signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def add_bgcolor ( self , colname , cmap = 'copper' , mode = 'absmax' , threshold = 2 ) :
"""Change column content into HTML paragraph with background color
: param colname :
: param cmap : a colormap ( matplotlib ) or created using
colormap package ( from pypi ) .
: param mode : type of normalisation in ' a... | try : # if a cmap is provided , it may be just a known cmap name
cmap = cmap_builder ( cmap )
except :
pass
data = self . df [ colname ] . values
if len ( data ) == 0 :
return
if mode == 'clip' :
data = [ min ( x , threshold ) / float ( threshold ) for x in data ]
elif mode == 'absmax' :
m = abs ( d... |
def submitter ( self ) :
"""| Comment : The user who submitted the ticket . The submitter always becomes the author of the first comment on the ticket""" | if self . api and self . submitter_id :
return self . api . _get_user ( self . submitter_id ) |
def getFileDescription ( self , fileInfo ) :
"""Function to get the description of a file .""" | data = 'Description'
result = fileInfo [ fileInfo . find ( data + "</td>" ) + len ( data + "</td>" ) : ]
result . lstrip ( )
result = result [ : result . find ( "</td>" ) ]
result = result [ result . rfind ( "<" ) : ]
if "<td" in result :
result = result [ result . find ( ">" ) + 1 : ]
return result |
def map_plus ( target : Callable , mi , ma , a , mk , k ) :
"""The builtin ` map ( ) ` , but with superpowers .""" | if a is None :
a = [ ]
if k is None :
k = { }
if mi is None and ma is None and mk is None :
return [ ]
elif mi is None and ma is None :
return [ target ( * a , ** mki , ** k ) for mki in mk ]
elif ma is None and mk is None :
return [ target ( mii , * a , ** k ) for mii in mi ]
elif mk is None and mi... |
def imagej_description ( shape , rgb = None , colormaped = False , version = None , hyperstack = None , mode = None , loop = None , ** kwargs ) :
"""Return ImageJ image description from data shape .
ImageJ can handle up to 6 dimensions in order TZCYXS .
> > > imagej _ description ( ( 51 , 5 , 2 , 196 , 171 ) ) ... | if colormaped :
raise NotImplementedError ( 'ImageJ colormapping not supported' )
if version is None :
version = '1.11a'
shape = imagej_shape ( shape , rgb = rgb )
rgb = shape [ - 1 ] in ( 3 , 4 )
result = [ 'ImageJ=%s' % version ]
append = [ ]
result . append ( 'images=%i' % product ( shape [ : - 3 ] ) )
if hy... |
def get_neutralized_variable ( variable ) :
"""Return a new neutralized variable ( to be used by reforms ) .
A neutralized variable always returns its default value , and does not cache anything .""" | result = variable . clone ( )
result . is_neutralized = True
result . label = '[Neutralized]' if variable . label is None else '[Neutralized] {}' . format ( variable . label ) ,
return result |
def _retrieve_tag ( self , text ) :
"""Tag text with chosen tagger and clean tags .
Tag format : [ ( ' word ' , ' tag ' ) ]
: param text : string
: return : list of tuples , with each tuple containing the word and its pos tag
: rtype : list""" | if self . tagger == 'tag_ngram_123_backoff' : # Data format : Perseus Style ( see https : / / github . com / cltk / latin _ treebank _ perseus )
tags = POSTag ( 'latin' ) . tag_ngram_123_backoff ( text . lower ( ) )
return [ ( tag [ 0 ] , tag [ 1 ] ) for tag in tags ]
elif self . tagger == 'tag_tnt' :
tags ... |
def associations ( self , association_resource ) :
"""Retrieve Association for this resource of the type in association _ resource .
This method will return all * resources * ( group , indicators , task , victims , etc ) for this
resource that are associated with the provided association resource _ type .
* *... | resource = self . copy ( )
resource . _request_entity = association_resource . api_entity
resource . _request_uri = '{}/{}' . format ( resource . _request_uri , association_resource . request_uri )
return resource |
def second_parameter ( self , singular_value ) :
"""get the solution space contribution to parameter error variance
at a singular value ( G * obscov * G ^ T )
Parameters
singular _ value : int
singular value to calc second term at
Returns
second _ parameter : pyemu . Cov
second term contribution to pa... | self . log ( "calc second term parameter @" + str ( singular_value ) )
result = self . G ( singular_value ) * self . obscov * self . G ( singular_value ) . T
self . log ( "calc second term parameter @" + str ( singular_value ) )
return result |
def execute_service_endpoint_request ( self , service_endpoint_request , project , endpoint_id ) :
"""ExecuteServiceEndpointRequest .
[ Preview API ] Proxy for a GET request defined by a service endpoint .
: param : class : ` < ServiceEndpointRequest > < azure . devops . v5_0 . service _ endpoint . models . Ser... | route_values = { }
if project is not None :
route_values [ 'project' ] = self . _serialize . url ( 'project' , project , 'str' )
query_parameters = { }
if endpoint_id is not None :
query_parameters [ 'endpointId' ] = self . _serialize . query ( 'endpoint_id' , endpoint_id , 'str' )
content = self . _serialize .... |
def null_advance_strain ( self , blocksize ) :
"""Advance and insert zeros
Parameters
blocksize : int
The number of seconds to attempt to read from the channel""" | sample_step = int ( blocksize * self . sample_rate )
csize = sample_step + self . corruption * 2
self . strain . roll ( - sample_step )
# We should roll this off at some point too . . .
self . strain [ len ( self . strain ) - csize + self . corruption : ] = 0
self . strain . start_time += blocksize
# The next time we n... |
def _init_level_set ( init_level_set , image_shape ) :
"""Auxiliary function for initializing level sets with a string .
