY ] = float ( parts [ 1 ] )
meta_data [ PCENT_S1_INDELS_KEY ] = float ( parts [ 2 ] )
meta_data [ PCENT_S2_INDELS_KEY ] = float ( parts [ 3 ] )
meta_data [ ANNOTATION_KEY ] = ""
if parts [ 8 ] == "C" :
meta_data [ UNKNOWN_RM_HEADER_FIELD_KEY ] = pa... |
def make_gaussian_sources_image ( shape , source_table , oversample = 1 ) :
"""Make an image containing 2D Gaussian sources .
Parameters
shape : 2 - tuple of int
The shape of the output 2D image .
source _ table : ` ~ astropy . table . Table `
Table of parameters for the Gaussian sources . Each row of the... | model = Gaussian2D ( x_stddev = 1 , y_stddev = 1 )
if 'x_stddev' in source_table . colnames :
xstd = source_table [ 'x_stddev' ]
else :
xstd = model . x_stddev . value
# default
if 'y_stddev' in source_table . colnames :
ystd = source_table [ 'y_stddev' ]
else :
ystd = model . y_stddev . value
# def... |
def save ( self ) :
"""save or update this entity on Ariane server
: return :""" | LOGGER . debug ( "InjectorUITreeEntity.save" )
if self . id and self . value and self . type :
ok = True
if InjectorUITreeService . find_ui_tree_entity ( self . id ) is None : # SAVE
self_string = str ( self . injector_ui_tree_menu_entity_2_json ( ignore_genealogy = True ) ) . replace ( "'" , '"' )
... |
def geneinfo ( args ) :
"""% prog geneinfo pineapple . 20141004 . bed liftover . bed pineapple . 20150413 . bed note . txt interproscan . txt
Build gene info table from various sources . The three beds contain
information on the original scaffolds , linkage groups , and final selected
loci ( after removal of ... | p = OptionParser ( geneinfo . __doc__ )
opts , args = p . parse_args ( args )
if len ( args ) != 5 :
sys . exit ( not p . print_help ( ) )
scfbed , liftoverbed , lgbed , note , ipr = args
note = DictFile ( note , delimiter = "\t" )
scfbed = Bed ( scfbed )
lgorder = Bed ( lgbed ) . order
liftover = Bed ( liftoverbed... |
def _register_handler ( event , fun , external = False ) :
"""Register a function to be an event handler""" | registry = core . HANDLER_REGISTRY
if external :
registry = core . EXTERNAL_HANDLER_REGISTRY
if not isinstance ( event , basestring ) : # If not basestring , it is a BaseEvent subclass .
# This occurs when class methods are registered as handlers
event = core . parse_event_to_name ( event )
if event in registry... |
def set_sequestered ( self , sequestered ) :
"""Sets the sequestered flag .
arg : sequestered ( boolean ) : the new sequestered flag
raise : InvalidArgument - ` ` sequestered ` ` is invalid
raise : NoAccess - ` ` Metadata . isReadOnly ( ) ` ` is ` ` true ` `
* compliance : mandatory - - This method must be ... | if sequestered is None :
raise errors . NullArgument ( )
if self . get_sequestered_metadata ( ) . is_read_only ( ) :
raise errors . NoAccess ( )
if not isinstance ( sequestered , bool ) :
raise errors . InvalidArgument ( )
self . _my_map [ 'sequestered' ] = sequestered |
def to_sint ( self ) :
"""Converts the word to a BinInt , treating it as a signed number .""" | if self . _width == 0 :
return BinInt ( 0 )
sbit = 1 << ( self . _width - 1 )
return BinInt ( ( self . _val - sbit ) ^ - sbit ) |
def validate_wrap ( self , value ) :
'''Checks that value is a ` ` dict ` ` , that every key is a valid MongoDB
key , and that every value validates based on DictField . value _ type''' | if not isinstance ( value , dict ) :
self . _fail_validation_type ( value , dict )
for k , v in value . items ( ) :
self . _validate_key_wrap ( k )
try :
self . value_type . validate_wrap ( v )
except BadValueException as bve :
self . _fail_validation ( value , 'Bad value for key %s' % k... |
def read_magic_file ( self , path , sort_by_this_name ) :
"""reads a magic formated data file from path and sorts the keys
according to sort _ by _ this _ name
Parameters
path : path to file to read
sort _ by _ this _ name : variable to sort data by""" | DATA = { }
try :
with open ( path , 'r' ) as finput :
lines = list ( finput . readlines ( ) [ 1 : ] )
except FileNotFoundError :
return [ ]
# fin = open ( path , ' r ' )
# fin . readline ( )
line = lines [ 0 ]
header = line . strip ( '\n' ) . split ( '\t' )
error_strings = [ ]
for line in lines [ 1 : ] ... |
def status_reblogged_by ( self , id ) :
"""Fetch a list of users that have reblogged a status .
