signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def get_parent_gradebooks ( self , gradebook_id ) :
"""Gets the parents of the given gradebook .
arg : gradebook _ id ( osid . id . Id ) : the ` ` Id ` ` of a gradebook
return : ( osid . grading . GradebookList ) - the parents of the
gradebook
raise : NotFound - ` ` gradebook _ id ` ` is not found
raise :... | # Implemented from template for
# osid . resource . BinHierarchySession . get _ parent _ bins
if self . _catalog_session is not None :
return self . _catalog_session . get_parent_catalogs ( catalog_id = gradebook_id )
return GradebookLookupSession ( self . _proxy , self . _runtime ) . get_gradebooks_by_ids ( list (... |
def instance_for_arguments ( self , arguments : { Prior : float } ) :
"""Create an instance of the associated class for a set of arguments
Parameters
arguments : { Prior : float }
Dictionary mapping _ matrix priors to attribute analysis _ path and value pairs
Returns
An instance of the class""" | for prior , value in arguments . items ( ) :
prior . assert_within_limits ( value )
model_arguments = { t . name : arguments [ t . prior ] for t in self . direct_prior_tuples }
constant_arguments = { t . name : t . constant . value for t in self . direct_constant_tuples }
for tuple_prior in self . tuple_prior_tuple... |
def process_soundcloud ( vargs ) :
"""Main SoundCloud path .""" | artist_url = vargs [ 'artist_url' ]
track_permalink = vargs [ 'track' ]
keep_previews = vargs [ 'keep' ]
folders = vargs [ 'folders' ]
id3_extras = { }
one_track = False
likes = False
client = get_client ( )
if 'soundcloud' not in artist_url . lower ( ) :
if vargs [ 'group' ] :
artist_url = 'https://soundcl... |
def tabSeparatedSummary ( self , sortOn = None ) :
"""Summarize all the alignments for this title as multi - line string with
TAB - separated values on each line .
@ param sortOn : A C { str } attribute to sort titles on . One of ' length ' ,
' maxScore ' , ' medianScore ' , ' readCount ' , or ' title ' .
@... | # The order of the fields returned here is somewhat arbitrary . The
# subject titles are last because they are so variable in length .
# Putting them last makes it more likely that the initial columns in
# printed output will be easier to read down .
# Note that post - processing scripts will be relying on the field
# ... |
def fit ( self , X , y = None ) :
"""Fit a transformation from the pipeline
: param X ( DataSet ) : the data to fit""" | for columns , transformer in self . mapping :
if transformer is not None :
transformer . fit ( self . _get_columns ( X , columns ) )
return self |
def _geocode ( self , pq ) :
""": arg PlaceQuery pq : PlaceQuery object to use for geocoding
: returns : list of location Candidates""" | # : List of desired output fields
# : See ` ESRI docs < https : / / developers . arcgis . com / rest / geocode / api - reference / geocoding - geocode - addresses . htm > _ ` for details
outFields = ( 'Loc_name' , # ' Shape ' ,
'Score' , 'Match_addr' , # based on address standards for the country
# ' Address ' , # retu... |
def js_reverse_inline ( context ) :
"""Outputs a string of javascript that can generate URLs via the use
of the names given to those URLs .""" | if 'request' in context :
default_urlresolver = get_resolver ( getattr ( context [ 'request' ] , 'urlconf' , None ) )
else :
default_urlresolver = get_resolver ( None )
return mark_safe ( generate_js ( default_urlresolver ) ) |
def stripe_to_db ( self , data ) :
"""Convert the raw value to decimal representation .""" | val = data . get ( self . name )
# Note : 0 is a possible return value , which is ' falseish '
if val is not None :
return val / decimal . Decimal ( "100" ) |
def u2open ( self , u2request ) :
"""Open a connection .
@ param u2request : A urllib2 request .
@ type u2request : urllib2 . Requet .
@ return : The opened file - like urllib2 object .
@ rtype : fp""" | tm = self . options . timeout
url = build_opener ( HTTPSClientAuthHandler ( self . context ) )
if self . u2ver ( ) < 2.6 :
socket . setdefaulttimeout ( tm )
return url . open ( u2request )
else :
return url . open ( u2request , timeout = tm ) |
def save ( self , force = False , uuid = False , ** kwargs ) :
"""REPLACES the object in DB . This is forbidden with objects from find ( ) methods unless force = True is given .""" | if not self . _initialized_with_doc and not force :
raise Exception ( "Cannot save a document not initialized from a Python dict. This might remove fields from the DB!" )
self . _initialized_with_doc = False
if '_id' not in self :
if uuid :
self [ '_id' ] = str ( "%s-%s" % ( self . mongokat_collection .... |
def write_keys ( self , records_in , clean = True ) :
"""Write the keywords to the header .
parameters
records : FITSHDR or list or dict
Can be one of these :
- FITSHDR object
- list of dictionaries containing ' name ' , ' value ' and optionally
a ' comment ' field ; the order is preserved .
