signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def _build_filename_from_browserstack_json ( j ) :
"""Build a useful filename for an image from the screenshot json metadata""" | filename = ''
device = j [ 'device' ] if j [ 'device' ] else 'Desktop'
if j [ 'state' ] == 'done' and j [ 'image_url' ] :
detail = [ device , j [ 'os' ] , j [ 'os_version' ] , j [ 'browser' ] , j [ 'browser_version' ] , '.jpg' ]
filename = '_' . join ( item . replace ( " " , "_" ) for item in detail if item )
e... |
def login ( self , username , password , token ) :
'''Login to Salesforce . com and starts a client session .
Unlike other toolkits , token is a separate parameter , because
Salesforce doesn ' t explicitly tell you to append it when it gives
you a login error . Folks that are new to the API may not know this ... | self . _setHeaders ( 'login' )
result = self . _sforce . service . login ( username , password + token )
# set session header
header = self . generateHeader ( 'SessionHeader' )
header . sessionId = result [ 'sessionId' ]
self . setSessionHeader ( header )
self . _sessionId = result [ 'sessionId' ]
self . _userId = resu... |
def List ( self , * branches , ** kwargs ) :
"""While ` Seq ` is sequential , ` phi . dsl . Expression . List ` allows you to split the computation and get back a list with the result of each path . While the list literal should be the most incarnation of this expresion , it can actually be any iterable ( implement... | gs = [ _parse ( code ) . _f for code in branches ]
def h ( x , state ) :
ys = [ ]
for g in gs :
y , state = g ( x , state )
ys . append ( y )
return ( ys , state )
return self . __then__ ( h , ** kwargs ) |
def _adjust_width ( self ) :
"""Shrinks bar if number of iterations is less than the bar width""" | if self . bar_width > self . max_iter :
self . bar_width = int ( self . max_iter ) |
def _calc ( self , x , y ) :
"""List based implementation of binary tree algorithm for concordance
measure after : cite : ` Christensen2005 ` .""" | x = np . array ( x )
y = np . array ( y )
n = len ( y )
perm = list ( range ( n ) )
perm . sort ( key = lambda a : ( x [ a ] , y [ a ] ) )
vals = y [ perm ]
ExtraY = 0
ExtraX = 0
ACount = 0
BCount = 0
CCount = 0
DCount = 0
ECount = 0
DCount = 0
Concordant = 0
Discordant = 0
# ids for left child
li = [ None ] * ( n - 1 ... |
def is_the_same_indel ( self , other_record , ref_seq ) :
'''Returns True iff this record and other _ record are the " same "
indel . At repeats , there is more than one way to report the same
variant . eg :
pos = 42 , ref = CAAA , alt = CAA
pos = 43 , ref = AAA , alt = AA
pos = 44 , ref = AA , alt = A''' | if self . CHROM != other_record . CHROM or len ( self . ALT ) > 1 or len ( other_record . ALT ) > 1 or self . is_snp ( ) or other_record . is_snp ( ) :
return False
# The number of nuleotides that have been added or removed
# is a necessary condition of the indels being the same ,
# so check that before devling int... |
def cnst_AT ( self , Y ) :
r"""Compute : math : ` A ^ T \ mathbf { y } ` . In this case
: math : ` A ^ T \ mathbf { y } = ( I \ ; \ ; \ Gamma _ 0 ^ T \ ; \ ; \ Gamma _ 1 ^ T \ ; \ ;
\ ldots ) \ mathbf { y } ` .""" | return self . cnst_A0T ( self . block_sep0 ( Y ) ) + np . sum ( self . cnst_A1T ( self . block_sep1 ( Y ) ) , axis = - 1 ) |
def checkGeneTreeMatchesSpeciesTree ( speciesTree , geneTree , processID ) :
"""Function to check ids in gene tree all match nodes in species tree""" | def fn ( tree , l ) :
if tree . internal :
fn ( tree . left , l )
fn ( tree . right , l )
else :
l . append ( processID ( tree . iD ) )
l = [ ]
fn ( speciesTree , l )
l2 = [ ]
fn ( geneTree , l2 )
for i in l2 : # print " node " , i , l
assert i in l |
def create_inline ( project , resource , offset ) :
"""Create a refactoring object for inlining
Based on ` resource ` and ` offset ` it returns an instance of
` InlineMethod ` , ` InlineVariable ` or ` InlineParameter ` .""" | pyname = _get_pyname ( project , resource , offset )
message = 'Inline refactoring should be performed on ' 'a method, local variable or parameter.'
if pyname is None :
raise rope . base . exceptions . RefactoringError ( message )
if isinstance ( pyname , pynames . ImportedName ) :
pyname = pyname . _get_import... |
def format_string ( string , foreground = None , background = None , reset = True , bold = False , faint = False , italic = False , underline = False , blink = False , inverted = False ) :
"""Returns a Unicode string formatted with an ANSI escape sequence .
string
String to format
foreground
Foreground colo... | colour_format = format_escape ( foreground , background , bold , faint , italic , underline , blink , inverted )
reset_format = '' if not reset else ANSI_FORMAT_RESET
return '{}{}{}' . format ( colour_format , string , reset_format ) |
def _get_connection ( self ) :
"""Returns connection to the postgres database .
Returns :
connection to postgres database who stores mpr data .""" | if not getattr ( self , '_connection' , None ) :
logger . debug ( 'Creating new connection.\n dsn: {}' . format ( self . _dsn ) )
d = parse_url_to_dict ( self . _dsn )
self . _connection = psycopg2 . connect ( database = d [ 'path' ] . strip ( '/' ) , user = d [ 'username' ] , password = d [ 'password' ] ... |
def decode ( self , codes ) :
"""Given PQ - codes , reconstruct original D - dimensional vectors via : func : ` PQ . decode ` ,
and applying an inverse - rotation .