Does not require authentication for publicly visible statuses .
Returns a list of ` user dicts ` _ .""" | id = self . __unpack_id ( id )
url = '/api/v1/statuses/{0}/reblogged_by' . format ( str ( id ) )
return self . __api_request ( 'GET' , url ) |
def graph_from_incidence_matrix ( matrix , node_prefix = '' , directed = False ) :
"""Creates a basic graph out of an incidence matrix .
The matrix has to be a list of rows of values
representing an incidence matrix .
The values can be anything : bool , int , float , as long
as they can evaluate to True or ... | if directed :
graph = Dot ( graph_type = 'digraph' )
else :
graph = Dot ( graph_type = 'graph' )
for row in matrix :
nodes = [ ]
c = 1
for node in row :
if node :
nodes . append ( c * node )
c += 1
nodes . sort ( )
if len ( nodes ) == 2 :
graph . add_edge ... |
def get_assets_by_search ( self , asset_query , asset_search ) :
"""Gets the search results matching the given search query using the given search .
arg : asset _ query ( osid . repository . AssetQuery ) : the asset
query
arg : asset _ search ( osid . repository . AssetSearch ) : the asset
search
return :... | # Implemented from template for
# osid . resource . ResourceSearchSession . get _ resources _ by _ search _ template
# Copied from osid . resource . ResourceQuerySession . get _ resources _ by _ query _ template
and_list = list ( )
or_list = list ( )
for term in asset_query . _query_terms :
and_list . append ( { te... |
def flexifunction_read_req_send ( self , target_system , target_component , read_req_type , data_index , force_mavlink1 = False ) :
'''Reqest reading of flexifunction data
target _ system : System ID ( uint8 _ t )
target _ component : Component ID ( uint8 _ t )
read _ req _ type : Type of flexifunction data r... | return self . send ( self . flexifunction_read_req_encode ( target_system , target_component , read_req_type , data_index ) , force_mavlink1 = force_mavlink1 ) |
def SVD ( stream_list , full = False ) :
"""Depreciated . Use svd .""" | warnings . warn ( 'Depreciated, use svd instead.' )
return svd ( stream_list = stream_list , full = full ) |
def importData ( directory ) :
"""Parse the input files and return two dictionnaries""" | dataTask = OrderedDict ( )
dataQueue = OrderedDict ( )
for fichier in sorted ( os . listdir ( directory ) ) :
try :
with open ( "{directory}/{fichier}" . format ( ** locals ( ) ) , 'rb' ) as f :
fileName , fileType = fichier . rsplit ( '-' , 1 )
if fileType == "QUEUE" :
... |
def _set_area ( self , v , load = False ) :
"""Setter method for area , mapped from YANG variable / routing _ system / interface / ve / ip / interface _ vlan _ ospf _ conf / ospf1 / area ( ospf - area - id )
If this variable is read - only ( config : false ) in the
source YANG file , then _ set _ area is consid... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = RestrictedClassType ( base_type = unicode , restriction_dict = { 'pattern' : u'((([0-9]|[1-9][0-9]|1[0-9][0-9]|2[0-4][0-9]|25[0-5])\\.)(([0-9]|[1-9][0-9]|1[0-9][0-9]|2[0-4][0-9]|25[0-5])\\.){2}([0-9]|[1-9][0-9]|1[0-9][0-9]|2[... |
def set_folder ( self , folder = 'assets' ) :
"""Changes the file folder to look at
: param folder : str [ images , assets ]
: return : None""" | folder = folder . replace ( '/' , '.' )
self . _endpoint = 'files/{folder}' . format ( folder = folder ) |
def load ( self , id_code ) :
"""Loads a workflow identified by id _ code
id _ code - unique identifier , previously must have called save with same id _ code""" | filestream = open ( '{0}/{1}' . format ( self . data_path , id_code ) , 'rb' )
workflow = pickle . load ( filestream )
return workflow |
def doControl ( self , controlCode , bytes = [ ] ) :
"""Transmit a control command to the reader and return response .
