signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def mutate ( self , row ) :
"""Add a row to the batch . If the current batch meets one of the size
limits , the batch is sent synchronously .
For example :
. . literalinclude : : snippets . py
: start - after : [ START bigtable _ batcher _ mutate ]
: end - before : [ END bigtable _ batcher _ mutate ]
: ... | mutation_count = len ( row . _get_mutations ( ) )
if mutation_count > MAX_MUTATIONS :
raise MaxMutationsError ( "The row key {} exceeds the number of mutations {}." . format ( row . row_key , mutation_count ) )
if ( self . total_mutation_count + mutation_count ) >= MAX_MUTATIONS :
self . flush ( )
self . rows .... |
def _raise_or_append_exception ( self ) :
"""The connection is presumably dead and we need to raise or
append an exception .
If we have a list for exceptions , append the exception and let
the connection handle it , if not raise the exception here .
: return :""" | message = ( 'Connection dead, no heartbeat or data received in >= ' '%ds' % ( self . _interval * 2 ) )
why = AMQPConnectionError ( message )
if self . _exceptions is None :
raise why
self . _exceptions . append ( why ) |
def register ( self , classes = [ ] ) :
"""Registers new plugins .
The registration only creates a new entry for a plugin inside the _ classes dictionary .
It does not activate or even initialise the plugin .
A plugin must be a class , which inherits directly or indirectly from GwBasePattern .
: param class... | if not isinstance ( classes , list ) :
raise AttributeError ( "plugins must be a list, not %s." % type ( classes ) )
plugin_registered = [ ]
for plugin_class in classes :
plugin_name = plugin_class . __name__
self . register_class ( plugin_class , plugin_name )
self . _log . debug ( "Plugin %s registere... |
def delete_posix_account ( self , name , retry = google . api_core . gapic_v1 . method . DEFAULT , timeout = google . api_core . gapic_v1 . method . DEFAULT , metadata = None , ) :
"""Deletes a POSIX account .
Example :
> > > from google . cloud import oslogin _ v1
> > > client = oslogin _ v1 . OsLoginService... | # Wrap the transport method to add retry and timeout logic .
if "delete_posix_account" not in self . _inner_api_calls :
self . _inner_api_calls [ "delete_posix_account" ] = google . api_core . gapic_v1 . method . wrap_method ( self . transport . delete_posix_account , default_retry = self . _method_configs [ "Delet... |
def get_models ( self , columns = None ) :
"""Get the hydrated models without eager loading .
: param columns : The columns to get
: type columns : list
: return : A list of models
: rtype : list""" | results = self . _query . get ( columns )
connection = self . _model . get_connection_name ( )
return self . _model . hydrate ( results , connection ) . all ( ) |
def opened ( self , block_identifier : BlockSpecification ) -> bool :
"""Returns if the channel is opened .""" | return self . token_network . channel_is_opened ( participant1 = self . participant1 , participant2 = self . participant2 , block_identifier = block_identifier , channel_identifier = self . channel_identifier , ) |
def clear_dead_threads ( self ) :
"""Remove Thread objects from the snapshot
referring to threads no longer running .""" | for tid in self . get_thread_ids ( ) :
aThread = self . get_thread ( tid )
if not aThread . is_alive ( ) :
self . _del_thread ( aThread ) |
def decode_iter ( data , codec_options = DEFAULT_CODEC_OPTIONS ) :
"""Decode BSON data to multiple documents as a generator .
Works similarly to the decode _ all function , but yields one document at a
time .
` data ` must be a string of concatenated , valid , BSON - encoded
documents .
: Parameters :
-... | if not isinstance ( codec_options , CodecOptions ) :
raise _CODEC_OPTIONS_TYPE_ERROR
position = 0
end = len ( data ) - 1
while position < end :
obj_size = _UNPACK_INT ( data [ position : position + 4 ] ) [ 0 ]
elements = data [ position : position + obj_size ]
position += obj_size
yield _bson_to_dic... |
def process_checkpoint ( self , msg : Checkpoint , sender : str ) -> bool :
"""Process checkpoint messages
: return : whether processed ( True ) or stashed ( False )""" | self . logger . info ( '{} processing checkpoint {} from {}' . format ( self , msg , sender ) )
result , reason = self . validator . validate_checkpoint_msg ( msg )
if result == DISCARD :
self . discard ( msg , "{} discard message {} from {} " "with the reason: {}" . format ( self , msg , sender , reason ) , self .... |
def import_teamocil ( sconf ) :
"""Return tmuxp config from a ` teamocil ` _ yaml config .
. . _ teamocil : https : / / github . com / remiprev / teamocil
Parameters
sconf : dict
python dict for session configuration
Notes
Todos :
- change ' root ' to a cd or start _ directory
- width in pane - > ma... | tmuxp_config = { }
if 'session' in sconf :
sconf = sconf [ 'session' ]
if 'name' in sconf :
tmuxp_config [ 'session_name' ] = sconf [ 'name' ]
else :
tmuxp_config [ 'session_name' ] = None
if 'root' in sconf :
tmuxp_config [ 'start_directory' ] = sconf . pop ( 'root' )
tmuxp_config [ 'windows' ] = [ ]
f... |
def calculate_eclipses ( M1s , M2s , R1s , R2s , mag1s , mag2s , u11s = 0.394 , u21s = 0.296 , u12s = 0.394 , u22s = 0.296 , Ps = None , period = None , logperkde = RAGHAVAN_LOGPERKDE , incs = None , eccs = None , mininc = None , calc_mininc = True , maxecc = 0.97 , ecc_fn = draw_eccs , band = 'Kepler' , return_probabi... | if MAfn is None :
logging . warning ( 'MAInterpolationFunction not passed, so generating one...' )
MAfn = MAInterpolationFunction ( nzs = 200 , nps = 400 , pmin = 0.007 , pmax = 1 / 0.007 )
M1s = np . atleast_1d ( M1s )
M2s = np . atleast_1d ( M2s )
R1s = np . atleast_1d ( R1s )
R2s = np . atleast_1d ( R2s )
nb... |
def all ( self ) :
"""Returns list with vids of all indexed partitions .""" | partitions = [ ]
query = text ( """
SELECT dataset_vid, vid
FROM partition_index;""" )
for result in self . backend . library . database . connection . execute ( query ) :
dataset_vid , vid = result
partitions . append ( PartitionSearchResult ( dataset_vid = dataset_vid , vid = vid , sco... |
def recordWidget ( xparent , widget ) :
"""Records the inputed widget to the parent profile .
