signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def navigate ( self , name , * args ) :
"""Navigate to a route
* @ param { String } name Route name
* @ param { * } arg A single argument to pass to the route handler""" | if name not in self . routes :
raise Exception ( 'invalid route name \'%s\'' % name )
elif callable ( self . routes [ name ] ) :
return self . routes [ name ] ( self , * args )
raise Exception ( 'route %s not callable' , name ) |
def up_ec2 ( connection , region , instance_id , wait_for_ssh_available = True , log = False , timeout = 600 ) :
"""boots an existing ec2 _ instance""" | # boot the ec2 instance
instance = connection . start_instances ( instance_ids = instance_id ) [ 0 ]
instance . update ( )
while instance . state != "running" and timeout > 1 :
log_yellow ( "Instance state: %s" % instance . state )
if log :
log_yellow ( "Instance state: %s" % instance . state )
slee... |
def main ( ) :
"""This is a Toil pipeline used to perform alignment of fastqs .""" | # Define Parser object and add to Toil
if mock_mode ( ) :
usage_msg = 'You have the TOIL_SCRIPTS_MOCK_MODE environment variable set, so this pipeline ' 'will run in mock mode. To disable mock mode, set TOIL_SCRIPTS_MOCK_MODE=0'
else :
usage_msg = None
parser = argparse . ArgumentParser ( usage = usage_msg )
sub... |
def get_cardinality ( self , node = None ) :
"""Returns the cardinality of the node . Throws an error if the CPD for the
queried node hasn ' t been added to the network .
Parameters
node : Any hashable python object ( optional ) .
The node whose cardinality we want . If node is not specified returns a
dic... | if node :
return self . get_cpds ( node ) . cardinality [ 0 ]
else :
cardinalities = defaultdict ( int )
for cpd in self . cpds :
cardinalities [ cpd . variable ] = cpd . cardinality [ 0 ]
return cardinalities |
def getLinkedAnalyses ( self ) :
"""Lookup linked Analyses
: returns : sorted list of ANs , where the latest AN comes first""" | # Fetch the linked Analyses UIDs
refs = get_backreferences ( self , "AnalysisAttachment" )
# fetch the objects by UID and handle nonexisting UIDs gracefully
ans = map ( lambda uid : api . get_object_by_uid ( uid , None ) , refs )
# filter out None values ( nonexisting UIDs )
ans = filter ( None , ans )
# sort by physic... |
def center_land ( world ) :
"""Translate the map horizontally and vertically to put as much ocean as
possible at the borders . It operates on elevation and plates map""" | y_sums = world . layers [ 'elevation' ] . data . sum ( 1 )
# 1 = = sum along x - axis
y_with_min_sum = y_sums . argmin ( )
if get_verbose ( ) :
print ( "geo.center_land: height complete" )
x_sums = world . layers [ 'elevation' ] . data . sum ( 0 )
# 0 = = sum along y - axis
x_with_min_sum = x_sums . argmin ( )
if g... |
def _get_token ( ) :
'''Get an auth token''' | username = __opts__ . get ( 'rallydev' , { } ) . get ( 'username' , None )
password = __opts__ . get ( 'rallydev' , { } ) . get ( 'password' , None )
path = 'https://rally1.rallydev.com/slm/webservice/v2.0/security/authorize'
result = salt . utils . http . query ( path , decode = True , decode_type = 'json' , text = Tr... |
def get_docargs ( self , args = None , prt = None ) :
"""Pare down docopt . Return a minimal dictionary and a set containing runtime arg values .""" | # docargs = self . objdoc . get _ docargs ( args , exp _ letters = set ( [ ' o ' , ' t ' , ' p ' , ' c ' ] ) )
docargs = self . objdoc . get_docargs ( args , prt )
self . _chk_docopts ( docargs )
return docargs |
def clean_query_Dict ( cls , query_Dict ) :
"""removes NoneTypes from the dict""" | return { k : v for k , v in query_Dict . items ( ) if v } |
def set_data ( self , index , data ) :
"""Set the complete data for a single line strip .
Parameters
index : int
The index of the line strip to be replaced .
data : array - like
The data to assign to the selected line strip .""" | self . _pos_tex [ index , : ] = data
self . update ( ) |
def remove_user_from_group ( self , username , groupname ) :
"""Remove a user from a group .
: param username : The user to remove from the group .
: param groupname : The group that the user will be removed from .""" | url = self . _options [ 'server' ] + '/rest/api/latest/group/user'
x = { 'groupname' : groupname , 'username' : username }
self . _session . delete ( url , params = x )
return True |
def assign_issue ( issue_key , assignee , server = None , username = None , password = None ) :
'''Assign the issue to an existing user . Return ` ` True ` ` when the issue has
been properly assigned .
issue _ key
The JIRA ID of the ticket to manipulate .
assignee
The name of the user to assign the ticket... | jira_ = _get_jira ( server = server , username = username , password = password )
assigned = jira_ . assign_issue ( issue_key , assignee )
return assigned |
def _compute_bgid ( self , bg = None ) :
"""Return a unique identifier for the background data""" | if bg is None :
bg = self . _bgdata
if isinstance ( bg , qpimage . QPImage ) : # Single QPImage
if "identifier" in bg :
return bg [ "identifier" ]
else :
data = [ bg . amp , bg . pha ]
for key in sorted ( list ( bg . meta . keys ( ) ) ) :
val = bg . meta [ key ]
... |
def get_combined_size ( tiles ) :
"""Calculate combined size of tiles .""" | # TODO : Refactor calculating layout to avoid repetition .
