signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def n_to_c ( self , var_n ) :
"""Given a parsed n . variant , return a c . variant on the specified
transcript using the specified alignment method ( default is
" transcript " indicating a self alignment ) .
: param hgvs . sequencevariant . SequenceVariant var _ n : a variant object
: returns : variant obje... | if not ( var_n . type == "n" ) :
raise HGVSInvalidVariantError ( "Expected n. variant; got " + str ( var_n ) )
if self . _validator :
self . _validator . validate ( var_n )
var_n . fill_ref ( self . hdp )
tm = self . _fetch_AlignmentMapper ( tx_ac = var_n . ac , alt_ac = var_n . ac , alt_aln_method = "transcrip... |
def update_resource ( self , resource , filename , change = None ) :
"""Update resource from uri to filename on local system .
Update means three things :
1 . GET resources
2 . set mtime in local time to be equal to timestamp in UTC ( should perhaps
or at least warn if different from LastModified from the G... | path = os . path . dirname ( filename )
distutils . dir_util . mkpath ( path )
num_updated = 0
if ( self . dryrun ) :
self . logger . info ( "dryrun: would GET %s --> %s" % ( resource . uri , filename ) )
else : # 1 . GET
for try_i in range ( 1 , self . tries + 1 ) :
try :
r = requests . get... |
def real_time_statistics ( self ) :
"""Access the real _ time _ statistics
: returns : twilio . rest . taskrouter . v1 . workspace . workspace _ real _ time _ statistics . WorkspaceRealTimeStatisticsList
: rtype : twilio . rest . taskrouter . v1 . workspace . workspace _ real _ time _ statistics . WorkspaceReal... | if self . _real_time_statistics is None :
self . _real_time_statistics = WorkspaceRealTimeStatisticsList ( self . _version , workspace_sid = self . _solution [ 'sid' ] , )
return self . _real_time_statistics |
def _configure_send ( self , request , ** kwargs ) : # type : ( ClientRequest , Any ) - > Dict [ str , str ]
"""Configure the kwargs to use with requests .
See " send " for kwargs details .
: param ClientRequest request : The request object to be sent .
: returns : The requests . Session . request kwargs
: ... | requests_kwargs = { }
# type : Any
session = kwargs . pop ( 'session' , self . session )
# If custom session was not create here
if session is not self . session :
self . _init_session ( session )
session . max_redirects = int ( self . config . redirect_policy ( ) )
session . trust_env = bool ( self . config . prox... |
def get_items ( self , repository_id , project = None , scope_path = None , recursion_level = None , include_content_metadata = None , latest_processed_change = None , download = None , include_links = None , version_descriptor = None ) :
"""GetItems .
[ Preview API ] Get Item Metadata and / or Content for a coll... | route_values = { }
if project is not None :
route_values [ 'project' ] = self . _serialize . url ( 'project' , project , 'str' )
if repository_id is not None :
route_values [ 'repositoryId' ] = self . _serialize . url ( 'repository_id' , repository_id , 'str' )
query_parameters = { }
if scope_path is not None :... |
def stop ( self , timeout = 15 ) :
"""Stop the subprocess .
Keyword Arguments
* * timeout * *
Time in seconds to wait for a process and its
children to exit .""" | pp = self . pid
if pp :
try :
kill_process_nicely ( pp , timeout = timeout )
except psutil . NoSuchProcess :
pass |
def to_networkx ( self , labels = None , edge_labels = False ) :
"""Get a networkx representation of the binary search tree .""" | import networkx as nx
graph = nx . DiGraph ( )
for node in self . _traverse_nodes ( ) :
u = node . key
graph . add_node ( u )
# Minor redundancy
# Set node properties
graph . nodes [ u ] [ 'value' ] = node . value
if labels is not None :
label = ',' . join ( [ str ( getattr ( node , k ) ... |
def modify_instance_attribute ( self , instance_id , attribute , value ) :
"""Changes an attribute of an instance
: type instance _ id : string
: param instance _ id : The instance id you wish to change
: type attribute : string
: param attribute : The attribute you wish to change .
* AttributeName - Expe... | # Allow a bool to be passed in for value of disableApiTermination
if attribute == 'disableApiTermination' :
if isinstance ( value , bool ) :
if value :
value = 'true'
else :
value = 'false'
params = { 'InstanceId' : instance_id , 'Attribute' : attribute , 'Value' : value }
re... |
def query_neighbors ( self , nodes : List [ Node ] ) -> List [ Edge ] :
"""Get all edges incident to any of the given nodes .""" | return self . session . query ( Edge ) . filter ( self . _edge_one_node ( nodes ) ) . all ( ) |
def get_changeset ( args ) :
"""Dump the changeset objects as JSON , reading the provided bundle YAML .
The YAML can be provided either from stdin or by passing a file path as
first argument .""" | # Parse the arguments .
parser = argparse . ArgumentParser ( description = get_changeset . __doc__ )
parser . add_argument ( 'infile' , nargs = '?' , type = argparse . FileType ( 'r' ) , default = sys . stdin , help = 'path to the bundle YAML file' )
parser . add_argument ( '--version' , action = 'version' , version = ... |
def render ( self , renderer = None , ** kwargs ) :
"""Render the navigational item using a renderer .
: param renderer : An object implementing the : class : ` ~ . Renderer `
interface .
: return : A markupsafe string with the rendered result .""" | return Markup ( get_renderer ( current_app , renderer ) ( ** kwargs ) . visit ( self ) ) |
def search_for_devices_by_serial_number ( self , sn ) :
"""Returns a list of device objects that match the serial number
in param ' sn ' .
