signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def set_max_connections_per_host ( self , host_distance , max_connections ) :
"""Sets the maximum number of connections per Session that will be opened
for each host with : class : ` ~ . HostDistance ` equal to ` host _ distance ` .
The default is 2 for : attr : ` ~ HostDistance . LOCAL ` and 1 for
: attr : `... | if self . protocol_version >= 3 :
raise UnsupportedOperation ( "Cluster.set_max_connections_per_host() only has an effect " "when using protocol_version 1 or 2." )
self . _max_connections_per_host [ host_distance ] = max_connections |
def add_notes ( self , note , duration = None ) :
"""Add a Note , note as string or NoteContainer to the last Bar .
If the Bar is full , a new one will automatically be created .
If the Bar is not full but the note can ' t fit in , this method will
return False . True otherwise .
An InstrumentRangeError exc... | if self . instrument != None :
if not self . instrument . can_play_notes ( note ) :
raise InstrumentRangeError , "Note '%s' is not in range of the instrument (%s)" % ( note , self . instrument )
if duration == None :
duration = 4
# Check whether the last bar is full , if so create a new bar and add the
... |
def get_client ( self ) :
"""Retrieves or creates a client instance from this configuration object . If instantiated from this configuration ,
the resulting object is also cached in the property ` ` client ` ` and a reference to this configuration is stored
on the client object .
: return : Client object inst... | client = self . _client
if not client :
self . _client = client = self . client_constructor ( ** self . get_init_kwargs ( ) )
client . client_configuration = self
# Client might update the version number after construction .
updated_version = getattr ( client , 'api_version' , None )
if updated_vers... |
def trim_nearby_peaks ( peaks , dt ) :
r"""Finds pairs of peaks that are nearer to each other than to the solid phase ,
and removes the peak that is closer to the solid .
Parameters
peaks : ND - array
A boolean image containing True values to mark peaks in the distance
transform ( ` ` dt ` ` )
dt : ND -... | peaks = sp . copy ( peaks )
if dt . ndim == 2 :
from skimage . morphology import square as cube
else :
from skimage . morphology import cube
peaks , N = spim . label ( peaks , structure = cube ( 3 ) )
crds = spim . measurements . center_of_mass ( peaks , labels = peaks , index = sp . arange ( 1 , N + 1 ) )
crds... |
def _add_timedelta ( self , delta ) :
"""Add timedelta duration to the instance .
: param delta : The timedelta instance
: type delta : pendulum . Duration or datetime . timedelta
: rtype : Date""" | if isinstance ( delta , pendulum . Duration ) :
return self . add ( years = delta . years , months = delta . months , weeks = delta . weeks , days = delta . remaining_days , )
return self . add ( days = delta . days ) |
def get ( self ) :
"""Get the script content from the URL using the decided downloader .""" | method_name = "_download_" + self . name
method = getattr ( self , method_name )
return method ( ) |
def create_user ( self , projects = None , tasks = None ) :
"""Create and return a new user
: param projects : the projects for the user
: type projects : list of : class : ` jukeboxcore . djadapter . models . Project `
: param tasks : the tasks for the user
: type tasks : list of : class : ` jukeboxcore . ... | projects = projects or [ ]
tasks = tasks or [ ]
dialog = UserCreatorDialog ( projects = projects , tasks = tasks , parent = self )
dialog . exec_ ( )
user = dialog . user
if user :
userdata = djitemdata . UserItemData ( user )
treemodel . TreeItem ( userdata , self . users_model . root )
return user |
def decorators ( self , relation ) :
"""Return prefixes for tuple .
: param int relation : relation of string value to actual value""" | if self . CONFIG . show_approx_str :
approx_str = Decorators . relation_to_symbol ( relation )
else :
approx_str = ''
return _Decorators ( approx_str = approx_str ) |
def _normalize_window ( window , nfft , library , dtype ) :
"""Normalise a window specification for a PSD calculation
Parameters
window : ` str ` , ` numpy . ndarray ` , ` None `
the input window specification
nfft : ` int `
the length of the Fourier transform , in samples
library : ` str `
the name o... | if library == '_lal' and isinstance ( window , numpy . ndarray ) :
from . _lal import window_from_array
return window_from_array ( window )
if library == '_lal' :
from . _lal import generate_window
return generate_window ( nfft , window = window , dtype = dtype )
if isinstance ( window , string_types ) ... |
def avgwave ( self , wavelengths = None ) :
"""Calculate the : ref : ` average wavelength < synphot - formula - avgwv > ` .
Parameters
wavelengths : array - like , ` ~ astropy . units . quantity . Quantity ` , or ` None `
Wavelength values for sampling .
If not a Quantity , assumed to be in Angstrom .
If ... | x = self . _validate_wavelengths ( wavelengths ) . value
y = self ( x ) . value
num = np . trapz ( y * x , x = x )
den = np . trapz ( y , x = x )
if den == 0 : # pragma : no cover
avg_wave = 0.0
else :
avg_wave = abs ( num / den )
return avg_wave * self . _internal_wave_unit |
def change_authentication ( self , client_id = None , client_secret = None , access_token = None , refresh_token = None ) :
"""Change the current authentication .""" | # TODO : Add error checking so you cannot change client _ id and retain
# access _ token . Because that doesn ' t make sense .
self . client_id = client_id or self . client_id
self . client_secret = client_secret or self . client_secret
self . access_token = access_token or self . access_token
self . refresh_token = re... |
def warnconfig ( action = 'default' ) :
"""Configure the Python warnings .