: param xparent | < xml . etree . Element >
widget | < QWidget >""" | # record a splitter
if isinstance ( widget , XSplitter ) :
xwidget = ElementTree . SubElement ( xparent , 'split' )
if ( widget . orientation ( ) == Qt . Horizontal ) :
xwidget . set ( 'orient' , 'horizontal' )
else :
xwidget . set ( 'orient' , 'vertical' )
xwidget . set ( 'state' , nati... |
def construct_time_based_gas_price_strategy ( max_wait_seconds , sample_size = 120 , probability = 98 ) :
"""A gas pricing strategy that uses recently mined block data to derive a gas
price for which a transaction is likely to be mined within X seconds with
probability P .
: param max _ wait _ seconds : The d... | def time_based_gas_price_strategy ( web3 , transaction_params ) :
avg_block_time = _get_avg_block_time ( web3 , sample_size = sample_size )
wait_blocks = int ( math . ceil ( max_wait_seconds / avg_block_time ) )
raw_miner_data = _get_raw_miner_data ( web3 , sample_size = sample_size )
miner_data = _aggr... |
def tensor_markov ( * args ) :
"""Computes the product of two independent markov chains .
: param m1 : a tuple containing the nodes and the transition matrix of the first chain
: param m2 : a tuple containing the nodes and the transition matrix of the second chain
: return : a tuple containing the nodes and t... | if len ( args ) > 2 :
m1 = args [ 0 ]
m2 = args [ 1 ]
tail = args [ 2 : ]
prod = tensor_markov ( m1 , m2 )
return tensor_markov ( prod , tail )
elif len ( args ) == 2 :
m1 , m2 = args
n1 , t1 = m1
n2 , t2 = m2
n1 = np . array ( n1 , dtype = float )
n2 = np . array ( n2 , dtype = ... |
def reshape_1d ( df ) :
"""If parameter is 1D row vector then convert it into 2D matrix .""" | shape = df . shape
if len ( shape ) == 1 :
return df . reshape ( shape [ 0 ] , 1 )
else :
return df |
def get_segment_efforts ( self , segment_id , athlete_id = None , start_date_local = None , end_date_local = None , limit = None ) :
"""Gets all efforts on a particular segment sorted by start _ date _ local
Returns an array of segment effort summary representations sorted by
start _ date _ local ascending or b... | params = { "segment_id" : segment_id }
if athlete_id is not None :
params [ 'athlete_id' ] = athlete_id
if start_date_local :
if isinstance ( start_date_local , six . string_types ) :
start_date_local = arrow . get ( start_date_local ) . naive
params [ "start_date_local" ] = start_date_local . strft... |
def get_parsed_args ( self , comp_words ) :
"""gets the parsed args from a patched parser""" | active_parsers = self . _patch_argument_parser ( )
parsed_args = argparse . Namespace ( )
self . completing = True
if USING_PYTHON2 : # Python 2 argparse only properly works with byte strings .
comp_words = [ ensure_bytes ( word ) for word in comp_words ]
try :
active_parsers [ 0 ] . parse_known_args ( comp_wor... |
def nodeInLanguageStem ( _ : Context , n : Node , s : ShExJ . LanguageStem ) -> bool :
"""http : / / shex . io / shex - semantics / # values
* * nodeIn * * : asserts that an RDF node n is equal to an RDF term s or is in a set defined by a
: py : class : ` ShExJ . IriStem ` , : py : class : ` LiteralStem ` or : ... | return isinstance ( s , ShExJ . Wildcard ) or ( isinstance ( n , Literal ) and n . language is not None and str ( n . language ) . startswith ( str ( s ) ) ) |
def create_new_account ( data_dir , password , ** geth_kwargs ) :
"""Creates a new Ethereum account on geth .
This is useful for testing when you want to stress
interaction ( transfers ) between Ethereum accounts .