controlCode : control command
bytes : command data to transmit ( list of bytes )
return : response are the response bytes ( if any )""" | CardConnection . doControl ( self , controlCode , bytes )
hresult , response = SCardControl ( self . hcard , controlCode , bytes )
if hresult != 0 :
raise SmartcardException ( 'Failed to control ' + SCardGetErrorMessage ( hresult ) )
data = [ ( x + 256 ) % 256 for x in response ]
return list ( data ) |
def resolve_aliases ( self , chunks ) :
'''Preserve backward compatibility by rewriting the ' state ' key in the low
chunks if it is using a legacy type .''' | for idx , _ in enumerate ( chunks ) :
new_state = self . aliases . get ( chunks [ idx ] [ 'state' ] )
if new_state is not None :
chunks [ idx ] [ 'state' ] = new_state |
def from_bytes ( self , raw ) :
'''Return an Ethernet object reconstructed from raw bytes , or an
Exception if we can ' t resurrect the packet .''' | if len ( raw ) < UDP . _MINLEN :
raise NotEnoughDataError ( "Not enough bytes ({}) to reconstruct an UDP object" . format ( len ( raw ) ) )
fields = struct . unpack ( UDP . _PACKFMT , raw [ : UDP . _MINLEN ] )
self . _src = fields [ 0 ]
self . _dst = fields [ 1 ]
self . _len = fields [ 2 ]
self . _checksum = fields... |
def get_message_id ( self ) :
"""Method to get messageId of group created .""" | message_id = self . json_response . get ( "messageId" , None )
self . logger . info ( "%s\t%s" % ( self . request_method , self . request_url ) )
return message_id |
def gen_age ( output , ascii_props = False , append = False , prefix = "" ) :
"""Generate ` age ` property .""" | obj = { }
all_chars = ALL_ASCII if ascii_props else ALL_CHARS
with codecs . open ( os . path . join ( HOME , 'unicodedata' , UNIVERSION , 'DerivedAge.txt' ) , 'r' , 'utf-8' ) as uf :
for line in uf :
if not line . startswith ( '#' ) :
data = line . split ( '#' ) [ 0 ] . split ( ';' )
... |
def urlopen ( self , method , url , ** kw ) :
"Same as HTTP ( S ) ConnectionPool . urlopen , ` ` url ` ` must be absolute ." | kw [ 'assert_same_host' ] = False
return self . proxy_pool . urlopen ( method , url , ** kw ) |
def update_vm_result ( self , context , msg ) :
"""Update VM ' s result field in the DB .
The result reflects the success of failure of operation when an
agent processes the vm info .""" | args = jsonutils . loads ( msg )
agent = context . get ( 'agent' )
port_id = args . get ( 'port_uuid' )
result = args . get ( 'result' )
LOG . debug ( 'update_vm_result received from %(agent)s: ' '%(port_id)s %(result)s' , { 'agent' : agent , 'port_id' : port_id , 'result' : result } )
# Add the request into queue for ... |
def buildTables ( self ) :
"""Compile OpenType feature tables from the source .
Raises a FeaLibError if the feature compilation was unsuccessful .
* * This should not be called externally . * * Subclasses
may override this method to handle the table compilation
in a different way if desired .""" | if not self . features :
return
# the path is used by the lexer to follow ' include ' statements ;
# if we generated some automatic features , includes have already been
# resolved , and we work from a string which does ' t exist on disk
path = self . ufo . path if not self . featureWriters else None
try :
addO... |
def add_data_set ( self , data , series_type = "line" , name = None , ** kwargs ) :
"""set data for series option in highcharts""" | self . data_set_count += 1
if not name :
name = "Series %d" % self . data_set_count
kwargs . update ( { 'name' : name } )
if series_type == 'treemap' :
self . add_JSsource ( 'http://code.highcharts.com/modules/treemap.js' )
series_data = Series ( data , series_type = series_type , ** kwargs )
series_data . __op... |
def to_json ( record , extraneous = True , prop = None ) :
"""JSON conversion function : a ' visitor ' function which implements marshall
out ( to JSON data form ) , honoring JSON property types / hints but does not
require them . To convert to an actual JSON document , pass the return value
to ` ` json . dum... | if prop :
if isinstance ( prop , basestring ) :
prop = type ( record ) . properties [ prop ]
val = prop . __get__ ( record )
if hasattr ( prop , "to_json" ) :
return prop . to_json ( val , extraneous , _json_data )
else :
return _json_data ( val , extraneous )
elif isinstance ( r... |
def _check_avail ( cmd ) :
'''Check to see if the given command can be run''' | if isinstance ( cmd , list ) :
cmd = ' ' . join ( [ six . text_type ( x ) if not isinstance ( x , six . string_types ) else x for x in cmd ] )
bret = True
wret = False
if __salt__ [ 'config.get' ] ( 'cmd_blacklist_glob' ) :
blist = __salt__ [ 'config.get' ] ( 'cmd_blacklist_glob' , [ ] )
for comp in blist :... |
def apply_modification ( self ) :
"""Modifications on the right side need to be committed""" | self . __changing_model = True
if self . adding_model :
self . model . add ( self . adding_model )
elif self . editing_model and self . editing_iter : # notifies the currencies model
path = self . model . get_path ( self . editing_iter )
self . model . row_changed ( path , self . editing_iter )
pass
sel... |
def dynacRepresentation ( self ) :