: type action : string
: param action : The configuration to set . Options are : ' default ' , ' error ' , ' ignore ' , ' always ' , ' module ' and ' once ' .""" | # If action is ' default '
if action . lower ( ) == 'default' : # Change warning settings
warnings . filterwarnings ( 'default' )
# If action is ' error '
elif action . lower ( ) == 'error' : # Change warning settings
warnings . filterwarnings ( 'error' )
# If action is ' ignore '
elif action . lower ( ) == 'ig... |
def make_es_id ( uri ) :
"""Creates the id based off of the uri value
Args :
uri : the uri to conver to an elasticsearch id""" | try :
uri = uri . clean_uri
except AttributeError :
pass
return sha1 ( uri . encode ( ) ) . hexdigest ( ) |
def next_prime ( starting_value ) :
"Return the smallest prime larger than the starting value ." | if starting_value < 2 :
return 2
result = ( starting_value + 1 ) | 1
while not is_prime ( result ) :
result = result + 2
return result |
def merge ( files , out_file , config ) :
"""merge smartly fastq files . It recognizes paired fastq files .""" | pair1 = [ fastq_file [ 0 ] for fastq_file in files ]
if len ( files [ 0 ] ) > 1 :
path = splitext_plus ( out_file )
pair1_out_file = path [ 0 ] + "_R1" + path [ 1 ]
pair2 = [ fastq_file [ 1 ] for fastq_file in files ]
pair2_out_file = path [ 0 ] + "_R2" + path [ 1 ]
_merge_list_fastqs ( pair1 , pair... |
def delete_many ( self , uris ) :
"""Remove many nodes from cache .
No return .""" | cache_keys = ( self . _build_cache_key ( uri ) for uri in uris )
self . _delete_many ( cache_keys ) |
def _padleft ( width , s , has_invisible = True ) :
"""Flush right .
> > > _ padleft ( 6 , ' \u044f \u0439 \u0446 \u0430 ' ) = = ' \u044f \u0439 \u0446 \u0430 '
True""" | def impl ( val ) :
iwidth = width + len ( val ) - len ( _strip_invisible ( val ) ) if has_invisible else width
fmt = "{0:>%ds}" % iwidth
return fmt . format ( val )
num_lines = s . splitlines ( )
return len ( num_lines ) > 1 and '\n' . join ( map ( impl , num_lines ) ) or impl ( s ) |
def finalize ( self ) :
"""Output the number of instances that contained dead code .""" | if self . total_instances > 1 :
print ( '{} of {} instances contained dead code.' . format ( self . dead_code_instances , self . total_instances ) ) |
def parse_token ( self , token , tags = [ WORD , POS , CHUNK , PNP , REL , ANCHOR , LEMMA ] ) :
"""Returns the arguments for Sentence . append ( ) from a tagged token representation .
The order in which token tags appear can be specified .
The default order is ( separated by slashes ) :
- word ,
- part - of... | p = { WORD : "" , POS : None , IOB : None , CHUNK : None , PNP : None , REL : None , ROLE : None , ANCHOR : None , LEMMA : None }
# Split the slash - formatted token into separate tags in the given order .
# Decode & slash ; characters ( usually in words and lemmata ) .
# Assume None for missing tags ( except the word ... |
def fix_coordinate_decimal ( d ) :
"""Coordinate decimal degrees calculated by an excel formula are often too long as a repeating decimal .
Round them down to 5 decimals
: param dict d : Metadata
: return dict d : Metadata""" | try :
for idx , n in enumerate ( d [ "geo" ] [ "geometry" ] [ "coordinates" ] ) :
d [ "geo" ] [ "geometry" ] [ "coordinates" ] [ idx ] = round ( n , 5 )
except Exception as e :
logger_misc . error ( "fix_coordinate_decimal: {}" . format ( e ) )
return d |
def fn_check_full ( fn ) :
"""Check for file existence
Avoids race condition , but slower than os . path . exists .
Parameters
fn : str
Input filename string .
Returns
status
True if file exists , False otherwise .""" | status = True
if not os . path . isfile ( fn ) :
status = False
else :
try :
open ( fn )
except IOError :
status = False
return status |
def delete_Variable ( self , name ) :
'''pops a variable from class and delete it from parameter list
: parameter name : name of the parameter to delete''' | self . message ( 1 , 'Deleting variable {0}' . format ( name ) )
self . par_list = self . par_list [ self . par_list != name ]
return self . __dict__ . pop ( name ) |
def inject ( self , span_context , format , carrier ) :
"""Injects ` span _ context ` into ` carrier ` .
The type of ` carrier ` is determined by ` format ` . See the
: class : ` Format ` class / namespace for the built - in OpenTracing formats .
Implementations * must * raise : exc : ` UnsupportedFormatExcep... | if format in Tracer . _supported_formats :
return
raise UnsupportedFormatException ( format ) |
def upload_backup_bundle_from_file ( self , file_path , deployment_groups_id_or_uri ) :
"""Restore an Artifact Bundle from a backup file .
Args :
file _ path ( str ) : The File Path to restore the Artifact Bundle .
deployment _ groups _ id _ or _ uri : ID or URI of the Deployment Groups .
Returns :
dict :... | deployment_groups_uri = deployment_groups_id_or_uri
if self . DEPLOYMENT_GROUPS_URI not in deployment_groups_id_or_uri :
deployment_groups_uri = self . DEPLOYMENT_GROUPS_URI + deployment_groups_id_or_uri
uri = self . BACKUP_ARCHIVE_PATH + "?deploymentGrpUri=" + deployment_groups_uri
return self . _client . upload (... |
def add_vbar_widget ( self , ref , x = 1 , y = 1 , length = 10 ) :
"""Add Vertical Bar Widget""" | if ref not in self . widgets :
widget = widgets . VBarWidget ( screen = self , ref = ref , x = x , y = y , length = length )
self . widgets [ ref ] = widget
return self . widgets [ ref ] |
def unlist ( list_thing , complain = True ) :
"""transforms [ Something ] - > Something . By default , raises a ValueError for
any other list values .""" | if complain and len ( list_thing ) > 1 :
raise ValueError ( "More than one element in {}" . format ( list_thing ) )
elif len ( list_thing ) == 1 :
return list_thing [ 0 ]
if complain :
raise ValueError ( "Nothing in {}" . format ( list_thing ) )
return None |
def function_exists ( self , fun ) :
"""get function ' s existense""" | res = fun in self . _rule_functions
self . say ( 'function exists:' + str ( fun ) + ':' + str ( res ) , verbosity = 10 )
return res |
def _use_datastore ( self , key , options = None ) :
"""Return whether to use the datastore for this key .