If ` init _ level _ set ` is not a string , it is returned as is .""" | if isinstance ( init_level_set , str ) :
if init_level_set == 'checkerboard' :
res = checkerboard_level_set ( image_shape )
elif init_level_set == 'circle' :
res = circle_level_set ( image_shape )
else :
raise ValueError ( "`init_level_set` not in " "['checkerboard', 'circle']" )
els... |
def delete_resource_subscription ( self , device_id , _resource_path , ** kwargs ) : # noqa : E501
"""Remove a subscription # noqa : E501
To remove an existing subscription from a resource path . * * Example usage : * * curl - X DELETE \\ https : / / api . us - east - 1 . mbedcloud . com / v2 / subscriptions / { ... | kwargs [ '_return_http_data_only' ] = True
if kwargs . get ( 'asynchronous' ) :
return self . delete_resource_subscription_with_http_info ( device_id , _resource_path , ** kwargs )
# noqa : E501
else :
( data ) = self . delete_resource_subscription_with_http_info ( device_id , _resource_path , ** kwargs )
... |
def map_ids ( queries , frm = 'ACC' , to = 'ENSEMBL_PRO_ID' , organism_taxid = 9606 , test = False ) :
"""https : / / www . uniprot . org / help / api _ idmapping""" | url = 'https://www.uniprot.org/uploadlists/'
params = { 'from' : frm , 'to' : to , 'format' : 'tab' , 'organism' : organism_taxid , 'query' : ' ' . join ( queries ) , }
response = requests . get ( url , params = params )
if test :
print ( response . url )
if response . ok :
df = pd . read_table ( response . url... |
def decode ( self , packet ) :
"""Check a parsed packet and figure out if it is an Eddystone Beacon .
If it is , return the relevant data as a dictionary .
Return None , it is not an Eddystone Beacon advertising packet""" | ssu = packet . retrieve ( "Complete uuids" )
found = False
for x in ssu :
if EDDY_UUID in x :
found = True
break
if not found :
return None
found = False
adv = packet . retrieve ( "Advertised Data" )
for x in adv :
luuid = x . retrieve ( "Service Data uuid" )
for uuid in luuid :
... |
def highpass ( timeseries , frequency , filter_order = 8 , attenuation = 0.1 ) :
"""Return a new timeseries that is highpassed .
Return a new time series that is highpassed above the ` frequency ` .
Parameters
Time Series : TimeSeries
The time series to be high - passed .
frequency : float
The frequency... | if not isinstance ( timeseries , TimeSeries ) :
raise TypeError ( "Can only resample time series" )
if timeseries . kind is not 'real' :
raise TypeError ( "Time series must be real" )
lal_data = timeseries . lal ( )
_highpass_func [ timeseries . dtype ] ( lal_data , frequency , 1 - attenuation , filter_order )
... |
async def destroy ( self , token ) :
"""Destroys a given token .
Parameters :
token ( ObjectID ) : Token ID
Returns :
bool : ` ` True ` ` on success""" | token_id = extract_attr ( token , keys = [ "ID" ] )
response = await self . _api . put ( "/v1/acl/destroy" , token_id )
return response . body |
def hybrid_meco_frequency ( m1 , m2 , chi1 , chi2 , qm1 = None , qm2 = None ) :
"""Return the frequency of the hybrid MECO
Parameters
m1 : float
Mass of the primary object in solar masses .
m2 : float
Mass of the secondary object in solar masses .
chi1 : float
Dimensionless spin of the primary object ... | if qm1 is None :
qm1 = 1
if qm2 is None :
qm2 = 1
return velocity_to_frequency ( hybrid_meco_velocity ( m1 , m2 , chi1 , chi2 , qm1 , qm2 ) , m1 + m2 ) |
def set_provider_links ( self , resource_ids = None ) :
"""Sets a provider chain in order from the most recent source to
the originating source .
: param resource _ ids : the new source
: type resource _ ids : ` ` osid . id . Id [ ] ` `
: raise : ` ` InvalidArgument ` ` - - ` ` resource _ ids ` ` is invalid... | if resource_ids is None :
raise NullArgument ( )
metadata = Metadata ( ** settings . METADATA [ 'provider_link_ids' ] )
if metadata . is_read_only ( ) :
raise NoAccess ( )
if self . _is_valid_input ( resource_ids , metadata , array = True ) :
self . _my_map [ 'providerLinkIds' ] = [ ]
for i in resource_... |
def from_frame ( klass , frame , connection ) :
"""Create a new TaskStateChange event from a Stompest Frame .""" | event = frame . headers [ 'new' ]
data = json . loads ( frame . body )
info = data [ 'info' ]
task = Task . fromDict ( info )
task . connection = connection
return klass ( task , event ) |
def read ( self , x ) :
"""Read from the memory .
An external component can use the results via a simple MLP ,
e . g . , fn ( x W _ x + retrieved _ mem W _ m ) .
Args :
x : a tensor in the shape of [ batch _ size , length , depth ] .
Returns :
access _ logits : the logits for accessing the memory in sha... | access_logits = self . _address_content ( x )
weights = tf . nn . softmax ( access_logits )
retrieved_mem = tf . reduce_sum ( tf . multiply ( tf . expand_dims ( weights , 3 ) , tf . expand_dims ( self . mem_vals , axis = 1 ) ) , axis = 2 )
return access_logits , retrieved_mem |
def universal_transformer_with_lstm_as_transition_function ( layer_inputs , step , hparams , ffn_unit , attention_unit , pad_remover = None ) :
"""Universal Transformer which uses a lstm as transition function .