columns , rows = calc_columns_rows ( len ( tiles ) )
tile_size = tiles [ 0 ] . image . size
return ( tile_size [ 0 ] * columns , tile_size [ 1 ] * rows ) |
def calculate_mrcas ( self , c1 : ClassId , c2 : ClassId ) -> Set [ ClassId ] :
"""Calculate the MRCA for a class pair""" | G = self . G
# reflexive ancestors
ancs1 = self . _ancestors ( c1 ) | { c1 }
ancs2 = self . _ancestors ( c2 ) | { c2 }
common_ancestors = ancs1 & ancs2
redundant = set ( )
for a in common_ancestors :
redundant = redundant | nx . ancestors ( G , a )
return common_ancestors - redundant |
def get_mean_and_stddevs ( self , sites , rup , dists , imt , stddev_types ) :
"""See : meth : ` superclass method
< . base . GroundShakingIntensityModel . get _ mean _ and _ stddevs > `
for spec of input and result values .""" | # extracting dictionary of coefficients specific to required
# intensity measure type .
C = self . COEFFS [ imt ]
imean = self . _get_mean ( C , rup , dists , sites )
if imt . name in "SA PGA" : # Convert units to g ,
# but only for PGA and SA ( not PGV ) :
mean = np . log ( ( 10.0 ** ( imean - 2.0 ) ) / g )
else :... |
def get_metric ( self , timestamp ) :
"""Get a metric including all current time series .
Get a : class : ` opencensus . metrics . export . metric . Metric ` with one
: class : ` opencensus . metrics . export . time _ series . TimeSeries ` for each
set of label values with a recorded measurement . Each ` Time... | if not self . points :
return None
with self . _points_lock :
ts_list = get_timeseries_list ( self . points , timestamp )
return metric . Metric ( self . descriptor , ts_list ) |
def r_get_numbers ( matchgroup , num ) :
"""A helper function which can be used similarly to fscanf ( fid , ' % f ' , num ) to extract num arguments from the regex iterator""" | res = [ ]
for i in range ( num ) :
res . append ( float ( matchgroup . next ( ) . group ( ) ) )
return np . array ( res ) |
def _initialize_context ( self , trace_header ) :
"""Create a facade segment based on environment variables
set by AWS Lambda and initialize storage for subsegments .""" | sampled = None
if not global_sdk_config . sdk_enabled ( ) : # Force subsequent subsegments to be disabled and turned into DummySegments .
sampled = False
elif trace_header . sampled == 0 :
sampled = False
elif trace_header . sampled == 1 :
sampled = True
segment = FacadeSegment ( name = 'facade' , traceid =... |
def multiply_adjacent_elements ( input_list ) :
"""This function multiplies neighbouring elements in a given list .
Args :
input _ list : The list whose consecutive elements are to be multiplied .
Returns :
A list of the products of neighbouring elements in the input list .
Examples :
> > > multiply _ a... | product_list = [ input_list [ i ] * input_list [ i + 1 ] for i in range ( len ( input_list ) - 1 ) ]
return product_list |
def parse_link ( self , node ) :
"""Parses < Link >
@ param node : Node containing the < Link > element
@ type node : xml . etree . Element""" | if 'name' in node . lattrib :
name = node . lattrib [ 'name' ]
else :
self . raise_error ( '<Link> must specify a name' )
if 'type' in node . lattrib :
type_ = node . lattrib [ 'type' ]
else :
self . raise_error ( "Link '{0}' must specify a type" , name )
description = node . lattrib . get ( 'descriptio... |
def get_wallet_height ( self , id = None , endpoint = None ) :
"""Get the current wallet index height .
Args :
id : ( int , optional ) id to use for response tracking
endpoint : ( RPCEndpoint , optional ) endpoint to specify to use
Returns :
json object of the result or the error encountered in the RPC ca... | return self . _call_endpoint ( GET_WALLET_HEIGHT , id = id , endpoint = endpoint ) |
def voronoi_partition ( G , outline ) :
"""For 2D - embedded graph ` G ` , within the boundary given by the shapely polygon
` outline ` , returns ` G ` with the Voronoi cell region as an additional node
attribute .""" | # following line from vresutils . graph caused a bug
# G = polygon _ subgraph ( G , outline , copy = False )
points = list ( vresutils . graph . get_node_attributes ( G , 'pos' ) . values ( ) )
regions = vresutils . graph . voronoi_partition_pts ( points , outline , no_multipolygons = True )
nx . set_node_attributes ( ... |
def add_to_manifest ( self , manifest ) :
"""Add useful details to the manifest about this service
so that it can be used in an application .
: param manifest : An predix . admin . app . Manifest object
instance that manages reading / writing manifest config
for a cloud foundry app .""" | # Add this service to list of services
manifest . add_service ( self . service . name )
# Add environment variables
manifest . add_env_var ( self . __module__ + '.uri' , self . service . settings . data [ 'url' ] )
manifest . add_env_var ( self . __module__ + '.zone_id' , self . get_predix_zone_id ( ) )
manifest . writ... |
def set_address ( self , host , port ) :
"""Add host and port attributes""" | self . host = host
self . port = port |
def _req_fix ( self , line ) :
"""Fix slacky and salix requirements because many dependencies splitting
with " , " and others with " | " """ | deps = [ ]
for dep in line [ 18 : ] . strip ( ) . split ( "," ) :
dep = dep . split ( "|" )
if self . repo == "slacky" :
if len ( dep ) > 1 :
for d in dep :
deps . append ( d . split ( ) [ 0 ] )
dep = "" . join ( dep )
deps . append ( dep . split ( ) [ 0 ] )
... |
def fetch_file ( dataset_name , url , dataset_dir , dataset_prefix = None , default_paths = None , filetype = None , resume = True , overwrite = False , md5sum = None , username = None , password = None , retry = 0 , verbose = 1 , temp_downloads = None ) :
"""Load requested file , downloading it if needed or reques... | final_path , cached = _get_dataset ( dataset_name , dataset_prefix = dataset_prefix , data_dir = dataset_dir , default_paths = default_paths , verbose = verbose )
if cached and not overwrite :
return final_path
data_dir = final_path . parent
if temp_downloads is None :
temp_downloads = NIWORKFLOWS_CACHE_DIR / '... |
def reindex ( self , indexers = None , method = None , tolerance = None , copy = True , ** indexers_kwargs ) :
"""Conform this object onto a new set of indexes , filling in
missing values with NaN .
