signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def get_authentication_tokens ( self ) :
"""get _ auth _ url ( self )
Returns an authorization URL for a user to hit .""" | callback_url = self . callback_url or 'oob'
request_args = { }
if OAUTH_LIB_SUPPORTS_CALLBACK :
request_args [ 'callback_url' ] = callback_url
resp , content = self . client . request ( self . request_token_url , "GET" , ** request_args )
if resp [ 'status' ] != '200' :
raise AuthError ( "Seems something couldn... |
def endBy1 ( p , sep ) :
'''` endBy1 ( p , sep ) parses one or more occurrences of ` p ` , separated and
ended by ` sep ` . Returns a list of values returned by ` p ` .''' | return separated ( p , sep , 1 , maxt = float ( 'inf' ) , end = True ) |
def _raw_name_string ( bufr , strings_offset , str_offset , length ) :
"""Return the * length * bytes comprising the encoded string in * bufr * at
* str _ offset * in the strings area beginning at * strings _ offset * .""" | offset = strings_offset + str_offset
tmpl = '%ds' % length
return unpack_from ( tmpl , bufr , offset ) [ 0 ] |
def size ( self , table = None ) :
"""Return the size , in bytes , of the profile or * table * .
If * table * is ` None ` , this function returns the size of the
whole profile ( i . e . the sum of the table sizes ) . Otherwise , it
returns the size of * table * .
Note : if the file is gzipped , it returns t... | size = 0
if table is None :
for table in self . relations :
size += self . size ( table )
else :
try :
fn = _table_filename ( os . path . join ( self . root , table ) )
size += os . stat ( fn ) . st_size
except ItsdbError :
pass
return size |
def id ( self ) :
"""Computes the signature of the record , a SHA - 512 of significant values
: return : SHa - 512 Hex string""" | h = hashlib . new ( 'sha512' )
for value in ( self . machine . name , self . machine . os , self . user , self . application . name , self . application . path , self . event . report_type , self . event . type , self . event . time . isoformat ( ) ) :
h . update ( str ( value ) . encode ( 'utf-8' ) )
for parameter... |
def create_intent ( self , workspace_id , intent , description = None , examples = None , ** kwargs ) :
"""Create intent .
Create a new intent .
This operation is limited to 2000 requests per 30 minutes . For more information ,
see * * Rate limiting * * .
: param str workspace _ id : Unique identifier of th... | if workspace_id is None :
raise ValueError ( 'workspace_id must be provided' )
if intent is None :
raise ValueError ( 'intent must be provided' )
if examples is not None :
examples = [ self . _convert_model ( x , Example ) for x in examples ]
headers = { }
if 'headers' in kwargs :
headers . update ( kwa... |
def _type_insert ( self , handle , key , value ) :
'''Insert the value into the series .''' | if value != 0 :
if isinstance ( value , float ) :
handle . incrbyfloat ( key , value )
else :
handle . incr ( key , value ) |
def ask_list ( question : str , default : list = None ) -> list :
"""Asks for a comma seperated list of strings""" | default_q = " [default: {0}]: " . format ( "," . join ( default ) ) if default is not None else ""
answer = input ( "{0} [{1}]: " . format ( question , default_q ) )
if answer == "" :
return default
return [ ans . strip ( ) for ans in answer . split ( "," ) ] |
def _file_size ( file_path , uncompressed = False ) :
"""Return size of a single file , compressed or uncompressed""" | _ , ext = os . path . splitext ( file_path )
if uncompressed :
if ext in { ".gz" , ".gzip" } :
with gzip . GzipFile ( file_path , mode = "rb" ) as fp :
try :
fp . seek ( 0 , os . SEEK_END )
return fp . tell ( )
except ValueError : # on python2 , cannot... |