Args :
key : Key instance .
options : ContextOptions instance , or None .
Returns :
True if the datastore should be used , False otherwise .""" | flag = ContextOptions . use_datastore ( options )
if flag is None :
flag = self . _datastore_policy ( key )
if flag is None :
flag = ContextOptions . use_datastore ( self . _conn . config )
if flag is None :
flag = True
return flag |
def unique_size ( self ) :
"""Size of ONLY this particular layer
: return : int or None""" | self . _virtual_size = self . _virtual_size or graceful_chain_get ( self . data , "VirtualSize" , default = 0 )
try :
return self . _virtual_size - self . _shared_size
except TypeError :
return 0 |
def vlans ( self ) :
"""list [ dict ] : A list of dictionary items describing the details of
vlan interfaces .
This method fetches the VLAN interfaces
Examples :
> > > import pynos . device
> > > switch = ' 10.24.39.202'
> > > auth = ( ' admin ' , ' password ' )
> > > conn = ( switch , ' 22 ' )
> > ... | urn = "{urn:brocade.com:mgmt:brocade-interface-ext}"
result = [ ]
has_more = ''
last_vlan_id = ''
while ( has_more == '' ) or ( has_more == 'true' ) :
request_interface = self . get_vlan_brief_request ( last_vlan_id )
interface_result = self . _callback ( request_interface , 'get' )
has_more = self . get_no... |
def headers ( self ) :
"""Return the headers for the resource . Returns the AltName , if specified ; if not , then the
Name , and if that is empty , a name based on the column position . These headers
are specifically applicable to the output table , and may not apply to the resource source . FOr those headers ... | t = self . schema_term
if t :
return [ self . _name_for_col_term ( c , i ) for i , c in enumerate ( t . children , 1 ) if c . term_is ( "Table.Column" ) ]
else :
return None |
def add ( self , * args ) :
"""Add object ( s ) to the Container .
: param * args : Any objects to add to the Container .
: returns : full list of Container ' s child objects""" | self . children . extend ( args )
bump_child_depth ( self , self . _depth )
return self . children |
def get_pkg_names ( pkgs ) :
"""Get PyPI package names from a list of imports .
Args :
pkgs ( List [ str ] ) : List of import names .
Returns :
List [ str ] : The corresponding PyPI package names .""" | result = set ( )
with open ( join ( "mapping" ) , "r" ) as f :
data = dict ( x . strip ( ) . split ( ":" ) for x in f )
for pkg in pkgs : # Look up the mapped requirement . If a mapping isn ' t found ,
# simply use the package name .
result . add ( data . get ( pkg , pkg ) )
# Return a sorted list for backward ... |
def add_final_training_ops ( self , embeddings , all_labels_count , bottleneck_tensor_size , hidden_layer_size = BOTTLENECK_TENSOR_SIZE / 4 , dropout_keep_prob = None ) :
"""Adds a new softmax and fully - connected layer for training .
The set up for the softmax and fully - connected layers is based on :
https ... | with tf . name_scope ( 'input' ) :
bottleneck_input = tf . placeholder_with_default ( embeddings , shape = [ None , bottleneck_tensor_size ] , name = 'ReshapeSqueezed' )
bottleneck_with_no_gradient = tf . stop_gradient ( bottleneck_input )
with tf . name_scope ( 'Wx_plus_b' ) :
hidden = layers . ful... |
def symget ( self , name ) :
""": param name : name of the macro varable to set :
- name is a character""" | ll = self . submit ( "%put " + name + "=&" + name + ";\n" )
l2 = ll [ 'LOG' ] . rpartition ( name + "=" )
l2 = l2 [ 2 ] . partition ( "\n" )
try :
var = int ( l2 [ 0 ] )
except :
try :
var = float ( l2 [ 0 ] )
except :
var = l2 [ 0 ]
return var |
def list_jobs ( config , * , status = JobStatus . Active , filter_by_type = None , filter_by_worker = None ) :
"""Return a list of Celery jobs .
Args :
config ( Config ) : Reference to the configuration object from which the
settings are retrieved .
status ( JobStatus ) : The status of the jobs that should ... | celery_app = create_app ( config )
# option to filter by the worker ( improves performance )
if filter_by_worker is not None :
inspect = celery_app . control . inspect ( destination = filter_by_worker if isinstance ( filter_by_worker , list ) else [ filter_by_worker ] )
else :
inspect = celery_app . control . i... |
def transpose ( self , name = None , output_channels = None , kernel_shapes = None , strides = None , paddings = None , activation = None , activate_final = None , normalization_ctor = None , normalization_kwargs = None , normalize_final = None , initializers = None , partitioners = None , regularizers = None , use_bat... | for rate in self . _rates :
if rate != 1 :
raise NotImplementedError ( "Transpose dilated convolutions " "are not supported" )
output_shapes = [ ]
if data_format is None :
data_format = self . _data_format
if data_format == DATA_FORMAT_NHWC :
start_dim , end_dim = 1 , - 1
elif data_format == DATA_FO... |
def OnUpdate ( self , event ) :
"""Updates the toolbar states""" | attributes = event . attr
self . _update_font ( attributes [ "textfont" ] )
self . _update_pointsize ( attributes [ "pointsize" ] )
self . _update_font_weight ( attributes [ "fontweight" ] )
self . _update_font_style ( attributes [ "fontstyle" ] )
self . _update_frozencell ( attributes [ "frozen" ] )
self . _update_loc... |
def lookup_string ( conn , kstr ) :
"""Finds the keycode associated with a string representation of a keysym .