Args :
codes ( np . ndarray ) : PQ - cdoes with shape = ( N , M ) and dtype = self . code _ dtype .
Each row is a PQ - code
Returns :
np . ... | # Because R is a rotation matrix ( R ^ t * R = I ) , R ^ - 1 should be R ^ t
return self . pq . decode ( codes ) @ self . R . T |
def _resource_index ( self , resource ) :
"""Get index for given resource .
by default it will be ` self . index ` , but it can be overriden via app . config
: param resource : resource name""" | datasource = self . get_datasource ( resource )
indexes = self . _resource_config ( resource , 'INDEXES' ) or { }
default_index = self . _resource_config ( resource , 'INDEX' )
return indexes . get ( datasource [ 0 ] , default_index ) |
def ping ( self ) :
"""Check connectivity to InfluxDB .
: returns : The version of the InfluxDB the client is connected to""" | response = self . request ( url = "ping" , method = 'GET' , expected_response_code = 204 )
return response . headers [ 'X-Influxdb-Version' ] |
def _get_gene_info ( self , limit ) :
"""Currently loops through the gene _ info file and
creates the genes as classes , typed with SO . It will add their label ,
any alternate labels as synonyms , alternate ids as equivlaent classes .
HPRDs get added as protein products .
The chromosome and chr band get ad... | src_key = 'gene_info'
if self . test_mode :
graph = self . testgraph
else :
graph = self . graph
geno = Genotype ( graph )
model = Model ( graph )
# not unzipping the file
LOG . info ( "Processing 'Gene Info' records" )
line_counter = 0
gene_info = '/' . join ( ( self . rawdir , self . files [ src_key ] [ 'file... |
def clear_data ( self ) :
"""Removes the content data .
raise : NoAccess - ` ` Metadata . isRequired ( ) ` ` is ` ` true ` ` or
` ` Metadata . isReadOnly ( ) ` ` is ` ` true ` `
* compliance : mandatory - - This method must be implemented . *""" | # cjshaw @ mit . edu , Jan 9 , 2015
# Removes the item from AWS S3 and resets URL to ' '
odl_repo , url = get_aws_s3_handle ( self . _config_map )
existing_url = self . _payload . get_url_metadata ( ) . get_existing_string_values ( ) [ 0 ]
# try to clear from payload first , in case that fails we won ' t mess with AWS
... |
def create_cmd ( self , args ) :
'''' create ' sub - command
: param args : cli arguments
: return :''' | cmd = args . get ( 'cmd_create' )
if cmd == 'conf' :
conf_file = args [ 'conf_file' ]
conf_id = args [ 'id' ]
return self . load_xml_conf ( conf_file , conf_id )
else :
print ( "Error: Create %s is invalid or not implemented" % cmd ) |
def Main ( ) :
"""The main function .
Returns :
bool : True if successful or False otherwise .""" | tool = image_export_tool . ImageExportTool ( )
if not tool . ParseArguments ( ) :
return False
if tool . list_signature_identifiers :
tool . ListSignatureIdentifiers ( )
return True
if not tool . has_filters :
logging . warning ( 'No filter defined exporting all files.' )
# TODO : print more status info... |
def _add_tip_during_transfer ( self , tips , ** kwargs ) :
"""Performs a : any : ` pick _ up _ tip ` when running a : any : ` transfer ` ,
: any : ` distribute ` , or : any : ` consolidate ` .""" | if self . has_tip_rack ( ) and tips > 0 and not self . current_tip ( ) :
self . pick_up_tip ( ) |
def raw ( self , use_local = True ) :
"""Load the raw dataset from remote URL or local file
Parameters
use _ local : boolean
If True ( default ) , then attempt to load the dataset locally . If
False or if the dataset is not available locally , then load the
data from an external URL .""" | if use_local and self . is_local :
return pkgutil . get_data ( 'vega_datasets' , self . pkg_filename )
else :
return urlopen ( self . url ) . read ( ) |
def load_tensor ( f , format = None ) : # type : ( Union [ IO [ bytes ] , Text ] , Optional [ Any ] ) - > TensorProto
'''Loads a serialized TensorProto into memory
@ params
f can be a file - like object ( has " read " function ) or a string containing a file name
format is for future use
@ return
Loaded i... | s = _load_bytes ( f )
return load_tensor_from_string ( s , format = format ) |
def send_game ( self , chat_id : Union [ int , str ] , game_short_name : str , disable_notification : bool = None , reply_to_message_id : int = None , reply_markup : Union [ "pyrogram.InlineKeyboardMarkup" , "pyrogram.ReplyKeyboardMarkup" , "pyrogram.ReplyKeyboardRemove" , "pyrogram.ForceReply" ] = None ) -> "pyrogram.... | r = self . send ( functions . messages . SendMedia ( peer = self . resolve_peer ( chat_id ) , media = types . InputMediaGame ( id = types . InputGameShortName ( bot_id = types . InputUserSelf ( ) , short_name = game_short_name ) , ) , message = "" , silent = disable_notification or None , reply_to_msg_id = reply_to_mes... |
def extract_subtree ( self , node ) :
'''Return a copy of the subtree rooted at ` ` node ` `
Args :
` ` node ` ` ( ` ` Node ` ` ) : The root of the desired subtree
Returns :
` ` Tree ` ` : A copy of the subtree rooted at ` ` node ` `''' | if not isinstance ( node , Node ) :
raise TypeError ( "node must be a Node" )
r = self . root ;
self . root = node ;
o = copy ( self ) ;
self . root = r ;
return o |
def make_arrow ( self , portal ) :
"""Make an : class : ` Arrow ` to represent a : class : ` Portal ` , store it ,
and return it .""" | if ( portal [ "origin" ] not in self . spot or portal [ "destination" ] not in self . spot ) :
raise ValueError ( "An :class:`Arrow` should only be made after " "the :class:`Spot`s it connects" )
if ( portal [ "origin" ] in self . arrow and portal [ "destination" ] in self . arrow [ portal [ "origin" ] ] ) :
ra... |
def _analyze_txt_config ( self , config_string = None ) :
"""Analyze the given container and return the corresponding job .