This command communicates with ` ` geth ` ` command over
terminal interaction . It creates ke... | if os . path . exists ( password ) :
geth_kwargs [ 'password' ] = password
command , proc = spawn_geth ( dict ( data_dir = data_dir , suffix_args = [ 'account' , 'new' ] , ** geth_kwargs ) )
if os . path . exists ( password ) :
stdoutdata , stderrdata = proc . communicate ( )
else :
stdoutdata , stderrdata ... |
def parse_parameter ( self , tup_tree ) :
"""< ! ELEMENT PARAMETER ( QUALIFIER * ) >
< ! ATTLIST PARAMETER
% CIMName ;
% CIMType ; # REQUIRED >""" | self . check_node ( tup_tree , 'PARAMETER' , ( 'NAME' , 'TYPE' ) , ( ) , ( 'QUALIFIER' , ) )
attrl = attrs ( tup_tree )
qualifiers = self . list_of_matching ( tup_tree , ( 'QUALIFIER' , ) )
return CIMParameter ( attrl [ 'NAME' ] , type = attrl [ 'TYPE' ] , is_array = False , qualifiers = qualifiers , embedded_object = ... |
def filter_N_top ( self , inst_rc , N_top , rank_type = 'sum' ) :
'''Filter the matrix rows or columns based on sum / variance , and only keep the top''' | inst_df = self . dat_to_df ( )
inst_df = run_filter . filter_N_top ( inst_rc , inst_df , N_top , rank_type )
self . df_to_dat ( inst_df ) |
def clear ( self ) :
"""Brutely clears the key value store for keys with THUMBNAIL _ KEY _ PREFIX
prefix . Use this in emergency situations . Normally you would probably
want to use the ` ` cleanup ` ` method instead .""" | all_keys = self . _find_keys_raw ( settings . THUMBNAIL_KEY_PREFIX )
if all_keys :
self . _delete_raw ( * all_keys ) |
def total_ordering ( cls ) : # pragma : no cover
"""Class decorator that fills in missing ordering methods""" | convert = { '__lt__' : [ ( '__gt__' , lambda self , other : not ( self < other or self == other ) ) , ( '__le__' , lambda self , other : self < other or self == other ) , ( '__ge__' , lambda self , other : not self < other ) ] , '__le__' : [ ( '__ge__' , lambda self , other : not self <= other or self == other ) , ( '_... |
def save_current_nb_as_html ( info = False ) :
"""Save the current notebook as html file in the same directory""" | assert in_ipynb ( )
full_path = get_notebook_name ( )
path , filename = os . path . split ( full_path )
wd_save = os . getcwd ( )
os . chdir ( path )
cmd = 'jupyter nbconvert --to html "{}"' . format ( filename )
os . system ( cmd )
os . chdir ( wd_save )
if info :
print ( "target dir: " , path )
print ( "cmd: ... |
def get_root_folder ( ) :
"""returns the home folder and program root depending on OS""" | locations = { 'linux' : { 'hme' : '/home/duncan/' , 'core_folder' : '/home/duncan/dev/src/python/AIKIF' } , 'win32' : { 'hme' : 'T:\\user\\' , 'core_folder' : 'T:\\user\\dev\\src\\python\\AIKIF' } , 'cygwin' : { 'hme' : os . getcwd ( ) + os . sep , 'core_folder' : os . getcwd ( ) } , 'darwin' : { 'hme' : os . getcwd ( ... |
def _default_ising_beta_range ( h , J ) :
"""Determine the starting and ending beta from h J
Args :
h ( dict )
J ( dict )
Assume each variable in J is also in h .
We use the minimum bias to give a lower bound on the minimum energy gap , such at the
final sweeps we are highly likely to settle into the cu... | # Get nonzero , absolute biases
abs_h = [ abs ( hh ) for hh in h . values ( ) if hh != 0 ]
abs_J = [ abs ( jj ) for jj in J . values ( ) if jj != 0 ]
abs_biases = abs_h + abs_J
if not abs_biases :
return [ 0.1 , 1.0 ]
# Rough approximation of min change in energy when flipping a qubit
min_delta_energy = min ( abs_b... |
def describe ( self , language = DEFAULT_LANGUAGE , min_score : int = 75 ) -> dict :
"""Return a dictionary that describes a given language tag in a specified
natural language .
See ` language _ name ` and related methods for more specific versions of this .
The desired ` language ` will in fact be matched ag... | names = { }
if self . language :
names [ 'language' ] = self . language_name ( language , min_score )
if self . script :
names [ 'script' ] = self . script_name ( language , min_score )
if self . region :
names [ 'region' ] = self . region_name ( language , min_score )
if self . variants :
names [ 'vari... |
def get_methods_by_name ( self , name ) :
"""generator of methods matching name . This will include any bridges
present .""" | return ( m for m in self . methods if m . get_name ( ) == name ) |
def list_protocols ( profile , ** libcloud_kwargs ) :
'''Return a list of supported protocols .
: param profile : The profile key
: type profile : ` ` str ` `
: param libcloud _ kwargs : Extra arguments for the driver ' s list _ protocols method
: type libcloud _ kwargs : ` ` dict ` `
: return : a list of... | conn = _get_driver ( profile = profile )
libcloud_kwargs = salt . utils . args . clean_kwargs ( ** libcloud_kwargs )
return conn . list_protocols ( ** libcloud_kwargs ) |
def firmware_drivers ( self ) :
"""Gets the FirmwareDrivers API client .
Returns :
FirmwareDrivers :""" | if not self . __firmware_drivers :
self . __firmware_drivers = FirmwareDrivers ( self . __connection )
return self . __firmware_drivers |
def classorder ( self , classes ) :
"""Return a list of class IDs in order for presentational purposes : order is determined first and foremost by explicit ordering , else alphabetically by label or as a last resort by class ID""" | return [ classid for classid , classitem in sorted ( ( ( classid , classitem ) for classid , classitem in classes . items ( ) if 'seqnr' in classitem ) , key = lambda pair : pair [ 1 ] [ 'seqnr' ] ) ] + [ classid for classid , classitem in sorted ( ( ( classid , classitem ) for classid , classitem in classes . items ( ... |
def problem_serializing ( value , e = None ) :
"""THROW ERROR ABOUT SERIALIZING""" | from mo_logs import Log
try :
typename = type ( value ) . __name__
except Exception :
typename = "<error getting name>"
try :
rep = text_type ( repr ( value ) )
except Exception as _ :
rep = None
if rep == None :
Log . error ( "Problem turning value of type {{type}} to json" , type = typename , caus... |
def logit ( self , msg , pid , user , cname , priority = None ) :
"""Function for formatting content and logging to syslog""" | if self . stream :
print ( msg , file = self . stream )
elif priority == logging . WARNING :
self . logger . warning ( "{0}[pid:{1}] user:{2}: WARNING - {3}" . format ( cname , pid , user , msg ) )
elif priority == logging . ERROR :
self . logger . error ( "{0}[pid:{1}] user:{2}: ERROR - {3}" . format ( cna... |
def ReplaceStoredProcedure ( self , sproc_link , sproc , options = None ) :
"""Replaces a stored procedure and returns it .
: param str sproc _ link :
The link to the stored procedure .
: param dict sproc :
: param dict options :
The request options for the request .