This will match partial serial numbers .""" | import re
sn_search = re . compile ( sn )
matches = [ ]
for dev_o in self . get_all_devices_in_portal ( ) : # print ( " Checking { 0 } " . format ( dev _ o [ ' sn ' ] ) )
try :
if sn_search . match ( dev_o [ 'sn' ] ) :
matches . append ( dev_o )
except TypeError as err :
print ( "Pro... |
def _loglikelihood ( self , y , mu , weights = None , rescale_y = True ) :
"""compute the log - likelihood of the dataset using the current model
Parameters
y : array - like of shape ( n , )
containing target values
mu : array - like of shape ( n _ samples , )
expected value of the targets given the model... | if rescale_y :
y = np . round ( y * weights ) . astype ( 'int' )
return self . distribution . log_pdf ( y = y , mu = mu , weights = weights ) . sum ( ) |
def retrieve_ocsps ( self , cert , issuer ) :
""": param cert :
An asn1crypto . x509 . Certificate object
: param issuer :
An asn1crypto . x509 . Certificate object of cert ' s issuer
: return :
A list of asn1crypto . ocsp . OCSPResponse objects""" | if not self . _allow_fetching :
return self . _ocsps
if cert . issuer_serial not in self . _fetched_ocsps :
try :
ocsp_response = ocsp_client . fetch ( cert , issuer , ** self . _ocsp_fetch_params )
self . _fetched_ocsps [ cert . issuer_serial ] = [ ocsp_response ]
# Responses can contai... |
def endline_handle ( self , original , loc , tokens ) :
"""Add line number information to end of line .""" | internal_assert ( len ( tokens ) == 1 , "invalid endline tokens" , tokens )
lines = tokens [ 0 ] . splitlines ( True )
if self . minify :
lines = lines [ 0 ]
out = [ ]
ln = lineno ( loc , original )
for endline in lines :
out . append ( self . wrap_line_number ( self . adjust ( ln ) ) + endline )
ln += 1
re... |
def start_transports ( self ) :
"""start thread transports .""" | self . transport = Transport ( self . queue , self . batch_size , self . batch_interval , self . session_factory )
thread = threading . Thread ( target = self . transport . loop )
self . threads . append ( thread )
thread . daemon = True
thread . start ( ) |
def _represent_undefined ( self , data ) :
"""Raises flag for objects that cannot be represented""" | raise RepresenterError ( _format ( "Cannot represent an object: {0!A} of type: {1}; " "yaml_representers: {2!A}, " "yaml_multi_representers: {3!A}" , data , type ( data ) , self . yaml_representers . keys ( ) , self . yaml_multi_representers . keys ( ) ) ) |
def ensure_open ( f , mode = 'r' ) :
r"""Return a file pointer using gzip . open if filename ends with . gz otherwise open ( )
TODO : try to read a gzip rather than relying on gz extension , likewise for zip and other formats
TODO : monkey patch the file so that . write _ bytes = . write and . write writes both... | fin = f
if isinstance ( f , basestring ) :
if len ( f ) <= MAX_LEN_FILEPATH :
f = find_filepath ( f ) or f
if f and ( not hasattr ( f , 'seek' ) or not hasattr ( f , 'readlines' ) ) :
if f . lower ( ) . endswith ( '.gz' ) :
return gzip . open ( f , mode = mode )
... |
def ip_address ( ) :
"""Get the IP address used for public connections .""" | s = socket . socket ( socket . AF_INET , socket . SOCK_DGRAM )
# 8.8.8.8 is the google public DNS
s . connect ( ( "8.8.8.8" , 53 ) )
ip = s . getsockname ( ) [ 0 ]
s . close ( )
return ip |
def fromTerm ( cls , term ) :
"""Create a functor from a Term or term handle .""" | if isinstance ( term , Term ) :
term = term . handle
elif not isinstance ( term , ( c_void_p , int ) ) :
raise ArgumentTypeError ( ( str ( Term ) , str ( int ) ) , str ( type ( term ) ) )
f = functor_t ( )
if PL_get_functor ( term , byref ( f ) ) : # get args
args = [ ]
arity = PL_functor_arity ( f . va... |
def vprintf ( self , alevel , format , * args ) :
'''A verbosity - aware printf .''' | if self . _verbosity and self . _verbosity >= alevel :
sys . stdout . write ( format % args ) |
def pop_row ( self , idr = None , tags = False ) :
"""Pops a row , default the last""" | idr = idr if idr is not None else len ( self . body ) - 1
row = self . body . pop ( idr )
return row if tags else [ cell . childs [ 0 ] for cell in row ] |
def _get_host_ref ( service_instance , host , host_name = None ) :
'''Helper function that returns a host object either from the host location or the host _ name .
If host _ name is provided , that is the host _ object that will be returned .
The function will first search for hosts by DNS Name . If no hosts ar... | search_index = salt . utils . vmware . get_inventory ( service_instance ) . searchIndex
# First , try to find the host reference by DNS Name .
if host_name :
host_ref = search_index . FindByDnsName ( dnsName = host_name , vmSearch = False )
else :
host_ref = search_index . FindByDnsName ( dnsName = host , vmSea... |
def map_vnics ( vm ) :
"""maps the vnic on the vm by name
: param vm : virtual machine
: return : dictionary : { ' vnic _ name ' : vnic }""" | return { device . deviceInfo . label : device for device in vm . config . hardware . device if isinstance ( device , vim . vm . device . VirtualEthernetCard ) } |
def _filter_packages ( self ) :
"""Run the package filtering plugins and remove any packages from the
packages _ to _ sync that match any filters .
- Logging of action will be done within the check _ match methods""" | global LOG_PLUGINS
filter_plugins = filter_project_plugins ( )
if not filter_plugins :
if LOG_PLUGINS :
logger . info ( "No project filters are enabled. Skipping filtering" )
LOG_PLUGINS = False
return
# Make a copy of self . packages _ to _ sync keys
# as we may delete packages during iteration... |
def _notify_single_item ( self , item ) :
"""Route inbound items to individual channels""" | # channels that this individual item has already triggered
# ( dont want to trigger them again )
triggered_channels = set ( )
for key_set in self . watch_keys : # only pluck keys if they exist
plucked = { key_name : item [ key_name ] for key_name in key_set if key_name in item }
route_keys = expand_dict_as_keys... |
def write ( self , bucket , rows ) :
"""https : / / github . com / frictionlessdata / tableschema - pandas - py # storage""" | # Prepare
descriptor = self . describe ( bucket )
new_data_frame = self . __mapper . convert_descriptor_and_rows ( descriptor , rows )
# Just set new DataFrame if current is empty
if self . __dataframes [ bucket ] . size == 0 :
self . __dataframes [ bucket ] = new_data_frame
# Append new data frame to the old one s... |
def register_channel ( model_class , search_fields = ( ) ) :
"""Register channel for model
: param model _ class : model to register channel for
: param search _ fields :
: return :""" | if len ( search_fields ) == 0 :
search_fields = get_fields_with_icontains_filter ( model_class )
channel_class = type ( model_class . __name__ + "LookupChannel" , ( AutoLookupChannelBase , ) , { "model" : model_class , "dynamical_search_fields" : search_fields , } )
channel_name = class_name_to_low_case ( model_cla... |
def classify ( self , text = u'' ) :
"""Predicts the Language of a given text .