If ` ` config _ string ` ` is ` ` None ` ` ,
try reading it from the TXT config file inside the container .
: param string config _ string : the configuration string
: rtype : : class ... | self . log ( u"Analyzing container with TXT config string" )
if config_string is None :
self . log ( u"Analyzing container with TXT config file" )
config_entry = self . container . entry_config_txt
self . log ( [ u"Found TXT config entry '%s'" , config_entry ] )
config_dir = os . path . dirname ( config... |
def request ( self , method , endpoint , payload = None , timeout = 5 ) :
"""Send request to API .""" | url = self . api_url + endpoint
data = None
headers = { }
if payload is not None :
data = json . dumps ( payload )
headers [ 'Content-Type' ] = 'application/json'
try :
if self . auth_token is not None :
headers [ API_AUTH_HEADER ] = self . auth_token
response = self . session . request ( me... |
def get_response ( url , plugins , timeout = SPLASH_TIMEOUT ) :
"""Return response with HAR , inline scritps and software detected by JS matchers .
: rtype : dict""" | lua_script = create_lua_script ( plugins )
lua = urllib . parse . quote_plus ( lua_script )
page_url = f'{SPLASH_URL}/execute?url={url}&timeout={timeout}&lua_source={lua}'
try :
with docker_container ( ) :
logger . debug ( '[+] Sending request to Splash instance' )
res = requests . get ( page_url )
... |
def parse ( self , path ) :
"""Extracts a dictionary of values from the XML file at the specified path .""" | # Load the template that will be used for parsing the values .
expath , template , root = self . _load_template ( path )
if expath is not None :
values = template . parse ( root )
return ( values , template ) |
def _search ( self , search_terms , begins_with = None ) :
"""Returns a list of Archive id ' s in the table on Dynamo""" | kwargs = dict ( ProjectionExpression = '#id' , ExpressionAttributeNames = { "#id" : "_id" } )
if len ( search_terms ) > 0 :
kwargs [ 'FilterExpression' ] = reduce ( lambda x , y : x & y , [ Attr ( 'tags' ) . contains ( arg ) for arg in search_terms ] )
if begins_with :
if 'FilterExpression' in kwargs :
... |
def to_code_array ( self ) :
"""Replaces everything in code _ array from xls _ file""" | self . _xls2shape ( )
worksheets = self . workbook . sheet_names ( )
for tab , worksheet_name in enumerate ( worksheets ) :
worksheet = self . workbook . sheet_by_name ( worksheet_name )
self . _xls2code ( worksheet , tab )
self . _xls2attributes ( worksheet , tab )
self . _xls2row_heights ( worksheet ,... |
def _extract_blocks ( x , block_h , block_w ) :
"""Helper function for local 2d attention .
Args :
x : a [ batch , height , width , depth ] tensor
block _ h : An integer . block height
block _ w : An inteter . block width
returns :
a [ batch , num _ heads , height / block _ h , width / block _ w , depth... | ( _ , height , width , depth ) = common_layers . shape_list ( x )
assert height % block_h == 0
assert width % block_w == 0
x = tf . reshape ( x , [ - 1 , height // block_h , block_h , width // block_w , block_w , depth ] )
return tf . transpose ( x , [ 0 , 1 , 3 , 2 , 4 , 5 ] ) |
def package_meta ( ) :
"""Read _ _ init _ _ . py for global package metadata .
Do this without importing the package .""" | _version_re = re . compile ( r'__version__\s+=\s+(.*)' )
_url_re = re . compile ( r'__url__\s+=\s+(.*)' )
_license_re = re . compile ( r'__license__\s+=\s+(.*)' )
with open ( 'lambda_uploader/__init__.py' , 'rb' ) as ffinit :
initcontent = ffinit . read ( )
version = str ( ast . literal_eval ( _version_re . sea... |
def rotate_bitmaps_to_roots ( bitmaps , roots ) :
"""Circularly shift a relative bitmaps to asbolute pitch classes .
See : func : ` rotate _ bitmap _ to _ root ` for more information .
Parameters
bitmap : np . ndarray , shape = ( N , 12)
Bitmap of active notes , relative to the given root .
root : np . nd... | abs_bitmaps = [ ]
for bitmap , chord_root in zip ( bitmaps , roots ) :
abs_bitmaps . append ( rotate_bitmap_to_root ( bitmap , chord_root ) )
return np . asarray ( abs_bitmaps ) |
def cli ( env , volume_id , capacity , tier , upgrade ) :
"""Order snapshot space for a file storage volume .""" | file_manager = SoftLayer . FileStorageManager ( env . client )
if tier is not None :
tier = float ( tier )
try :
order = file_manager . order_snapshot_space ( volume_id , capacity = capacity , tier = tier , upgrade = upgrade )
except ValueError as ex :
raise exceptions . ArgumentError ( str ( ex ) )
if 'pla... |
def receive ( self , path , diffTo , diffFrom ) :
"""Receive a btrfs diff .""" | diff = self . toObj . diff ( diffTo , diffFrom )
self . _open ( self . butterStore . receive ( diff , [ path , ] ) ) |
def scale ( self , width : int , height : int ) -> None :
"""Scale this Image to the new width and height .