: return :
The replaced Stored Pro... | if options is None :
options = { }
CosmosClient . __ValidateResource ( sproc )
sproc = sproc . copy ( )
if sproc . get ( 'serverScript' ) :
sproc [ 'body' ] = str ( sproc [ 'serverScript' ] )
elif sproc . get ( 'body' ) :
sproc [ 'body' ] = str ( sproc [ 'body' ] )
path = base . GetPathFromLink ( sproc_link... |
def get_contributor_sort_value ( self , obj ) :
"""Generate display name for contributor .""" | user = obj . contributor
if user . first_name or user . last_name :
contributor = user . get_full_name ( )
else :
contributor = user . username
return contributor . strip ( ) . lower ( ) |
def addNotice ( self , data ) :
"""Add custom notice to front - end for this NodeServers
: param data : String of characters to add as a notification in the front - end .""" | LOGGER . info ( 'Sending addnotice to Polyglot: {}' . format ( data ) )
message = { 'addnotice' : data }
self . send ( message ) |
def search ( pattern , sentence , * args , ** kwargs ) :
"""Returns a list of all matches found in the given sentence .""" | return compile ( pattern , * args , ** kwargs ) . search ( sentence ) |
def init_fftw_plan ( self , planning_effort = 'measure' , ** kwargs ) :
"""Initialize the FFTW plan for this transform for later use .
If the implementation of this operator is not ' pyfftw ' , this
method should not be called .
Parameters
planning _ effort : str , optional
Flag for the amount of effort p... | if self . impl != 'pyfftw' :
raise ValueError ( 'cannot create fftw plan without fftw backend' )
# Using available temporaries if possible
inverse = isinstance ( self , FourierTransformInverse )
if inverse :
rspace = self . range
fspace = self . domain
else :
rspace = self . domain
fspace = self . r... |
def epoch_cb ( self ) :
"""Callback function after each epoch . Now it records each epoch time
and append it to epoch dataframe .""" | metrics = { }
metrics [ 'elapsed' ] = self . elapsed ( )
now = datetime . datetime . now ( )
metrics [ 'epoch_time' ] = now - self . last_epoch_time
self . append_metrics ( metrics , 'epoch' )
self . last_epoch_time = now |
def sam_readline ( sock , partial = None ) :
"""read a line from a sam control socket""" | response = b''
exception = None
while True :
try :
c = sock . recv ( 1 )
if not c :
raise EOFError ( 'SAM connection died. Partial response %r %r' % ( partial , response ) )
elif c == b'\n' :
break
else :
response += c
except ( BlockingIOError ... |
def hacking_no_removed_module ( logical_line , noqa ) :
r"""Check for removed modules in Python 3.
Examples :
Okay : from os import path
Okay : from os import path as p
Okay : from os import ( path as p )
Okay : import os . path
H237 : import thread
Okay : import thread # noqa
H237 : import commands... | if noqa :
return
line = core . import_normalize ( logical_line . strip ( ) )
if line and line . split ( ) [ 0 ] == 'import' :
module_name = line . split ( ) [ 1 ] . split ( '.' ) [ 0 ]
if module_name in removed_modules :
yield 0 , ( "H237: module %s is " "removed in Python 3" % module_name ) |
def must_open ( filename , mode = "r" , checkexists = False , skipcheck = False , oappend = False ) :
"""Accepts filename and returns filehandle .
Checks on multiple files , stdin / stdout / stderr , . gz or . bz2 file .""" | if isinstance ( filename , list ) :
assert "r" in mode
if filename [ 0 ] . endswith ( ( ".gz" , ".bz2" ) ) :
filename = " " . join ( filename )
# allow opening multiple gz / bz2 files
else :
import fileinput
return fileinput . input ( filename )
if filename . startswith ( "s3... |
def update_values ( self ) :
"""Update form values when detection method is selected .""" | self . method = self . idx_method . currentText ( )
sw_det = DetectSlowWave ( method = self . method )
self . index [ 'f1' ] . set_value ( sw_det . det_filt [ 'freq' ] [ 0 ] )
self . index [ 'f2' ] . set_value ( sw_det . det_filt [ 'freq' ] [ 1 ] )
self . index [ 'min_trough_dur' ] . set_value ( sw_det . trough_duratio... |
def value ( self ) :
"""returns the class as a dictionary""" | val = { }
for k in self . __allowed_keys :
v = getattr ( self , "_" + k )
if v is not None :
val [ k ] = v
return val |
def obo ( self ) :
"""str : the ontology serialized in obo format .""" | meta = self . _obo_meta ( )
meta = [ meta ] if meta else [ ]
newline = "\n\n" if six . PY3 else "\n\n" . encode ( 'utf-8' )
try : # if ' namespace ' in self . meta :
return newline . join ( meta + [ r . obo for r in self . typedefs ] + [ t . obo for t in self if t . id . startswith ( self . meta [ 'namespace' ] [ 0... |
def stop ( self ) -> None :
"""Stops the running simulation once the current event is done executing .""" | if self . is_running :
if _logger is not None :
self . _log ( INFO , "stop" , __now = self . now ( ) )
self . _is_running = False |
def render_template ( self , plain , rich = None , ** context ) :
'''Render the body of the message from a template . The plain
body will be rendered from a template named ` ` plain ` ` or
` ` plain + ' . txt ' ` ` ( in that order of preference ) . The rich
body will be rendered from ` ` rich ` ` if given , o... | self . plain = render_template ( [ plain , plain + '.txt' ] , ** context )
if rich is not None :
self . rich = render_template ( rich , ** context )
else :
try :
self . rich = render_template ( plain + '.html' , ** context )
except TemplateNotFound :
pass |
def result ( self , r = None , ** kwargs ) :
'''Validates a result , stores it in self . results and prints it .
Accepts the same kwargs as the binwalk . core . module . Result class .
@ r - An existing instance of binwalk . core . module . Result .