: param kstr : English representation of a keysym .
: return : Keycode , if one exists .
: rtype : int""" | if kstr in keysyms :
return get_keycode ( conn , keysyms [ kstr ] )
elif len ( kstr ) > 1 and kstr . capitalize ( ) in keysyms :
return get_keycode ( conn , keysyms [ kstr . capitalize ( ) ] )
return None |
def cmd ( send , * _ ) :
"""Returns the Discordian date .
Syntax : { command }""" | try :
output = subprocess . check_output ( [ 'ddate' ] , universal_newlines = True )
except subprocess . CalledProcessError :
output = 'Today is the day you install ddate!'
for line in output . splitlines ( ) :
send ( line ) |
def _dumpArrayToFile ( filelike , array ) :
"""Serializes a 1 - dimensional ` ` numpy . array ` ` to bytes , writes the bytes to
the filelike object and returns a dictionary with metadata , necessary to
restore the ` ` numpy . array ` ` from the file .
: param filelike : can be a file or a file - like object ... | bytedata = array . tobytes ( 'C' )
start = filelike . tell ( )
end = start + len ( bytedata )
metadata = { 'start' : start , 'end' : end , 'size' : array . size , 'dtype' : array . dtype . name }
filelike . write ( bytedata )
return metadata |
def scatter ( adata , x = None , y = None , color = None , use_raw = None , layers = 'X' , sort_order = True , alpha = None , basis = None , groups = None , components = None , projection = '2d' , legend_loc = 'right margin' , legend_fontsize = None , legend_fontweight = None , color_map = None , palette = None , frame... | if basis is not None :
axs = _scatter_obs ( adata = adata , x = x , y = y , color = color , use_raw = use_raw , layers = layers , sort_order = sort_order , alpha = alpha , basis = basis , groups = groups , components = components , projection = projection , legend_loc = legend_loc , legend_fontsize = legend_fontsiz... |
def get_group_by_id ( self , group_id ) -> typing . Optional [ 'Group' ] :
"""Args :
group _ id : group ID
Returns : Group""" | VALID_POSITIVE_INT . validate ( group_id , 'get_group_by_id' )
for group in self . groups :
if group . group_id == group_id :
return group
return None |
def download_items ( self , items , file_path , file_format = 'zip' ) :
"""Retrieve a file from the server containing the metadata
and documents for the speficied items
: type items : List or ItemGroup
: param items : List of the the URLs of the items to download ,
or an ItemGroup object
: type file _ pat... | download_url = '/catalog/download_items'
download_url += '?' + urlencode ( ( ( 'format' , file_format ) , ) )
item_data = { 'items' : list ( items ) }
data = self . api_request ( download_url , method = 'POST' , data = json . dumps ( item_data ) , raw = True )
with open ( file_path , 'w' ) as f :
f . write ( data )... |
async def synchronize ( self , pid , vendor_specific = None ) :
"""Send an object synchronization request to the CN .""" | return await self . _request_pyxb ( "post" , [ "synchronize" , pid ] , { } , mmp_dict = { "pid" : pid } , vendor_specific = vendor_specific , ) |
def create_diff_storage ( self , target , variant ) :
"""Starts creating an empty differencing storage unit based on this
medium in the format and at the location defined by the @ a target
argument .
The target medium must be in : py : attr : ` MediumState . not _ created `
state ( i . e . must not have an ... | if not isinstance ( target , IMedium ) :
raise TypeError ( "target can only be an instance of type IMedium" )
if not isinstance ( variant , list ) :
raise TypeError ( "variant can only be an instance of type list" )
for a in variant [ : 10 ] :
if not isinstance ( a , MediumVariant ) :
raise TypeErro... |
def cli ( ctx ) :
"""Check the latest Apio version .""" | current_version = get_distribution ( 'apio' ) . version
latest_version = get_pypi_latest_version ( )
if latest_version is None :
ctx . exit ( 1 )
if latest_version == current_version :
click . secho ( 'You\'re up-to-date!\nApio {} is currently the ' 'newest version available.' . format ( latest_version ) , fg =... |
def highlight_block ( self , text ) :
"""Implement highlight specific for C / C + + .""" | text = to_text_string ( text )
inside_comment = tbh . get_state ( self . currentBlock ( ) . previous ( ) ) == self . INSIDE_COMMENT
self . setFormat ( 0 , len ( text ) , self . formats [ "comment" if inside_comment else "normal" ] )
match = self . PROG . search ( text )
index = 0
while match :
for key , value in li... |
def read_clusters ( self , min_cluster_size ) :
"""Read and parse OSLOM clusters output file .""" | num_found = 0
clusters = [ ]
with open ( self . get_path ( OslomRunner . OUTPUT_FILE ) , "r" ) as reader : # Read the output file every two lines
for line1 , line2 in itertools . izip_longest ( * [ reader ] * 2 ) :
info = OslomRunner . RE_INFOLINE . match ( line1 . strip ( ) ) . groups ( )
nodes = l... |
def list_subscriptions ( self , target_id = None , ids = None , query_flags = None ) :
"""ListSubscriptions .