"""Return the Pynac representation of this Set4DAperture instance .""" | details = [ self . energyDefnFlag . val , self . energy . val , self . phase . val , self . x . val , self . y . val , self . radius . val , ]
return [ 'REJECT' , [ details ] ] |
def add_user_email ( self , user , ** kwargs ) :
"""Add a UserEmail object , with properties specified in ` ` * * kwargs ` ` .""" | # If User and UserEmail are separate classes
if self . UserEmailClass :
user_email = self . UserEmailClass ( user = user , ** kwargs )
self . db_adapter . add_object ( user_email )
# If there is only one User class
else :
for key , value in kwargs . items ( ) :
setattr ( user , key , value )
use... |
def requires_swimlane_version ( min_version = None , max_version = None ) :
"""Decorator for SwimlaneResolver methods verifying Swimlane server build version is within a given inclusive range
Raises :
InvalidVersion : Raised before decorated method call if Swimlane server version is out of provided range
Valu... | if min_version is None and max_version is None :
raise ValueError ( 'Must provide either min_version, max_version, or both' )
if min_version and max_version and compare_versions ( min_version , max_version ) < 0 :
raise ValueError ( 'min_version must be <= max_version ({}, {})' . format ( min_version , max_vers... |
def autogroups_states_changed ( sender , instance , action , reverse , model , pk_set , * args , ** kwargs ) :
"""Trigger group membership update when a state is added or removed from
an autogroup config .""" | if action . startswith ( 'post_' ) :
for pk in pk_set :
try :
state = State . objects . get ( pk = pk )
instance . update_group_membership_for_state ( state )
except State . DoesNotExist : # Deleted States handled by the profile state change
pass |
def horizontal_infrared_radiation_intensity ( self , value = 9999.0 ) :
"""Corresponds to IDD Field ` horizontal _ infrared _ radiation _ intensity `
Args :
value ( float ) : value for IDD Field ` horizontal _ infrared _ radiation _ intensity `
Unit : Wh / m2
value > = 0.0
Missing value : 9999.0
if ` va... | if value is not None :
try :
value = float ( value )
except ValueError :
raise ValueError ( 'value {} need to be of type float ' 'for field `horizontal_infrared_radiation_intensity`' . format ( value ) )
if value < 0.0 :
raise ValueError ( 'value need to be greater or equal 0.0 ' 'fo... |
def _getproject ( self , config , section , ** kwargs ) :
"""Creates a VSG project from a configparser instance .
: param object config : The instance of the configparser class
: param str section : The section name to read .
: param kwargs : List of additional keyworded arguments to be passed into the VSGPro... | if section not in config :
raise ValueError ( 'Section [{}] not found in [{}]' . format ( section , ', ' . join ( config . sections ( ) ) ) )
type = config . get ( section , 'type' , fallback = None )
if not type :
raise ValueError ( 'Section [{}] mandatory option "{}" not found' . format ( section , "type" ) )... |
def exception_to_unicode ( e , traceback = False ) :
"""Convert an ` Exception ` to an ` unicode ` object .
In addition to ` to _ unicode ` , this representation of the exception
also contains the class name and optionally the traceback .""" | message = '%s: %s' % ( e . __class__ . __name__ , to_unicode ( e ) )
if traceback :
from docido_sdk . toolbox import get_last_traceback
traceback_only = get_last_traceback ( ) . split ( '\n' ) [ : - 2 ]
message = '\n%s\n%s' % ( to_unicode ( '\n' . join ( traceback_only ) ) , message )
return message |
def skip_storing_namespace ( self , namespace : Optional [ str ] ) -> bool :
"""Check if the namespace should be skipped .
: param namespace : The keyword of the namespace to check .""" | return ( namespace is not None and namespace in self . namespace_url and self . namespace_url [ namespace ] in self . uncached_namespaces ) |
def get_kb_mapping ( kb_name = "" , key = "" , value = "" , match_type = "e" , default = "" , limit = None ) :
"""Get one unique mapping . If not found , return default .
: param kb _ name : the name of the kb
: param key : include only lines matching this on left side in the results
: param value : include o... | mappings = get_kb_mappings ( kb_name , key = key , value = value , match_type = match_type , limit = limit )
if len ( mappings ) == 0 :
return default
else :
return mappings [ 0 ] |
def stage_subset ( self , * files_to_add : str ) :
"""Stages a subset of files
: param files _ to _ add : files to stage
: type files _ to _ add : str""" | LOGGER . info ( 'staging files: %s' , files_to_add )
self . repo . git . add ( * files_to_add , A = True ) |
def add_config_file ( self , config_filename ) :
"""Parses the content . types file and updates the content types database .
: param config _ filename :
The path to the configuration file .""" | with open ( config_filename , 'rb' ) as f :
content = f . read ( )
config = yaml . load ( content )
self . add_config ( config , config_filename ) |
def complete_definition ( subj : Node , source_graph : Graph , target_graph : Optional [ Graph ] = None ) -> PrettyGraph :
"""Return the transitive closure of subject .