Args :
width ( int ) : The new width of the Image after scaling .
height ( int ) : The new height of the Image after scaling .""" | lib . TCOD_image_scale ( self . image_c , width , height )
self . width , self . height = width , height |
def p_print_list_at ( p ) :
"""print _ at : AT expr COMMA expr""" | p [ 0 ] = make_sentence ( 'PRINT_AT' , make_typecast ( TYPE . ubyte , p [ 2 ] , p . lineno ( 1 ) ) , make_typecast ( TYPE . ubyte , p [ 4 ] , p . lineno ( 3 ) ) ) |
def _make_temp_directory ( prefix ) :
'''Generate a temporary directory that would not live beyond the lifetime of
unity _ server .
Caller is expected to clean up the temp file as soon as the directory is no
longer needed . But the directory will be cleaned as unity _ server restarts''' | temp_dir = _make_temp_filename ( prefix = str ( prefix ) )
_os . makedirs ( temp_dir )
return temp_dir |
def fetchUserJobs ( self , jobs ) :
"""Takes a user input array of jobs , verifies that they are in the jobStore
and returns the array of jobsToReport .
: param list jobs : A list of jobs to be verified .
: returns jobsToReport : A list of jobs which are verified to be in the jobStore .""" | jobsToReport = [ ]
for jobID in jobs :
try :
jobsToReport . append ( self . jobStore . load ( jobID ) )
except JobException :
print ( 'The job %s could not be found.' % jobID , file = sys . stderr )
raise
return jobsToReport |
def _validate_platforms_in_image ( self , image ) :
"""Ensure that the image provides all platforms expected for the build .""" | expected_platforms = get_platforms ( self . workflow )
if not expected_platforms :
self . log . info ( 'Skipping validation of available platforms ' 'because expected platforms are unknown' )
return
if len ( expected_platforms ) == 1 :
self . log . info ( 'Skipping validation of available platforms for base... |
def save ( self ) :
"""Saves pypirc file with new configuration information .""" | for server , conf in self . servers . iteritems ( ) :
self . _add_index_server ( )
for conf_k , conf_v in conf . iteritems ( ) :
if not self . conf . has_section ( server ) :
self . conf . add_section ( server )
self . conf . set ( server , conf_k , conf_v )
with open ( self . rc_fil... |
def search ( self , index = None , doc_type = None , body = None , ** query_params ) :
"""Make a search query on the elastic search
` < http : / / www . elastic . co / guide / en / elasticsearch / reference / current / search - search . html > ` _
: param index : the index name to query
: param doc _ type : h... | path = self . _es_parser . make_path ( index , doc_type , EsMethods . SEARCH )
result = yield self . _perform_request ( HttpMethod . POST , path , body = body , params = query_params )
returnValue ( result ) |
def response_hook ( self , r , ** kwargs ) :
"""The actual hook handler .""" | if r . status_code == 401 : # Handle server auth .
www_authenticate = r . headers . get ( 'www-authenticate' , '' ) . lower ( )
auth_type = _auth_type_from_header ( www_authenticate )
if auth_type is not None :
return self . retry_using_http_NTLM_auth ( 'www-authenticate' , 'Authorization' , r , aut... |
def _get_cached_stats ( self , app_stats ) :
"""Process :
* cached _ host _ check _ stats
* cached _ service _ check _ stats""" | stats = { }
app_keys = [ "cached_host_check_stats" , "cached_service_check_stats" , ]
for app_key in app_keys :
if app_key not in app_stats . keys ( ) :
continue
( x01 , x05 , x15 ) = self . _convert_tripplet ( app_stats [ app_key ] )
scratch = app_key . split ( "_" ) [ 1 ]
stats [ "%ss.cached.0... |
def by_id ( cls , user_id , db_session = None ) :
"""fetch user by user id
: param user _ id :
: param db _ session :
: return :""" | db_session = get_db_session ( db_session )
query = db_session . query ( cls . model )
query = query . filter ( cls . model . id == user_id )
query = query . options ( sa . orm . eagerload ( "groups" ) )
return query . first ( ) |
def get_n_header ( f , header_char = '"' ) :
'''Get the nummber of header rows in a Little Leonardo data file
Args
f : file stream
File handle for the file from which header rows will be read
header _ char : str
Character array at beginning of each header line
Returns
n _ header : int
Number of head... | n_header = 0
reading_headers = True
while reading_headers :
line = f . readline ( )
if line . startswith ( header_char ) :
n_header += 1
else :
reading_headers = False
return n_header |
def get_config ( self , budget ) :
"""Function to sample a new configuration
This function is called inside BOHB to query a new configuration
Parameters :
budget : float
the budget for which this configuration is scheduled
Returns
config
return a valid configuration with parameters and budget""" | logger . debug ( 'start sampling a new configuration.' )
sample = None
info_dict = { }
# If no model is available , sample from prior
# also mix in a fraction of random configs
if len ( self . kde_models . keys ( ) ) == 0 or np . random . rand ( ) < self . random_fraction :
sample = self . configspace . sample_conf... |
def validate_term ( term , so = None , method = "verify" ) :
"""Validate an SO term against so . obo""" | if so is None :
so = load_GODag ( )
oterm = term
if term not in so . valid_names :
if "resolve" in method :
if "_" in term :
tparts = deque ( term . split ( "_" ) )
tparts . pop ( ) if "prefix" in method else tparts . popleft ( )
nterm = "_" . join ( tparts ) . strip ... |
def expand_groups ( config_ids , maps ) :
"""Iterates over a list of container configuration ids , expanding groups of container configurations .
: param config _ ids : List of container configuration ids .