: param text : Unicode text to be classified .""" | text = self . lm . normalize ( text )
tokenz = LM . tokenize ( text , mode = 'c' )
result = self . lm . calculate ( doc_terms = tokenz )
# print ' Karbasa : ' , self . karbasa ( result )
if self . unk and self . lm . karbasa ( result ) < self . min_karbasa :
lang = 'unk'
else :
lang = result [ 'calc_id' ]
retur... |
def resolve_structure ( self , fc , ct ) :
"""Resolve structure specifications .""" | if self . debug :
print ( "++++++++ Resolving structure of (%s) with %s" % ( fc , ct ) )
for w in ct . structure . withs :
try :
if w . instance == 'parent' or w . instance == 'this' :
w2 = With ( w . instance , w . as_ )
else :
w2 = With ( fc . paths [ w . instance ] . v... |
def addAnswers ( self , answers , callback = None , errback = None , ** kwargs ) :
"""Add answers to the record .
: param answers : answers structure . See the class note on answer format .""" | if not self . data :
raise RecordException ( 'record not loaded' )
orig_answers = self . data [ 'answers' ]
new_answers = self . _rest . _getAnswersForBody ( answers )
orig_answers . extend ( new_answers )
return self . update ( answers = orig_answers , callback = callback , errback = errback , ** kwargs ) |
def _create_cadvisor_prometheus_instance ( self , instance ) :
"""Create a copy of the instance and set default values .
This is so the base class can create a scraper _ config with the proper values .""" | cadvisor_instance = deepcopy ( instance )
cadvisor_instance . update ( { 'namespace' : self . NAMESPACE , # We need to specify a prometheus _ url so the base class can use it as the key for our config _ map ,
# we specify a dummy url that will be replaced in the ` check ( ) ` function . We append it with " cadvisor "
#... |
def _set_view ( self ) :
"""Assign a view to current graph""" | if self . logarithmic :
view_class = PolarLogView
else :
view_class = PolarView
self . view = view_class ( self . width - self . margin_box . x , self . height - self . margin_box . y , self . _box ) |
def wait_for_any_log ( nodes , pattern , timeout , filename = 'system.log' , marks = None ) :
"""Look for a pattern in the system . log of any in a given list
of nodes .
@ param nodes The list of nodes whose logs to scan
@ param pattern The target pattern
@ param timeout How long to wait for the pattern . N... | if marks is None :
marks = { }
for _ in range ( timeout ) :
for node in nodes :
found = node . grep_log ( pattern , filename = filename , from_mark = marks . get ( node , None ) )
if found :
return node
time . sleep ( 1 )
raise TimeoutError ( time . strftime ( "%d %b %Y %H:%M:%S"... |
def tx_max ( tasmax , freq = 'YS' ) :
r"""Highest max temperature
The maximum value of daily maximum temperature .
Parameters
tasmax : xarray . DataArray
Maximum daily temperature [ ° C ] or [ K ]
freq : str , optional
Resampling frequency
Returns
xarray . DataArray
Maximum value of daily maximum ... | return tasmax . resample ( time = freq ) . max ( dim = 'time' , keep_attrs = True ) |
def laplace ( affinity_matrix , shi_malik_type = False ) :
"""Converts affinity matrix into normalised graph Laplacian ,
for spectral clustering .
( At least ) two forms exist :
L = ( D ^ - 0.5 ) . A . ( D ^ - 0.5 ) - default
L = ( D ^ - 1 ) . A - ` Shi - Malik ` type , from Shi Malik paper""" | diagonal = affinity_matrix . sum ( axis = 1 ) - affinity_matrix . diagonal ( )
zeros = diagonal <= 1e-10
diagonal [ zeros ] = 1
if ( diagonal <= 1e-10 ) . any ( ) : # arbitrarily small value
raise ZeroDivisionError
if shi_malik_type :
inv_d = np . diag ( 1 / diagonal )
return inv_d . dot ( affinity_matrix )... |
def block ( self , * args , ** kwargs ) :
"""Call the wrapped function , and wait for the result in a blocking fashion
Returns the result of the function call .
: param args :
: param kwargs :
: return : result of function call""" | LOG . debug ( '%s on %s (awaitable %s async %s provider %s)' , 'blocking' , self . _func , self . _is_awaitable , self . _is_asyncio_provider , self . _concurrency_provider )
if self . _deferable :
raise RuntimeError ( 'Already activated this call by deferring it' )
with self . _lock :
if not hasattr ( self , '... |
def arith_prog_term ( a , n , d ) :
"""Function to compute the n - th term of an Arithmetic Progression ( AP ) .
The n - th term " Tn " of an AP where " a " is the first term , and " d " the common difference , is computed using the formula :
Tn = a + ( n - 1 ) * d
Examples :
arith _ prog _ term ( 1 , 5 , 2... | term = ( a + ( ( n - 1 ) * d ) )
return term |
def auto_labels ( df ) :
"""Transforms atomic system information into well - formatted labels .
Parameters
df : Pandas DataFrame .