It ' s kind of like having a lstm , filliped vertically next to the Universal
Transformer that contr... | state , unused_inputs , memory = tf . unstack ( layer_inputs , num = None , axis = 0 , name = "unstack" )
# NOTE :
# state ( ut _ state ) : output of the lstm in the previous step
# inputs ( ut _ input ) : original input - - > we don ' t use it here
# memory : lstm memory
# Multi _ head _ attention :
assert not hparams... |
def intersect_regions ( flist ) :
"""Construct a region which is the intersection of all regions described in the given
list of file names .
Parameters
flist : list
A list of region filenames .
Returns
region : : class : ` AegeanTools . regions . Region `
The intersection of all regions , possibly emp... | if len ( flist ) < 2 :
raise Exception ( "Require at least two regions to perform intersection" )
a = Region . load ( flist [ 0 ] )
for b in [ Region . load ( f ) for f in flist [ 1 : ] ] :
a . intersect ( b )
return a |
def reset ( self ) :
"""Reseting wrapped function""" | super ( SinonSpy , self ) . unwrap ( )
super ( SinonSpy , self ) . wrap2spy ( ) |
def run ( self , script_file , args = None , verbose = False ) :
"""The run command will execute a command script from the file pointed to
by the file argument , which should contain Cytoscape commands , one per
line . Arguments to the script are provided by the args argument .
: param script _ file : file to... | PARAMS = set_param ( [ "file" , "args" ] , [ script_file , args ] )
response = api ( url = self . __url + "/run" , PARAMS = PARAMS , verbose = verbose )
return response |
def get_measurements_from_kal_scan ( kal_out ) :
"""Return a list of all measurements from kalibrate channel scan .""" | result = [ ]
for line in kal_out . splitlines ( ) :
if "offset " in line :
p_line = line . split ( ' ' )
result . append ( p_line [ - 1 ] )
return result |
def unique_authors ( self , limit ) :
"""Unique list of authors , but preserving order .""" | seen = set ( )
if limit == 0 :
limit = None
seen_add = seen . add
# Assign to variable , so not resolved each time
return [ x . author for x in self . sorted_commits [ : limit ] if not ( x . author in seen or seen_add ( x . author ) ) ] |
def daterange_end ( value ) :
'''Parse a date range end boundary''' | if not value :
return None
elif isinstance ( value , datetime ) :
return value . date ( )
elif isinstance ( value , date ) :
return value
result = parse_dt ( value ) . date ( )
dashes = value . count ( '-' )
if dashes >= 2 : # Full date
return result
elif dashes == 1 : # Year / Month
return result +... |
def get_compositions_by_repositories ( self , repository_ids ) :
"""Gets the list of ` ` Compositions ` ` corresponding to a list of ` ` Repository ` ` objects .
arg : repository _ ids ( osid . id . IdList ) : list of repository
` ` Ids ` `
return : ( osid . repository . CompositionList ) - list of Compositio... | # Implemented from template for
# osid . resource . ResourceBinSession . get _ resources _ by _ bins
composition_list = [ ]
for repository_id in repository_ids :
composition_list += list ( self . get_compositions_by_repository ( repository_id ) )
return objects . CompositionList ( composition_list ) |
def formfield_for_dbfield ( self , db_field , ** kwargs ) :
"""Hook for specifying the form Field instance for a given
database Field instance . If kwargs are given , they ' re
passed to the form Field ' s constructor .
Default implementation uses the overrides returned by
` get _ formfield _ overrides ` . ... | overides = self . get_formfield_overrides ( )
# If we ' ve got overrides for the formfield defined , use ' em . * * kwargs
# passed to formfield _ for _ dbfield override the defaults .
for klass in db_field . __class__ . mro ( ) :
if klass in overides :
kwargs = dict ( overides [ klass ] , ** kwargs )
... |
def disable_oozie_ha ( self , active_name ) :
"""Disable high availability for Oozie
@ param active _ name : Name of the Oozie Server that will be active after
High Availability is disabled .
@ return : Reference to the submitted command .
@ since : API v6""" | args = dict ( activeName = active_name )
return self . _cmd ( 'oozieDisableHa' , data = args , api_version = 6 ) |
def sample ( self , count , ** kwargs ) :
"""Use rejection sampling to generate random points inside a
polygon .
Parameters
count : int
Number of points to return
If there are multiple bodies , there will
be up to count * bodies points returned
factor : float
How many points to test per loop
IE , ... | poly = self . polygons_full
if len ( poly ) == 0 :
samples = np . array ( [ ] )
elif len ( poly ) == 1 :
samples = polygons . sample ( poly [ 0 ] , count = count , ** kwargs )
else :
samples = util . vstack_empty ( [ polygons . sample ( i , count = count , ** kwargs ) for i in poly ] )
return samples |
def reconstitute ( html ) :
"""Given a file - like object as ` ` html ` ` , reconstruct it into models .""" | try :
htree = etree . parse ( html )
except etree . XMLSyntaxError :
html . seek ( 0 )
htree = etree . HTML ( html . read ( ) )
xhtml = etree . tostring ( htree , encoding = 'utf-8' )
return adapt_single_html ( xhtml ) |
def builtin ( self , ref , context = None ) :
"""Get whether the specified reference is an ( xs ) builtin .
@ param ref : A str or qref .
@ type ref : ( str | qref )
@ return : True if builtin , else False .