Returns an instance of binwalk . core . module . Result .''' | if r is None :
r = Result ( ** kwargs )
# Add the name of the current module to the result
r . module = self . __class__ . __name__
# Any module that is reporting results , valid or not , should be marked
# as enabled
if not self . enabled :
self . enabled = True
self . validate ( r )
self . _plugins_result ( r... |
def _wait_for_reader ( self ) :
"""Checks for backpressure by the downstream reader .""" | if self . max_size <= 0 : # Unlimited queue
return
if self . write_item_offset - self . cached_remote_offset <= self . max_size :
return
# Hasn ' t reached max size
remote_offset = internal_kv . _internal_kv_get ( self . read_ack_key )
if remote_offset is None : # logger . debug ( " [ writer ] Waiting for r... |
def hexdiff ( x , y ) :
"""Show differences between 2 binary strings""" | x = bytes_encode ( x ) [ : : - 1 ]
y = bytes_encode ( y ) [ : : - 1 ]
SUBST = 1
INSERT = 1
d = { ( - 1 , - 1 ) : ( 0 , ( - 1 , - 1 ) ) }
for j in range ( len ( y ) ) :
d [ - 1 , j ] = d [ - 1 , j - 1 ] [ 0 ] + INSERT , ( - 1 , j - 1 )
for i in range ( len ( x ) ) :
d [ i , - 1 ] = d [ i - 1 , - 1 ] [ 0 ] + INSE... |
def setColor ( self , color ) :
"""Convenience method to set the border , fill and highlight colors based
on the inputed color .
: param color | < QColor >""" | # sets the border color as the full value
self . setBorderColor ( color )
# set the highlight color as the color with a 140 % alpha
clr = QColor ( color )
clr . setAlpha ( 150 )
self . setHighlightColor ( clr )
# set the fill color as the color with a 50 % alpha
clr = QColor ( color )
clr . setAlpha ( 80 )
self . setFi... |
def _internal_write ( out_stream , arr ) :
"""Writes numpy . ndarray arr to a file - like object ( with write ( ) method ) in
IDX format .""" | if arr . size == 0 :
raise FormatError ( 'Cannot encode empty array.' )
try :
type_byte , struct_lib_type = _DATA_TYPES_NUMPY [ str ( arr . dtype ) ]
except KeyError :
raise FormatError ( 'numpy ndarray type not supported by IDX format.' )
if arr . ndim > _MAX_IDX_DIMENSIONS :
raise FormatError ( 'IDX f... |
def get_object ( self , identifier , mask = None ) :
"""Get a Reserved Capacity Group
: param int identifier : Id of the SoftLayer _ Virtual _ ReservedCapacityGroup
: param string mask : override default object Mask""" | if mask is None :
mask = "mask[instances[billingItem[item[keyName],category], guest], backendRouter[datacenter]]"
result = self . client . call ( self . rcg_service , 'getObject' , id = identifier , mask = mask )
return result |
def fetch_file_handler ( unused_build_context , target , fetch , package_dir , tar ) :
"""Handle remote downloadable file URI .
Download the file and cache it under the private builer workspace
( unless already downloaded ) , and add it to the package tar .
TODO ( itamar ) : Support re - downloading if remote... | dl_dir = join ( package_dir , fetch . name ) if fetch . name else package_dir
fetch_url ( fetch . uri , join ( dl_dir , basename ( urlparse ( fetch . uri ) . path ) ) , dl_dir )
tar . add ( package_dir , arcname = split_name ( target . name ) ) |
def merge_upwards_if_smaller_than ( self , small_size , a_or_u ) :
"""After prune _ if _ smaller _ than is run , we may still have excess
nodes .
For example , with a small _ size of 609710690:
28815419 / data / *
32 / data / srv / *
925746 / data / srv / docker . bak / *
12 / data / srv / docker . bak ... | # Assert that we ' re not messing things up .
prev_app_size = self . app_size ( )
prev_use_size = self . use_size ( )
small_nodes = self . _find_small_nodes ( small_size , ( ) , a_or_u )
for node , parents in small_nodes : # Check immediate grandparent for isdir = None and if it
# exists , move this there . The isdir =... |
def add_cron ( self , name , command , minute = "*" , hour = "*" , mday = "*" , month = "*" , wday = "*" , who = "root" , env = None ) :
"""Write a file to / etc / cron . d to schedule a command
env is a dict containing environment variables you want to set in the file
name will be used as the name of the file"... | if minute == 'random' :
minute = str ( random . randrange ( 60 ) )
if hour == 'random' :
hour = str ( random . randrange ( 24 ) )
fp = open ( '/etc/cron.d/%s' % name , "w" )
if env :
for key , value in env . items ( ) :
fp . write ( '%s=%s\n' % ( key , value ) )
fp . write ( '%s %s %s %s %s %s %s\n'... |
def as_set ( obj ) :
"""Convert obj into a set , returns None if obj is None .
> > > assert as _ set ( None ) is None and as _ set ( 1 ) = = set ( [ 1 ] ) and as _ set ( range ( 1,3 ) ) = = set ( [ 1 , 2 ] )""" | if obj is None or isinstance ( obj , collections . Set ) :
return obj
if not isinstance ( obj , collections . Iterable ) :
return set ( ( obj , ) )
else :
return set ( obj ) |
def fire ( self , * args , ** kwargs ) :
"""Fire event and call all handler functions
You can call EventHandler object itself like e ( * args , * * kwargs ) instead of
e . fire ( * args , * * kwargs ) .""" | for func in self . _getfunctionlist ( ) :
if type ( func ) == EventHandler :
func . fire ( * args , ** kwargs )
else :
func ( self . obj , * args , ** kwargs ) |
def find_by_organization ( self , organization , params = { } , ** options ) :
"""Returns the compact records for all teams in the organization visible to
the authorized user .
Parameters
organization : { Id } Globally unique identifier for the workspace or organization .