Returns
labels : list of system labels .""" | systems = list ( df . system )
facets = list ( df . facet )
systems_labels = [ w . replace ( '_' , '\ ' ) for w in systems ]
systems_labels = [ sub ( w ) for w in systems_labels ]
systems_labels = [ w . replace ( '}$$_{' , '' ) for w in systems_labels ]
systems_labels = [ w . replace ( '$' , '' ) for w in systems_label... |
def match_string ( pattern , search_string ) :
'''Match a pattern in a string''' | rexobj = REX ( pattern , None )
rexpatstr = reformat_pattern ( pattern )
# print " rexpatstr : " , rexpatstr
rexpat = re . compile ( rexpatstr )
rexobj . rex_patternstr = rexpatstr
rexobj . rex_pattern = rexpat
line_count = 1
for line in search_string . splitlines ( ) :
line = line . strip ( )
mobj = rexpat . m... |
def print_summary ( self ) -> None :
"""Prints the tasks ' timing summary .""" | print ( "Tasks execution time summary:" )
for mon_task in self . _monitor_tasks :
print ( "%s:\t%.4f (sec)" % ( mon_task . task_name , mon_task . total_time ) ) |
def _get_model_fitting ( self , mf_id ) :
"""Retreive model fitting with identifier ' mf _ id ' from the list of model
fitting objects stored in self . model _ fitting""" | for model_fitting in self . model_fittings :
if model_fitting . activity . id == mf_id :
return model_fitting
raise Exception ( "Model fitting activity with id: " + str ( mf_id ) + " not found." ) |
def cli ( env ) :
"""Server order options for a given chassis .""" | hardware_manager = hardware . HardwareManager ( env . client )
options = hardware_manager . get_create_options ( )
tables = [ ]
# Datacenters
dc_table = formatting . Table ( [ 'datacenter' , 'value' ] )
dc_table . sortby = 'value'
for location in options [ 'locations' ] :
dc_table . add_row ( [ location [ 'name' ] ... |
def get_driver_class ( provider ) :
"""Return the driver class
: param provider : str - provider name
: return :""" | if "." in provider :
parts = provider . split ( '.' )
kls = parts . pop ( )
path = '.' . join ( parts )
module = import_module ( path )
if not hasattr ( module , kls ) :
raise ImportError ( '{0} provider not found at {1}' . format ( kls , path ) )
driver = getattr ( module , kls )
else :... |
def vn_free_ar ( call = None , kwargs = None ) :
'''Frees a reserved address range from a virtual network .
. . versionadded : : 2016.3.0
vn _ id
The ID of the virtual network from which to free an address range .
Can be used instead of ` ` vn _ name ` ` .
vn _ name
The name of the virtual network from ... | if call != 'function' :
raise SaltCloudSystemExit ( 'The vn_free_ar function must be called with -f or --function.' )
if kwargs is None :
kwargs = { }
vn_id = kwargs . get ( 'vn_id' , None )
vn_name = kwargs . get ( 'vn_name' , None )
ar_id = kwargs . get ( 'ar_id' , None )
if ar_id is None :
raise SaltClou... |
def callback ( self , filename , lines , ** kwargs ) :
"""publishes lines one by one to the given topic""" | timestamp = self . get_timestamp ( ** kwargs )
if kwargs . get ( 'timestamp' , False ) :
del kwargs [ 'timestamp' ]
for line in lines :
try :
import warnings
with warnings . catch_warnings ( ) :
warnings . simplefilter ( 'error' )
# produce message
if self . _... |
def join ( self , other , on = None , how = 'left' , lsuffix = None , rsuffix = None , algorithm = 'merge' , is_on_sorted = True , is_on_unique = True ) :
"""Database - like join this DataFrame with the other DataFrame .
Currently assumes the ` on ` columns are sorted and the on - column ( s ) values are unique !... | check_type ( lsuffix , str )
check_type ( rsuffix , str )
self_names = self . _gather_column_names ( )
other_names = other . _gather_column_names ( )
common_names = set ( self_names ) . intersection ( set ( other_names ) )
if len ( common_names ) > 0 and lsuffix is None and rsuffix is None :
raise ValueError ( 'Col... |
def get_trust ( self ) :
"""Gets the ` ` Trust ` ` for this authorization .
return : ( osid . authentication . process . Trust ) - the ` ` Trust ` `
raise : IllegalState - ` ` has _ trust ( ) ` ` is ` ` false ` `
raise : OperationFailed - unable to complete request
* compliance : mandatory - - This method m... | # Implemented from template for osid . resource . Resource . get _ avatar _ template
if not bool ( self . _my_map [ 'trustId' ] ) :
raise errors . IllegalState ( 'this Authorization has no trust' )
mgr = self . _get_provider_manager ( 'AUTHENTICATION.PROCESS' )
if not mgr . supports_trust_lookup ( ) :
raise err... |
def showSegmentation ( segmentation , voxelsize_mm = np . ones ( [ 3 , 1 ] ) , degrad = 4 , label = 1 , smoothing = True ) :
"""Funkce vrací trojrozměrné porobné jako data [ ' segmentation ' ]
v data [ ' slab ' ] je popsáno , co která hodnota znamená""" | labels = [ ]
segmentation = segmentation [ : : degrad , : : degrad , : : degrad ]
# import pdb ; pdb . set _ trace ( )
mesh_data = seg2fem . gen_mesh_from_voxels_mc ( segmentation , voxelsize_mm * degrad )
if smoothing :
mesh_data . coors = seg2fem . smooth_mesh ( mesh_data )
else :
mesh_data = seg2fem . gen_me... |
def get_params ( self ) :
"""Get parameters from this object""" | params = super ( ) . get_params ( )
params . update ( { 'knn' : self . knn , 'decay' : self . decay , 'bandwidth' : self . bandwidth , 'bandwidth_scale' : self . bandwidth_scale , 'distance' : self . distance , 'thresh' : self . thresh , 'n_jobs' : self . n_jobs , 'random_state' : self . random_state , 'verbose' : self... |
def queue_get_stoppable ( self , q ) :
"""Take obj from queue , but will give up when the thread is stopped""" | while not self . stopped ( ) :
try :
return q . get ( timeout = 5 )
except queue . Empty :
pass |
def safe_mult ( a , b ) :
"""safe version of multiply""" | if isinstance ( a , str ) and isinstance ( b , int ) and len ( a ) * b > MAX_STR_LEN :
raise RuntimeError ( "String length exceeded, max string length is {}" . format ( MAX_STR_LEN ) )
return a * b |
def get_github_login ( self , user , rol , commit_hash , repo ) :
"""rol : author or committer""" | login = None
try :
login = self . github_logins [ user ]
except KeyError : # Get the login from github API
GITHUB_API_URL = "https://api.github.com"
commit_url = GITHUB_API_URL + "/repos/%s/commits/%s" % ( repo , commit_hash )
headers = { 'Authorization' : 'token ' + self . github_token }
r = self .... |
def listen ( self , topic , timeout = 1 , limit = 1 ) :
"""Listen to a topic and return a list of message payloads received
within the specified time . Requires an async Subscribe to have been called previously .