[ Preview API ]
: param str target _ id :
: param [ str ] ids :
: param str query _ flags :
: rtype : [ NotificationSubscription ]""" | query_parameters = { }
if target_id is not None :
query_parameters [ 'targetId' ] = self . _serialize . query ( 'target_id' , target_id , 'str' )
if ids is not None :
ids = "," . join ( ids )
query_parameters [ 'ids' ] = self . _serialize . query ( 'ids' , ids , 'str' )
if query_flags is not None :
quer... |
def segment_file ( self , value ) :
"""Setter for _ segment _ file attribute""" | assert os . path . isfile ( value ) , "%s is not a valid file" % value
self . _segment_file = value |
def load_country_map_data ( ) :
"""Loading data for map with country map""" | csv_bytes = get_example_data ( 'birth_france_data_for_country_map.csv' , is_gzip = False , make_bytes = True )
data = pd . read_csv ( csv_bytes , encoding = 'utf-8' )
data [ 'dttm' ] = datetime . datetime . now ( ) . date ( )
data . to_sql ( # pylint : disable = no - member
'birth_france_by_region' , db . engine , if_e... |
def _get_ghp_command ( self ) -> str :
'''Generate ` ` mkdocs gh - deploy ` ` command to deploy the site to GitHub Pages .''' | components = [ self . _mkdocs_config . get ( 'mkdocs_path' , 'mkdocs' ) ]
components . append ( 'gh-deploy' )
command = ' ' . join ( components )
self . logger . debug ( f'GHP upload command: {command}' )
return command |
def psicomputations ( variance , Z , variational_posterior , return_psi2_n = False ) :
"""Compute psi - statistics for ss - linear kernel""" | # here are the " statistics " for psi0 , psi1 and psi2
# Produced intermediate results :
# psi0 N
# psi1 NxM
# psi2 MxM
mu = variational_posterior . mean
S = variational_posterior . variance
psi0 = ( variance * ( np . square ( mu ) + S ) ) . sum ( axis = 1 )
Zv = variance * Z
psi1 = np . dot ( mu , Zv . T )
if return_p... |
def pomegranate ( args ) :
"""% prog cotton seqids karyotype . layout mcscan . out all . bed synteny . layout
Build a figure that calls graphics . karyotype to illustrate the high ploidy
of WGD history of pineapple genome . The script calls both graphics . karyotype
and graphic . synteny .""" | p = OptionParser ( pomegranate . __doc__ )
opts , args , iopts = p . set_image_options ( args , figsize = "9x7" )
if len ( args ) != 5 :
sys . exit ( not p . print_help ( ) )
seqidsfile , klayout , datafile , bedfile , slayout = args
fig = plt . figure ( 1 , ( iopts . w , iopts . h ) )
root = fig . add_axes ( [ 0 ,... |
def _update_secret ( namespace , name , data , apiserver_url ) :
'''Replace secrets data by a new one''' | # Prepare URL
url = "{0}/api/v1/namespaces/{1}/secrets/{2}" . format ( apiserver_url , namespace , name )
# Prepare data
data = [ { "op" : "replace" , "path" : "/data" , "value" : data } ]
# Make request
ret = _kpatch ( url , data )
if ret . get ( "status" ) == 404 :
return "Node {0} doesn't exist" . format ( url )... |
def get ( self , status_code ) :
"""Returns the requested status .
: param int status _ code : the status code to return
: queryparam str reason : optional reason phrase""" | status_code = int ( status_code )
if status_code >= 400 :
kwargs = { 'status_code' : status_code }
if self . get_query_argument ( 'reason' , None ) :
kwargs [ 'reason' ] = self . get_query_argument ( 'reason' )
if self . get_query_argument ( 'log_message' , None ) :
kwargs [ 'log_message' ] ... |
def results ( self , project_key = None , plan_key = None , job_key = None , build_number = None , expand = None , favourite = False , clover_enabled = False , issue_key = None , start_index = 0 , max_results = 25 ) :
"""Get results as generic method
: param project _ key :
: param plan _ key :
: param job _ ... | resource = "result"
if project_key and plan_key and job_key and build_number :
resource += "/{}-{}-{}/{}" . format ( project_key , plan_key , job_key , build_number )
elif project_key and plan_key and build_number :
resource += "/{}-{}/{}" . format ( project_key , plan_key , build_number )
elif project_key and ... |
def extract ( self , file_path , is_drum = False ) :
'''Extract MIDI file .
Args :
file _ path : File path of MIDI .
is _ drum : Extract drum data or not .
Returns :
pd . DataFrame ( columns = [ " program " , " start " , " end " , " pitch " , " velocity " , " duration " ] )''' | midi_data = pretty_midi . PrettyMIDI ( file_path )
note_tuple_list = [ ]
for instrument in midi_data . instruments :
if ( is_drum is False and instrument . is_drum is False ) or ( is_drum is True and instrument . is_drum is True ) :
for note in instrument . notes :
note_tuple_list . append ( ( i... |
def _ts_parse ( ts ) :
"""Parse alert timestamp , return UTC datetime object to maintain Python 2 compatibility .""" | dt = datetime . strptime ( ts [ : 19 ] , "%Y-%m-%dT%H:%M:%S" )
if ts [ 19 ] == '+' :
dt -= timedelta ( hours = int ( ts [ 20 : 22 ] ) , minutes = int ( ts [ 23 : ] ) )
elif ts [ 19 ] == '-' :
dt += timedelta ( hours = int ( ts [ 20 : 22 ] ) , minutes = int ( ts [ 23 : ] ) )
return dt . replace ( tzinfo = pytz .... |
def listen ( self , * , host , port , override = False , forever = False , ** kwargs ) :
"""Listen on TCP / IP socket .