: param subj : URI or BNode for subject
: param source _ graph : Graph containing defininition
: param target _ graph : return graph ( for re... | if target_graph is None :
target_graph = PrettyGraph ( )
for p , o in source_graph . predicate_objects ( subj ) :
target_graph . add ( ( subj , p , o ) )
if isinstance ( o , BNode ) :
complete_definition ( o , source_graph , target_graph )
return target_graph |
def polygon_diameter ( points ) :
'''Compute the maximun euclidian distance between any two points
in a list of points''' | return max ( point_dist ( p0 , p1 ) for ( p0 , p1 ) in combinations ( points , 2 ) ) |
def query_position ( self , strand , chr , genome_coord ) :
"""Provides the relative position on the coding sequence for a given
genomic position .
Parameters
chr : str
chromosome , provided to check validity of query
genome _ coord : int
0 - based position for mutation , actually used to get relative c... | # first check if valid
pos = None
# initialize to invalid pos
if chr != self . chrom : # logger . debug ( ' Wrong chromosome queried . You provided { 0 } but gene is '
# ' on { 1 } . ' . format ( chr , self . chrom ) )
# return pos
pass
if type ( genome_coord ) is list : # handle case for indels
pos_left = self... |
def elem_find ( self , field , value ) :
"""Return the indices of elements whose field first satisfies the given values
` ` value ` ` should be unique in self . field .
This function does not check the uniqueness .
: param field : name of the supplied field
: param value : value of field of the elemtn to fi... | if isinstance ( value , ( int , float , str ) ) :
value = [ value ]
f = list ( self . __dict__ [ field ] )
uid = np . vectorize ( f . index ) ( value )
return self . get_idx ( uid ) |
def cli ( ctx , group_id , new_name ) :
"""Update the name of a group
Output :
a dictionary containing group information""" | return ctx . gi . groups . update_group ( group_id , new_name ) |
def read_table ( filename , usecols = ( 0 , 1 ) , sep = '\t' , comment = '#' , encoding = 'utf-8' , skip = 0 ) :
"""Parse data files from the data directory
Parameters
filename : string
Full path to file
usecols : list , default [ 0 , 1]
A list of two elements representing the columns to be parsed into a ... | with io . open ( filename , 'r' , encoding = encoding ) as f : # skip initial lines
for _ in range ( skip ) :
next ( f )
# filter comment lines
lines = ( line for line in f if not line . startswith ( comment ) )
d = dict ( )
for line in lines :
columns = line . split ( sep )
... |
def create_record ( self , bucket_name , record_key , record_data , record_metadata = None , record_mimetype = '' , record_encoding = '' , overwrite = True ) :
'''a method for adding a record to an S3 bucket
: param bucket _ name : string with name of bucket
: param record _ key : string with name of key ( path... | title = '%s.create_record' % self . __class__ . __name__
import sys
from hashlib import md5
from base64 import b64encode
# define size limitations
metadata_max = self . fields . metadata [ 'limits' ] [ 'metadata_max_bytes' ]
record_max = self . fields . metadata [ 'limits' ] [ 'record_max_bytes' ]
record_optimal = self... |
def update ( preset , clean ) :
"""Update a local preset
This command will cause ` be ` to pull a preset already
available locally .
Usage :
$ be update ad
Updating " ad " . .""" | if self . isactive ( ) :
lib . echo ( "ERROR: Exit current project first" )
sys . exit ( lib . USER_ERROR )
presets = _extern . github_presets ( )
if preset not in presets :
sys . stdout . write ( "\"%s\" not found" % preset )
sys . exit ( lib . USER_ERROR )
lib . echo ( "Are you sure you want to update... |
def webui_data_stores_data_store_value ( self , ** kwargs ) :
"""Auto Generated Code""" | config = ET . Element ( "config" )
webui = ET . SubElement ( config , "webui" , xmlns = "http://tail-f.com/ns/webui" )
data_stores = ET . SubElement ( webui , "data-stores" )
data_store = ET . SubElement ( data_stores , "data-store" )
key_key = ET . SubElement ( data_store , "key" )
key_key . text = kwargs . pop ( 'key... |
def sync_file ( self , clusters ) :
"""Generates new HAProxy config file content and writes it to the
file at ` haproxy _ config _ path ` .