: type config _ ids : collections . Iterable [ dockermap . map . input . InputConfigId | dockermap . map ... | for config_id in config_ids :
if config_id . map_name == '__all__' :
c_maps = six . iteritems ( maps )
else :
c_maps = ( config_id . map_name , maps [ config_id . map_name ] ) ,
if isinstance ( config_id , InputConfigId ) :
instance_name = config_id . instance_names
elif isinstan... |
def _merge_user_attrs ( self , attrs_backend , attrs_out , backend_name ) :
"""merge attributes from one backend search to the attributes dict
output""" | for attr in attrs_backend :
if attr in self . attributes . backend_attributes [ backend_name ] :
attrid = self . attributes . backend_attributes [ backend_name ] [ attr ]
if attrid not in attrs_out :
attrs_out [ attrid ] = attrs_backend [ attr ] |
def _update_length ( self ) :
"""Update the length field of the struct .""" | action_length = 4 + len ( self . field . pack ( ) )
overflow = action_length % 8
self . length = action_length
if overflow :
self . length = action_length + 8 - overflow |
def _split ( self , string ) :
"""Iterates over the ngrams of a string ( no padding ) .
> > > from ngram import NGram
> > > n = NGram ( )
> > > list ( n . _ split ( " hamegg " ) )
[ ' ham ' , ' ame ' , ' meg ' , ' egg ' ]""" | for i in range ( len ( string ) - self . N + 1 ) :
yield string [ i : i + self . N ] |
def parse_names ( cls , expression ) :
"""Return the list of identifiers used in the expression .""" | names = set ( )
try :
ast_node = ast . parse ( expression , "ast" )
class Visitor ( ast . NodeVisitor ) :
def visit_Name ( self , node ) :
names . add ( node . id )
Visitor ( ) . visit ( ast_node )
except Exception :
pass
return names |
def rdist ( x , y ) :
"""Reduced Euclidean distance .
Parameters
x : array of shape ( embedding _ dim , )
y : array of shape ( embedding _ dim , )
Returns
The squared euclidean distance between x and y""" | result = 0.0
for i in range ( x . shape [ 0 ] ) :
result += ( x [ i ] - y [ i ] ) ** 2
return result |
def __set_formula ( self , formula ) :
"""Sets a formula in this cell .
Any cell value can be set using this method . Actual formulas must
start with an equal sign .""" | array = ( ( self . _clean_formula ( formula ) , ) , )
return self . _get_target ( ) . setFormulaArray ( array ) |
def _symmetrize_correlograms ( correlograms ) :
"""Return the symmetrized version of the CCG arrays .""" | n_clusters , _ , n_bins = correlograms . shape
assert n_clusters == _
# We symmetrize c [ i , j , 0 ] .
# This is necessary because the algorithm in correlograms ( )
# is sensitive to the order of identical spikes .
correlograms [ ... , 0 ] = np . maximum ( correlograms [ ... , 0 ] , correlograms [ ... , 0 ] . T )
sym ... |
def multihead_attention_vars ( mesh , heads , io_channels , kv_channels , master_dtype , slice_dtype , activation_dtype ) :
"""Deprecated version of multihead _ attention _ params with combine = True .""" | return multihead_attention_params ( mesh , heads , io_channels , kv_channels , mtf . VariableDType ( master_dtype , slice_dtype , activation_dtype ) , combine = True ) |
def remove_connection ( provider_id , provider_user_id ) :
"""Remove a specific connection for the authenticated user to the
specified provider""" | provider = get_provider_or_404 ( provider_id )
ctx = dict ( provider = provider . name , user = current_user , provider_user_id = provider_user_id )
deleted = _datastore . delete_connection ( user_id = current_user . get_id ( ) , provider_id = provider_id , provider_user_id = provider_user_id )
if deleted :
after_t... |
def download_and_calibrate_parallel ( list_of_ids , n = None ) :
"""Download and calibrate in parallel .
Parameters
list _ of _ ids : list , optional
container with img _ ids to process
n : int
Number of cores for the parallel processing . Default : n _ cores _ system / / 2""" | setup_cluster ( n_cores = n )
c = Client ( )
lbview = c . load_balanced_view ( )
lbview . map_async ( download_and_calibrate , list_of_ids )
subprocess . Popen ( [ "ipcluster" , "stop" , "--quiet" ] ) |
def exponential ( x , y , xscale , yscale ) :
"""Two - dimensional oriented exponential decay pattern .""" | if xscale == 0.0 or yscale == 0.0 :
return x * 0.0
with float_error_ignore ( ) :
x_w = np . divide ( x , xscale )
y_h = np . divide ( y , yscale )
return np . exp ( - np . sqrt ( x_w * x_w + y_h * y_h ) ) |
def calculate_signature ( key , data , timestamp = None ) :
"""Calculates the signature for the given request data .""" | # Create a timestamp if one was not given
if timestamp is None :
timestamp = int ( time . time ( ) )
# Construct the message from the timestamp and the data in the request
message = str ( timestamp ) + '' . join ( "%s%s" % ( k , v ) for k , v in sorted ( data . items ( ) ) )
# Calculate the signature ( HMAC SHA256 ... |
def to_html ( sample , stats_object ) :
"""Generate a HTML report from summary statistics and a given sample .
Parameters
sample : DataFrame
the sample you want to print
stats _ object : dict
Summary statistics . Should be generated with an appropriate describe ( ) function
Returns
str
containing pr... | n_obs = stats_object [ 'table' ] [ 'n' ]
value_formatters = formatters . value_formatters
row_formatters = formatters . row_formatters
if not isinstance ( sample , pd . DataFrame ) :
raise TypeError ( "sample must be of type pandas.DataFrame" )
if not isinstance ( stats_object , dict ) :
raise TypeError ( "stat... |
def msvs_parse_version ( s ) :
"""Split a Visual Studio version , which may in fact be something like
'7.0Exp ' , into is version number ( returned as a float ) and trailing
" suite " portion .""" | num , suite = version_re . match ( s ) . groups ( )
return float ( num ) , suite |
def getTotalPrice ( self ) :
"""compute total price""" | price = self . getPrice ( )
price = Decimal ( price or '0.00' )
vat = Decimal ( self . getVAT ( ) )
vat = vat and vat / 100 or 0
price = price + ( price * vat )
return price . quantize ( Decimal ( '0.00' ) ) |
def to_datetime ( self , column ) :
'''This function converts epoch timestamps to datetimes .