Parameters
host : str
Host like ' 127.0.0.1'
port :
Port like 80.""" | if override :
argv = dict ( enumerate ( sys . argv ) )
host = argv . get ( 1 , host )
port = int ( argv . get ( 2 , port ) )
server = self . loop . create_server ( self . __handler . fork , host , port , ** kwargs )
server = self . loop . run_until_complete ( server )
self . log ( 'info' , 'Start listening ... |
def decorate_with_metadata ( obj , result ) :
"""Return obj decorated with es _ meta object""" | # Create es _ meta object with Elasticsearch metadata about this
# search result
obj . es_meta = Metadata ( # Elasticsearch id
id = result . get ( '_id' , 0 ) , # Source data
source = result . get ( '_source' , { } ) , # The search result score
score = result . get ( '_score' , None ) , # The document type
type = resul... |
def duplicate_lines ( self ) :
"""Duplicates the document lines under cursor .
: return : Method success .
: rtype : bool""" | cursor = self . textCursor ( )
self . __select_text_under_cursor_blocks ( cursor )
text = cursor . selectedText ( )
cursor . setPosition ( cursor . block ( ) . next ( ) . position ( ) )
cursor . position ( ) == cursor . document ( ) . firstBlock ( ) . position ( ) and cursor . setPosition ( cursor . document ( ) . last... |
def _get_url_doc ( self ) :
"""Return a list of URLs that map to this resource .""" | resolver = get_resolver ( None )
possibilities = resolver . reverse_dict . getlist ( self )
urls = [ possibility [ 0 ] for possibility in possibilities ]
return urls |
def make_path_relative ( path ) :
"""makes an absolute path name to a relative pathname .""" | if os . path . isabs ( path ) :
drive_s , path = os . path . splitdrive ( path )
import re
if not drive_s :
path = re . compile ( "/*(.*)" ) . findall ( path ) [ 0 ]
else :
path = path [ 1 : ]
assert ( not os . path . isabs ( path ) ) , path
return path |
def send_update_port_statuses ( self , context , port_ids , status ) :
"""Call the pluging to update the port status which updates the DB .
: param context : contains user information
: param port _ ids : list of ids of the ports associated with the status
: param status : value of the status for the given po... | cctxt = self . client . prepare ( version = '1.1' )
return cctxt . call ( context , 'update_port_statuses_cfg' , port_ids = port_ids , status = status ) |
def train_model_from_args ( args : argparse . Namespace ) :
"""Just converts from an ` ` argparse . Namespace ` ` object to string paths .""" | train_model_from_file ( args . param_path , args . serialization_dir , args . overrides , args . file_friendly_logging , args . recover , args . force , args . cache_directory , args . cache_prefix ) |
def PMISc ( S , method = 'JP' ) :
"""C / F splitting using Parallel Modified Independent Set ( in color ) .
PMIS - c , or PMIS in color , improves PMIS by perturbing the initial
random weights with weights determined by a vertex coloring .
Parameters
S : csr _ matrix
Strength of connection matrix indicati... | S = remove_diagonal ( S )
weights , G , S , T = preprocess ( S , coloring_method = method )
return MIS ( G , weights ) |
def logger_has_handlers ( logger ) :
"""Check if given logger has at least 1 handler associated , return a boolean value .
Since Python 2 doesn ' t provide Logger . hasHandlers ( ) , we have to perform the lookup by ourself .""" | if six . PY3 :
return logger . hasHandlers ( )
else :
c = logger
rv = False
while c :
if c . handlers :
rv = True
break
if not c . propagate :
break
else :
c = c . parent
return rv |
def schema_org ( builder ) : # pylint : disable = line - too - long
"""Builds schema . org microdata for DatasetSearch from DatasetBuilder .
Markup spec : https : / / developers . google . com / search / docs / data - types / dataset # dataset
Testing tool : https : / / search . google . com / structured - data... | # pylint : enable = line - too - long
properties = [ ( lambda x : x . name , SCHEMA_ORG_NAME ) , ( lambda x : x . description , SCHEMA_ORG_DESC ) , ( lambda x : x . name , SCHEMA_ORG_URL ) , ( lambda x : ( x . urls and x . urls [ 0 ] ) or "" , SCHEMA_ORG_SAMEAS ) ]
info = builder . info
out_str = SCHEMA_ORG_PRE
for ext... |
def update_info ( self , info ) :
"""set / update the info for this indexable with the key / value
if there is a conflict raise / warn as needed""" | for key in self . _info_fields :
value = getattr ( self , key , None )
idx = _get_info ( info , self . name )
existing_value = idx . get ( key )
if key in idx and value is not None and existing_value != value : # frequency / name just warn
if key in [ 'freq' , 'index_name' ] :
ws = a... |
def logout ( request , redirect_url = settings . LOGOUT_REDIRECT_URL ) :
"""Nothing hilariously hidden here , logs a user out . Strip this out if your
application already has hooks to handle this .""" | django_logout ( request )
return HttpResponseRedirect ( request . build_absolute_uri ( redirect_url ) ) |
def reverse ( self ) :
"""Generate the reverse of a directed graph , returns an identical graph if not directed .
Attributes & weights are preserved .
@ rtype : digraph
@ return : The directed graph that should be reversed .""" | assert self . DIRECTED , "Undirected graph types such as %s cannot be reversed" % self . __class__ . __name__
N = self . __class__ ( )
# - Add the nodes
N . add_nodes ( n for n in self . nodes ( ) )
# - Add the reversed edges
for ( u , v ) in self . edges ( ) :
wt = self . edge_weight ( ( u , v ) )
label = self... |
def remote ( self , name = 'origin' ) :
""": return : Remote with the specified name
: raise ValueError : if no remote with such a name exists""" | r = Remote ( self , name )
if not r . exists ( ) :
raise ValueError ( "Remote named '%s' didn't exist" % name )
return r |
def _fire_master ( self , data = None , tag = None , events = None , pretag = None , timeout = 60 , sync = True , timeout_handler = None ) :
'''Fire an event on the master , or drop message if unable to send .''' | load = { 'id' : self . opts [ 'id' ] , 'cmd' : '_minion_event' , 'pretag' : pretag , 'tok' : self . tok }
if events :
load [ 'events' ] = events
elif data and tag :
load [ 'data' ] = data
load [ 'tag' ] = tag
elif not data and tag :
load [ 'data' ] = { }
load [ 'tag' ] = tag
else :
return
if syn... |
def get_create_parameter ( model , param ) :
"""Return parameter with given name , creating it if needed .