[ params ] : { Object } Parameters ... | path = "/organizations/%s/teams" % ( organization )
return self . client . get_collection ( path , params , ** options ) |
def get_by_username ( cls , username ) :
"""Return a User by email address""" | return cls . query ( ) . filter ( cls . username == username ) . first ( ) |
def _split_sequences_multitraj ( dtrajs , lag ) :
"""splits the discrete trajectories into conditional sequences by starting state
Parameters
dtrajs : list of int - iterables
discrete trajectories
nstates : int
total number of discrete states
lag : int
lag time""" | n = number_of_states ( dtrajs )
res = [ ]
for i in range ( n ) :
res . append ( [ ] )
for dtraj in dtrajs :
states , seqs = _split_sequences_singletraj ( dtraj , n , lag )
for i in range ( len ( states ) ) :
res [ states [ i ] ] . append ( seqs [ i ] )
return res |
def load_config ( self , config ) :
"""Load the outputs section of the configuration file .""" | # Limit the number of processes to display in the WebUI
if config is not None and config . has_section ( 'outputs' ) :
logger . debug ( 'Read number of processes to display in the WebUI' )
n = config . get_value ( 'outputs' , 'max_processes_display' , default = None )
logger . debug ( 'Number of processes t... |
def trimLeft ( self , amount ) :
"""Trim this fastqSequence in - place by removing < amount > nucleotides from
the 5 ' end ( left end ) .
: param amount : the number of nucleotides to trim from the left - side of
this sequence .""" | if amount == 0 :
return
self . sequenceData = self . sequenceData [ amount : ]
self . sequenceQual = self . sequenceQual [ amount : ] |
def function_call ( self , function , arguments ) :
"""Generates code for a function call
function - function index in symbol table
arguments - list of arguments ( indexes in symbol table )""" | # push each argument to stack
for arg in arguments :
self . push ( self . symbol ( arg ) )
self . free_if_register ( arg )
self . newline_text ( "CALL\t" + self . symtab . get_name ( function ) , True )
args = self . symtab . get_attribute ( function )
# generates stack cleanup if function has arguments
if args... |
def divide ( n , iterable ) :
"""split an iterable into n groups , per https : / / more - itertools . readthedocs . io / en / latest / api . html # grouping
: param int n : Number of unique groups
: param iter iterable : An iterable to split up
: return : a list of new iterables derived from the original iter... | seq = tuple ( iterable )
q , r = divmod ( len ( seq ) , n )
ret = [ ]
for i in range ( n ) :
start = ( i * q ) + ( i if i < r else r )
stop = ( ( i + 1 ) * q ) + ( i + 1 if i + 1 < r else r )
ret . append ( iter ( seq [ start : stop ] ) )
return ret |
def from_content ( cls , content ) :
"""Parses a Tibia . com response into a House object .
Parameters
content : : class : ` str `
HTML content of the page .
Returns
: class : ` House `
The house contained in the page , or None if the house doesn ' t exist .
Raises
InvalidContent
If the content is... | parsed_content = parse_tibiacom_content ( content )
image_column , desc_column , * _ = parsed_content . find_all ( 'td' )
if "Error" in image_column . text :
return None
image = image_column . find ( 'img' )
for br in desc_column . find_all ( "br" ) :
br . replace_with ( "\n" )
description = desc_column . text ... |
def reset ( self ) :
'''Reset the state of the container and its internal fields''' | super ( Container , self ) . reset ( )
for field in self . _fields :
field . reset ( )
self . _field_idx = 0 |
def __create_remote_webdriver_from_config ( self , testname = None ) :
'''Reads the config value for browser type .''' | desired_capabilities = self . _generate_desired_capabilities ( testname )
remote_url = self . _config_reader . get ( WebDriverFactory . REMOTE_URL_CONFIG )
# Instantiate remote webdriver .
driver = webdriver . Remote ( desired_capabilities = desired_capabilities , command_executor = remote_url )
# Log IP Address of nod... |
def dbnsfp ( self ) :
"""dbnsfp""" | tstart = datetime . now ( )
# python . . / scripts / annotate _ vcfs . py - i mm13173_14 . ug . target1 . vcf - r 1000genomes dbsnp138 clinvar esp6500 - a . . / data / 1000genomes / ALL . wgs . integrated _ phase1 _ v3.20101123 . snps _ indels _ sv . sites . vcf . gz . . / data / dbsnp138/00 - All . vcf . gz . . / data... |
def diff_json_files ( left_files , right_files ) :
'''Compute the difference between two sets of basis set JSON files
The output is a set of files that correspond to each file in
` left _ files ` . Each resulting dictionary will contain only the elements / shells
that exist in that entry and not in any of the... | left_data = [ fileio . read_json_basis ( x ) for x in left_files ]
right_data = [ fileio . read_json_basis ( x ) for x in right_files ]
d = diff_basis_dict ( left_data , right_data )
for idx , diff_bs in enumerate ( d ) :
fpath = left_files [ idx ]
fileio . write_json_basis ( fpath + '.diff' , diff_bs ) |
def confd_state_rest_listen_tcp_port ( self , ** kwargs ) :
"""Auto Generated Code""" | config = ET . Element ( "config" )
confd_state = ET . SubElement ( config , "confd-state" , xmlns = "http://tail-f.com/yang/confd-monitoring" )
rest = ET . SubElement ( confd_state , "rest" )
listen = ET . SubElement ( rest , "listen" )
tcp = ET . SubElement ( listen , "tcp" )
port = ET . SubElement ( tcp , "port" )
po... |
def on_before_transform_template ( self , template_dict ) :
"""Hook method that gets called before the SAM template is processed .
The template has pass the validation and is guaranteed to contain a non - empty " Resources " section .