: param column : column to convert from current state - > datetime''' | if column in self :
if self [ column ] . dtype in NUMPY_NUMERICAL :
self [ column ] = pd . to_datetime ( self [ column ] , unit = 's' )
else :
self [ column ] = pd . to_datetime ( self [ column ] , utc = True ) |
def parse ( cls , args ) :
"""Parse command line arguments to construct a dictionary of command
parameters that can be used to create a command
Args :
` args ` : sequence of arguments
Returns :
Dictionary that can be used in create method
Raises :
ParseError : when the arguments are not correct""" | try :
( options , args ) = cls . optparser . parse_args ( args )
if options . inline is None and options . script_location is None :
raise ParseError ( "One of script or it's location" " must be specified" , cls . optparser . format_help ( ) )
except OptionParsingError as e :
raise ParseError ( e . ... |
def __generate_tree ( self , top , src , resources , models , ctrls , views , utils ) :
"""Creates directories and packages""" | res = self . __mkdir ( top )
for fn in ( src , models , ctrls , views , utils ) :
res = self . __mkpkg ( fn ) or res
res = self . __mkdir ( resources ) or res
res = self . __mkdir ( os . path . join ( resources , "ui" , "builder" ) ) or res
res = self . __mkdir ( os . path . join ( resources , "ui" , "styles" ) ) o... |
def rotate ( name , pattern = None , conf_file = default_conf , ** kwargs ) :
'''Set up pattern for logging .
name : string
alias for entryname
pattern : string
alias for log _ file
conf _ file : string
optional path to alternative configuration file
kwargs : boolean | string | int
optional addition... | # # cleanup kwargs
kwargs = salt . utils . args . clean_kwargs ( ** kwargs )
# # inject name into kwargs
if 'entryname' not in kwargs and name and not name . startswith ( '/' ) :
kwargs [ 'entryname' ] = name
# # inject pattern into kwargs
if 'log_file' not in kwargs :
if pattern and pattern . startswith ( '/' ... |
def wrap_line ( line , maxline = 79 , result = [ ] , count = count ) :
"""We have a line that is too long ,
so we ' re going to try to wrap it .""" | # Extract the indentation
append = result . append
extend = result . extend
indentation = line [ 0 ]
lenfirst = len ( indentation )
indent = lenfirst - len ( indentation . lstrip ( ) )
assert indent in ( 0 , lenfirst )
indentation = line . pop ( 0 ) if indent else ''
# Get splittable / non - splittable groups
dgroups =... |
def pprint ( sequence_file , annotation = None , annotation_file = None , block_length = 10 , blocks_per_line = 6 ) :
"""Pretty - print sequence ( s ) from a file .""" | annotations = [ ]
if annotation :
annotations . append ( [ ( first - 1 , last ) for first , last in annotation ] )
try : # Peek to see if this looks like a FASTA file .
line = next ( sequence_file )
if line . startswith ( '>' ) :
_pprint_fasta ( itertools . chain ( [ line ] , sequence_file ) , annot... |
def contents ( self ) :
"""Return the list of contained directory entries , loading them
if not already loaded .""" | if not self . contents_read :
self . contents_read = True
base = self . path
for entry in os . listdir ( self . source_path ) :
source_path = os . path . join ( self . source_path , entry )
target_path = os . path . join ( base , entry )
if os . path . isdir ( source_path ) :
... |
def _canBeExpanded ( self , headVerbRoot , headVerbWID , suitableNomAdvExpansions , expansionVerbs , widToToken ) :
'''Teeb kindlaks , kas kontekst on verbiahela laiendamiseks piisavalt selge / yhene :
1 ) Nii ' nom / adv ' kandidaate kui ka Vinf kandidaate on täpselt üks ;
2 ) Nom / adv ei kuulu mingi suurem... | if len ( suitableNomAdvExpansions ) == 1 and expansionVerbs : # Kontrollime , kas leidub t2pselt yks laiendiks sobiv verb ( kui leidub
# rohkem , on kontekst kahtlane ja raske otsustada , kas tasub laiendada
# v6i mitte )
suitableExpansionVerbs = [ expVerb for expVerb in expansionVerbs if expVerb [ 2 ] == suitableN... |
def finish_async_rpc ( self , address , rpc_id , response ) :
"""Finish a previous asynchronous RPC .
This method should be called by a peripheral tile that previously
had an RPC called on it and chose to response asynchronously by
raising ` ` AsynchronousRPCResponse ` ` in the RPC handler itself .
The resp... | pending = self . _pending_rpcs . get ( address )
if pending is None :
raise ArgumentError ( "No asynchronously RPC currently in progress on tile %d" % address )
responder = pending . get ( rpc_id )
if responder is None :
raise ArgumentError ( "RPC %04X is not running asynchronous on tile %d" % ( rpc_id , addres... |
async def get_creds_display_coarse ( self , filt : dict = None ) -> str :
"""Return human - readable credentials from wallet by input filter for
schema identifier and / or credential definition identifier components ;
return all credentials for no filter .