If a restart is not necessary the nodes configured in HAProxy will
be synced on the fly . If a restart * is * necessary , one will be
triggered .""" | logger . info ( "Updating HAProxy config file." )
if not self . restart_required :
self . sync_nodes ( clusters )
version = self . control . get_version ( )
with open ( self . haproxy_config_path , "w" ) as f :
f . write ( self . config_file . generate ( clusters , version = version ) )
if self . restart_requir... |
def intty ( cls ) :
"""Check if we are in a tty .""" | # XXX : temporary hack until we can detect if we are in a pipe or not
return True
if hasattr ( sys . stdout , 'isatty' ) and sys . stdout . isatty ( ) :
return True
return False |
def location_gmap ( context , location ) :
"""Display a link to Google maps iff we are using WagtailGMaps""" | gmapq = None
if getattr ( MapFieldPanel , "UsingWagtailGMaps" , False ) :
gmapq = location
return { 'gmapq' : gmapq } |
def Boi ( compiler , cont ) :
'''end of parse _ state''' | return il . If ( il . Le ( il . GetItem ( il . parse_state , il . Integer ( 1 ) ) , 0 ) , cont ( TRUE ) , il . failcont ( FALSE ) ) |
def digit ( m : Union [ int , pd . Series ] , n : int ) -> Union [ int , pd . Series ] :
"""Returns the nth digit of each number in m .""" | return ( m // ( 10 ** n ) ) % 10 |
def validate ( self , obj , ** kwargs ) :
"""Check if a thing is a valid date .""" | obj = stringify ( obj )
if obj is None :
return False
return self . DATE_RE . match ( obj ) is not None |
def postinit ( self , type = None , name = None , body = None ) :
"""Do some setup after initialisation .
: param type : The types that the block handles .
: type type : Tuple or NodeNG or None
: param name : The name that the caught exception is assigned to .
: type name : AssignName or None
: param body... | self . type = type
self . name = name
self . body = body |
def send ( self , msg , timeout = None ) :
"""Sends one CAN message .
When a transmission timeout is set the firmware tries to send
a message within this timeout . If it could not be sent the firmware sets
the " auto delete " state . Within this state all transmit CAN messages for
this channel will be delet... | if timeout is not None and timeout >= 0 :
self . _ucan . set_tx_timeout ( self . channel , int ( timeout * 1000 ) )
message = CanMsg ( msg . arbitration_id , MsgFrameFormat . MSG_FF_STD | ( MsgFrameFormat . MSG_FF_EXT if msg . is_extended_id else 0 ) | ( MsgFrameFormat . MSG_FF_RTR if msg . is_remote_frame else 0 )... |
def add_stack_frame ( self , stack_frame ) :
"""Add StackFrame to frames list .""" | if len ( self . stack_frames ) >= MAX_FRAMES :
self . dropped_frames_count += 1
else :
self . stack_frames . append ( stack_frame . format_stack_frame_json ( ) ) |
def matchiter ( r , s , flags = 0 ) :
"""Yields contiguous MatchObjects of r in s .
Raises ValueError if r eventually doesn ' t match contiguously .""" | if isinstance ( r , basestring ) :
r = re . compile ( r , flags )
i = 0
while s :
m = r . match ( s )
g = m and m . group ( 0 )
if not m or not g :
raise ValueError ( "{}: {!r}" . format ( i , s [ : 50 ] ) )
i += len ( g )
s = s [ len ( g ) : ]
yield m |
def list_cards ( self , * args , ** kwargs ) :
"""List the cards of the customer .
: param page : the page number
: type page : int | None
: param per _ page : number of customers per page . It ' s a good practice to increase this number if you know that you
will need a lot of payments .
: type per _ page... | return payplug . Card . list ( self , * args , ** kwargs ) |
def set_mindays ( name , mindays ) :
'''Set the minimum number of days between password changes . See man passwd .
CLI Example :
. . code - block : : bash
salt ' * ' shadow . set _ mindays username 7''' | pre_info = info ( name )
if mindays == pre_info [ 'min' ] :
return True
cmd = 'passwd -n {0} {1}' . format ( mindays , name )
__salt__ [ 'cmd.run' ] ( cmd , python_shell = False )
post_info = info ( name )
if post_info [ 'min' ] != pre_info [ 'min' ] :
return post_info [ 'min' ] == mindays
return False |
def getProperty ( self , orgresource , dummy = 56184 ) :
"""GetProperty
Args :
dummy : ? ? ?
orgresource : File path
Returns :
FileInfo object :
False : Failed to get property""" | url = nurls [ 'getProperty' ]
data = { 'userid' : self . user_id , 'useridx' : self . useridx , 'dummy' : dummy , 'orgresource' : orgresource , }
r = self . session . post ( url = url , data = data )
j = json . loads ( r . text )
if self . resultManager ( r . text ) :
f = FileInfo ( )
result = j [ 'resultvalue'... |
def script_file ( self ) :
"""Returns the startup script file for this VPCS VM .
: returns : path to startup script file""" | # use the default VPCS file if it exists
path = os . path . join ( self . working_dir , 'startup.vpc' )
if os . path . exists ( path ) :
return path
else :
return None |
def _get_all_forecast_from_api ( api_result : dict ) -> OrderedDict :
"""Converts results fråm API to SmhiForeCast list""" | # Total time in hours since last forecast
total_hours_last_forecast = 1.0
# Last forecast time
last_time = None
# Need the ordered dict to get
# the days in order in next stage
forecasts_ordered = OrderedDict ( )
# Get the parameters
for forecast in api_result [ 'timeSeries' ] :
valid_time = datetime . strptime ( f... |
def ptb_producer ( raw_data , batch_size , num_steps , name = None ) :
"""Iterate on the raw PTB data .