@ rtype : bool""" | w3 = 'http://www.w3.org'
try :
if isqref ( ref ) :
ns = ref [ 1 ]
return ref [ 0 ] in Factory . tags and ns . startswith ( w3 )
if context is None :
context = self . root
prefix = splitPrefix ( ref ) [ 0 ]
prefixes = context . findPrefixes ( w3 , 'startswith' )
return prefix ... |
def _list_queues ( self , prefix = None , marker = None , max_results = None , include = None , timeout = None , _context = None ) :
'''Returns a list of queues under the specified account . Makes a single list
request to the service . Used internally by the list _ queues method .
: param str prefix :
Filters... | request = HTTPRequest ( )
request . method = 'GET'
request . host_locations = self . _get_host_locations ( secondary = True )
request . path = _get_path ( )
request . query = { 'comp' : 'list' , 'prefix' : _to_str ( prefix ) , 'marker' : _to_str ( marker ) , 'maxresults' : _int_to_str ( max_results ) , 'include' : _to_... |
def reset_topology_change_flag ( self ) :
"""Set topology _ change attribute to False in all hosts and services
: return : None""" | for i in self . hosts :
i . topology_change = False
for i in self . services :
i . topology_change = False |
def get_rank ( self , member , reverse = False , pipe = None ) :
"""Return the rank of * member * in the collection .
By default , the member with the lowest score has rank 0.
If * reverse * is ` ` True ` ` , the member with the highest score has rank 0.""" | pipe = self . redis if pipe is None else pipe
method = getattr ( pipe , 'zrevrank' if reverse else 'zrank' )
rank = method ( self . key , self . _pickle ( member ) )
return rank |
def set_address ( self , address ) :
"""Set the radio address to be used""" | if len ( address ) != 5 :
raise Exception ( 'Crazyradio: the radio address shall be 5' ' bytes long' )
if address != self . current_address :
_send_vendor_setup ( self . handle , SET_RADIO_ADDRESS , 0 , 0 , address )
self . current_address = address |
def increase_i ( self ) :
"""i means the ith round . Increase i by 1""" | self . i += 1
if self . i > self . bracket_id :
self . no_more_trial = True |
async def settings ( dev : Device ) :
"""Print out all possible settings .""" | settings_tree = await dev . get_settings ( )
for module in settings_tree :
await traverse_settings ( dev , module . usage , module . settings ) |
def _check_stack_for_module_return ( stack ) :
"""Verify that the stack is in the expected state before the dummy
RETURN _ VALUE instruction of a module or class .""" | fail = ( len ( stack ) != 1 or not isinstance ( stack [ 0 ] , instrs . LOAD_CONST ) or stack [ 0 ] . arg is not None )
if fail :
raise DecompilationError ( "Reached end of non-function code " "block with unexpected stack: %s." % stack ) |
def _groups_of ( length , total_length ) :
"""Return an iterator of tuples for slicing , in ' length ' chunks .
Parameters
length : int
Length of each chunk .
total _ length : int
Length of the object we are slicing
Returns
iterable of tuples
Values defining a slice range resulting in length ' lengt... | indices = tuple ( range ( 0 , total_length , length ) ) + ( None , )
return _pairwise ( indices ) |
def get_whitelist_page ( self , page_number = None , page_size = None ) :
"""Gets a paginated list of indicators that the user ' s company has whitelisted .
: param int page _ number : the page number to get .
: param int page _ size : the size of the page to be returned .
: return : A | Page | of | Indicator... | params = { 'pageNumber' : page_number , 'pageSize' : page_size }
resp = self . _client . get ( "whitelist" , params = params )
return Page . from_dict ( resp . json ( ) , content_type = Indicator ) |
def initialize ( ) :
"""All named pins in OUTPUT _ PINS and INPUT _ PINS are exported , and set the
HALT pin high ( normal running state ) , since the default value after export
is low .""" | for pin in sorted ( OUTPUT_PINS . values ( ) ) :
_enable_pin ( pin , OUT )
for pin in sorted ( INPUT_PINS . values ( ) ) :
_enable_pin ( pin , IN ) |
def notify ( name , states , callback ) :
'''executes the callback function with no parameters when the container reaches the specified state or states
states can be or - ed or and - ed
notify ( ' test ' , ' STOPPED ' , letmeknow )
notify ( ' test ' , ' STOPPED | RUNNING ' , letmeknow )''' | if not exists ( name ) :
raise ContainerNotExists ( "The container (%s) does not exist!" % name )
cmd = [ 'lxc-wait' , '-n' , name , '-s' , states ]
def th ( ) :
subprocess . check_call ( cmd )
callback ( )
_logger . info ( "Waiting on states %s for container %s" , states , name )
threading . Thread ( targe... |
def click ( self , x , y ) :
'''click at arbitrary coordinates .''' | return self . server . jsonrpc . click ( x , y ) |
def plot_profile_histogram ( x , y , n_bins = 100 , title = None , x_label = None , y_label = None , log_y = False , filename = None ) :
'''Takes 2D point data ( x , y ) and creates a profile histogram similar to the TProfile in ROOT . It calculates
the y mean for every bin at the bin center and gives the y mean ... | if len ( x ) != len ( y ) :
raise ValueError ( 'x and y dimensions have to be the same' )
n , bin_edges = np . histogram ( x , bins = n_bins )
# needed to calculate the number of points per bin
sy = np . histogram ( x , bins = n_bins , weights = y ) [ 0 ]
# the sum of the bin values
sy2 = np . histogram ( x , bins ... |
def update ( gandi , resource , memory , cores , console , password , background , reboot ) :
"""Update a virtual machine .