: param filt : indy - sdk filter for credentials ; i ... | LOGGER . debug ( 'HolderProver.get_creds_display_coarse >>> filt: %s' , filt )
rv_json = await anoncreds . prover_get_credentials ( self . wallet . handle , json . dumps ( filt or { } ) )
LOGGER . debug ( 'HolderProver.get_creds_display_coarse <<< %s' , rv_json )
return rv_json |
def rebin ( a , * args ) :
"""See http : / / scipy - cookbook . readthedocs . io / items / Rebinning . html
Note : integer division in the computation of ' factor ' has been
included to avoid the following runtime message :
VisibleDeprecationWarning : using a non - integer number instead of
an integer will ... | shape = a . shape
len_shape = len ( shape )
factor = np . asarray ( shape ) // np . asarray ( args )
ev_list = [ 'a.reshape(' ] + [ 'args[%d], factor[%d], ' % ( i , i ) for i in range ( len_shape ) ] + [ ')' ] + [ '.mean(%d)' % ( i + 1 ) for i in range ( len_shape ) ]
# print ( ' ' . join ( ev _ list ) )
return eval ( ... |
def _ProcessSources ( self , sources , parser_factory ) :
"""Iterates through sources yielding action responses .""" | for source in sources :
for action , request in self . _ParseSourceType ( source ) :
yield self . _RunClientAction ( action , request , parser_factory , source . path_type ) |
def normalizeGlyphUnicode ( value ) :
"""Normalizes glyph unicode .
* * * value * * must be an int or hex ( represented as a string ) .
* * * value * * must be in a unicode range .
* Returned value will be an ` ` int ` ` .""" | if not isinstance ( value , ( int , basestring ) ) or isinstance ( value , bool ) :
raise TypeError ( "Glyph unicode must be a int or hex string, not %s." % type ( value ) . __name__ )
if isinstance ( value , basestring ) :
try :
value = int ( value , 16 )
except ValueError :
raise ValueErro... |
def list_indexes ( cls ) :
"""Returns a dictionary with the key as the es _ index name and the
object is a list of rdfclasses for that index
args :
None""" | cls_list = cls . list_mapped_classes ( )
rtn_obj = { }
for key , value in cls_list . items ( ) :
idx = value . es_defs . get ( 'kds_esIndex' ) [ 0 ]
try :
rtn_obj [ idx ] . append ( value )
except KeyError :
rtn_obj [ idx ] = [ value ]
return rtn_obj |
def replaceChild ( self , new_child : 'WdomElement' , old_child : 'WdomElement' ) -> Node :
"""Replace child nodes .""" | if self . connected :
self . _replace_child_web ( new_child , old_child )
return self . _replace_child ( new_child , old_child ) |
def export_configuration_generator ( self , sql , sql_args ) :
"""Generator for : class : ` meteorpi _ model . ExportConfiguration `
: param sql :
A SQL statement which must return rows describing export configurations
: param sql _ args :
Any variables required to populate the query provided in ' sql '
:... | self . con . execute ( sql , sql_args )
results = self . con . fetchall ( )
output = [ ]
for result in results :
if result [ 'exportType' ] == "observation" :
search = mp . ObservationSearch . from_dict ( json . loads ( result [ 'searchString' ] ) )
elif result [ 'exportType' ] == "file" :
searc... |
def json_loads ( cls , s , ** kwargs ) :
"""A rewrap of json . loads done for one reason - to inject a custom ` cls ` kwarg
: param s :
: param kwargs :
: return :
: rtype : dict""" | if 'cls' not in kwargs :
kwargs [ 'cls' ] = cls . json_decoder
return json . loads ( s , ** kwargs ) |
def send ( self , msg ) :
"""send message to client .""" | assert isinstance ( msg , str ) , "String is required"
if self . _debug :
log . info ( "outgoing message: %s, %s" , self . id , str ( msg ) [ : 200 ] )
if self . state != STATE_OPEN :
return
self . _feed ( FRAME_MESSAGE , msg ) |
def runGetRnaQuantificationSet ( self , id_ ) :
"""Runs a getRnaQuantificationSet request for the specified ID .""" | compoundId = datamodel . RnaQuantificationSetCompoundId . parse ( id_ )
dataset = self . getDataRepository ( ) . getDataset ( compoundId . dataset_id )
rnaQuantificationSet = dataset . getRnaQuantificationSet ( id_ )
return self . runGetRequest ( rnaQuantificationSet ) |
def field_elongation ( ra , dec , date ) :
"""For a given field , calculate the solar elongation at the given date .
: param ra : field ' s right ascension . unit = " h " format = " RAh : RAm : RAs "
: param dec : field ' s declination . degrees
: param date : date at which to calculate elongation
: return ... | sun = ephem . Sun ( )
sun . compute ( date )
sep = ephem . separation ( ( ra , dec ) , sun )
retval = 180. - math . degrees ( sep )
return retval |
def num_examples ( self ) :
"""The number of examples this subset spans .""" | if self . is_list :
return len ( self . list_or_slice )
else :
start , stop , step = self . slice_to_numerical_args ( self . list_or_slice , self . original_num_examples )
return stop - start |
def get_file_path_validator ( default_file_param = None ) :
"""Creates a namespace validator that splits out ' path ' into ' directory _ name ' and ' file _ name ' .
Allows another path - type parameter to be named which can supply a default filename .""" | def validator ( namespace ) :
if not hasattr ( namespace , 'path' ) :
return
path = namespace . path
dir_name , file_name = os . path . split ( path ) if path else ( None , '' )
if default_file_param and '.' not in file_name :
dir_name = path
file_name = os . path . split ( getat... |
def fast_sweep_time_evolution ( Ep , epsilonp , gamma , omega_level , rm , xi , theta , semi_analytic = True , file_name = None , return_code = False ) :
r"""Return a spectrum of time evolutions of the density matrix .
We test a basic two - level system .
> > > import numpy as np
> > > from sympy import symbo... | # We unpack variables .
if True :
Nl = xi . shape [ 0 ]
# We determine which arguments are constants .
if True :
try :
Ep = np . array ( [ complex ( Ep [ l ] ) for l in range ( Nl ) ] )
variable_Ep = False
except :
variable_Ep = True
try :
epsilonp = [ np . array ( [ comp... |
def get_id_generator ( self , name ) :
"""Creates cluster - wide : class : ` ~ hazelcast . proxy . id _ generator . IdGenerator ` .