Parameters
indexers : dict , optional
Dictionary with keys given by dimension names and values given by
arr... | indexers = either_dict_or_kwargs ( indexers , indexers_kwargs , 'reindex' )
ds = self . _to_temp_dataset ( ) . reindex ( indexers = indexers , method = method , tolerance = tolerance , copy = copy )
return self . _from_temp_dataset ( ds ) |
def getHostsFromFile ( filename ) :
"""Parse a file to return a list of hosts .""" | valid_hostname = r"^[^ /\t=\n]+"
workers = r"\d+"
hostname_re = re . compile ( valid_hostname )
worker_re = re . compile ( workers )
hosts = [ ]
with open ( filename ) as f :
for line in f : # check to see if it is a SLURM grouping instead of a
# regular list of hosts
if re . search ( '[\[\]]' , line ) ... |
def connect_edges ( graph ) :
"""Given a Graph element containing abstract edges compute edge
segments directly connecting the source and target nodes . This
operation just uses internal HoloViews operations and will be a
lot slower than the pandas equivalent .""" | paths = [ ]
for start , end in graph . array ( graph . kdims ) :
start_ds = graph . nodes [ : , : , start ]
end_ds = graph . nodes [ : , : , end ]
if not len ( start_ds ) or not len ( end_ds ) :
raise ValueError ( 'Could not find node positions for all edges' )
start = start_ds . array ( start_d... |
def worker_task ( work_item , config ) :
"""The celery task which performs a single mutation and runs a test suite .
This runs ` cosmic - ray worker ` in a subprocess and returns the results ,
passing ` config ` to it via stdin .
Args :
work _ item : A dict describing a WorkItem .
config : The configurati... | global _workspace
_ensure_workspace ( config )
result = worker ( work_item . module_path , config . python_version , work_item . operator_name , work_item . occurrence , config . test_command , config . timeout )
return work_item . job_id , result |
def cover ( ctx , html = False ) :
'''Run tests suite with coverage''' | header ( 'Run tests suite with coverage' )
cmd = 'pytest --cov udata --cov-report term'
if html :
cmd = ' ' . join ( ( cmd , '--cov-report html:reports/python/cover' ) )
with ctx . cd ( ROOT ) :
ctx . run ( cmd , pty = True ) |
def extract_file_from_zip ( bytes_io , expected_file ) :
"""Extracts a file from a bytes _ io zip . Returns bytes""" | zipf = zipfile . ZipFile ( bytes_io )
return zipf . read ( expected_file ) |
def cap ( self ) :
"""" Caps " the construction of the pipeline , signifying that no more inputs
and outputs are expected to be added and therefore the input and output
nodes can be created along with the provenance .""" | to_cap = ( self . _inputnodes , self . _outputnodes , self . _prov )
if to_cap == ( None , None , None ) :
self . _inputnodes = { f : self . _make_inputnode ( f ) for f in self . input_frequencies }
self . _outputnodes = { f : self . _make_outputnode ( f ) for f in self . output_frequencies }
self . _prov =... |
def vqa_recurrent_self_attention_base ( ) :
"""VQA attention baseline hparams .""" | hparams = universal_transformer . universal_transformer_base ( )
hparams . batch_size = 1024
hparams . use_fixed_batch_size = True
hparams . weight_decay = 0.
hparams . clip_grad_norm = 0.
# use default initializer
# hparams . initializer = " xavier "
hparams . learning_rate_schedule = ( "constant*linear_warmup*rsqrt_n... |
def write_languages ( f , l ) :
"""Write language information .""" | f . write ( "Languages = {%s" % os . linesep )
for lang in sorted ( l ) :
f . write ( " %r: %r,%s" % ( lang , l [ lang ] , os . linesep ) )
f . write ( "}%s" % os . linesep ) |
def _parse ( jsonOutput ) :
'''Parses JSON response from Tika REST API server
: param jsonOutput : JSON output from Tika Server
: return : a dictionary having ' metadata ' and ' content ' values''' | parsed = { }
if not jsonOutput :
return parsed
parsed [ "status" ] = jsonOutput [ 0 ]
if jsonOutput [ 1 ] == None or jsonOutput [ 1 ] == "" :
return parsed
realJson = json . loads ( jsonOutput [ 1 ] )
content = ""
for js in realJson :
if "X-TIKA:content" in js :
content += js [ "X-TIKA:content" ]
if... |
def list_nodes_select ( call = None ) :
'''Return a list of the VMs that are on the provider , with select fields''' | if call == 'action' :
raise SaltCloudSystemExit ( 'The list_nodes_select function must be called ' 'with -f or --function.' )
selection = __opts__ . get ( 'query.selection' )
if not selection :
raise SaltCloudSystemExit ( 'query.selection not found in /etc/salt/cloud' )
# TODO : somewhat doubt the implementatio... |
def full_value ( self ) :
"""Returns the full value with the path also ( ie , name = value ( path ) )
: returns : String""" | s = self . name_value ( )
s += self . path_value ( )
s += "\n\n"
return s |
def store_array_elements ( self , array , start_idx , data ) :
"""Stores either a single element or a range of elements in the array .