- a dicti... | if isinstance ( records_in , FITSHDR ) :
hdr = records_in
else :
hdr = FITSHDR ( records_in )
if clean :
is_table = hasattr ( self , '_table_type_str' )
# is _ table = isinstance ( self , TableHDU )
hdr . clean ( is_table = is_table )
for r in hdr . records ( ) :
name = r [ 'name' ] . upper ( )
... |
def task ( func ) :
"""Decorator to run the decorated function as a Task""" | def task_wrapper ( * args , ** kwargs ) :
return spawn ( func , * args , ** kwargs )
return task_wrapper |
def add_to_stmts_rules ( stmts , rules ) :
"""Use by plugins to add extra rules to the existing rules for
a statement .""" | def is_rule_less_than ( ra , rb ) :
rka = ra [ 0 ]
rkb = rb [ 0 ]
if not util . is_prefixed ( rkb ) : # old rule is non - prefixed ; append new rule after
return False
if not util . is_prefixed ( rka ) : # old rule prefixed , but new rule is not , insert
return True
# both are prefix... |
def moments_match_ep ( self , data_i , tau_i , v_i , Y_metadata_i = None ) :
"""Moments match of the marginal approximation in EP algorithm
: param i : number of observation ( int )
: param tau _ i : precision of the cavity distribution ( float )
: param v _ i : mean / variance of the cavity distribution ( fl... | sigma2_hat = 1. / ( 1. / self . variance + tau_i )
mu_hat = sigma2_hat * ( data_i / self . variance + v_i )
sum_var = self . variance + 1. / tau_i
Z_hat = 1. / np . sqrt ( 2. * np . pi * sum_var ) * np . exp ( - .5 * ( data_i - v_i / tau_i ) ** 2. / sum_var )
return Z_hat , mu_hat , sigma2_hat |
def _build_dependent_model_list ( self , obj_schema ) :
'''Helper function to build the list of models the given object schema is referencing .''' | dep_models_list = [ ]
if obj_schema :
obj_schema [ 'type' ] = obj_schema . get ( 'type' , 'object' )
if obj_schema [ 'type' ] == 'array' :
dep_models_list . extend ( self . _build_dependent_model_list ( obj_schema . get ( 'items' , { } ) ) )
else :
ref = obj_schema . get ( '$ref' )
if ref :
ref_... |
def pivot_table ( self , index , columns , values = 'value' , aggfunc = 'count' , fill_value = None , style = None ) :
"""Returns a pivot table
Parameters
index : str or list of strings
rows for Pivot table
columns : str or list of strings
columns for Pivot table
values : str , default ' value '
dataf... | index = [ index ] if isstr ( index ) else index
columns = [ columns ] if isstr ( columns ) else columns
df = self . data
# allow ' aggfunc ' to be passed as string for easier user interface
if isstr ( aggfunc ) :
if aggfunc == 'count' :
df = self . data . groupby ( index + columns , as_index = False ) . cou... |
def constants_pyx ( ) :
"""generate CONST = ZMQ _ CONST and _ _ all _ _ for constants . pxi""" | all_lines = [ ]
assign_lines = [ ]
for name in all_names :
if name == "NULL" : # avoid conflict with NULL in Cython
assign_lines . append ( "globals()['NULL'] = ZMQ_NULL" )
else :
assign_lines . append ( '{0} = ZMQ_{0}' . format ( name ) )
all_lines . append ( ' "{0}",' . format ( name ) )
... |
def _parse_broadcast ( self , msg ) :
"""Given a broacast message , returns the message that was broadcast .""" | # get message , remove surrounding quotes , and unescape
return self . _unescape ( self . _get_type ( msg [ self . broadcast_prefix_len : ] ) ) |
def image_summary ( tag , image ) :
"""Outputs a ` Summary ` protocol buffer with image ( s ) .
Parameters
tag : str
A name for the generated summary . Will also serve as a series name in TensorBoard .
image : MXNet ` NDArray ` or ` numpy . ndarray `
Image data that is one of the following layout : ( H , ... | tag = _clean_tag ( tag )
image = _prepare_image ( image )
image = _make_image ( image )
return Summary ( value = [ Summary . Value ( tag = tag , image = image ) ] ) |
def abstracts ( self , key , value ) :
"""Populate the ` ` abstracts ` ` key .""" | result = [ ]
source = force_single_element ( value . get ( '9' ) )
for a_value in force_list ( value . get ( 'a' ) ) :
result . append ( { 'source' : source , 'value' : a_value , } )
return result |
def get_artifact_info ( self ) :
"""Returns a tuple composed of a : class : ` pants . java . jar . JarDependency `
describing the jar for this target and a bool indicating if this target is exportable .""" | exported = bool ( self . provides )
org = self . provides . org if exported else 'internal'
name = self . provides . name if exported else self . identifier
# TODO ( John Sirois ) : This should return something less than a JarDependency encapsulating just
# the org and name . Perhaps a JarFamily ?
return JarDependency ... |
def next ( self ) :
"""Returns the next ( object , nextPageToken ) pair .""" | if self . _currentObject is None :
raise StopIteration ( )
nextPageToken = None
if self . _nextObject is not None :
start = self . _getStart ( self . _nextObject )
# If start > the search anchor , move the search anchor . Otherwise ,
# increment the distance from the anchor .
if start > self . _sear... |
def line_spacing ( self ) :
"""The spacing between baselines of successive lines in this paragraph .
A float value indicates a number of lines . A | Length | value indicates
a fixed spacing . Value is contained in ` . / a : lnSpc / a : spcPts / @ val ` or
` . / a : lnSpc / a : spcPct / @ val ` . Value is | No... | lnSpc = self . lnSpc
if lnSpc is None :
return None
if lnSpc . spcPts is not None :
return lnSpc . spcPts . val
return lnSpc . spcPct . val |
def compute_equiv_class ( atom ) :
"""( atom ) - > Computes a unique integer for an atom""" | try :
equiv_class = atom . number + 1000 * ( atom . charge + 10 ) + 100000 * ( atom . hcount ) + 1000000 * ( atom . weight )
except TypeError :
raise ValueError , "Can't compute number from atom.number %s atom.charge %s atom.hcount %s" " atom.weight %s" % ( atom . number , atom . charge , atom . hcount , atom .... |
def walk ( textRoot , currentTag , level , prefix = None , postfix = None , unwrapUntilPara = False ) :
'''. . note : :
This method does not cover all possible input doxygen types ! This means that
when an unsupported / unrecognized doxygen tag appears in the xml listing , the
* * raw xml will appear on the f... | if not currentTag :
return
if prefix :
currentTag . insert_before ( prefix )
if postfix :
currentTag . insert_after ( postfix )
children = currentTag . findChildren ( recursive = False )
indent = " " * level
if currentTag . name == "orderedlist" :
idx = 1
for child in children :
walk ( tex... |
def start_tree ( self , tree , name ) :
"""Skip this fixer if " _ _ future _ _ . division " is already imported .""" | super ( FixDivisionSafe , self ) . start_tree ( tree , name )
self . skip = "division" in tree . future_features |
def _slice_bam ( in_bam , region , tmp_dir , config ) :
"""Use sambamba to slice a bam region""" | name_file = os . path . splitext ( os . path . basename ( in_bam ) ) [ 0 ]
out_file = os . path . join ( tmp_dir , os . path . join ( tmp_dir , name_file + _to_str ( region ) + ".bam" ) )
sambamba = config_utils . get_program ( "sambamba" , config )
region = _to_sambamba ( region )
with file_transaction ( out_file ) as... |
def log_update ( self , service , to_update , status , count ) :
"""lets log everything at the end
: param service : service object
: param to _ update : boolean to check if we have to update
: param status : is everything worked fine ?