This chunks up raw _ data into batches of examples and returns Tensors that
are drawn from these batches .
Args :
raw _ data : one of the raw data outputs from ptb _ raw _ data .
batch _ size : int , th... | with tf . name_scope ( name , "PTBProducer" , [ raw_data , batch_size , num_steps ] ) :
raw_data = tf . convert_to_tensor ( raw_data , name = "raw_data" , dtype = tf . int32 )
data_len = tf . size ( raw_data )
batch_len = data_len // batch_size
data = tf . reshape ( raw_data [ 0 : batch_size * batch_len... |
def mouseUp ( x = None , y = None , button = 'left' , duration = 0.0 , tween = linear , pause = None , _pause = True ) :
"""Performs releasing a mouse button up ( but not down beforehand ) .
The x and y parameters detail where the mouse event happens . If None , the
current mouse position is used . If a float v... | if button not in ( 'left' , 'middle' , 'right' , 1 , 2 , 3 ) :
raise ValueError ( "button argument must be one of ('left', 'middle', 'right', 1, 2, 3), not %s" % button )
_failSafeCheck ( )
x , y = _unpackXY ( x , y )
_mouseMoveDrag ( 'move' , x , y , 0 , 0 , duration = 0 , tween = None )
x , y = platformModule . _... |
def init ( parser = None ) :
"""module needs to be initialized by ' init ' .
Can be called with parser to use a pre - built parser , otherwise
a simple default parser is created""" | global p , subparsers
if parser is None :
p = argparse . ArgumentParser ( )
else :
p = parser
arg = p . add_argument
subparsers = p . add_subparsers ( ) |
def to_string_monkey ( df , highlight_cols = None , latex = False ) :
"""monkey patch to pandas to highlight the maximum value in specified
cols of a row
Example :
> > > from utool . experimental . pandas _ highlight import *
> > > import pandas as pd
> > > df = pd . DataFrame (
> > > np . array ( [ [ 0... | try :
import pandas as pd
import utool as ut
import numpy as np
import six
if isinstance ( highlight_cols , six . string_types ) and highlight_cols == 'all' :
highlight_cols = np . arange ( len ( df . columns ) )
# kwds = dict ( buf = None , columns = None , col _ space = None , header =... |
def synchronize ( self ) :
"""Perform sync of the security groups between ML2 and EOS .""" | # Get expected ACLs and rules
expected_acls = self . get_expected_acls ( )
# Get expected interface to ACL mappings
all_expected_bindings = self . get_expected_bindings ( )
# Check that config is correct on every registered switch
for switch_ip in self . _switches . keys ( ) :
expected_bindings = all_expected_bindi... |
def normalize_frame ( self , module = None , function = None , file = None , line = None , module_offset = None , offset = None , normalized = None , ** kwargs # eat any extra kwargs passed in
) :
"""Normalizes a single frame
Returns a structured conglomeration of the input parameters to serve as
a signature . ... | # If there ' s a cached normalized value , use that so we don ' t spend time
# figuring it out again
if normalized is not None :
return normalized
if function : # If there ' s a filename and it ends in . rs , then normalize using
# Rust rules
if file and ( parse_source_file ( file ) or '' ) . endswith ( '.rs' )... |
def children ( self ) :
"""~ TermList : the children of all the terms in the list .""" | return TermList ( unique_everseen ( y for x in self for y in x . children ) ) |
def get_permissions ( self ) :
""": returns : list of dicts , or an empty list if there are no permissions .""" | path = Client . urls [ 'all_permissions' ]
conns = self . _call ( path , 'GET' )
return conns |
def checkState ( self ) :
"""Returns Qt . Checked or Qt . Unchecked if all children are checked or unchecked , else
returns Qt . PartiallyChecked""" | # commonData = self . childItems [ 0 ] . data if self . childItems else Qt . PartiallyChecked
commonData = None
for child in self . childItems :
if isinstance ( child , BoolCti ) :
if commonData is not None and child . data != commonData :
return Qt . PartiallyChecked
commonData = child ... |
def resetToPreviousLoc ( self ) :
"""Resets the loc of the dragger to place where dragging started .