def _lstree ( files , dirs ) :
"""Make git ls - tree like output .""" | for f , sha1 in files :
yield "100644 blob {}\t{}\0" . format ( sha1 , f )
for d , sha1 in dirs :
yield "040000 tree {}\t{}\0" . format ( sha1 , d ) |
def to_team ( team ) :
"""Serializes team to id string
: param team : object to serialize
: return : string id""" | from sevenbridges . models . team import Team
if not team :
raise SbgError ( 'Team is required!' )
elif isinstance ( team , Team ) :
return team . id
elif isinstance ( team , six . string_types ) :
return team
else :
raise SbgError ( 'Invalid team parameter!' ) |
def wb_db004 ( self , value = None ) :
"""Corresponds to IDD Field ` wb _ db004 `
mean coincident wet - bulb temperature to
Dry - bulb temperature corresponding to 0.4 % annual cumulative frequency of occurrence ( warm conditions )
Args :
value ( float ) : value for IDD Field ` wb _ db004 `
Unit : C
if ... | if value is not None :
try :
value = float ( value )
except ValueError :
raise ValueError ( 'value {} need to be of type float ' 'for field `wb_db004`' . format ( value ) )
self . _wb_db004 = value |
def _cx_counters_psutil ( self , tags = None ) :
"""Collect metrics about interfaces counters using psutil""" | tags = [ ] if tags is None else tags
for iface , counters in iteritems ( psutil . net_io_counters ( pernic = True ) ) :
metrics = { 'bytes_rcvd' : counters . bytes_recv , 'bytes_sent' : counters . bytes_sent , 'packets_in.count' : counters . packets_recv , 'packets_in.error' : counters . errin , 'packets_out.count'... |
def load ( self ) :
"""Loads the prefixes that are available is the workdir
Returns :
None
Raises :
MalformedWorkdir : if the wordir is malformed""" | if self . loaded :
LOGGER . debug ( 'Already loaded' )
return
try :
basepath , dirs , _ = os . walk ( self . path ) . next ( )
except StopIteration :
raise MalformedWorkdir ( 'Empty dir %s' % self . path )
full_path = partial ( os . path . join , basepath )
found_current = False
for dirname in dirs :
... |
def update_checksum ( self , progress_callback = None , chunk_size = None , checksum_kwargs = None , ** kwargs ) :
"""Update checksum based on file .""" | self . checksum = self . storage ( ** kwargs ) . checksum ( progress_callback = progress_callback , chunk_size = chunk_size , ** ( checksum_kwargs or { } ) ) |
def _validate_name ( name ) :
'''Checks if the provided name fits Linode ' s labeling parameters .
. . versionadded : : 2015.5.6
name
The VM name to validate''' | name = six . text_type ( name )
name_length = len ( name )
regex = re . compile ( r'^[a-zA-Z0-9][A-Za-z0-9_-]*[a-zA-Z0-9]$' )
if name_length < 3 or name_length > 48 :
ret = False
elif not re . match ( regex , name ) :
ret = False
else :
ret = True
if ret is False :
log . warning ( 'A Linode label may on... |
def save_function_effect ( module ) :
"""Recursively save function effect for pythonic functions .""" | for intr in module . values ( ) :
if isinstance ( intr , dict ) : # Submodule case
save_function_effect ( intr )
else :
fe = FunctionEffects ( intr )
IntrinsicArgumentEffects [ intr ] = fe
if isinstance ( intr , intrinsic . Class ) :
save_function_effect ( intr . fiel... |
def handle_program_options ( ) :
"""Uses the built - in argparse module to handle command - line options for the
program .
: return : The gathered command - line options specified by the user
: rtype : argparse . ArgumentParser""" | parser = argparse . ArgumentParser ( description = "Convert Sanger-sequencing \
derived data files for use with the \
metagenomics analysis program QIIME, by \
extracting Sample ID information, adding\
... |
def kill_raylet ( self , check_alive = True ) :
"""Kill the raylet .