: param count : number of data to update
: type service : service obj... | if to_update :
if status :
msg = "{} - {} new data" . format ( service , count )
update_result ( service . id , msg = "OK" , status = status )
logger . info ( msg )
else :
msg = "{} AN ERROR OCCURS " . format ( service )
update_result ( service . id , msg = msg , status =... |
def _weighted_formula ( form , weight_func ) :
"""Yield weight of each formula element .""" | for e , mf in form . items ( ) :
if e == Atom . H :
continue
yield e , mf , weight_func ( e ) |
def _identify_eds_ing ( first , second ) :
"""Find nodes connecting adjacent edges .
Args :
first ( Edge ) : Edge object representing the first edge .
second ( Edge ) : Edge object representing the second edge .
Returns :
tuple [ int , int , set [ int ] ] : The first two values represent left and right no... | A = set ( [ first . L , first . R ] )
A . update ( first . D )
B = set ( [ second . L , second . R ] )
B . update ( second . D )
depend_set = A & B
left , right = sorted ( list ( A ^ B ) )
return left , right , depend_set |
def get_file_descriptor ( self ) :
"""Returns the file descriptor used for passing to the select call when listening
on the message queue .""" | return self . _subscription . connection and self . _subscription . connection . _sock . fileno ( ) |
def spmatrix ( self , reordered = True , symmetric = False ) :
"""Converts the : py : class : ` cspmatrix ` : math : ` A ` to a sparse matrix . A reordered
matrix is returned if the optional argument ` reordered ` is
` True ` ( default ) , and otherwise the inverse permutation is applied . Only the
default op... | n = self . symb . n
snptr = self . symb . snptr
snode = self . symb . snode
relptr = self . symb . relptr
snrowidx = self . symb . snrowidx
sncolptr = self . symb . sncolptr
blkptr = self . symb . blkptr
blkval = self . blkval
if self . is_factor :
if symmetric :
raise ValueError ( "'symmetric = True' not i... |
def _write ( self , f ) :
"""Serialize an NDEF record to a file - like object .""" | log . debug ( "writing ndef record at offset {0}" . format ( f . tell ( ) ) )
record_type = self . type
record_name = self . name
record_data = self . data
if record_type == '' :
header_flags = 0 ;
record_name = '' ;
record_data = ''
elif record_type . startswith ( "urn:nfc:wkt:" ) :
header_flags = 1 ;
... |
def fetch ( self , minutes = values . unset , start_date = values . unset , end_date = values . unset , task_channel = values . unset ) :
"""Fetch a WorkerStatisticsInstance
: param unicode minutes : Filter cumulative statistics by up to ' x ' minutes in the past .
: param datetime start _ date : Filter cumulat... | return self . _proxy . fetch ( minutes = minutes , start_date = start_date , end_date = end_date , task_channel = task_channel , ) |
def get_group_for_col ( self , table_name , col_name ) :
"""Check data model to find group name for a given column header
Parameters
table _ name : str
col _ name : str
Returns
group _ name : str""" | df = self . dm [ table_name ]
try :
group_name = df . loc [ col_name , 'group' ]
except KeyError :
return ''
return group_name |
def _read_para_reg_failed ( self , code , cbit , clen , * , desc , length , version ) :
"""Read HIP REG _ FAILED parameter .
Structure of HIP REG _ FAILED parameter [ RFC 8003 ] :
0 1 2 3
0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1
| Type | Length |
| Lifetime | Reg Type # 1 | Reg Type... | _life = collections . namedtuple ( 'Lifetime' , ( 'min' , 'max' ) )
_mint = self . _read_unpack ( 1 )
_maxt = self . _read_unpack ( 1 )
_type = list ( )
for _ in range ( clen - 2 ) :
_code = self . _read_unpack ( 1 )
_kind = _REG_FAILURE_TYPE . get ( _code )
if _kind is None :
if 0 <= _code <= 200 :... |
def get_pickup_time_estimates ( self , start_latitude , start_longitude , product_id = None , ) :
"""Get pickup time estimates for products at a given location .
Parameters
start _ latitude ( float )
The latitude component of a start location .
start _ longitude ( float )
The longitude component of a star... | args = OrderedDict ( [ ( 'start_latitude' , start_latitude ) , ( 'start_longitude' , start_longitude ) , ( 'product_id' , product_id ) , ] )
return self . _api_call ( 'GET' , 'v1.2/estimates/time' , args = args ) |
def dragMoveEvent ( self , event ) :
"""Processes the drag drop event using the filter set by the setDragDropFilter
: param event | < QDragEvent >""" | filt = self . dragDropFilter ( )
if ( filt and filt ( self , event ) ) :
return
super ( XTableWidget , self ) . dragMoveEvent ( event ) |
def convert_epoch_to_timestamp ( cls , timestamp , tsformat ) :
"""Converts the given float representing UNIX - epochs into an actual timestamp .
: param float timestamp : Timestamp as UNIX - epochs .
: param string tsformat : Format of the given timestamp . This is used to convert the
timestamp from UNIX epo... | return time . strftime ( tsformat , time . gmtime ( timestamp ) ) |
def set_auth_request ( self , interface_id , address = None ) :
"""Set the authentication request field for the specified
engine .""" | self . interface . set_auth_request ( interface_id , address )
self . _engine . update ( ) |
def get_crumbs ( self ) :
"""Get crumbs for navigation links .