: param dict template _ dict : Dictionary of the SAM template
: return : No... | template = SamTemplate ( template_dict )
# Temporarily add Serverless : : Api resource corresponding to Implicit API to the template .
# This will allow the processing code to work the same way for both Implicit & Explicit APIs
# If there are no implicit APIs , we will remove from the template later .
# If the customer... |
def _clean_dic ( self , dic ) :
"""Clean recursively all empty or None values inside a dict .""" | aux_dic = dic . copy ( )
for key , value in iter ( dic . items ( ) ) :
if value is None or value == '' :
del aux_dic [ key ]
elif type ( value ) is dict :
cleaned_dict = self . _clean_dic ( value )
if not cleaned_dict :
del aux_dic [ key ]
continue
aux_dic... |
def linear_insert ( self , item , priority ) :
"""Linear search . Performance is O ( n ^ 2 ) .""" | with self . lock :
self_data = self . data
rotate = self_data . rotate
maxlen = self . _maxlen
length = len ( self_data )
count = length
# in practice , this is better than doing a rotate ( - 1 ) every
# loop and getting self . data [ 0 ] each time only because deque
# implements a very ... |
def _evaluate_sql_query_subprocess ( self , predicted_query : str , sql_query_labels : List [ str ] ) -> int :
"""We evaluate here whether the predicted query and the query label evaluate to the
exact same table . This method is only called by the subprocess , so we just exit with
1 if it is correct and 0 other... | postprocessed_predicted_query = self . postprocess_query_sqlite ( predicted_query )
try :
self . _cursor . execute ( postprocessed_predicted_query )
predicted_rows = self . _cursor . fetchall ( )
except sqlite3 . Error as error :
logger . warning ( f'Error executing predicted: {error}' )
exit ( 0 )
# If... |
def running_window ( iterable , size ) :
"""Generate n - size running window .
Example : :
> > > for i in running _ windows ( [ 1 , 2 , 3 , 4 , 5 ] , size = 3 ) :
. . . print ( i )
[1 , 2 , 3]
[2 , 3 , 4]
[3 , 4 , 5]
* * 中文文档 * *
简单滑窗函数 。""" | if size > len ( iterable ) :
raise ValueError ( "size can not be greater than length of iterable." )
fifo = collections . deque ( maxlen = size )
for i in iterable :
fifo . append ( i )
if len ( fifo ) == size :
yield list ( fifo ) |
def add_domain_to_toctree ( app , doctree , docname ) :
"""Add domain objects to the toctree dynamically .
This should be attached to the ` ` doctree - resolved ` ` event .
This works by :
* Finding each domain node ( addnodes . desc )
* Figuring out it ' s parent that will be in the toctree
( nodes . sec... | toc = app . env . tocs [ docname ]
for desc_node in doctree . traverse ( addnodes . desc ) :
try :
ref_id = desc_node . children [ 0 ] . attributes [ "ids" ] [ 0 ]
except ( KeyError , IndexError ) as e :
LOGGER . warning ( "Invalid desc node: %s" % e )
continue
try : # Python domain ... |
def is_blocked ( self , ip ) :
"""Determine if an IP address should be considered blocked .""" | blocked = True
if ip in self . allowed_admin_ips :
blocked = False
for allowed_range in self . allowed_admin_ip_ranges :
if ipaddress . ip_address ( ip ) in ipaddress . ip_network ( allowed_range ) :
blocked = False
return blocked |
def wait ( self , log_file ) :
"Wait until the process is ready ." | lines = map ( self . log_line , self . filter_lines ( self . get_lines ( log_file ) ) )
return any ( std . re . search ( self . pattern , line ) for line in lines ) |
def set_config_for_routing_entity ( self , routing_entity : Union [ web . Resource , web . StaticResource , web . ResourceRoute ] , config ) :
"""Record configuration for resource or it ' s route .""" | if isinstance ( routing_entity , ( web . Resource , web . StaticResource ) ) :
resource = routing_entity
# Add resource configuration or fail if it ' s already added .
if resource in self . _resource_config :
raise ValueError ( "CORS is already configured for {!r} resource." . format ( resource ) )
... |
def space_labels ( document ) :
"""Ensure space around bold compound labels .""" | for label in document . xpath ( './/bold' ) : # TODO : Make this more permissive to match chemical _ label in parser
if not label . text or not re . match ( '^\(L?\d\d?[a-z]?\):?$' , label . text , re . I ) :
continue
parent = label . getparent ( )
previous = label . getprevious ( )
if previous ... |
def add_case ( self , case_obj ) :
"""Add a case obj with individuals to adapter
Args :
case _ obj ( puzzle . models . Case )""" | for ind_obj in case_obj . individuals :
self . _add_individual ( ind_obj )
logger . debug ( "Adding case {0} to plugin" . format ( case_obj . case_id ) )
self . case_objs . append ( case_obj )
if case_obj . tabix_index :
logger . debug ( "Setting filters.can_filter_range to True" )
self . filters . can_filt... |
def save_object ( collection , obj ) :
"""Save an object ` ` obj ` ` to the given ` ` collection ` ` .
` ` obj . id ` ` must be unique across all other existing objects in
the given collection . If ` ` id ` ` is not present in the object , a
* UUID * is assigned as the object ' s ` ` id ` ` .
Indexes alread... | if 'id' not in obj :
obj . id = uuid ( )
id = obj . id
path = object_path ( collection , id )
temp_path = '%s.temp' % path
with open ( temp_path , 'w' ) as f :
data = _serialize ( obj )
f . write ( data )
shutil . move ( temp_path , path )
if id in _db [ collection ] . cache :
_db [ collection ] . cache... |
def update_http_rules ( rules , content_type = 'text/plain' ) :
"""Adds rules to global http mock .
It permits to set mock in a more global way than decorators , cf . :
https : / / github . com / openstack / requests - mock
Here we assume urls in the passed dict are regex we recompile before adding
a rule .... | for kw in deepcopy ( rules ) :
kw [ 'url' ] = re . compile ( kw [ 'url' ] )
# ensure headers dict for at least have a default content type
if 'Content-Type' not in kw . get ( 'headers' , { } ) :
kw [ 'headers' ] = dict ( kw . get ( 'headers' , { } ) , ** { 'Content-Type' : content_type , } )
met... |
def dallinger_package_path ( ) :
"""Return the absolute path of the root directory of the installed
Dallinger package :
> > > utils . dallinger _ package _ location ( )
' / Users / janedoe / projects / Dallinger3 / dallinger '""" | dist = get_distribution ( "dallinger" )
src_base = os . path . join ( dist . location , dist . project_name )
return src_base |
def getmeths ( method_type ) :
"""returns MagIC method codes available for a given type""" | meths = [ ]
if method_type == 'GM' :
meths . append ( 'GM-PMAG-APWP' )
meths . append ( 'GM-ARAR' )
meths . append ( 'GM-ARAR-AP' )
meths . append ( 'GM-ARAR-II' )
meths . append ( 'GM-ARAR-NI' )
meths . append ( 'GM-ARAR-TF' )
meths . append ( 'GM-CC-ARCH' )
meths . append ( 'GM-CC-ARCH... |
def _setup_appium ( self ) :
"""Setup Appium webdriver
: returns : a new remote Appium driver""" | self . config . set ( 'Server' , 'host' , '127.0.0.1' )
self . config . set ( 'Server' , 'port' , '4723' )
return self . _create_remote_driver ( ) |
def rdann ( record_name , extension , sampfrom = 0 , sampto = None , shift_samps = False , pb_dir = None , return_label_elements = [ 'symbol' ] , summarize_labels = False ) :
"""Read a WFDB annotation file record _ name . extension and return an
Annotation object .