: param array : Reference to the array .
: param start _ idx : Starting index for the store .
: param data : Either a single value or a list of values .""" | # we process data as a list of elements
# = > if there is only a single element , wrap it in a list
data = data if isinstance ( data , list ) else [ data ]
# concretize start index
concrete_start_idxes = self . concretize_store_idx ( start_idx )
if len ( concrete_start_idxes ) == 1 : # only one start index
# = > concre... |
def get_editor_buffer_for_location ( self , location ) :
"""Return the ` EditorBuffer ` for this location .
When this file was not yet loaded , return None""" | for eb in self . editor_buffers :
if eb . location == location :
return eb |
def parse_resource_extended ( self , session , resource_name ) :
"""Parse a resource string to get extended interface information .
Corresponds to viParseRsrcEx function of the VISA library .
: param session : Resource Manager session ( should always be the Default Resource Manager for VISA
returned from open... | try :
parsed = rname . parse_resource_name ( resource_name )
return ( ResourceInfo ( parsed . interface_type_const , parsed . board , parsed . resource_class , str ( parsed ) , None ) , constants . StatusCode . success )
except ValueError :
return 0 , constants . StatusCode . error_invalid_resource_name |
def select_gist ( self , allow_none = False ) :
"""Given the requested filename , it selects the proper gist ; if more than
one gist is found with the given filename , user is asked to choose .
: allow _ none : ( bool ) for ` getgist ` it should raise error if no gist is
found , but setting this argument to T... | # pick up all macthing gists
matches = list ( )
for gist in self . get_gists ( ) :
for gist_file in gist . get ( "files" ) :
if self . filename == gist_file . get ( "filename" ) :
matches . append ( gist )
# abort if no match is found
if not matches :
if allow_none :
return None
... |
def calculate_column_sum ( matrix , column_index ) :
"""This function computes the sum of a given column in a given 2D list ( matrix ) .
For example ,
Given matrix = [ [ 1 , 2 , 3 , 2 ] , [ 4 , 5 , 6 , 2 ] , [ 7 , 8 , 9 , 5 ] ] ,
calculate _ column _ sum ( matrix , 0 ) will give 12,
calculate _ column _ sum... | column_total = sum ( row [ column_index ] for row in matrix )
return column_total |
def revise_sql ( query , id_column , output_table , max_date_column , min_date_column , date_column , date , source_id_column = None ) :
"""Given an expensive query that aggregates temporal data ,
Revise the results to censor before a particular date""" | if source_id_column is None :
source_id_column = id_column
if hasattr ( id_column , '__iter__' ) :
id_column = str . join ( ', ' , id_column )
if hasattr ( source_id_column , '__iter__' ) :
source_id_column = str . join ( ', ' , source_id_column )
sql_vars = dict ( query = query , id_column = id_column , ou... |
def snmp_server_group_group_auth_mode ( self , ** kwargs ) :
"""Auto Generated Code""" | config = ET . Element ( "config" )
snmp_server = ET . SubElement ( config , "snmp-server" , xmlns = "urn:brocade.com:mgmt:brocade-snmp" )
group = ET . SubElement ( snmp_server , "group" )
group_name_key = ET . SubElement ( group , "group-name" )
group_name_key . text = kwargs . pop ( 'group_name' )
group_version_key = ... |
def com_google_fonts_check_metadata_valid_name_values ( style , font_metadata , font_familynames , typographic_familynames ) :
"""METADATA . pb font . name field contains font name in right format ?""" | from fontbakery . constants import RIBBI_STYLE_NAMES
if style in RIBBI_STYLE_NAMES :
familynames = font_familynames
else :
familynames = typographic_familynames
failed = False
for font_familyname in familynames :
if font_familyname not in font_metadata . name :
failed = True
yield FAIL , ( "... |
def convertShape ( shapeString ) :
"""Convert xml shape string into float tuples .
This method converts the 2d or 3d shape string from SUMO ' s xml file
into a list containing 3d float - tuples . Non existant z coordinates default
to zero . If shapeString is empty , an empty list will be returned .""" | cshape = [ ]
for pointString in shapeString . split ( ) :
p = [ float ( e ) for e in pointString . split ( "," ) ]
if len ( p ) == 2 :
cshape . append ( ( p [ 0 ] , p [ 1 ] , 0. ) )
elif len ( p ) == 3 :
cshape . append ( tuple ( p ) )
else :
raise ValueError ( 'Invalid shape poi... |
def create_node ( ctx , path ) :
"""Create node for given relative path .
: param ctx : BuildContext object .
: param path : Relative path relative to top directory .
: return : Created Node .""" | # Ensure given context object is BuildContext object
_ensure_build_context ( ctx )
# Get top directory ' s relative path relative to ` wscript ` directory
top_dir_relpath = os . path . relpath ( # Top directory ' s absolute path
ctx . top_dir , # ` wscript ` directory ' s absolute path
ctx . run_dir , )
# Convert given... |
def raises ( self , expected_exception ) :
"""Ensures preceding predicates ( specifically , : meth : ` called _ with ( ) ` ) result in * expected _ exception * being raised .""" | return unittest_case . assertRaises ( expected_exception , self . _orig_subject , * self . _args , ** self . _kwargs ) |
def validate ( self , sig = None ) :
'''Check if file matches its signature''' | if sig is not None :
sig_mtime , sig_size , sig_md5 = sig
else :
try :
with open ( self . sig_file ( ) ) as sig :
sig_mtime , sig_size , sig_md5 = sig . read ( ) . strip ( ) . split ( )
except :
return False
if not self . exists ( ) :
if ( self + '.zapped' ) . is_file ( ) :
... |
def _convert_rename ( self , fc ) :
"""Convert a FileRenameCommand into a new FileCommand .