Returns :
tuple :
concatenated list of crumbs using these crumbs and the
crumbs of the parent classes through ` ` _ _ mro _ _ ` ` .""" | crumbs = [ ]
for cls in reversed ( type ( self ) . __mro__ [ 1 : ] ) :
crumbs . extend ( getattr ( cls , 'crumbs' , ( ) ) )
crumbs . extend ( list ( self . crumbs ) )
return tuple ( crumbs ) |
def properties ( self , name = None , pk = None , category = Category . INSTANCE , ** kwargs ) : # type : ( Optional [ str ] , Optional [ str ] , Optional [ str ] , * * Any ) - > List [ Property ]
"""Retrieve properties .
If additional ` keyword = value ` arguments are provided , these are added to the request pa... | request_params = { 'name' : name , 'id' : pk , 'category' : category }
if kwargs :
request_params . update ( ** kwargs )
response = self . _request ( 'GET' , self . _build_url ( 'properties' ) , params = request_params )
if response . status_code != requests . codes . ok : # pragma : no cover
raise NotFoundErro... |
def stop_event_loop ( self , event = None ) :
"""Stop an event loop . This is used to stop a blocking event
loop so that interactive functions , such as ginput and
waitforbuttonpress , can wait for events .
Call signature : :
stop _ event _ loop _ default ( self )""" | if hasattr ( self , '_event_loop' ) :
if self . _event_loop . IsRunning ( ) :
self . _event_loop . Exit ( )
del self . _event_loop |
def on_headers ( self , response , exc = None ) :
'''Websocket upgrade as ` ` on _ headers ` ` event .''' | if response . status_code == 101 :
connection = response . connection
request = response . request
handler = request . websocket_handler
if not handler :
handler = WS ( )
parser = request . client . frame_parser ( kind = 1 )
consumer = partial ( WebSocketClient . create , response , hand... |
def get_query ( self , q , request ) :
"""return a query set searching for the query string q
either implement this method yourself or set the search _ field
in the LookupChannel class definition""" | return Group . objects . filter ( Q ( name__icontains = q ) | Q ( description__icontains = q ) ) |
def generate_plates ( seed , world_name , output_dir , width , height , num_plates = 10 ) :
"""Eventually this method should be invoked when generation is called at
asked to stop at step " plates " , it should not be a different operation
: param seed :
: param world _ name :
: param output _ dir :
: para... | elevation , plates = generate_plates_simulation ( seed , width , height , num_plates = num_plates )
world = World ( world_name , Size ( width , height ) , seed , GenerationParameters ( num_plates , - 1.0 , "plates" ) )
world . elevation = ( numpy . array ( elevation ) . reshape ( height , width ) , None )
world . plate... |
def evaluate ( self , input_data , targets , return_cache = False , prediction = True ) :
"""Evaluate the loss function without computing gradients .
* * Parameters : * *
input _ data : GPUArray
Data to evaluate
targets : GPUArray
Targets
return _ cache : bool , optional
Whether to return intermediary... | # Forward pass
activations , hidden_cache = self . feed_forward ( input_data , return_cache = True , prediction = prediction )
loss = self . top_layer . train_error ( None , targets , average = False , cache = activations , prediction = prediction )
for hl in self . hidden_layers :
if hl . l1_penalty_weight :
... |
def augment_usage_errors ( ctx , param = None ) :
"""Context manager that attaches extra information to exceptions that
fly .""" | try :
yield
except BadParameter as e :
if e . ctx is None :
e . ctx = ctx
if param is not None and e . param is None :
e . param = param
raise
except UsageError as e :
if e . ctx is None :
e . ctx = ctx
raise |
def windows_df ( self ) :
"""Get Windows ( W ) W - row , W - col and W - index of windows e . g . loaded with : meth : ` block _ windows ` as a dataframe .
Returns :
[ dataframe ] - - A dataframe with the window information and indices ( row , col , index ) .""" | import pandas as pd
if self . windows is None :
raise Exception ( "You need to call the block_windows or windows before." )
df_wins = [ ]
for row , col , win in zip ( self . windows_row , self . windows_col , self . windows ) :
df_wins . append ( pd . DataFrame ( { "row" : [ row ] , "col" : [ col ] , "Window" :... |
def map_to_array ( pairs ) :
"""MAP THE ( tuid , line ) PAIRS TO A SINGLE ARRAY OF TUIDS
: param pairs :
: return :""" | if pairs :
pairs = [ TuidMap ( * p ) for p in pairs ]
max_line = max ( p . line for p in pairs )
tuids = [ None ] * max_line
for p in pairs :
if p . line : # line = = 0 IS A PLACEHOLDER FOR FILES THAT DO NOT EXIST
tuids [ p . line - 1 ] = p . tuid
return tuids
else :
return N... |
def _build_model ( self ) :
"""Build the model .""" | # Set up LSTM modules
self . lstms = nn . ModuleList ( [ RNN ( num_classes = 0 , num_tokens = self . word_dict . s , emb_size = self . settings [ "emb_dim" ] , lstm_hidden = self . settings [ "hidden_dim" ] , attention = self . settings [ "attention" ] , dropout = self . settings [ "dropout" ] , bidirectional = self . ... |
def morpho ( self , m ) :
"""Renvoie la chaîne de rang m dans la liste des morphologies donnée par le fichier data / morphos . la
: param m : Indice de morphologie
: type m : int
: return : Chaîne de rang m dans la liste des morphologies donnée par le fichier data / morphos . la
: rtype : str""" | l = "fr"
# TODO : Si ajout langue de traduction , il faudra convertir ce qui suit
# if self . _ morphos . keys ( ) . contains ( _ cible . mid ( 0,2 ) ) ) l = _ cible . mid ( 0,2:
# elif ( _ cible . size ( ) > 4 ) and ( _ morphos . keys ( ) . contains ( _ cible . mid ( 3,2 ) ) ) :
# l = _ cible . mid ( 3,2)
if m < 0 or ... |
def Emulation_setVisibleSize ( self , width , height ) :
"""Function path : Emulation . setVisibleSize
Domain : Emulation
Method name : setVisibleSize
WARNING : This function is marked ' Experimental ' !