This could be used in a test situation if the dragger was dragged to an incorrect location .""" | self . rect . left = self . startDraggingX
self . rect . top = self . startDraggingY |
def give_zip_element_z_and_names ( element_name ) :
'''create 2 indexes that , given the name of the element / specie , give the atomic number .''' | # import numpy as np
global z_bismuth
z_bismuth = 83
global z_for_elem
z_for_elem = [ ]
global index_stable
index_stable = [ ]
i_for_stable = 1
i_for_unstable = 0
for i in range ( z_bismuth ) :
z_for_elem . append ( int ( i + 1 ) )
# the only elements below bismuth with no stable isotopes are Tc and Pm
if i... |
def cleanup ( self ) :
"""Release resources used during memory capture""" | if self . sock is not None :
self . sock . close ( )
if self . outfile is not None :
self . outfile . close ( )
if self . bar is not None :
self . update_progress ( complete = True ) |
def describe_all ( self , full = False ) :
"""Prints description information about all tables registered
Args :
full ( bool ) : Also prints description of post processors .""" | for table in self . tabs :
yield self . tabs [ table ] ( ) . describe ( full ) |
def bootstrap_counts ( dtrajs , lagtime , corrlength = None ) :
"""Generates a randomly resampled count matrix given the input coordinates .
See API function for full documentation .""" | from scipy . stats import rv_discrete
# if we have just one trajectory , put it into a one - element list :
if ( isinstance ( dtrajs [ 0 ] , six . integer_types ) ) :
dtrajs = [ dtrajs ]
ntraj = len ( dtrajs )
# can we do the estimate ?
lengths = determine_lengths ( dtrajs )
Lmax = np . max ( lengths )
Ltot = np . ... |
def download_if_not_exists ( url : str , filename : str , skip_cert_verify : bool = True , mkdir : bool = True ) -> None :
"""Downloads a URL to a file , unless the file already exists .""" | if os . path . isfile ( filename ) :
log . info ( "No need to download, already have: {}" , filename )
return
if mkdir :
directory , basename = os . path . split ( os . path . abspath ( filename ) )
mkdir_p ( directory )
download ( url = url , filename = filename , skip_cert_verify = skip_cert_verify ) |
def SURFstar_compute_scores ( inst , attr , nan_entries , num_attributes , mcmap , NN_near , NN_far , headers , class_type , X , y , labels_std , data_type ) :
"""Unique scoring procedure for SURFstar algorithm . Scoring based on nearest neighbors within defined radius , as well as
' anti - scoring ' of far insta... | scores = np . zeros ( num_attributes )
for feature_num in range ( num_attributes ) :
if len ( NN_near ) > 0 :
scores [ feature_num ] += compute_score ( attr , mcmap , NN_near , feature_num , inst , nan_entries , headers , class_type , X , y , labels_std , data_type )
# Note that we are using the near sc... |
def subpoint ( self ) :
"""Return the latitude and longitude directly beneath this position .
Returns a : class : ` ~ skyfield . toposlib . Topos ` whose ` ` longitude ` `
and ` ` latitude ` ` are those of the point on the Earth ' s surface
directly beneath this position , and whose ` ` elevation ` ` is the
... | if self . center != 399 : # TODO : should an _ _ init _ _ ( ) check this ?
raise ValueError ( "you can only ask for the geographic subpoint" " of a position measured from Earth's center" )
t = self . t
xyz_au = einsum ( 'ij...,j...->i...' , t . M , self . position . au )
lat , lon , elevation_m = reverse_terra ( xy... |
def get_internal_classpath_entries_for_targets ( self , targets , respect_excludes = True ) :
"""Gets the internal classpath products for the given targets .
Products are returned in order , optionally respecting target excludes , and the products only
include internal artifact classpath elements ( ie : no reso... | classpath_tuples = self . get_classpath_entries_for_targets ( targets , respect_excludes = respect_excludes )
return [ ( conf , cp_entry ) for conf , cp_entry in classpath_tuples if ClasspathEntry . is_internal_classpath_entry ( cp_entry ) ] |
def ExpandWindowsPath ( cls , path , environment_variables ) :
"""Expands a Windows path containing environment variables .
Args :
path ( str ) : Windows path with environment variables .
environment _ variables ( list [ EnvironmentVariableArtifact ] ) : environment
variables .
Returns :
str : expanded ... | if environment_variables is None :
environment_variables = [ ]
lookup_table = { }
if environment_variables :
for environment_variable in environment_variables :
attribute_name = environment_variable . name . upper ( )
attribute_value = environment_variable . value
if not isinstance ( att... |
def find_grid_embedding ( dim , m , n = None , t = 4 ) :
"""Find an embedding for a grid in a Chimera graph .
Given a target : term : ` Chimera ` graph size , and grid dimensions , attempts to find an embedding .
Args :
dim ( iterable [ int ] ) :
Sizes of each grid dimension . Length can be between 1 and 3.... | m , n , t , target_edges = _chimera_input ( m , n , t , None )
indexer = dnx . generators . chimera . chimera_coordinates ( m , n , t )
dim = list ( dim )
num_dim = len ( dim )
if num_dim == 1 :
def _key ( row , col , aisle ) :
return row
dim . extend ( [ 1 , 1 ] )
elif num_dim == 2 :
def _key ( row... |
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