Resource can be a Hostname or an ID""" | pwd = None
if password :
pwd = click . prompt ( 'password' , hide_input = True , confirmation_prompt = True )
max_memory = None
if memory :
max_memory = gandi . iaas . required_max_memory ( resource , memory )
if max_memory and not reboot :
gandi . echo ( 'memory update must be done offline.' )
if not c... |
def raises_not_implemented ( self ) :
"""Check if this node raises a : class : ` NotImplementedError ` .
: returns : True if this node raises a : class : ` NotImplementedError ` ,
False otherwise .
: rtype : bool""" | if not self . exc :
return False
for name in self . exc . _get_name_nodes ( ) :
if name . name == "NotImplementedError" :
return True
return False |
def create_result ( self , ip , host_port , container_port , meta , val , dividers ) :
"""The format is the same as the default docker cli client : :
ip : hostPort : containerPort | ip : : containerPort | hostPort : containerPort | containerPort""" | if host_port in ( '' , NotSpecified ) and container_port in ( '' , NotSpecified ) :
container_port = ip
ip = NotSpecified
host_port = NotSpecified
elif container_port in ( '' , NotSpecified ) :
container_port = host_port
host_port = ip
ip = NotSpecified
elif host_port in ( '' , NotSpecified ) :
... |
def render ( self ) :
'''Renders widget to template''' | data = self . prepare_data ( )
if self . field . readable :
return self . env . template . render ( self . template , ** data )
return '' |
def unlock_account ( account ) :
"""Unlock the account .
: param account : Account
: return :""" | return Web3Provider . get_web3 ( ) . personal . unlockAccount ( account . address , account . password ) |
def _evaluate ( self , R , z , phi = 0. , t = 0. ) :
"""NAME :
_ evaluate
PURPOSE :
evaluate the potential at R , z
INPUT :
R - Galactocentric cylindrical radius
z - vertical height
phi - azimuth
t - time
OUTPUT :
Phi ( R , z )
HISTORY :
2015-02-07 - Written - Bovy ( IAS )""" | return self . _mn3 [ 0 ] ( R , z , phi = phi , t = t ) + self . _mn3 [ 1 ] ( R , z , phi = phi , t = t ) + self . _mn3 [ 2 ] ( R , z , phi = phi , t = t ) |
def get_token ( self ) :
"""Gets the authorization token""" | payload = { 'grant_type' : 'client_credentials' , 'client_id' : self . client_id , 'client_secret' : self . client_secret }
r = requests . post ( OAUTH_ENDPOINT , data = json . dumps ( payload ) , headers = { 'content-type' : 'application/json' } )
response = r . json ( )
if r . status_code != 200 and not ERROR_KEY in ... |
def contents ( self ) :
"""Returns the item in the container , if there is one .
This will be a standard item object .""" | rawitem = self . _item . get ( "contained_item" )
if rawitem :
return self . __class__ ( rawitem , self . _schema ) |
def _find_models ( self , constructor , table_name , constraints = None , * , columns = None , order_by = None , limiting = None ) :
"""Calls DataAccess . find _ all and passes the results to the given constructor .""" | for record in self . find_all ( table_name , constraints , columns = columns , order_by = order_by , limiting = limiting ) :
yield constructor ( record ) |
def unzip_manifest ( self , raw_manifest ) :
"""Decompress gzip encoded manifest
: type raw _ manifest : str
: param raw _ manifest : compressed gzip manifest file content""" | buf = BytesIO ( raw_manifest )
f = gzip . GzipFile ( fileobj = buf )
manifest = f . read ( )
return manifest |
def check ( self , records ) :
"""Check current value .""" | for value , target in records :
LOGGER . info ( "%s [%s]: %s" , self . name , target , value )
if value is None :
self . notify ( self . no_data , value , target )
continue
for rule in self . rules :
if self . evaluate_rule ( rule , value , target ) :
self . notify ( rule... |
def input_has_value ( step , field_name , value ) :
"""Check that the form input element has given value .""" | with AssertContextManager ( step ) :
text_field = find_any_field ( world . browser , DATE_FIELDS + TEXT_FIELDS , field_name )
assert_false ( step , text_field is False , 'Can not find a field named "%s"' % field_name )
assert_equals ( text_field . get_attribute ( 'value' ) , value ) |
def append_note ( self , player , text ) :
"""Append text to an already existing note .""" | note = self . _find_note ( player )
note . text += text |
def _preconditions_snapshots_postconditions ( checker : Callable ) -> _PrePostSnaps :
"""Collect the preconditions , snapshots and postconditions from a contract checker of a function .""" | preconditions = getattr ( checker , "__preconditions__" , [ ] )
# type : List [ List [ icontract . _ Contract ] ]
assert all ( isinstance ( precondition_group , list ) for precondition_group in preconditions )
assert ( all ( isinstance ( precondition , icontract . _Contract ) for precondition_group in preconditions for... |
def user ( self , username ) :
"""Returns the : class : ` ~ plexapi . myplex . MyPlexUser ` that matches the email or username specified .
Parameters :
username ( str ) : Username , email or id of the user to return .""" | for user in self . users ( ) : # Home users don ' t have email , username etc .
if username . lower ( ) == user . title . lower ( ) :
return user
elif ( user . username and user . email and user . id and username . lower ( ) in ( user . username . lower ( ) , user . email . lower ( ) , str ( user . id )... |
def _get_tough_method ( self , method ) :
"""Return a " tough " version of a connection class method .