Parameters :
Required arguments :
' width ' ( type : integer ) - > Frame width ( DIP ) .
' height ... | assert isinstance ( width , ( int , ) ) , "Argument 'width' must be of type '['int']'. Received type: '%s'" % type ( width )
assert isinstance ( height , ( int , ) ) , "Argument 'height' must be of type '['int']'. Received type: '%s'" % type ( height )
subdom_funcs = self . synchronous_command ( 'Emulation.setVisibleSi... |
def com_google_fonts_check_metadata_match_weight_postscript ( font_metadata ) :
"""METADATA . pb weight matches postScriptName .""" | WEIGHTS = { "Thin" : 100 , "ThinItalic" : 100 , "ExtraLight" : 200 , "ExtraLightItalic" : 200 , "Light" : 300 , "LightItalic" : 300 , "Regular" : 400 , "Italic" : 400 , "Medium" : 500 , "MediumItalic" : 500 , "SemiBold" : 600 , "SemiBoldItalic" : 600 , "Bold" : 700 , "BoldItalic" : 700 , "ExtraBold" : 800 , "ExtraBoldI... |
def dipole ( self ) :
"""Calculates the dipole of the Slab in the direction of the surface
normal . Note that the Slab must be oxidation state - decorated for this
to work properly . Otherwise , the Slab will always have a dipole of 0.""" | dipole = np . zeros ( 3 )
mid_pt = np . sum ( self . cart_coords , axis = 0 ) / len ( self )
normal = self . normal
for site in self :
charge = sum ( [ getattr ( sp , "oxi_state" , 0 ) * amt for sp , amt in site . species . items ( ) ] )
dipole += charge * np . dot ( site . coords - mid_pt , normal ) * normal
r... |
def findTargetNS ( self , node ) :
"""Return the defined target namespace uri for the given node .""" | attrget = self . getAttr
attrkey = ( self . NS_XMLNS , 'xmlns' )
DOCUMENT_NODE = node . DOCUMENT_NODE
ELEMENT_NODE = node . ELEMENT_NODE
while 1 :
if node . nodeType != ELEMENT_NODE :
node = node . parentNode
continue
result = attrget ( node , 'targetNamespace' , default = None )
if result i... |
def to_dict ( self ) :
"""Converts this embed object into a dict .""" | # add in the raw data into the dict
result = { key [ 1 : ] : getattr ( self , key ) for key in self . __slots__ if key [ 0 ] == '_' and hasattr ( self , key ) }
# deal with basic convenience wrappers
try :
colour = result . pop ( 'colour' )
except KeyError :
pass
else :
if colour :
result [ 'color' ... |
def _remove_layer_and_reconnect ( self , layer ) :
"""Remove the layer , and reconnect each of its predecessor to each of
its successor""" | successors = self . get_successors ( layer )
predecessors = self . get_predecessors ( layer )
# remove layer ' s edges
for succ in successors :
self . _remove_edge ( layer , succ )
for pred in predecessors :
self . _remove_edge ( pred , layer )
# connect predecessors and successors
for pred in predecessors :
... |
def gen_ref_docs ( gen_index = False ) : # type : ( int , bool ) - > None
"""Generate reference documentation for the project .
This will use * * sphinx - refdoc * * to generate the source . rst files for the
reference documentation .
Args :
gen _ index ( bool ) :
Set it to * * True * * if you want to gen... | try :
from refdoc import generate_docs
except ImportError as ex :
msg = ( "You need to install sphinx-refdoc if you want to generate " "code reference docs." )
print ( msg , file = sys . stderr )
log . err ( "Exception: {}" . format ( ex ) )
sys . exit ( - 1 )
pretend = context . get ( 'pretend' , F... |
def get_uses_implied_permission_list ( self ) :
"""Return all permissions implied by the target SDK or other permissions .
: rtype : list of string""" | target_sdk_version = self . get_effective_target_sdk_version ( )
READ_CALL_LOG = 'android.permission.READ_CALL_LOG'
READ_CONTACTS = 'android.permission.READ_CONTACTS'
READ_EXTERNAL_STORAGE = 'android.permission.READ_EXTERNAL_STORAGE'
READ_PHONE_STATE = 'android.permission.READ_PHONE_STATE'
WRITE_CALL_LOG = 'android.per... |
def kill_current_session ( ctx : Context_T ) -> None :
"""Force kill current session of the given context ,
despite whether it is running or not .
: param ctx : message context""" | ctx_id = context_id ( ctx )
if ctx_id in _sessions :
del _sessions [ ctx_id ] |
def write_grid_tpl ( name , tpl_file , suffix , zn_array = None , shape = None , spatial_reference = None , longnames = False ) :
"""write a grid - based template file
Parameters
name : str
the base parameter name
tpl _ file : str
the template file to write - include path
zn _ array : numpy . ndarray
... | if shape is None and zn_array is None :
raise Exception ( "must pass either zn_array or shape" )
elif shape is None :
shape = zn_array . shape
parnme , x , y = [ ] , [ ] , [ ]
with open ( tpl_file , 'w' ) as f :
f . write ( "ptf ~\n" )
for i in range ( shape [ 0 ] ) :
for j in range ( shape [ 1 ... |
def daemonize ( pid_file = None , cwd = None ) :
"""Detach a process from the controlling terminal and run it in the
background as a daemon .
Modified version of :
code . activestate . com / recipes / 278731 - creating - a - daemon - the - python - way /
author = " Chad J . Schroeder "
copyright = " Copyr... | cwd = cwd or '/'
try :
pid = os . fork ( )
except OSError as e :
raise Exception ( "%s [%d]" % ( e . strerror , e . errno ) )
if ( pid == 0 ) : # The first child .
os . setsid ( )
try :
pid = os . fork ( )
# Fork a second child .
except OSError as e :
raise Exception ( "%s [%... |
def set_dict_value ( dictionary , keys , value ) :
"""Set a value in a ( nested ) dictionary by defining a list of keys .