: param name : ( str ) , name of the IdGenerator proxy .
: return : ( : class : ` ~ hazelcast . proxy . id _ generator . IdGenerator ` ) , IdGenerator proxy for the given name .""" | atomic_long = self . get_atomic_long ( ID_GENERATOR_ATOMIC_LONG_PREFIX + name )
return self . proxy . get_or_create ( ID_GENERATOR_SERVICE , name , atomic_long = atomic_long ) |
def build_alignment ( self , score , pieces ) :
"""converts a score and pieces to an alignment""" | # build text
self . open_seqs ( )
text1 = text2 = ""
end1 = end2 = None
for ( start1 , start2 , length , pctId ) in pieces :
if ( end1 != None ) :
if ( start1 == end1 ) : # insertion in sequence 2
text1 += self . seq1_gap * ( start2 - end2 )
text2 += self . seq2_file . get ( end2 , s... |
def strip_exts ( s , exts ) :
"""Given a string and an interable of extensions , strip the extenion off the
string if the string ends with one of the extensions .""" | f_split = os . path . splitext ( s )
if f_split [ 1 ] in exts :
return f_split [ 0 ]
else :
return s |
def mask_file ( regionfile , infile , outfile , negate = False ) :
"""Created a masked version of file , using a region .
Parameters
regionfile : str
A file which can be loaded as a : class : ` AegeanTools . regions . Region ` .
The image will be masked according to this region .
infile : str
Input FITS... | # Check that the input file is accessible and then open it
if not os . path . exists ( infile ) :
raise AssertionError ( "Cannot locate fits file {0}" . format ( infile ) )
im = pyfits . open ( infile )
if not os . path . exists ( regionfile ) :
raise AssertionError ( "Cannot locate region file {0}" . format ( ... |
def _get_field_method ( self , tp ) :
"""Returns a reference to the form element ' s constructor method .""" | method = self . field_constructor . get ( tp )
if method and hasattr ( self , method . __name__ ) :
return getattr ( self , method . __name__ )
return method |
def load_EROS_lc ( filename = 'lm0010n22323.time' ) :
"""Read an EROS light curve and return its data .
Parameters
filename : str , optional
A light - curve filename .
Returns
dates : numpy . ndarray
An array of dates .
magnitudes : numpy . ndarray
An array of magnitudes .
errors : numpy . ndarray... | module_path = dirname ( __file__ )
file_path = join ( module_path , 'lightcurves' , filename )
data = np . loadtxt ( file_path )
date = data [ : , 0 ]
mag = data [ : , 1 ]
err = data [ : , 2 ]
return date , mag , err |
def all_packages ( self ) :
"""Returns a list of all packages .""" | p = dict ( self . parsed_pipfile . get ( "dev-packages" , { } ) )
p . update ( self . parsed_pipfile . get ( "packages" , { } ) )
return p |
def _add_rid_to_vrf_list ( self , ri ) :
"""Add router ID to a VRF list .
In order to properly manage VRFs in the ASR , their
usage has to be tracked . VRFs are provided with neutron
router objects in their hosting _ info fields of the gateway ports .
This means that the VRF is only available when the gatew... | if ri . ex_gw_port or ri . router . get ( 'gw_port' ) :
driver = self . driver_manager . get_driver ( ri . id )
vrf_name = driver . _get_vrf_name ( ri )
if not vrf_name :
return
if not self . _router_ids_by_vrf . get ( vrf_name ) :
LOG . debug ( "++ CREATING VRF %s" % vrf_name )
... |
def login ( session , user , password , database = None , server = None ) :
"""Logs into a MyGeotab server and stores the returned credentials .
: param session : The current Session object .
: param user : The username used for MyGeotab servers . Usually an email address .
: param password : The password ass... | if not user :
user = click . prompt ( "Username" , type = str )
if not password :
password = click . prompt ( "Password" , hide_input = True , type = str )
try :
with click . progressbar ( length = 1 , label = "Logging in..." ) as progressbar :
session . login ( user , password , database , server )... |
def stylemap ( self , definitions = True , all = True , cache = False ) :
"""return a dictionary of styles from . docx word / styles . xml , keyed to the id
( the id is used in the . docx word / document . xml rather than the style names ;
this method creates a mapping for us to use when outputting the document... | if self . _stylemap is not None and cache == True :
return self . _stylemap
else :
self . _stylemap = None
# expire the cache
x = self . xml ( src = 'word/styles.xml' )
document = self . xml ( src = 'word/document.xml' )
footnotes = self . xml ( src = 'word/footnotes.xml' )
# None if no foot... |
def _reset_state_mode ( self , state , mode ) :
"""Reset the state mode to the given mode , and apply the custom state options specified with this analysis .
: param state : The state to work with .
: param str mode : The state mode .
: return : None""" | state . set_mode ( mode )
state . options |= self . _state_add_options
state . options = state . options . difference ( self . _state_remove_options ) |
def is_unclaimed ( work ) :
"""Returns True if work piece is unclaimed .""" | if work [ 'is_completed' ] :
return False
cutoff_time = time . time ( ) - MAX_PROCESSING_TIME
if ( work [ 'claimed_worker_id' ] and work [ 'claimed_worker_start_time' ] is not None and work [ 'claimed_worker_start_time' ] >= cutoff_time ) :
return False
return True |
def make_name ( self ) :
"""Autogenerates a : attr : ` name ` from : attr : ` title _ for _ name `""" | if self . title :
self . name = six . text_type ( make_name ( self . title_for_name , maxlength = self . __name_length__ ) ) |
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