` topic ` topic to listen to
` timeout ` duration to listen
` limit ` the max number of payload... | if not self . _subscribed :
logger . warn ( 'Cannot listen when not subscribed to a topic' )
return [ ]
if topic not in self . _messages :
logger . warn ( 'Cannot listen when not subscribed to topic: %s' % topic )
return [ ]
# If enough messages have already been gathered , return them
if limit != 0 and... |
def add ( self , artifact_type : ArtifactType , src_path : str , dst_path : str = None ) :
"""Add an artifact of type ` artifact _ type ` at ` src _ path ` .
` src _ path ` should be the path of the file relative to project root .
` dst _ path ` , if given , is the desired path of the artifact in dependent
ta... | if dst_path is None :
dst_path = src_path
other_src_path = self . _artifacts [ artifact_type ] . setdefault ( dst_path , src_path )
if src_path != other_src_path :
raise RuntimeError ( '{} artifact with dest path {} exists with different src ' 'path: {} != {}' . format ( artifact_type , dst_path , src_path , ot... |
def prep_connection ( self , creds = None , keyspace = None , node_auto_discovery = True ) :
"""Do login and set _ keyspace tasks as necessary , and also check this
node ' s idea of the Cassandra ring . Expects that our connection is
alive .
Return a Deferred that will fire with the ring information , or be
... | d = defer . succeed ( None )
if creds is not None :
d . addCallback ( lambda _ : self . my_login ( creds ) )
if keyspace is not None :
d . addCallback ( lambda _ : self . my_set_keyspace ( keyspace ) )
if node_auto_discovery :
d . addCallback ( lambda _ : self . my_describe_ring ( keyspace ) )
return d |
def compute ( self , inputs , outputs ) :
"""Run one iteration of TemporalPoolerRegion ' s compute .
Note that if the reset signal is True ( 1 ) we assume this iteration
represents the * end * of a sequence . The output will contain the pooled
representation to this point and any history will then be reset . ... | resetSignal = False
if 'resetIn' in inputs :
if len ( inputs [ 'resetIn' ] ) != 1 :
raise Exception ( "resetIn has invalid length" )
if inputs [ 'resetIn' ] [ 0 ] != 0 :
resetSignal = True
outputs [ "mostActiveCells" ] [ : ] = numpy . zeros ( self . _columnCount , dtype = GetNTAReal ( ) )
if sel... |
def decompressBlocks ( self , startBlock , endBlock ) :
'''This is mostly a helper function to get BWT range , but I wanted it to be a separate thing for use possibly in
decompression
@ param startBlock - the index of the start block we will decode
@ param endBlock - the index of the final block we will decod... | expectedIndex = startBlock * self . binSize
trueIndex = np . sum ( self . partialFM [ startBlock ] ) - self . offsetSum
dist = expectedIndex - trueIndex
# find the end of the region of interest
startRange = self . refFM [ startBlock ]
if endBlock >= self . refFM . shape [ 0 ] - 1 :
endRange = self . bwt . shape [ 0... |
def fetchable_partitions ( self ) :
"""Return set of TopicPartitions that should be Fetched .""" | fetchable = set ( )
for partition , state in six . iteritems ( self . assignment ) :
if state . is_fetchable ( ) :
fetchable . add ( partition )
return fetchable |
def attention_bias_local_2d_block ( mesh , h_dim , w_dim , memory_h_dim , memory_w_dim , dtype = tf . int32 ) :
"""Bias for attention for local blocks where attention to right is disallowed .
Create the bias matrix by using two separate masks , one for the memory part
which doesn ' t overlap with the query and ... | memory_height = mtf . Dimension ( memory_h_dim . name , h_dim . size )
memory_width = mtf . Dimension ( memory_w_dim . name , w_dim . size )
mask_top_visible = mtf . zeros ( mesh , [ h_dim , memory_height ] , dtype = dtype )
mask_left_visible = mtf . zeros ( mesh , [ w_dim , memory_width ] , dtype = dtype )
mask_query ... |
def show_as_root_until_keypress ( self , w , key , afterwards = None ) :
"""Replaces root widget by given : class : ` urwid . Widget ` and makes the UI
ignore all further commands apart from cursor movement .
If later on ` key ` is pressed , the old root widget is reset , callable
` afterwards ` is called and... | self . mainloop . widget = w
self . _unlock_key = key
self . _unlock_callback = afterwards
self . _locked = True |
def check_param_ranges ( num_bins , num_groups , num_values , trim_outliers , trim_percentile ) :
"""Ensuring the parameters are in valid ranges .""" | if num_bins < minimum_num_bins :
raise ValueError ( 'Too few bins! The number of bins must be >= 5' )
if num_values < num_groups :
raise ValueError ( 'Insufficient number of values in features (< number of nodes), or invalid membership!' )
if trim_outliers :
if trim_percentile < 0 or trim_percentile >= 100 ... |
def apply ( self , func , ** kwargs ) :
"""apply the function to my values ; return a block if we are not
one""" | with np . errstate ( all = 'ignore' ) :
result = func ( self . values , ** kwargs )
if not isinstance ( result , Block ) :
result = self . make_block ( values = _block_shape ( result , ndim = self . ndim ) )
return result |
def install_custom_css ( destdir , cssfile , resource = PKGNAME ) :
"""Add the kernel CSS to custom . css""" | ensure_dir_exists ( destdir )
custom = os . path . join ( destdir , 'custom.css' )
prefix = css_frame_prefix ( resource )
# Check if custom . css already includes it . If so , let ' s remove it first
exists = False
if os . path . exists ( custom ) :
with io . open ( custom ) as f :
for line in f :
... |
def select_with_main_images ( self , limit = None , ** kwargs ) :
'''Select all objects with filters passed as kwargs .