Parameters
record _ name : str
The record ... | return_label_elements = check_read_inputs ( sampfrom , sampto , return_label_elements )
# Read the file in byte pairs
filebytes = load_byte_pairs ( record_name , extension , pb_dir )
# Get wfdb annotation fields from the file bytes
( sample , label_store , subtype , chan , num , aux_note ) = proc_ann_bytes ( filebytes ... |
def create ( self , image = None ) :
"""Create content and return url . In case of images add the image .""" | container = self . context
new = api . content . create ( container = container , type = self . portal_type , title = self . title , safe_id = True , )
if image :
namedblobimage = NamedBlobImage ( data = image . read ( ) , filename = safe_unicode ( image . filename ) )
new . image = namedblobimage
if new :
... |
def server_identity_is_verified ( self ) :
"""GPGAuth stage0""" | # Encrypt a uuid token for the server
server_verify_token = self . gpg . encrypt ( self . _nonce0 , self . server_fingerprint , always_trust = True )
if not server_verify_token . ok :
raise GPGAuthStage0Exception ( 'Encryption of the nonce0 (%s) ' 'to the server fingerprint (%s) failed.' % ( self . _nonce0 , self .... |
def run ( self , workflow_input , * args , ** kwargs ) :
''': param workflow _ input : Dictionary of the workflow ' s input arguments ; see below for more details
: type workflow _ input : dict
: param instance _ type : Instance type on which all stages ' jobs will be run , or a dict mapping function names to i... | return super ( DXWorkflow , self ) . run ( workflow_input , * args , ** kwargs ) |
def comment ( self , s , ** args ) :
"""Write DOT comment .""" | self . write ( u"// " )
self . writeln ( s = s , ** args ) |
def blacklistNode ( self , nodeName : str , reason : str = None , code : int = None ) :
"""Add the node specified by ` nodeName ` to this node ' s blacklist""" | msg = "{} blacklisting node {}" . format ( self , nodeName )
if reason :
msg += " for reason {}" . format ( reason )
if code :
msg += " for code {}" . format ( code )
logger . display ( msg )
self . nodeBlacklister . blacklist ( nodeName ) |
def write_file ( content , * path ) :
"""Simply write some content to a file , overriding the file if necessary .""" | with open ( os . path . join ( * path ) , "w" ) as file :
return file . write ( content ) |
def recurse_tree ( path , excludes , opts ) :
"""Look for every file in the directory tree and create the corresponding
ReST files .""" | # use absolute path for root , as relative paths like ' . . / . . / foo ' cause
# ' if " / . " in root . . . ' to filter out * all * modules otherwise
path = os . path . abspath ( path )
# check if the base directory is a package and get is name
if INIT in os . listdir ( path ) :
package_name = path . split ( os . ... |
def rename ( self , dn : str , new_rdn : str , new_base_dn : Optional [ str ] = None ) -> None :
"""rename a dn in the ldap database ; see ldap module . doesn ' t return a
result if transactions enabled .""" | _debug ( "rename" , self , dn , new_rdn , new_base_dn )
# split up the parameters
split_dn = tldap . dn . str2dn ( dn )
split_newrdn = tldap . dn . str2dn ( new_rdn )
assert ( len ( split_newrdn ) == 1 )
# make dn unqualified
rdn = tldap . dn . dn2str ( split_dn [ 0 : 1 ] )
# make newrdn fully qualified dn
tmplist = [ ... |
def _pick_unused_port_without_server ( ) : # Protected . pylint : disable = invalid - name
"""Pick an available network port without the help of a port server .
This code ensures that the port is available on both TCP and UDP .
This function is an implementation detail of PickUnusedPort ( ) , and
should not b... | # Try random ports first .
rng = random . Random ( )
for _ in range ( 10 ) :
port = int ( rng . randrange ( 15000 , 25000 ) )
if is_port_free ( port ) :
_random_ports . add ( port )
return port
# Next , try a few times to get an OS - assigned port .
# Ambrose discovered that on the 2.6 kernel , ... |
def findPolymorphisms ( self , strSeq , strict = False ) :
"""Compares strSeq with self . sequence .
If not ' strict ' , this function ignores the cases of matching heterozygocity ( ex : for a given position i , strSeq [ i ] = A and self . sequence [ i ] = ' A / G ' ) . If ' strict ' it returns all positions wher... | arr = self . encode ( strSeq ) [ 0 ]
res = [ ]
if not strict :
for i in range ( len ( arr ) + len ( self ) ) :
if i >= len ( arr ) or i > len ( self ) :
break
if arr [ i ] & self [ i ] == 0 :
res . append ( i )
else :
for i in range ( len ( arr ) + len ( self ) ) :
... |
def get_editor_nodes ( self , editor , node = None ) :
"""Returns the : class : ` umbra . components . factory . script _ editor . nodes . EditorNode ` class Nodes with given editor .
: param node : Node to start walking from .
: type node : AbstractNode or AbstractCompositeNode or Object
: param editor : Edi... | return [ editor_node for editor_node in self . list_editor_nodes ( node ) if editor_node . editor == editor ] |
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