. . note : : Side - effects
This function does not make a copy of dictionary , but directly
edits it .
Parameters
dictionary : dict
keys : List [ Any ]
value : object
Returns
d... | orig = dictionary
for key in keys [ : - 1 ] :
dictionary = dictionary . setdefault ( key , { } )
dictionary [ keys [ - 1 ] ] = value
return orig |
def findGlyph ( self , glyphName ) :
"""Returns a ` ` list ` ` of the group or groups associated with
* * glyphName * * .
* * glyphName * * will be an : ref : ` type - string ` . If no group is found
to contain * * glyphName * * an empty ` ` list ` ` will be returned . : :
> > > font . groups . findGlyph ( ... | glyphName = normalizers . normalizeGlyphName ( glyphName )
groupNames = self . _findGlyph ( glyphName )
groupNames = [ self . keyNormalizer . __func__ ( groupName ) for groupName in groupNames ]
return groupNames |
def _get_current_migration_state ( self , loader , apps ) :
"""Extract the most recent migrations from the relevant apps .
If no migrations have been performed , return ' zero ' as the most recent migration for the app .
This should only be called from list _ migrations ( ) .""" | # Only care about applied migrations for the passed - in apps .
apps = set ( apps )
relevant_applied = [ migration for migration in loader . applied_migrations if migration [ 0 ] in apps ]
# Sort them by the most recent migration and convert to a dictionary ,
# leaving apps as keys and most recent migration as values .... |
def get_hostfirmware ( self , callb = None ) :
"""Convenience method to request the device firmware info from the device
This method will check whether the value has already been retrieved from the device ,
if so , it will simply return it . If no , it will request the information from the device
and request ... | if self . host_firmware_version is None :
mypartial = partial ( self . resp_set_hostfirmware )
if callb :
mycallb = lambda x , y : ( mypartial ( y ) , callb ( x , y ) )
else :
mycallb = lambda x , y : mypartial ( y )
response = self . req_with_resp ( GetHostFirmware , StateHostFirmware ,... |
def clean ( cls , cpf ) :
u"""Retorna apenas os dígitos do CPF .
> > > CPF . clean ( ' 581.194.436-59 ' )
'58119443659'""" | if isinstance ( cpf , six . string_types ) :
cpf = int ( re . sub ( '[^0-9]' , '' , cpf ) )
return '{0:011d}' . format ( cpf ) |
def generate_version_file ( self , schema_filename , binding_filename ) :
"""Given a DataONE schema , generates a file that contains version information
about the schema .""" | version_filename = binding_filename + '_version.txt'
version_path = os . path . join ( self . binding_dir , version_filename )
schema_path = os . path . join ( self . schema_dir , schema_filename )
try :
tstamp , svnpath , svnrev , version = self . get_version_info_from_svn ( schema_path )
except TypeError :
pa... |
def get_objects ( self , queryset = None ) :
"""Return an iterator of Django model objects in Elasticsearch order ,
optionally using the given Django queryset . If no queryset is
given , a default queryset ( Model . objects . all ) is used .
: param queryset : Optional queryset to filter in .
: return :""" | if not self :
return
if not queryset :
queryset = self [ 0 ] . django_model . objects . all ( )
pks = [ res . pk for res in self if res . django_model == queryset . model ]
object_map = dict ( ( text_type ( obj . pk ) , obj ) for obj in queryset . filter ( pk__in = pks ) )
result_map = dict ( ( res . pk , res )... |
def get_timeseries ( self , child_agg_count = 0 , dataframe = False ) :
"""Get time series data for the specified fields and period of analysis
: param child _ agg _ count : the child aggregation count to be used
default = 0
: param dataframe : if dataframe = True , return a pandas . DataFrame object
: retu... | res = self . fetch_aggregation_results ( )
ts = { "date" : [ ] , "value" : [ ] , "unixtime" : [ ] }
if 'buckets' not in res [ 'aggregations' ] [ str ( self . parent_agg_counter - 1 ) ] :
raise RuntimeError ( "Aggregation results have no buckets in time series results." )
for bucket in res [ 'aggregations' ] [ str (... |
async def connect_to_endpoints ( self , * endpoints : ConnectionConfig ) -> None :
"""Connect to the given endpoints and await until all connections are established .""" | self . _throw_if_already_connected ( * endpoints )
await asyncio . gather ( * ( self . _await_connect_to_endpoint ( endpoint ) for endpoint in endpoints ) , loop = self . event_loop ) |
def download ( ctx ) :
"""Download blobs or files from Azure Storage""" | settings . add_cli_options ( ctx . cli_options , settings . TransferAction . Download )
ctx . initialize ( settings . TransferAction . Download )
specs = settings . create_download_specifications ( ctx . cli_options , ctx . config )
del ctx . cli_options
for spec in specs :
blobxfer . api . Downloader ( ctx . gener... |
def _propagate_packages ( self ) :
r"""Propogate packages .
Make sure that all the packages included in the previous containers
are part of the full list of packages .""" | super ( ) . _propagate_packages ( )
for item in ( self . preamble ) :
if isinstance ( item , LatexObject ) :
if isinstance ( item , Container ) :
item . _propagate_packages ( )
for p in item . packages :
self . packages . add ( p ) |
def is_local ( self , hadoop_conf = None , hadoop_home = None ) :
"""Is Hadoop configured to run in local mode ?