For each object it ' s main image instance is accessible as ` ` object . main _ image ` ` .
Results can be limited using ` ` limit ` ` parameter .
Selection is performed using only 2 or 3 sq... | objects = self . get_query_set ( ) . filter ( ** kwargs ) [ : limit ]
self . image_model_class . injector . inject_to ( objects , 'main_image' , is_main = True )
return objects |
def query ( searchstr , outformat = FORMAT_BIBTEX , allresults = False ) :
"""Query google scholar .
This method queries google scholar and returns a list of citations .
Parameters
searchstr : str
the query
outformat : int , optional
the output format of the citations . Default is bibtex .
allresults ... | logger . debug ( "Query: {sstring}" . format ( sstring = searchstr ) )
searchstr = '/scholar?q=' + quote ( searchstr )
url = GOOGLE_SCHOLAR_URL + searchstr
header = HEADERS
header [ 'Cookie' ] = "GSP=CF=%d" % outformat
request = Request ( url , headers = header )
response = urlopen ( request )
html = response . read ( ... |
def help ( subcommand = None ) :
"""Print help for subcommands .
Prints the help text for the specified subcommand .
If subcommand is not specified , prints one - line summaries for every command .""" | if not subcommand :
print ( "blurb version" , __version__ )
print ( )
print ( "Management tool for CPython Misc/NEWS and Misc/NEWS.d entries." )
print ( )
print ( "Usage:" )
print ( " blurb [subcommand] [options...]" )
print ( )
# print list of subcommands
summaries = [ ]
long... |
async def get ( self , key , param = None , extend_herd_timeout = None ) :
"""Use key or identity generate from key and param to
get cached content and expire time .
Compare expire time with time . now ( ) , return None and
set cache with extended timeout if cache is expired ,
else , return unpacked content... | identity = self . _gen_identity ( key , param )
res = await self . client . get ( identity )
if res :
res , timeout = self . _unpack ( res )
now = int ( time . time ( ) )
if timeout <= now :
extend_timeout = extend_herd_timeout or self . extend_herd_timeout
expected_expired_ts = now + extend... |
def main ( ) :
'''Example code , showing the instantiation of a ChebiEntity , a call to
get _ name ( ) , get _ outgoings ( ) and the calling of a number of methods of the
returned Relation objects .''' | chebi_entity = ChebiEntity ( 15903 )
print ( chebi_entity . get_name ( ) )
for outgoing in chebi_entity . get_outgoings ( ) :
target_chebi_entity = ChebiEntity ( outgoing . get_target_chebi_id ( ) )
print ( outgoing . get_type ( ) + '\t' + target_chebi_entity . get_name ( ) ) |
def _prepare_insert ( self , tmpl , record_class , field_names , placeholder_for_id = False ) :
"""With transaction isolation level of " read committed " this should
generate records with a contiguous sequence of integer IDs , assumes
an indexed ID column , the database - side SQL max function , the
insert - ... | field_names = list ( field_names )
if hasattr ( record_class , 'application_name' ) and 'application_name' not in field_names :
field_names . append ( 'application_name' )
if hasattr ( record_class , 'pipeline_id' ) and 'pipeline_id' not in field_names :
field_names . append ( 'pipeline_id' )
if hasattr ( recor... |
def get_active_title ( ) :
'''returns the window title of the active window''' | if os . name == 'posix' :
cmd = [ 'xdotool' , 'getactivewindow' , 'getwindowname' ]
proc = subprocess . Popen ( cmd , stdout = subprocess . PIPE , stderr = subprocess . PIPE )
title = proc . communicate ( ) [ 0 ] . decode ( 'utf-8' )
else :
raise NotImplementedError
return title |
def as_dataframe ( self , fillna = True , subjects = None ) :
"""Return association set as pandas DataFrame
Each row is a subject ( e . g . gene )
Each column is the inferred class used to describe the subject""" | entries = [ ]
selected_subjects = self . subjects
if subjects is not None :
selected_subjects = subjects
for s in selected_subjects :
vmap = { }
for c in self . inferred_types ( s ) :
vmap [ c ] = 1
entries . append ( vmap )
logging . debug ( "Creating DataFrame" )
df = pd . DataFrame ( entries ... |
def _set_secondary_path ( self , v , load = False ) :
"""Setter method for secondary _ path , mapped from YANG variable / mpls _ config / router / mpls / mpls _ cmds _ holder / lsp / secondary _ path ( list )
If this variable is read - only ( config : false ) in the
source YANG file , then _ set _ secondary _ p... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = YANGListType ( "secpath_name" , secondary_path . secondary_path , yang_name = "secondary-path" , rest_name = "secondary-path" , parent = self , is_container = 'list' , user_ordered = False , path_helper = self . _path_helper ... |
def on_invite ( self , connection , event ) :
"""Got an invitation to a channel""" | sender = self . get_nick ( event . source )
invited = self . get_nick ( event . target )
channel = event . arguments [ 0 ]
if invited == self . _nickname :
logging . info ( "! I am invited to %s by %s" , channel , sender )
connection . join ( channel )
else :
logging . info ( ">> %s invited %s to %s" , send... |
def fnmatches ( entry , * pattern_list ) :
"""returns true if entry matches any of the glob patterns , false
otherwise""" | for pattern in pattern_list :
if pattern and fnmatch ( entry , pattern ) :
return True
return False |
def add_new ( self , command ) :
"""Add a new entry to the queue .""" | self . queue [ self . next_key ] = command
self . queue [ self . next_key ] [ 'status' ] = 'queued'
self . queue [ self . next_key ] [ 'returncode' ] = ''
self . queue [ self . next_key ] [ 'stdout' ] = ''
self . queue [ self . next_key ] [ 'stderr' ] = ''
self . queue [ self . next_key ] [ 'start' ] = ''
self . queue ... |
def transform ( self , Xs ) :
"""Transports source samples Xs onto target ones Xt
Parameters
Xs : array - like , shape ( n _ source _ samples , n _ features )
The training input samples .