Args :
check _ alive ( bool ) : Raise an exception if the process was already
dead .""" | self . _kill_process_type ( ray_constants . PROCESS_TYPE_RAYLET , check_alive = check_alive ) |
def init_user ( ) :
"""Create and populate the ~ / . config / rapport directory tree if it ' s not existing .
Doesn ' t interfere with already existing directories or configuration files .""" | if not os . path . exists ( USER_CONFIG_DIR ) :
if rapport . config . get_int ( "rapport" , "verbosity" ) >= 1 :
print ( "Create user directory {0}" . format ( USER_CONFIG_DIR ) )
os . makedirs ( USER_CONFIG_DIR )
for subdir in [ "plugins" , "reports" , "templates/plugin" , "templates/email" , "template... |
def modify ( self , entry_id , ** kw ) :
'''Incremental version of : meth : ` update ` : instead of updating all
attributes of the entry to the specified values , this method only
updates the specified keywords . Returns True on success , or raises
an exception on failure .
Note : the default implementation... | entry = self . read ( entry_id )
for k , v in kw . items ( ) :
setattr ( entry , k , v )
self . update ( entry )
return True |
def symbol_scores ( self , symbol ) :
"""Find matches for symbol .
: param symbol : A . separated symbol . eg . ' os . path . basename '
: returns : A list of tuples of ( score , package , reference | None ) ,
ordered by score from highest to lowest .""" | scores = [ ]
path = [ ]
# sys . path sys path - > import sys
# os . path . basename os . path basename - > import os . path
# basename os . path basename - > from os . path import basename
# path . basename os . path basename - > from os import path
def fixup ( module , variable ) :
prefix = module . split ( '.' )
... |
def get_bounce_dump ( bounce_id , api_key = None , secure = None , test = None , ** request_args ) :
'''Get the raw email dump for a single bounce .
: param bounce _ id : The bounce ' s id . Get the id with : func : ` get _ bounces ` .
: param api _ key : Your Postmark API key . Required , if ` test ` is not ` ... | return _default_bounce_dump . get ( bounce_id , api_key = api_key , secure = secure , test = test , ** request_args ) |
def _add_jobs ( self ) :
"""Add configured jobs .""" | for name , params in self . jobs . items ( ) :
if params . active :
params . handler = params . handler ( params )
self . sched . add_cron_job ( params . handler . run , ** params . schedule ) |
def authorized_handler ( self , f ) :
"""Decorator for the route that is used as the callback for authorizing
with GitHub . This callback URL can be set in the settings for the app
or passed in during authorization .""" | @ wraps ( f )
def decorated ( * args , ** kwargs ) :
if 'code' in request . args :
data = self . _handle_response ( )
else :
data = self . _handle_invalid_response ( )
return f ( * ( ( data , ) + args ) , ** kwargs )
return decorated |
def shape ( self ) -> Tuple [ int , int ] :
"""Required shape of | NetCDFVariableAgg . array | .
For the default configuration , the first axis corresponds to the
number of devices , and the second one to the number of timesteps .