: return : None if the rename is being ignored , otherwise a
new FileCommand based on the whether the old and new paths
are inside or outside of the interesting locations .""" | old = fc . old_path
new = fc . new_path
keep_old = self . _path_to_be_kept ( old )
keep_new = self . _path_to_be_kept ( new )
if keep_old and keep_new :
fc . old_path = self . _adjust_for_new_root ( old )
fc . new_path = self . _adjust_for_new_root ( new )
return fc
elif keep_old : # The file has been renam... |
def create_mssql_pymssql ( username , password , host , port , database , ** kwargs ) : # pragma : no cover
"""create an engine connected to a mssql database using pymssql .""" | return create_engine ( _create_mssql_pymssql ( username , password , host , port , database ) , ** kwargs ) |
def set_next_week_day ( val , week_day , iso = False ) :
"""Set week day .
New date will be greater or equal than input date .
: param val : datetime or date
: type val : datetime . datetime | datetime . date
: param week _ day : Week day to set
: type week _ day : int
: param iso : week _ day in ISO fo... | return _set_week_day ( val , week_day , val . isoweekday ( ) if iso else val . weekday ( ) , sign = 1 ) |
def execute_streaming_sql ( self , session , sql , transaction = None , params = None , param_types = None , resume_token = None , query_mode = None , partition_token = None , seqno = None , retry = google . api_core . gapic_v1 . method . DEFAULT , timeout = google . api_core . gapic_v1 . method . DEFAULT , metadata = ... | # Wrap the transport method to add retry and timeout logic .
if "execute_streaming_sql" not in self . _inner_api_calls :
self . _inner_api_calls [ "execute_streaming_sql" ] = google . api_core . gapic_v1 . method . wrap_method ( self . transport . execute_streaming_sql , default_retry = self . _method_configs [ "Ex... |
def _thread_init ( cls ) :
"""Ensure thread local is initialized .""" | if not hasattr ( cls . _local , '_in_order_futures' ) :
cls . _local . _in_order_futures = set ( )
cls . _local . _activated = False |
def segmentlistdict_from_short_string ( s , boundtype = int ) :
"""Parse a string representation of a set of named segmentlists into a
segmentlistdict object . The string encoding is that generated by
segmentlistdict _ to _ short _ string ( ) . The optional boundtype argument
will be passed to from _ range _ ... | d = segments . segmentlistdict ( )
for token in s . strip ( ) . split ( "/" ) :
key , ranges = token . strip ( ) . split ( "=" )
d [ key . strip ( ) ] = from_range_strings ( ranges . strip ( ) . split ( "," ) , boundtype = boundtype )
return d |
def fit ( self , X ) :
"""Apply KMeans Clustering
X : dataset with feature vectors""" | self . centers_ , self . labels_ , self . sse_arr_ , self . n_iter_ = _kmeans ( X , self . n_clusters , self . max_iter , self . n_trials , self . tol ) |
def get_scope_by_name ( self , scope_name ) :
"""GetScopeByName .
[ Preview API ]
: param str scope _ name :
: rtype : : class : ` < IdentityScope > < azure . devops . v5_0 . identity . models . IdentityScope > `""" | query_parameters = { }
if scope_name is not None :
query_parameters [ 'scopeName' ] = self . _serialize . query ( 'scope_name' , scope_name , 'str' )
response = self . _send ( http_method = 'GET' , location_id = '4e11e2bf-1e79-4eb5-8f34-a6337bd0de38' , version = '5.0-preview.2' , query_parameters = query_parameters... |
def getChain ( self ) :
"returns a list of keys representing the chain of documents" | l = [ ]
h = self . head
while h :
l . append ( h . _key )
h = h . nextDoc
return l |
def asDictionary ( self ) :
"""returns the object as a dictionary""" | template = { "type" : "esriPMS" , "url" : self . _url , "imageData" : self . _imageDate , "contentType" : self . _contentType , "width" : self . _width , "height" : self . _height , "angle" : self . _angle , "xoffset" : self . _xoffset , "yoffset" : self . _yoffset , "xscale" : self . _xscale , "yscale" : self . _yscal... |
def annotate_proto ( self , text , annotators = None ) :
"""Return a Document protocol buffer from the CoreNLP server , containing annotations of the text .
: param ( str ) text : text to be annotated
: param ( list [ str ] ) annotators : a list of annotator names
: return ( CoreNLP _ pb2 . Document ) : a Doc... | properties = { 'annotators' : ',' . join ( annotators or self . default_annotators ) , 'outputFormat' : 'serialized' , 'serializer' : 'edu.stanford.nlp.pipeline.ProtobufAnnotationSerializer' }
r = self . _request ( text , properties )
buffer = r . content
# bytes
size , pos = _DecodeVarint ( buffer , 0 )
buffer = buffe... |
def new_connection ( self , remote_ip , remote_port ) :
"""This method is called when a new SMTP session is opened .