By default , it is . [ pseudo - ] distributed mode must be
explicitly configured .""" | conf = self . hadoop_params ( hadoop_conf , hadoop_home )
keys = ( 'mapreduce.framework.name' , 'mapreduce.jobtracker.address' , 'mapred.job.tracker' )
for k in keys :
if conf . get ( k , 'local' ) . lower ( ) != 'local' :
return False
return True |
def fastq_info ( path ) :
"""Found some info about how to ignore warnings in code blocks here :
- http : / / stackoverflow . com / questions / 14463277 / how - to - disable - python - warnings""" | numBases = 0
numReads = 0
readLengths = Counter ( )
GCTot = 0
with warnings . catch_warnings ( ) :
warnings . simplefilter ( "ignore" )
handle = gzip . open ( path , "rt" )
for record in SeqIO . parse ( handle , "fastq" ) :
numBases += len ( record )
numReads += 1
readLengths [ len (... |
def stop ( ) :
"""Stop the server , invalidating any viewer URLs .
This allows any previously - referenced data arrays to be garbage collected if there are no other
references to them .""" | global global_server
if global_server is not None :
ioloop = global_server . ioloop
def stop_ioloop ( ) :
ioloop . stop ( )
ioloop . close ( )
global_server . ioloop . add_callback ( stop_ioloop )
global_server = None |
def _packed_data ( self ) :
'''Returns the bit - packed data extracted from the data file . This is not so useful to analyze .
Use the complex _ data method instead .''' | header = self . header ( )
packed_data = np . frombuffer ( self . data , dtype = np . int8 ) . reshape ( ( header [ 'number_of_half_frames' ] , header [ 'half_frame_bytes' ] ) )
# create array of half frames
packed_data = packed_data [ : : - 1 , constants . header_offset : ]
# slice out header and flip half frame order... |
def assimilate ( self , path ) :
"""Parses vasp runs . Then insert the result into the db . and return the
task _ id or doc of the insertion .
Returns :
If in simulate _ mode , the entire doc is returned for debugging
purposes . Else , only the task _ id of the inserted doc is returned .""" | try :
d = self . get_task_doc ( path )
if self . mapi_key is not None and d [ "state" ] == "successful" :
self . calculate_stability ( d )
tid = self . _insert_doc ( d )
return tid
except Exception as ex :
import traceback
logger . error ( traceback . format_exc ( ) )
return False |
def _run_program ( self , bin , fastafile , params = None ) :
"""Run XXmotif and predict motifs from a FASTA file .
Parameters
bin : str
Command used to run the tool .
fastafile : str
Name of the FASTA input file .
params : dict , optional
Optional parameters . For some of the tools required parameter... | params = self . _parse_params ( params )
outfile = os . path . join ( self . tmpdir , os . path . basename ( fastafile . replace ( ".fa" , ".pwm" ) ) )
stdout = ""
stderr = ""
cmd = "%s %s %s --localization --batch %s %s" % ( bin , self . tmpdir , fastafile , params [ "background" ] , params [ "strand" ] , )
p = Popen ... |
def uncomment ( comment ) :
"""Converts the comment node received to a non - commented element , in place ,
and will return the new node .
This may fail , primarily due to special characters within the comment that
the xml parser is unable to handle . If it fails , this method will log an
error and return N... | parent = comment . parentNode
h = html . parser . HTMLParser ( )
data = h . unescape ( comment . data )
try :
node = minidom . parseString ( data ) . firstChild
except xml . parsers . expat . ExpatError : # Could not parse !
log . error ( 'Could not uncomment node due to parsing error!' )
return None
else :... |
def easeOutElastic ( n , amplitude = 1 , period = 0.3 ) :
"""An elastic tween function that overshoots the destination and then " rubber bands " into the destination .
Args :
n ( float ) : The time progress , starting at 0.0 and ending at 1.0.
Returns :
( float ) The line progress , starting at 0.0 and endi... | _checkRange ( n )
if amplitude < 1 :
amplitude = 1
s = period / 4
else :
s = period / ( 2 * math . pi ) * math . asin ( 1 / amplitude )
return amplitude * 2 ** ( - 10 * n ) * math . sin ( ( n - s ) * ( 2 * math . pi / period ) ) + 1 |
def package_install ( name , ** kwargs ) :
'''Install a " package " on the ssh server''' | cmd = 'pkg_install ' + name
if kwargs . get ( 'version' , False ) :
cmd += ' ' + kwargs [ 'version' ]
# Send the command to execute
out , err = DETAILS [ 'server' ] . sendline ( cmd )
# " scrape " the output and return the right fields as a dict
return parse ( out ) |
def page ( self , course , msg = "" , error = False ) :
"""Get all data and display the page""" | aggregations = OrderedDict ( )
taskids = list ( course . get_tasks ( ) . keys ( ) )
for aggregation in self . user_manager . get_course_aggregations ( course ) :
aggregations [ aggregation [ '_id' ] ] = dict ( list ( aggregation . items ( ) ) + [ ( "tried" , 0 ) , ( "done" , 0 ) , ( "url" , self . submission_url_ge... |
def classify ( self , url_path ) :
"""Classify an url""" | for dict_api_url in self . user_defined_rules :
api_url = dict_api_url [ 'str' ]
re_api_url = dict_api_url [ 're' ]
if re_api_url . match ( url_path [ 1 : ] ) :
return api_url
return self . RE_SIMPLIFY_URL . sub ( r'(\\d+)/' , url_path ) |
def fit ( self , ** skip_gram_params ) :
"""Creates the embeddings using gensim ' s Word2Vec .
: param skip _ gram _ params : Parameteres for gensim . models . Word2Vec - do not supply ' size ' it is taken from the Node2Vec ' dimensions ' parameter
: type skip _ gram _ params : dict
: return : A gensim word2v... | if 'workers' not in skip_gram_params :
skip_gram_params [ 'workers' ] = self . workers
if 'size' not in skip_gram_params :
skip_gram_params [ 'size' ] = self . dimensions
return gensim . models . Word2Vec ( self . walks , ** skip_gram_params ) |
import re
def discard_lowercase ( input_string ) :
"""This function discards lowercase characters from a given string using regex .