We show this for the 1 - dimensional input sequence | lland _ fluxes . NKor | :... | return self . sort_timeplaceentries ( len ( hydpy . pub . timegrids . init ) , len ( self . sequences ) ) |
def register_composite ( cls , name , handle = None , factory = None ) :
"""Maps a Postgresql type to this class . If the class ' s * table * attribute
is empty , and the class has an attribute * pg _ type * of tuple ( schema , type ) ,
it is calculated and set by querying Postgres . Register inherited / inheri... | class CustomCompositeCaster ( psycopg2 . extras . CompositeCaster ) :
def make ( self , values ) :
d_out ( "CustomCompositeCaster.make: cls={0} values={1}" . format ( repr ( cls ) , repr ( values ) ) )
return cls ( ** dict ( list ( zip ( self . attnames , values ) ) ) )
PG_TYPE_SQL = """SELECT array... |
def mutationhash ( strings , nedit ) :
"""produce a hash with each key a nedit distance substitution for a set of
strings . values of the hash is the set of strings the substitution could
have come from""" | maxlen = max ( [ len ( string ) for string in strings ] )
indexes = generate_idx ( maxlen , nedit )
muthash = defaultdict ( set )
for string in strings :
muthash [ string ] . update ( [ string ] )
for x in substitution_set ( string , indexes ) :
muthash [ x ] . update ( [ string ] )
return muthash |
def parse_quotes ( cmd , quotes = True , string = True ) :
"""parses quotes""" | import shlex
try :
args = shlex . split ( cmd ) if quotes else cmd . split ( )
except ValueError as exception :
logger . error ( exception )
return [ ]
return [ str ( arg ) for arg in args ] if string else args |
def OSLibraries ( self ) :
"""Microsoft Windows SDK Libraries""" | if self . vc_ver <= 10.0 :
arch_subdir = self . pi . target_dir ( hidex86 = True , x64 = True )
return [ os . path . join ( self . si . WindowsSdkDir , 'Lib%s' % arch_subdir ) ]
else :
arch_subdir = self . pi . target_dir ( x64 = True )
lib = os . path . join ( self . si . WindowsSdkDir , 'lib' )
li... |
def getWinner ( self , type = 'activation' ) :
"""Returns the winner of the type specified { ' activation ' or
' target ' } .""" | maxvalue = - 10000
maxpos = - 1
ttlvalue = 0
if type == 'activation' :
ttlvalue = Numeric . add . reduce ( self . activation )
maxpos = Numeric . argmax ( self . activation )
maxvalue = self . activation [ maxpos ]
elif type == 'target' : # note that backprop ( ) resets self . targetSet flag
if self . v... |
def join ( self ) :
"""Wait for root state to finish execution""" | self . _root_state . join ( )
# execution finished , close execution history log file ( if present )
if len ( self . _execution_histories ) > 0 :
if self . _execution_histories [ - 1 ] . execution_history_storage is not None :
set_read_and_writable_for_all = global_config . get_config_value ( "EXECUTION_LOG... |
def do_exists ( self , params ) :
"""\x1b [1mNAME \x1b [0m
exists - Gets the znode ' s stat information
\x1b [1mSYNOPSIS \x1b [0m
exists < path > [ watch ] [ pretty _ date ]
\x1b [1mOPTIONS \x1b [0m
* watch : set a ( data ) watch on the path ( default : false )
\x1b [1mEXAMPLES \x1b [0m
exists / foo
... | watcher = lambda evt : self . show_output ( str ( evt ) )
kwargs = { "watch" : watcher } if params . watch else { }
pretty = params . pretty_date
path = self . resolve_path ( params . path )
stat = self . _zk . exists ( path , ** kwargs )
if stat :
session = stat . ephemeralOwner if stat . ephemeralOwner else 0
... |
def between ( min_value , max_value ) :
'Numerical values limit' | message = N_ ( 'value should be between %(min)d and %(max)d' ) % dict ( min = min_value , max = max_value )
@ validator ( message )
def wrapper ( conv , value ) :
if value is None : # it meens that this value is not required
return True
if value < min_value :
return False
if value > max_valu... |
def _htpasswd ( username , password , ** kwargs ) :
'''Provide authentication via Apache - style htpasswd files''' | from passlib . apache import HtpasswdFile
pwfile = HtpasswdFile ( kwargs [ 'filename' ] )
# passlib below version 1.6 uses ' verify ' function instead of ' check _ password '
if salt . utils . versions . version_cmp ( kwargs [ 'passlib_version' ] , '1.6' ) < 0 :
return pwfile . verify ( username , password )
else :... |
def template ( * args , ** kwargs ) :
'''Get a rendered template as a string iterator .
You can use a name , a filename or a template string as first parameter .