[ PUBLIC API ]""" | self . state . set_state ( 'new' )
self . _message = Message ( Peer ( remote_ip , remote_port ) )
decision , response_sent = self . is_allowed ( 'accept_new_connection' , self . _message . peer )
if decision :
if not response_sent :
self . handle_input ( 'greet' )
self . _set_size_restrictions ( )
else ... |
def wait_until_exit ( self ) :
"""Wait until thread exit
Used for testing purpose only""" | if self . _timeout is None :
raise Exception ( "Thread will never exit. Use stop or specify timeout when starting it!" )
self . _thread . join ( )
self . stop ( ) |
def mark_dmag_rec ( s , ind , data ) :
"""Edits demagnetization data to mark " bad " points with measurement _ flag""" | datablock = [ ]
for rec in data :
if rec [ 'er_specimen_name' ] == s :
meths = rec [ 'magic_method_codes' ] . split ( ':' )
if 'LT-NO' in meths or 'LT-AF-Z' in meths or 'LT-T-Z' in meths :
datablock . append ( rec )
dmagrec = datablock [ ind ]
for k in range ( len ( data ) ) :
meths ... |
def get_command ( self , ctx , cmd_name ) :
"""gets the subcommands under the service name
Parameters
ctx : Context
the context object passed into the method
cmd _ name : str
the service name
Returns
EventTypeSubCommand :
returns subcommand if successful , None if not .""" | if cmd_name not in self . all_cmds :
return None
return EventTypeSubCommand ( self . events_lib , cmd_name , self . all_cmds [ cmd_name ] ) |
def on_lstSubcategories_itemSelectionChanged ( self ) :
"""Update subcategory description label .
. . note : : This is an automatic Qt slot
executed when the subcategory selection changes .""" | self . clear_further_steps ( )
# Set widgets
subcategory = self . selected_subcategory ( )
# Exit if no selection
if not subcategory :
return
# Set description label
self . lblDescribeSubcategory . setText ( subcategory [ 'description' ] )
icon_path = get_image_path ( subcategory )
self . lblIconSubcategory . setPi... |
def indexes ( self , recurse = True ) :
"""Returns the list of indexes that are associated with this schema .
: return [ < orb . Index > , . . ]""" | output = self . __indexes . copy ( )
if recurse and self . inherits ( ) :
schema = orb . system . schema ( self . inherits ( ) )
if not schema :
raise orb . errors . ModelNotFound ( schema = self . inherits ( ) )
else :
output . update ( schema . indexes ( recurse = recurse ) )
return output |
def fem ( ab , off , angle , zsrc , zrec , lsrc , lrec , depth , freq , etaH , etaV , zetaH , zetaV , xdirect , isfullspace , ht , htarg , use_ne_eval , msrc , mrec , loop_freq , loop_off , conv = True ) :
r"""Return the electromagnetic frequency - domain response .
This function is called from one of the above m... | # Preallocate array
fEM = np . zeros ( ( freq . size , off . size ) , dtype = complex )
# Initialize kernel count
# ( how many times the wavenumber - domain kernel was calld )
kcount = 0
# If < ab > = 36 ( or 63 ) , fEM - field is zero
if ab in [ 36 , ] :
return fEM , kcount , conv
# Get full - space - solution if ... |
def subtract ( self , other = None , ** kwargs ) :
"""Elements are subtracted from an * iterable * or from another
* mapping * ( or counter ) . Like : func : ` dict . update ` but subtracts
counts instead of replacing them .""" | if other is not None :
if self . _same_redis ( other , RedisCollection ) :
self . _update_helper ( other , operator . sub , use_redis = True )
elif hasattr ( other , 'keys' ) :
self . _update_helper ( other , operator . sub )
else :
self . _update_helper ( collections . Counter ( oth... |
def update_dataset ( self , dataStr , flatten = False ) :
'''update class with a data structure .
: keyword flatten : use this to automatically flatten variables ( squeeze dimensions )''' | # Load keys and dimensions
dataDim = dataStr . pop ( '_dimensions' , { } )
attrStr = dataStr . pop ( '_attributes' , { } )
ndims = dataDim . pop ( '_ndims' , 0 )
dimensions = [ dataDim . keys ( ) , dataDim . values ( ) ]
keys = dataStr . keys ( )
if len ( keys ) == 0 :
self . warning ( 2 , 'No data loaded' )
re... |
def parse_bowtie2_logs ( self , f ) :
"""Warning : This function may make you want to stab yourself .
Parse logs from bowtie2 . These miss several key bits of information
such as input files , so we try to look for logs from other wrapper tools
that may have logged this info . If not found , we default to usi... | # Regexes
regexes = { 'unpaired' : { 'unpaired_aligned_none' : r"(\d+) \([\d\.]+%\) aligned 0 times" , 'unpaired_aligned_one' : r"(\d+) \([\d\.]+%\) aligned exactly 1 time" , 'unpaired_aligned_multi' : r"(\d+) \([\d\.]+%\) aligned >1 times" } , 'paired' : { 'paired_aligned_none' : r"(\d+) \([\d\.]+%\) aligned concordan... |
def _report_self ( self ) :
"""Reports the crawler uuid to redis""" | if self . redis_connected :
self . logger . debug ( "Reporting self to redis" )
try :
key = "stats:rest:self:{m}:{u}" . format ( m = socket . gethostname ( ) , u = self . my_uuid )
self . redis_conn . set ( key , self . get_time ( ) )
self . redis_conn . expire ( key , self . settings [ ... |
def accumulate_from_superclasses ( cls , propname ) :
'''Traverse the class hierarchy and accumulate the special sets of names
` ` MetaHasProps ` ` stores on classes :
Args :
name ( str ) : name of the special attribute to collect .