Returns
transp _ Xs : array - like , shape ( n _ source _ samples , n _ features )
The transport source samples .""" | # check the necessary inputs parameters are here
if check_params ( Xs = Xs ) :
if np . array_equal ( self . xs_ , Xs ) : # perform standard barycentric mapping
transp = self . coupling_ / np . sum ( self . coupling_ , 1 ) [ : , None ]
# set nans to 0
transp [ ~ np . isfinite ( transp ) ] = 0... |
def register_nonzero_counter ( network , stats ) :
"""Register forward hooks to count the number of nonzero floating points
values from all the tensors used by the given network during inference .
: param network : The network to attach the counter
: param stats : Dictionary holding the counter .""" | if hasattr ( network , "__counter_nonzero__" ) :
raise ValueError ( "nonzero counter was already registered for this network" )
if not isinstance ( stats , dict ) :
raise ValueError ( "stats must be a dictionary" )
network . __counter_nonzero__ = stats
handles = [ ]
for name , module in network . named_modules ... |
def writeChunk ( self , stream , filename , chunkIdx = None ) :
"""Streams an uploaded chunk to a file .
: param stream : the binary stream that contains the file .
: param filename : the name of the file .
: param chunkIdx : optional chunk index ( for writing to a tmp dir )
: return : no of bytes written o... | import io
more = True
outputFileName = filename if chunkIdx is None else filename + '.' + str ( chunkIdx )
outputDir = self . _uploadDir if chunkIdx is None else self . _tmpDir
chunkFilePath = os . path . join ( outputDir , outputFileName )
if os . path . exists ( chunkFilePath ) and os . path . isfile ( chunkFilePath ... |
def disable ( name , stop = False , ** kwargs ) :
'''Don ' t start service ` ` name ` ` at boot
Returns ` ` True ` ` if operation is successful
name
the service ' s name
stop
if True , also stops the service
CLI Example :
. . code - block : : bash
salt ' * ' service . disable < name > [ stop = True ... | # non - existent as registrered service
if not enabled ( name ) :
return False
# down _ file : file that prevent sv autostart
svc_realpath = _get_svc_path ( name ) [ 0 ]
down_file = os . path . join ( svc_realpath , 'down' )
if stop :
stop ( name )
if not os . path . exists ( down_file ) :
try :
sal... |
def ExecutePackage ( self , package_id , parameters = { } ) :
"""Execute an existing Bluerprint package on the server .
https : / / t3n . zendesk . com / entries / 59727040 - Execute - Package
Requires package ID , currently only available by browsing control and browsing
for the package itself . The UUID par... | return ( clc . v2 . Requests ( clc . v2 . API . Call ( 'POST' , 'operations/%s/servers/executePackage' % ( self . alias ) , json . dumps ( { 'servers' : [ self . id ] , 'package' : { 'packageId' : package_id , 'parameters' : parameters } } ) , session = self . session ) , alias = self . alias , session = self . session... |
def _cursorLeft ( self ) :
"""Handles " cursor left " events""" | if self . cursorPos > 0 :
self . cursorPos -= 1
sys . stdout . write ( console . CURSOR_LEFT )
sys . stdout . flush ( ) |
def laplacian_calculation ( mesh , equal_weight = True ) :
"""Calculate a sparse matrix for laplacian operations .
Parameters
mesh : trimesh . Trimesh
Input geometry
equal _ weight : bool
If True , all neighbors will be considered equally
If False , all neightbors will be weighted by inverse distance
... | # get the vertex neighbors from the cache
neighbors = mesh . vertex_neighbors
# avoid hitting crc checks in loops
vertices = mesh . vertices . view ( np . ndarray )
# stack neighbors to 1D arrays
col = np . concatenate ( neighbors )
row = np . concatenate ( [ [ i ] * len ( n ) for i , n in enumerate ( neighbors ) ] )
i... |
def evaluate ( data_eval , model , nsp_loss , mlm_loss , vocab_size , ctx , log_interval , dtype ) :
"""Evaluation function .""" | mlm_metric = MaskedAccuracy ( )
nsp_metric = MaskedAccuracy ( )
mlm_metric . reset ( )
nsp_metric . reset ( )
eval_begin_time = time . time ( )
begin_time = time . time ( )
step_num = 0
running_mlm_loss = running_nsp_loss = 0
total_mlm_loss = total_nsp_loss = 0
running_num_tks = 0
for _ , dataloader in enumerate ( data... |
def get_env_macros ( self , data ) :
"""Get all environment macros from data
For each object in data : :
* Fetch all macros in object . _ _ class _ _ . macros
* Fetch all customs macros in o . custom
: param data : data to get macro
: type data :
: return : dict with macro name as key and macro value as... | env = { }
for obj in data :
cls = obj . __class__
macros = cls . macros
for macro in macros :
if macro . startswith ( "USER" ) :
continue
prop = macros [ macro ]
value = self . _get_value_from_element ( obj , prop )
env [ '%s%s' % ( self . env_prefix , macro ) ] =... |
def add_showanswer ( self , showanswer ) :
"""stub""" | if showanswer is None :
raise NullArgument ( 'showanswer cannot be None' )
if not self . my_osid_object_form . _is_valid_string ( showanswer , self . get_showanswer_metadata ( ) ) :
raise InvalidArgument ( 'showanswer' )
self . my_osid_object_form . _my_map [ 'showanswer' ] = showanswer |
def get_stp_mst_detail_output_cist_port_configured_path_cost ( self , ** kwargs ) :
"""Auto Generated Code""" | config = ET . Element ( "config" )
get_stp_mst_detail = ET . Element ( "get_stp_mst_detail" )
config = get_stp_mst_detail
output = ET . SubElement ( get_stp_mst_detail , "output" )
cist = ET . SubElement ( output , "cist" )
port = ET . SubElement ( cist , "port" )
configured_path_cost = ET . SubElement ( port , "config... |
def model_to_owl ( model , fname ) :
"""Save a BioPAX model object as an OWL file .