If unique is false and the parameter exists , the value is not changed ; if
it does not exist , it will be created . If unique is true then upon conflict
a number is added to the end of the parameter nam... | norm_name = _n ( param . name )
parameter = model . parameters . get ( norm_name )
if not param . unique and parameter is not None :
return parameter
if param . unique :
pnum = 1
while True :
pname = norm_name + '_%d' % pnum
if model . parameters . get ( pname ) is None :
break
... |
def getReadAlignments ( self , reference , start = None , end = None ) :
"""Returns an iterator over the specified reads""" | return self . _getReadAlignments ( reference , start , end , self , None ) |
def add_to_matching_blacklist ( session , term ) :
"""Add term to the matching blacklist .
This function adds a ` term ` to the matching blacklist .
The term to add cannot have a ` None ` or empty value ,
on this case an ` ValueError ` will be raised .
: param session : database session
: param term : ter... | if term is None :
raise ValueError ( "'term' to blacklist cannot be None" )
if term == '' :
raise ValueError ( "'term' to blacklist cannot be an empty string" )
mb = MatchingBlacklist ( excluded = term )
session . add ( mb )
return mb |
def is_available ( self ) -> bool :
"""Indicate if this Monitor is currently available .""" | status_response = self . _client . get_state ( 'api/monitors/daemonStatus/id:{}/daemon:zmc.json' . format ( self . _monitor_id ) )
if not status_response :
_LOGGER . warning ( 'Could not get availability for monitor {}' . format ( self . _monitor_id ) )
return False
# Monitor _ Status was only added in ZM 1.32.... |
def docker ( gandi , vm , args ) :
"""Manage docker instance""" | if not [ basedir for basedir in os . getenv ( 'PATH' , '.:/usr/bin' ) . split ( ':' ) if os . path . exists ( '%s/docker' % basedir ) ] :
gandi . echo ( """'docker' not found in $PATH, required for this command \
to work
See https://docs.docker.com/installation/#installation to install, or use:
# curl https://g... |
def _validate_version ( self ) :
"""If the version starts with a digit , it must be a sematic - versioning
style string .""" | self . _assert_type ( "version" , list ( six . string_types ) )
self . _assert_matches_re ( "version" , [ RELEASE_VERSION_RE ] ) |
def _variable_elimination ( self , variables , operation , evidence = None , elimination_order = None , joint = True ) :
"""Implementation of a generalized variable elimination .
Parameters
variables : list , array - like
variables that are not to be eliminated .
operation : str ( ' marginalize ' | ' maximi... | if isinstance ( variables , string_types ) :
raise TypeError ( "variables must be a list of strings" )
if isinstance ( evidence , string_types ) :
raise TypeError ( "evidence must be a list of strings" )
# Dealing with the case when variables is not provided .
if not variables :
all_factors = [ ]
for fa... |
def get_file_descriptor ( self ) :
"""Return the file descriptor for the given websocket""" | try :
return uwsgi . connection_fd ( )
except IOError as e :
self . close ( )
raise WebSocketError ( e ) |
def wait_for_service ( host , port , timeout = DEFAULT_TIMEOUT ) :
"""Return True if connection to the host and port is successful within the timeout .
@ param host : str : hostname of the server
@ param port : int : TCP port to which to connect
@ param timeout : int : length of time in seconds to try to conn... | service = ServiceURL ( 'tcp://{}:{}' . format ( host , port ) , timeout )
return service . wait ( ) |
def action ( arguments ) :
"""Trim the alignment as specified""" | # Determine file format for input and output
source_format = ( arguments . source_format or fileformat . from_handle ( arguments . source_file ) )
output_format = ( arguments . output_format or fileformat . from_handle ( arguments . output_file ) )
# Load the alignment
with arguments . source_file :
sequences = Seq... |
def _set_country ( self , c ) :
"""callback if we used Tor ' s GETINFO ip - to - country""" | self . location . countrycode = c . split ( ) [ 0 ] . split ( '=' ) [ 1 ] . strip ( ) . upper ( ) |
def copy_modified_gene ( self , modified_gene , ignore_model_attributes = True ) :
"""Copy attributes of a Gene object over to this Gene , given that the modified gene has the same ID .
Args :
modified _ gene ( Gene , GenePro ) : Gene with modified attributes that you want to copy over .
ignore _ model _ attr... | ignore = [ '_model' , '_reaction' , '_functional' , 'model' , 'reaction' , 'functional' ]
for attr in filter ( lambda a : not a . startswith ( '__' ) and not isinstance ( getattr ( type ( self ) , a , None ) , property ) and not callable ( getattr ( self , a ) ) , dir ( modified_gene ) ) :
if attr not in ignore and... |
def decrypt ( self , data ) :
"""DES decrypts the data based on the key it was initialised with .