Typically meaningful values are : ` ` _ _ container _ props _ _ ` ` ,
` `... | cachename = "__cached_all" + propname
# we MUST use cls . _ _ dict _ _ NOT hasattr ( ) . hasattr ( ) would also look at base
# classes , and the cache must be separate for each class
if cachename not in cls . __dict__ :
s = set ( )
for c in inspect . getmro ( cls ) :
if issubclass ( c , HasProps ) and h... |
def replaceelement ( oldelem , newelem ) :
'''Given a parent element , replace oldelem with newelem .''' | parent = oldelem . getparent ( )
if parent is not None :
size = len ( parent . getchildren ( ) )
for x in range ( 0 , size ) :
if parent . getchildren ( ) [ x ] == oldelem :
parent . remove ( oldelem )
parent . insert ( x , newelem ) |
def token_name ( tokens , expected ) :
"""Match a token name ( type ) .""" | try :
token = next ( iter ( tokens ) )
except StopIteration :
return
if token and token . name == expected :
return TokenMatch ( None , token . value , ( token , ) ) |
def run ( self , allow_interactive = True ) :
"""Enter the native GUI event loop .
Parameters
allow _ interactive : bool
Is the application allowed to handle interactive mode for console
terminals ? By default , typing ` ` python - i main . py ` ` results in
an interactive shell that also regularly calls ... | if allow_interactive and self . is_interactive ( ) :
inputhook . set_interactive ( enabled = True , app = self )
else :
return self . _backend . _vispy_run ( ) |
def logout_callback ( ) :
"""Route called by the OpenID provider when user logs out .
Clear the cookies here .""" | resp = make_response ( 'Logging Out' )
resp . set_cookie ( 'sub' , 'null' , expires = 0 )
resp . set_cookie ( 'session_id' , 'null' , expires = 0 )
return resp |
def fix_docs ( cls ) :
"""copies docstrings of derived attributes ( methods , properties , attrs ) from parent classes .""" | import inspect
public_undocumented_members = { name : func for name , func in inspect . getmembers ( cls ) if not name . startswith ( '_' ) and func . __doc__ is None }
for name , func in public_undocumented_members . items ( ) :
for parent in cls . __mro__ [ 1 : ] :
parfunc = getattr ( parent , name , None... |
def withNamedBits ( cls , ** values ) :
"""Creates a subclass with discreet named bits constraint .
Reduce fully duplicate enumerations along the way .""" | enums = set ( cls . namedValues . items ( ) )
enums . update ( values . items ( ) )
class X ( cls ) :
namedValues = namedval . NamedValues ( * enums )
X . __name__ = cls . __name__
return X |
def set_level ( self , position , channel = None ) :
"""Seek a specific value by specifying a float ( ) from 0.0 to 1.0.""" | try :
position = float ( position )
except Exception as err :
LOG . debug ( "HelperLevel.set_level: Exception %s" % ( err , ) )
return False
self . writeNodeData ( "LEVEL" , position , channel ) |
def expose_finish ( self , * args ) :
"""Finish drawing process""" | # Obtain a reference to the OpenGL drawable
# and rendering context .
gldrawable = self . get_gl_drawable ( )
# glcontext = self . get _ gl _ context ( )
if not gldrawable :
return
# Put the buffer on the screen !
if gldrawable . is_double_buffered ( ) :
gldrawable . swap_buffers ( )
else :
glFlush ( )
# Op... |
def LDRSH ( self , params ) :
"""LDRSH Ra , [ Rb , Rc ]
Load a half word from memory , sign extend , and put into Ra
Ra , Rb , and Rc must be low registers""" | # TODO LDRSH cant use immediates
Ra , Rb , Rc = self . get_three_parameters ( self . THREE_PARAMETER_WITH_BRACKETS , params )
self . check_arguments ( low_registers = ( Ra , Rb , Rc ) )
def LDRSH_func ( ) : # TODO does memory read up ?
if ( self . register [ Rb ] + self . register [ Rc ] ) % 2 != 0 :
raise ... |
def remove_config_to_machine_group ( self , project_name , config_name , group_name ) :
"""remove a logtail config to a machine group
Unsuccessful opertaion will cause an LogException .
: type project _ name : string
: param project _ name : the Project name
: type config _ name : string
: param config _ ... | headers = { }
params = { }
resource = "/machinegroups/" + group_name + "/configs/" + config_name
( resp , header ) = self . _send ( "DELETE" , project_name , None , resource , params , headers )
return RemoveConfigToMachineGroupResponse ( header , resp ) |
def register_model_resource ( self , resource : ModelResource ) :
"""Method to manually register a : class : ` ModelResource ` with APISpec .