Examples :
discard _ lowercase ( ' KDeoALOklOOHserfLoAJSIskdsf ' ) - > ' KDALOOOHLAJSI '
discard _ lowercase ( ' ProducTnamEstreAmIngMediAplAYer ' ) - > ' PTEAIMAAY '
discard _... | remove_lower_case = ( lambda text : re . sub ( '[a-z]' , '' , text ) )
return remove_lower_case ( input_string ) |
def _are_nearby_parallel_boxes ( self , b1 , b2 ) :
"Are two boxes nearby , parallel , and similar in width ?" | if not self . _are_aligned_angles ( b1 . angle , b2 . angle ) :
return False
# Otherwise pick the smaller angle and see whether the two boxes are close according to the " up " direction wrt that angle
angle = min ( b1 . angle , b2 . angle )
return abs ( np . dot ( b1 . center - b2 . center , [ - np . sin ( angle ) ... |
def get_datatype ( object_type , propid , vendor_id = 0 ) :
"""Return the datatype for the property of an object .""" | if _debug :
get_datatype . _debug ( "get_datatype %r %r vendor_id=%r" , object_type , propid , vendor_id )
# get the related class
cls = get_object_class ( object_type , vendor_id )
if not cls :
return None
# get the property
prop = cls . _properties . get ( propid )
if not prop :
return None
# return the d... |
def create_tokenizer ( self , name , config = dict ( ) ) :
"""Create a pipeline component from a factory .
name ( unicode ) : Factory name to look up in ` Language . factories ` .
config ( dict ) : Configuration parameters to initialise component .
RETURNS ( callable ) : Pipeline component .""" | if name not in self . factories :
raise KeyError ( Errors . E002 . format ( name = name ) )
factory = self . factories [ name ]
return factory ( self , ** config ) |
def set_object ( self , object , logmsg = None ) : # @ ReservedAssignment
"""Set the object we point to , possibly dereference our symbolic reference first .
If the reference does not exist , it will be created
: param object : a refspec , a SymbolicReference or an Object instance . SymbolicReferences
will be... | if isinstance ( object , SymbolicReference ) :
object = object . object
# @ ReservedAssignment
# END resolve references
is_detached = True
try :
is_detached = self . is_detached
except ValueError :
pass
# END handle non - existing ones
if is_detached :
return self . set_reference ( object , logmsg )
# s... |
def define_mask_borders ( image2d , sought_value , nadditional = 0 ) :
"""Generate mask avoiding undesired values at the borders .
Set to True image borders with values equal to ' sought _ value '
Parameters
image2d : numpy array
Initial 2D image .
sought _ value : int , float , bool
Pixel value that in... | # input image size
naxis2 , naxis1 = image2d . shape
# initialize mask
mask2d = np . zeros ( ( naxis2 , naxis1 ) , dtype = bool )
# initialize list to store borders
borders = [ ]
for i in range ( naxis2 ) : # only spectra with values different from ' sought _ value '
jborder_min , jborder_max = find_pix_borders ( i... |
def update_layers_esri_imageserver ( service ) :
"""Update layers for an ESRI REST ImageServer .
Sample endpoint : https : / / gis . ngdc . noaa . gov / arcgis / rest / services / bag _ bathymetry / ImageServer / ? f = json""" | try :
esri_service = ArcImageService ( service . url )
# set srs
# both mapserver and imageserver exposes just one srs at the service level
# not sure if other ones are supported , for now we just store this one
obj = json . loads ( esri_service . _contents )
srs_code = obj [ 'spatialReference' ... |
def get_project ( self , project_id , include_capabilities = None , include_history = None ) :
"""GetProject .
Get project with the specified id or name , optionally including capabilities .
: param str project _ id :
: param bool include _ capabilities : Include capabilities ( such as source control ) in the... | route_values = { }
if project_id is not None :
route_values [ 'projectId' ] = self . _serialize . url ( 'project_id' , project_id , 'str' )
query_parameters = { }
if include_capabilities is not None :
query_parameters [ 'includeCapabilities' ] = self . _serialize . query ( 'include_capabilities' , include_capab... |
def print_file ( self , file_format = 'ctfile' , f = sys . stdout ) :
"""Print representation of : class : ` ~ ctfile . ctfile . CTfile ` .
: param str file _ format : Format to use : ` ` ctfile ` ` or ` ` json ` ` .
: param f : Print to file or stdout .
: type f : File - like
: return : None .
: rtype : ... | print ( self . writestr ( file_format = file_format ) , file = f ) |
def _find_unprocessed ( config ) :
"""Find any finished directories that have not been processed .""" | reported = _read_reported ( config [ "msg_db" ] )
for dname in _get_directories ( config ) :
if os . path . isdir ( dname ) and dname not in reported :
if _is_finished_dumping ( dname ) :
yield dname |
def merge ( self , across = False ) :
"""Merge the range cells into one region in the worksheet .
: param bool across : Optional . Set True to merge cells in each row of the
specified range as separate merged cells .""" | url = self . build_url ( self . _endpoints . get ( 'merge_range' ) )
return bool ( self . session . post ( url , data = { 'across' : across } ) ) |
def bling ( self , target , sender ) :
"will print yo" | if target . startswith ( "#" ) :
self . message ( target , "%s: yo" % sender )
else :
self . message ( sender , "yo" ) |
def check_valid_package ( package , cyg_arch = 'x86_64' , mirrors = None ) :
'''Check if the package is valid on the given mirrors .
Args :
package : The name of the package
cyg _ arch : The cygwin architecture
mirrors : any mirrors to check
Returns ( bool ) : True if Valid , otherwise False
CLI Example... | if mirrors is None :
mirrors = [ { DEFAULT_MIRROR : DEFAULT_MIRROR_KEY } ]
LOG . debug ( 'Checking Valid Mirrors: %s' , mirrors )
for mirror in mirrors :
for mirror_url , key in mirror . items ( ) :
if package in _get_all_packages ( mirror_url , cyg_arch ) :
return True
return False |
def on_change ( self , callable_ ) :
"""Add a change observer to this entity .""" | self . model . add_observer ( callable_ , self . entity_type , 'change' , self . entity_id ) |
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