Parameters
model : org . biopax . paxtools . model . Model
A BioPAX model object ( java object ) .
fname : str
The name of the OWL file to save the model in .""" | io_class = autoclass ( 'org.biopax.paxtools.io.SimpleIOHandler' )
io = io_class ( autoclass ( 'org.biopax.paxtools.model.BioPAXLevel' ) . L3 )
try :
fileOS = autoclass ( 'java.io.FileOutputStream' ) ( fname )
except JavaException :
logger . error ( 'Could not open data file %s' % fname )
return
l3_factory =... |
def dof ( self ) :
"""Returns the DoF of the robot ( with grippers ) .""" | dof = self . mujoco_robot . dof
if self . has_gripper_left :
dof += self . gripper_left . dof
if self . has_gripper_right :
dof += self . gripper_right . dof
return dof |
def load_cache ( ) :
"""Load cache from the disk .
Return :
set : Deserialized data from disk .""" | if not os . path . exists ( settings . DUP_FILTER_FILE ) :
return set ( )
with open ( settings . DUP_FILTER_FILE ) as f :
return set ( json . loads ( f . read ( ) ) ) |
def _subscription_thread ( self , endpoint ) :
"""Thread Method , running the connection for each endpoint .
: param endpoint :
: return :""" | try :
conn = create_connection ( self . addr + endpoint , timeout = 5 )
except WebSocketTimeoutException :
self . restart_q . put ( endpoint )
return
while self . threads_running [ endpoint ] :
try :
msg = conn . recv ( )
except WebSocketTimeoutException :
self . _controller_q . put ... |
def add_custom_options ( parser ) :
"""Adds custom options to a parser .
: param parser : the parser to which to add options .
: type parser : argparse . ArgumentParser""" | parser . add_argument ( "--outliers-of" , type = str , metavar = "POP" , default = "CEU" , choices = [ "CEU" , "YRI" , "JPT-CHB" ] , help = ( "Finds the outliers of this population. " "[default: %(default)s]" ) )
parser . add_argument ( "--multiplier" , type = float , metavar = "FLOAT" , default = 1.9 , help = ( "To fi... |
def success_response ( self , method_resp , ** kw ) :
"""Make a standard " success " response ,
which contains some ancilliary data .
Also , detect if this node is too far behind the Bitcoin blockchain ,
and if so , convert this into an error message .""" | resp = { 'status' : True , 'indexing' : config . is_indexing ( self . working_dir ) , 'lastblock' : virtualchain_hooks . get_last_block ( self . working_dir ) , }
resp . update ( kw )
resp . update ( method_resp )
if self . is_stale ( ) : # our state is stale
resp [ 'stale' ] = True
resp [ 'warning' ] = 'Daemon... |
def count ( self , func ) :
"""Counts the number of elements in the sequence which satisfy the predicate func .
> > > seq ( [ - 1 , - 2 , 1 , 2 ] ) . count ( lambda x : x > 0)
: param func : predicate to count elements on
: return : count of elements that satisfy predicate""" | n = 0
for element in self :
if func ( element ) :
n += 1
return n |
def getInterval ( self , alpha ) :
"""Evaluate the interval corresponding to a C . L . of ( 1 - alpha ) % .
Parameters
alpha : limit confidence level .""" | dlnl = twosided_cl_to_dlnl ( 1.0 - alpha )
lo_lim = self . getDeltaLogLike ( dlnl , upper = False )
hi_lim = self . getDeltaLogLike ( dlnl , upper = True )
return ( lo_lim , hi_lim ) |
def _exclude_ss_bonded_cysteines ( self ) :
"""Pre - compute ss bonds to discard cystines for H - adding .""" | ss_bonds = self . nh_structure . search_ss_bonds ( )
for cys_pair in ss_bonds :
cys1 , cys2 = cys_pair
cys1 . resname = 'CYX'
cys2 . resname = 'CYX' |
def guess_payload_class ( self , payload ) :
"""the type of the payload encapsulation is given be the outer TZSP layers attribute encapsulation _ protocol # noqa : E501""" | under_layer = self . underlayer
tzsp_header = None
while under_layer :
if isinstance ( under_layer , TZSP ) :
tzsp_header = under_layer
break
under_layer = under_layer . underlayer
if tzsp_header :
return tzsp_header . get_encapsulated_payload_class ( )
else :
raise TZSPStructureExceptio... |
def check_entry ( self , entries , * args , ** kwargs ) :
"""With a list of entries , check each entry against every other""" | verbosity = kwargs . get ( 'verbosity' , 1 )
user_total_overlaps = 0
user = ''
for index_a , entry_a in enumerate ( entries ) : # Show the name the first time through
if index_a == 0 :
if args and verbosity >= 1 or verbosity >= 2 :
self . show_name ( entry_a . user )
user = entry_a .... |
def reqNewsArticle ( self , providerCode : str , articleId : str , newsArticleOptions : List [ TagValue ] = None ) -> NewsArticle :
"""Get the body of a news article .
This method is blocking .
https : / / interactivebrokers . github . io / tws - api / news . html
Args :
providerCode : Code indicating news ... | return self . _run ( self . reqNewsArticleAsync ( providerCode , articleId , newsArticleOptions ) ) |
def _get_first_urn ( self , urn ) :
"""Provisional route for GetFirstUrn request
: param urn : URN to filter the resource
: param inv : Inventory Identifier
: return : GetFirstUrn response""" | urn = URN ( urn )
subreference = None
textId = urn . upTo ( URN . NO_PASSAGE )
if urn . reference is not None :
subreference = str ( urn . reference )
firstId = self . resolver . getTextualNode ( textId = textId , subreference = subreference ) . firstId
r = render_template ( "cts/GetFirstUrn.xml" , firstId = firstI... |
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