The tough version checks whether the connection is bad ( lost )
and automatically and transparently tries to reset the connection
if this is the case ( for instance , the database has been restarted ) .""" | def tough_method ( * args , ** kwargs ) :
transaction = self . _transaction
if not transaction :
try : # check whether connection status is bad
if not self . _con . db . status :
raise AttributeError
if self . _maxusage : # or connection used too often
... |
def relevantindices ( self ) -> List [ int ] :
"""A | list | of all currently relevant indices , calculated as an
intercection of the ( constant ) class attribute ` RELEVANT _ VALUES `
and the ( variable ) property | IndexMask . refindices | .""" | return [ idx for idx in numpy . unique ( self . refindices . values ) if idx in self . RELEVANT_VALUES ] |
def by_filenumber ( self ) :
"""Iterates over categories and returns a filtered datamat .
If a categories object is attached , the images object for the given
category is returned as well ( else None is returned ) .
Returns :
( datamat , categories ) : A tuple that contains first the filtered
datamat ( ha... | for value in np . unique ( self . filenumber ) :
file_fm = self . filter ( self . filenumber == value )
if self . _categories :
yield ( file_fm , self . _categories [ self . category [ 0 ] ] [ value ] )
else :
yield ( file_fm , None ) |
def filter ( select , iterable , namespaces = None , flags = 0 , ** kwargs ) : # noqa : A001
"""Filter list of nodes .""" | return compile ( select , namespaces , flags , ** kwargs ) . filter ( iterable ) |
def mod_run_check ( onlyif , unless , creates ) :
'''Execute the onlyif / unless / creates logic . Returns a result dict if any of
the checks fail , otherwise returns True''' | cmd_kwargs = { 'use_vt' : False , 'bg' : False }
if onlyif is not None :
if isinstance ( onlyif , six . string_types ) :
onlyif = [ onlyif ]
if not isinstance ( onlyif , list ) or not all ( isinstance ( x , six . string_types ) for x in onlyif ) :
return { 'comment' : 'onlyif is not a string or ... |
def align_two_alignments ( aln1 , aln2 , moltype , params = None ) :
"""Returns an Alignment object from two existing Alignments .
aln1 , aln2 : cogent . core . alignment . Alignment objects , or data that can be
used to build them .
- Mafft profile alignment only works with aligned sequences . Alignment
ob... | # create SequenceCollection object from seqs
aln1 = Alignment ( aln1 , MolType = moltype )
# Create mapping between abbreviated IDs and full IDs
aln1_int_map , aln1_int_keys = aln1 . getIntMap ( )
# Create SequenceCollection from int _ map .
aln1_int_map = Alignment ( aln1_int_map , MolType = moltype )
# create Alignme... |
def diff_asymmetric ( self , catalogue , prime_label , tokenizer , output_fh ) :
"""Returns ` output _ fh ` populated with CSV results giving the
difference in n - grams between the witnesses of labelled sets
of works in ` catalogue ` , limited to those works labelled with
` prime _ label ` .
: param catalo... | labels = list ( self . _set_labels ( catalogue ) )
if len ( labels ) < 2 :
raise MalformedQueryError ( constants . INSUFFICIENT_LABELS_QUERY_ERROR )
try :
labels . remove ( prime_label )
except ValueError :
raise MalformedQueryError ( constants . LABEL_NOT_IN_CATALOGUE_ERROR )
label_placeholders = self . _g... |
def set_cells ( self , cells_location ) :
"""Set self . cells to function : cells in file pathname . py
: param cells _ location : cells location , format ' pathname . py : cells '
: return :""" | if ':' in cells_location :
pathname , func_name = cells_location . split ( ':' )
else :
pathname = cells_location
func_name = 'cells'
check_isfile ( pathname )
try :
self . cells = get_func ( func_name , pathname )
except SyntaxError as e :
fatal ( traceback . format_exc ( limit = 1 ) )
return pathn... |
def ifft ( self ) :
"""Compute the one - dimensional discrete inverse Fourier
transform of this ` FrequencySeries ` .
Returns
out : : class : ` ~ gwpy . timeseries . TimeSeries `
the normalised , real - valued ` TimeSeries ` .
See Also
: mod : ` scipy . fftpack ` for the definition of the DFT and conven... | from . . timeseries import TimeSeries
nout = ( self . size - 1 ) * 2
# Undo normalization from TimeSeries . fft
# The DC component does not have the factor of two applied
# so we account for it here
dift = npfft . irfft ( self . value * nout ) / 2
new = TimeSeries ( dift , epoch = self . epoch , channel = self . channe... |
def paths_wanted ( self ) :
"""The set of paths where we expect to find missing nodes .""" | return set ( address . new ( b , target = 'all' ) for b in self . missing_nodes ) |
def transfer ( self , name , local , remote , ** kwargs ) :
"""Transfers the file with the given name from the local to the remote
storage backend .
: param name : The name of the file to transfer
: param local : The local storage backend instance
: param remote : The remote storage backend instance
: ret... | try :
remote . save ( name , local . open ( name ) )
return True
except Exception as e :
logger . error ( "Unable to save '%s' to remote storage. " "About to retry." % name )
logger . exception ( e )
return False |
def remove_collisions ( self , min_dist = 0.5 ) :
"""Remove predicted sites that are too close to existing atoms in the
structure .