: param data : The encrypted bytes string to decrypt
: return : The decrypted bytes string""" | decrypted_data = b""
for i in range ( 0 , len ( data ) , 8 ) :
block = data [ i : i + 8 ]
block_length = len ( block )
if block_length != 8 :
raise ValueError ( "DES decryption must be a multiple of 8 " "bytes" )
decrypted_data += self . _decode_block ( block )
return decrypted_data |
def filter_accept_reftrack ( self , reftrack ) :
"""Return True , if the filter accepts the given reftrack
: param reftrack : the reftrack to filter
: type reftrack : : class : ` jukeboxcore . reftrack . Reftrack `
: returns : True , if the filter accepts the reftrack
: rtype : : class : ` bool `
: raises... | if reftrack . status ( ) in self . _forbidden_status :
return False
if reftrack . get_typ ( ) in self . _forbidden_types :
return False
if reftrack . uptodate ( ) in self . _forbidden_uptodate :
return False
if reftrack . alien ( ) in self . _forbidden_alien :
return False
return True |
def mavlink_packet ( self , m ) :
'''handle an incoming mavlink packet''' | if m . get_type ( ) == 'PPP' and self . ppp_fd != - 1 :
print ( "got ppp mavlink pkt len=%u" % m . length )
os . write ( self . ppp_fd , m . data [ : m . length ] ) |
def preprocess_text ( text , language ) :
"""This function applies pre - processing steps that convert forms of words
considered equivalent into one standardized form .
As one straightforward step , it case - folds the text . For the purposes of
wordfreq and related tools , a capitalized word shouldn ' t have... | # NFC or NFKC normalization , as needed for the language
info = get_language_info ( language )
text = unicodedata . normalize ( info [ 'normal_form' ] , text )
# Transliteration of multi - script languages
if info [ 'transliteration' ] is not None :
text = transliterate ( info [ 'transliteration' ] , text )
# Abjad... |
def safety_set_allowed_area_send ( self , target_system , target_component , frame , p1x , p1y , p1z , p2x , p2y , p2z , force_mavlink1 = False ) :
'''Set a safety zone ( volume ) , which is defined by two corners of a cube .
This message can be used to tell the MAV which
setpoints / MISSIONs to accept and whic... | return self . send ( self . safety_set_allowed_area_encode ( target_system , target_component , frame , p1x , p1y , p1z , p2x , p2y , p2z ) , force_mavlink1 = force_mavlink1 ) |
def setCmd ( self , cmd ) :
"""Check the cmd is valid , FrameError will be raised if its not .""" | cmd = cmd . upper ( )
if cmd not in VALID_COMMANDS :
raise FrameError ( "The cmd '%s' is not valid! It must be one of '%s' (STOMP v%s)." % ( cmd , VALID_COMMANDS , STOMP_VERSION ) )
else :
self . _cmd = cmd |
def get_turn_delta ( self , branch = None , turn = None , tick = None , start_tick = 0 ) :
"""Get a dictionary describing changes to the world within a given turn
Defaults to the present turn , and stops at the present tick unless specified .
See the documentation for ` ` get _ delta ` ` for a detailed descript... | branch = branch or self . branch
turn = turn or self . turn
tick = tick or self . tick
delta = super ( ) . get_turn_delta ( branch , turn , start_tick , tick )
if branch in self . _avatarness_cache . settings and turn in self . _avatarness_cache . settings [ branch ] :
for chara , graph , node , is_av in self . _av... |
def _apply_outputter ( self , func , mod ) :
'''Apply the _ _ outputter _ _ variable to the functions''' | if hasattr ( mod , '__outputter__' ) :
outp = mod . __outputter__
if func . __name__ in outp :
func . __outputter__ = outp [ func . __name__ ] |
def _get_msupdate_status ( ) :
'''Check to see if Microsoft Update is Enabled
Return Boolean''' | # To get the status of Microsoft Update we actually have to check the
# Microsoft Update Service Manager
# Initialize the PyCom system
with salt . utils . winapi . Com ( ) : # Create a ServiceManager Object
obj_sm = win32com . client . Dispatch ( 'Microsoft.Update.ServiceManager' )
# Return a collection of loaded S... |
def warn_explicit ( message , category , filename , lineno , module = None , registry = None , module_globals = None , emit_module = None ) :
"""Low level implementation of the warning functionality .
Duplicate of the standard library ` warnings . warn _ explicit ` ,
except it accepts the following arguments : ... | lineno = int ( lineno )
if module is None :
module = filename or "<unknown>"
if module [ - 3 : ] . lower ( ) == ".py" :
module = module [ : - 3 ]
# XXX What about leading pathname ?
if registry is None :
registry = { }
if registry . get ( 'version' , 0 ) != warnings . _filters_version :
... |
def read_annotations ( path_or_file , separator = '\t' , reset = True ) :
"""Read all annotations from the specified file .
> > > annotations = read _ annotations ( path _ or _ file , separator )
> > > colnames = annotations [ ' Column Name ' ]
> > > types = annotations [ ' Type ' ]
> > > annot _ row = anno... | annotations = OrderedDict ( { } )
with PathOrFile ( path_or_file , 'r' , reset = reset ) as f :
annotations [ 'Column Name' ] = f . readline ( ) . strip ( ) . split ( separator )
for line in f :
if line . startswith ( '#!{' ) :
tokens = line . strip ( ) . split ( separator )
_nam... |
def rescale_pixel_values ( images , order = "C" ) :
"""Rescale the range of values in images to be between [ 0 , 1]""" | images = np . asarray ( images , order = order ) . astype ( "float32" )
images -= images . min ( )
images /= images . max ( )
return images |
def run ( self , * args ) :
"""Get and set configuration parameters .
This command gets or sets parameter values from the user configuration
file . On Linux systems , configuration will be stored in the file
' ~ / . sortinghat ' .""" | params = self . parser . parse_args ( args )
config_file = os . path . expanduser ( '~/.sortinghat' )
if params . action == 'get' :
code = self . get ( params . parameter , config_file )
elif params . action == 'set' :
code = self . set ( params . parameter , params . value , config_file )
else :
raise Runt... |
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