: param resource :""" | model_name = resource . Meta . model . __name__
self . spec . add_tag ( { 'name' : model_name , 'description' : resource . Meta . model . __doc__ , } )
for method in resource . methods ( ) :
key = f'{resource.__name__}.{method}'
if key not in unchained . controller_bundle . controller_endpoints :
contin... |
def _cache_index ( self , dbname , collection , index , cache_for ) :
"""Add an index to the index cache for ensure _ index operations .""" | now = datetime . datetime . utcnow ( )
expire = datetime . timedelta ( seconds = cache_for ) + now
with self . __index_cache_lock :
if dbname not in self . __index_cache :
self . __index_cache [ dbname ] = { }
self . __index_cache [ dbname ] [ collection ] = { }
self . __index_cache [ dbname... |
def _get_description ( self , args : Tuple , kwargs : Dict [ str , Any ] ) -> Dict [ str , Any ] :
"""Return the dictionary to be sent to the queue .""" | return { 'id' : uuid1 ( ) . hex , 'args' : args , 'kwargs' : kwargs , 'module' : self . _module_name , 'function' : self . f . __name__ , 'sender_hostname' : socket . gethostname ( ) , 'sender_pid' : os . getpid ( ) , 'sender_cmd' : ' ' . join ( sys . argv ) , 'sender_timestamp' : datetime . utcnow ( ) . isoformat ( ) ... |
def clearCache ( ) :
"""Clears any cached data we have stored about specific engine versions""" | if os . path . exists ( CachedDataManager . _cacheDir ( ) ) == True :
shutil . rmtree ( CachedDataManager . _cacheDir ( ) ) |
def software_fibonacci ( n ) :
"""a normal old python function to return the Nth fibonacci number .""" | a , b = 0 , 1
for i in range ( n ) :
a , b = b , a + b
return a |
def phi_inv ( p ) :
"""phi _ inv : inverse of gaussian ( normal ) CDF
Source :
Handbook of Mathematical Functions
Dover Books on Mathematics
Milton Abramowitz and Irene A . Stegun ( Editors )
Formula 26.2.23.""" | if p < 0.5 :
t = math . sqrt ( - 2.0 * math . log ( p ) )
return ( ( 0.010328 * t + 0.802853 ) * t + 2.515517 ) / ( ( ( 0.001308 * t + 0.189269 ) * t + 1.432788 ) * t + 1.0 ) - t
else :
t = math . sqrt ( - 2.0 * math . log ( 1.0 - p ) )
return t - ( ( 0.010328 * t + 0.802853 ) * t + 2.515517 ) / ( ( ( 0... |
def set_weekly ( self , interval , * , days_of_week , first_day_of_week , ** kwargs ) :
"""Set to repeat every week on specified days for every x no . of days
: param int interval : no . of days to repeat at
: param str first _ day _ of _ week : starting day for a week
: param list [ str ] days _ of _ week : ... | self . set_daily ( interval , ** kwargs )
self . __days_of_week = set ( days_of_week )
self . __first_day_of_week = first_day_of_week |
def set_session_token ( self , session_token ) :
"""Sets session token and new login time .
: param str session _ token : Session token from request .""" | self . session_token = session_token
self . _login_time = datetime . datetime . now ( ) |
def end_timing ( self ) :
"""Ends timing of an execution block , calculates elapsed time and updates the associated counter .""" | if self . _callback != None :
elapsed = time . perf_counter ( ) * 1000 - self . _start
self . _callback . end_timing ( self . _counter , elapsed ) |
def get_path ( self ) :
'''获取选择的路径 , 如果没有选择 , 就返回根目录''' | model , tree_iter = self . selection . get_selected ( )
if not tree_iter :
return '/'
else :
return model [ tree_iter ] [ PATH_COL ] |
def summary_reporter ( self ) :
"""Parse individual MOB Recon reports into a summary report""" | logging . info ( 'Creating MOB-recon summary report' )
with open ( os . path . join ( self . reportpath , 'mob_recon_summary.csv' ) , 'w' ) as summary :
data = 'Strain,Location,Contig,Incompatibility,IncompatibilityAccession,RelaxaseType,' 'MashNearestNeighbor,MashNeighborDistance\n'
for sample in self . metada... |
def create ( window , root ) :
"""Create a notification object .
Args :
window ( : py : class : ` BrowserWindow ` ) : Window object this region
appears in .
root
( : py : class : ` ~ selenium . webdriver . remote . webelement . WebElement ` ) :
WebDriver element object that serves as the root for the
... | notifications = { }
_id = root . get_property ( "id" )
from foxpuppet . windows . browser . notifications import addons
notifications . update ( addons . NOTIFICATIONS )
return notifications . get ( _id , BaseNotification ) ( window , root ) |
def _warn ( self , problem , kind = BrotherQLRasterError ) :
"""Logs the warning message ` problem ` or raises a
` BrotherQLRasterError ` exception ( changeable via ` kind ` )
if ` self . exception _ on _ warning ` is set to True .
: raises BrotherQLRasterError : Or other exception set via the ` kind ` keywor... | if self . exception_on_warning :
raise kind ( problem )
else :
logger . warning ( problem ) |
def presence_handler ( type_ , from_ ) :
"""Register the decorated function as presence stanza handler .
: param type _ : Presence type to listen for
: type type _ : : class : ` ~ . PresenceType `
: param from _ : Sender JIDs to listen for
: type from _ : : class : ` aioxmpp . JID ` or : data : ` None `
:... | def decorator ( f ) :
if asyncio . iscoroutinefunction ( f ) :
raise TypeError ( "presence_handler must not be a coroutine function" )
aioxmpp . service . add_handler_spec ( f , aioxmpp . service . HandlerSpec ( ( _apply_presence_handler , ( type_ , from_ ) ) , require_deps = ( SimplePresenceDispatcher ... |
def _validate_arguments ( self ) :
"""method to sanitize model parameters
Parameters
None
Returns
None""" | if self . _has_terms ( ) :
[ term . _validate_arguments ( ) for term in self . _terms ]
else :
super ( TensorTerm , self ) . _validate_arguments ( )
return self |
def p_InDecrement ( p ) :
'''InDecrement : INDECREMENT Expression
| Expression INDECREMENT''' | from . helper import isString
if isString ( p [ 1 ] ) :
p [ 0 ] = InDecrement ( p [ 1 ] , p [ 2 ] , False )
else :
p [ 0 ] = InDecrement ( p [ 2 ] , p [ 1 ] , True ) |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.