Args :
min _ dist ( float ) : The minimum distance ( in Angstrom ) that
a predicted site needs to be from existing atoms . A min _ dist
with value < = 0 returns all sites wit... | s_f_coords = self . structure . frac_coords
f_coords = self . extrema_coords
if len ( f_coords ) == 0 :
if self . extrema_type is None :
logger . warning ( "Please run ChargeDensityAnalyzer.get_local_extrema first!" )
return
new_f_coords = [ ]
self . _update_extrema ( new_f_coords , self . e... |
def show_guiref ( self ) :
"""Show qtconsole help""" | from qtconsole . usage import gui_reference
self . main . help . show_rich_text ( gui_reference , collapse = True ) |
def compressBWT ( inputFN , outputFN , numProcs , logger ) :
'''Current encoding scheme uses 3 LSB for the letter and 5 MSB for a count , note that consecutive ones of the same character
combine to create one large count . So to represent 34A , you would have 00010 | 001 followed by 00001 | 001 which can be thoug... | # create bit spacings
letterBits = 3
numberBits = 8 - letterBits
numPower = 2 ** numberBits
mask = 255 >> letterBits
# load the thing to compress
logger . info ( 'Loading src file...' )
bwt = np . load ( inputFN , 'r' )
logger . info ( 'Original size:' + str ( bwt . shape [ 0 ] ) + 'B' )
numProcs = min ( numProcs , bwt... |
def optimise_levenberg_marquardt ( x , a , c , damping = 0.001 , tolerance = 0.001 ) :
"""Optimise value of x using levenberg - marquardt""" | x_new = x
x_old = x - 1
# dummy value
f_old = f ( x_new , a , c )
while np . abs ( x_new - x_old ) . sum ( ) > tolerance :
x_old = x_new
x_tmp = levenberg_marquardt_update ( x_old , a , c , damping )
f_new = f ( x_tmp , a , c )
if f_new < f_old :
damping = np . max ( damping / 10. , 1e-20 )
... |
def oscltx ( state , et , mu ) :
"""Determine the set of osculating conic orbital elements that
corresponds to the state ( position , velocity ) of a body at some
epoch . In additional to the classical elements , return the true
anomaly , semi - major axis , and period , if applicable .
https : / / naif . j... | state = stypes . toDoubleVector ( state )
et = ctypes . c_double ( et )
mu = ctypes . c_double ( mu )
elts = stypes . emptyDoubleVector ( 20 )
libspice . oscltx_c ( state , et , mu , elts )
return stypes . cVectorToPython ( elts ) [ 0 : 11 ] |
def on_shutdown ( self ) :
"""Respond to shutdown by sending close ( ) to every target , allowing their
receive loop to exit and clean up gracefully .""" | LOG . debug ( '%r.on_shutdown()' , self )
for stream , state in self . _state_by_stream . items ( ) :
state . lock . acquire ( )
try :
for sender , fp in reversed ( state . jobs ) :
sender . close ( )
fp . close ( )
state . jobs . pop ( )
finally :
state .... |
def get_nonconflicting_path_old ( base_fmtstr , dpath , offset = 0 ) :
r"""base _ fmtstr must have a % d in it""" | import utool as ut
from os . path import basename
pattern = '*'
dname_list = ut . glob ( dpath , pattern , recursive = False , with_files = True , with_dirs = True )
conflict_set = set ( [ basename ( dname ) for dname in dname_list ] )
newname = ut . get_nonconflicting_string ( base_fmtstr , conflict_set , offset = off... |
def value_from_datadict ( self , data , files , name ) :
"""Returns uploaded file from serialized value .""" | upload = super ( StickyUploadWidget , self ) . value_from_datadict ( data , files , name )
if upload is not None : # File was posted or cleared as normal
return upload
else : # Try the hidden input
hidden_name = self . get_hidden_name ( name )
value = data . get ( hidden_name , None )
if value is not No... |
def get_context ( self , ** kwargs ) :
"""Use this method to built context data for the template
Mix django wizard context data with django - xadmin context""" | context = self . get_context_data ( form = self . form_obj , ** kwargs )
context . update ( super ( FormAdminView , self ) . get_context ( ) )
return context |
def create_resource_quota ( self , name , quota_json ) :
"""Prevent builds being scheduled and wait for running builds to finish .
: return :""" | url = self . _build_k8s_url ( "resourcequotas/" )
response = self . _post ( url , data = json . dumps ( quota_json ) , headers = { "Content-Type" : "application/json" } )
if response . status_code == http_client . CONFLICT :
url = self . _build_k8s_url ( "resourcequotas/%s" % name )
response = self . _put ( url... |
def wait_until_exit ( self ) :
"""Wait until all the threads are finished .""" | [ t . join ( ) for t in self . threads ]
self . threads = list ( ) |
def create_checkbox ( self , name , margin = 10 ) :
"""Function creates a checkbox with his name""" | chk_btn = Gtk . CheckButton ( name )
chk_btn . set_margin_right ( margin )
return chk_btn |
def load_zip_data ( zipname , f_sino_real , f_sino_imag , f_angles = None , f_phantom = None , f_info = None ) :
"""Load example sinogram data from a . zip file""" | ret = [ ]
with zipfile . ZipFile ( str ( zipname ) ) as arc :
sino_real = np . loadtxt ( arc . open ( f_sino_real ) )
sino_imag = np . loadtxt ( arc . open ( f_sino_imag ) )
sino = sino_real + 1j * sino_imag
ret . append ( sino )
if f_angles :
angles = np . loadtxt ( arc . open ( f_angles ) ... |
def n_segments ( neurites , neurite_type = NeuriteType . all ) :
'''Number of segments in a collection of neurites''' | return sum ( len ( s . points ) - 1 for s in iter_sections ( neurites , neurite_filter = is_type ( neurite_type ) ) ) |
def name_conversion ( caffe_layer_name ) :
"""Convert a caffe parameter name to a tensorflow parameter name as
defined in the above model""" | # beginning & end mapping
NAME_MAP = { 'bn_conv1/beta' : 'conv0/bn/beta' , 'bn_conv1/gamma' : 'conv0/bn/gamma' , 'bn_conv1/mean/EMA' : 'conv0/bn/mean/EMA' , 'bn_conv1/variance/EMA' : 'conv0/bn/variance/EMA' , 'conv1/W' : 'conv0/W' , 'conv1/b' : 'conv0/b' , 'fc1000/W' : 'linear/W' , 'fc1000/b' : 'linear/b' }
if caffe_la... |
def is_dxlink ( x ) :
''': param x : A potential DNAnexus link
Returns whether * x * appears to be a DNAnexus link ( is a dict with
key ` ` " $ dnanexus _ link " ` ` ) with a referenced data object .''' | if not isinstance ( x , dict ) :
return False
if '$dnanexus_link' not in x :
return False
link = x [ '$dnanexus_link' ]
if isinstance ( link , basestring ) :
return True
elif isinstance ( link , dict ) :
return any ( key in link for key in ( 'id' , 'job' ) )
return False |
def delete_repository ( self , namespace , repository ) :
"""DELETE / v1 / repositories / ( namespace ) / ( repository ) /""" | return self . _http_call ( self . REPO , delete , namespace = namespace , repository = repository ) |
async def read_message ( self ) -> Optional [ Data ] :
"""Read a single message from the connection .
Re - assemble data frames if the message is fragmented .
Return ` ` None ` ` when the closing handshake is started .""" | frame = await self . read_data_frame ( max_size = self . max_size )
# A close frame was received .
if frame is None :
return None
if frame . opcode == OP_TEXT :
text = True
elif frame . opcode == OP_BINARY :
text = False
else : # frame . opcode = = OP _ CONT
raise WebSocketProtocolError ( "Unexpected op... |
def publish_api ( self , ret , stage_variables ) :
'''this method tie the given stage _ name to a deployment matching the given swagger _ file''' | stage_desc = dict ( )
stage_desc [ 'current_deployment_label' ] = self . deployment_label
stage_desc_json = _dict_to_json_pretty ( stage_desc )
if self . _deploymentId : # just do a reassociate of stage _ name to an already existing deployment
res = self . _set_current_deployment ( stage_desc_json , stage_variables... |
def process_request_thread ( self , request , client_address ) :
"""Process the request .""" | try :
self . finish_request ( request , client_address )
self . shutdown_request ( request )
except Exception as e :
self . logger . error ( e )
self . handle_error ( request , client_address )
self . shutdown_request ( request ) |
def set_position ( self , pos ) :
"""Seek in the current playing media .""" | time_in_ms = int ( pos ) * 1000
return self . apple_tv . set_property ( 'dacp.playingtime' , time_in_ms ) |
def list_users ( self , instance , limit = None , marker = None ) :
"""Returns all users for the specified instance .""" | return instance . list_users ( limit = limit , marker = marker ) |
def _set_attributes ( self , response , attribute_dict ) :
"""Set user attributes based on response code
: param response : HTTP response from Cognito
: attribute dict : Dictionary of attribute name and values""" | status_code = response . get ( 'HTTPStatusCode' , response [ 'ResponseMetadata' ] [ 'HTTPStatusCode' ] )
if status_code == 200 :
for k , v in attribute_dict . items ( ) :
setattr ( self , k , v ) |
def _get_task_host ( ) :
"""Get the Host header value for all mr tasks .
Task Host header determines which instance this task would be routed to .
Current version id format is : v7.368834058928280579
Current module id is just the module ' s name . It could be " default "
Default version hostname is app _ id... | version = os . environ [ "CURRENT_VERSION_ID" ] . split ( "." ) [ 0 ]
default_host = os . environ [ "DEFAULT_VERSION_HOSTNAME" ]
module = os . environ [ "CURRENT_MODULE_ID" ]
if os . environ [ "CURRENT_MODULE_ID" ] == "default" :
return "%s.%s" % ( version , default_host )
return "%s.%s.%s" % ( version , module , d... |
def getrepaymentsurl ( idcred , * args , ** kwargs ) :
"""Request loan Repayments URL .
If idcred is set , you ' ll get a response adequate for a
MambuRepayments object . There ' s a MambuRepayment object too , but
you ' ll get a list first and each element of it will be automatically
converted to a MambuRe... | url = getmambuurl ( * args , ** kwargs ) + "loans/" + idcred + "/repayments"
return url |
def scan ( self , file_or_stream ) :
""": param file _ or _ stream : : class : ` Blob ` instance , filename or file object
: returns : True if file is ' clean ' , False if a virus is detected , None if
file could not be scanned .
If ` file _ or _ stream ` is a Blob , scan result is stored in
Blob . meta [ '... | if not clamd :
return None
res = self . _scan ( file_or_stream )
if isinstance ( file_or_stream , Blob ) :
file_or_stream . meta [ "antivirus" ] = res
return res |
def getCurrentItem ( self ) : # TODO : rename ? getCurrentItemAndIndex ? getCurrentTuple ? getCurrent ?
"""Find the current tree item ( and the current index while we ' re at it )
Returns a tuple with the current item , and its index . The item may be None .
See also the notes at the top of this module on curre... | currentIndex = self . getRowCurrentIndex ( )
currentItem = self . model ( ) . getItem ( currentIndex )
return currentItem , currentIndex |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.