Template rendering arguments can be passed as dictionaries
or directly ( as keyword arguments ) .''' | tpl = args [ 0 ] if args else None
template_adapter = kwargs . pop ( 'template_adapter' , SimpleTemplate )
if tpl not in TEMPLATES or DEBUG :
settings = kwargs . pop ( 'template_settings' , { } )
lookup = kwargs . pop ( 'template_lookup' , TEMPLATE_PATH )
if isinstance ( tpl , template_adapter ) :
T... |
def replace_if_changed ( localfile , jottapath , JFS ) :
"""Compare md5 hash to determine if contents have changed .
Upload a file from local disk and replace file on JottaCloud if the md5s differ ,
or continue uploading if the file is incompletely uploaded .
Returns the JottaFile object""" | jf = JFS . getObject ( jottapath )
lf_hash = getxattrhash ( localfile )
# try to read previous hash , stored in xattr
if lf_hash is None : # no valid hash found in xattr ,
with open ( localfile ) as lf :
lf_hash = calculate_md5 ( lf )
# ( re ) calculate it
if type ( jf ) == JFSIncompleteFile :
l... |
def keys ( self , history = None ) :
"""Get the set of I { all } property names .
@ param history : A history of nodes checked to prevent
circular hunting .
@ type history : [ L { Properties } , . . ]
@ return : A set of property names .
@ rtype : list""" | if history is None :
history = [ ]
history . append ( self )
keys = set ( )
keys . update ( self . definitions . keys ( ) )
for x in self . links :
if x in history :
continue
keys . update ( x . keys ( history ) )
history . remove ( self )
return keys |
def childgroup ( self , field ) :
"""Return a list of fields stored by row regarding the configured grid
: param field : The original field this widget is attached to""" | grid = getattr ( self , "grid" , None )
named_grid = getattr ( self , "named_grid" , None )
if grid is not None :
childgroup = self . _childgroup ( field . children , grid )
elif named_grid is not None :
childgroup = self . _childgroup_by_name ( field . children , named_grid )
else :
raise AttributeError ( ... |
def quit_banner ( self ) -> None :
"""Print a banner for running the system""" | print ( "=" * 80 )
print ( "Done." )
print ( dtm . datetime . now ( ) . strftime ( "%Y/%m/%d - %H:%M:%S" ) )
print ( "=" * 80 ) |
from typing import List
from collections import Counter
def count_element_frequency ( elements : List [ int ] ) -> dict :
"""Calculate frequency of each element in the given list .
Examples :
> > > count _ element _ frequency ( [ 10 , 10 , 10 , 10 , 20 , 20 , 20 , 20 , 40 , 40 , 50 , 50 , 30 ] )
{10 : 4 , 20 ... | return Counter ( elements ) |
def to_plain_text ( str ) :
'''Return a plain - text version of a given string
This is a dumb approach that tags and then removing entity markers
but this is fine for the content from biocyc where entities are & beta ; etc .
Stripping in this way turns these into plaintext ' beta ' which is preferable
to un... | str = strip_tags_re . sub ( '' , str )
str = strip_entities_re . sub ( '' , str )
return str |
def connect_delete_namespaced_pod_proxy ( self , name , namespace , ** kwargs ) : # noqa : E501
"""connect _ delete _ namespaced _ pod _ proxy # noqa : E501
connect DELETE requests to proxy of Pod # noqa : E501
This method makes a synchronous HTTP request by default . To make an
asynchronous HTTP request , pl... | kwargs [ '_return_http_data_only' ] = True
if kwargs . get ( 'async_req' ) :
return self . connect_delete_namespaced_pod_proxy_with_http_info ( name , namespace , ** kwargs )
# noqa : E501
else :
( data ) = self . connect_delete_namespaced_pod_proxy_with_http_info ( name , namespace , ** kwargs )
# noqa... |
def _keyword_expander ( word , language , lemmatized = False , threshold = 0.70 ) :
"""Find similar terms in Word2Vec models . Accepts string and returns a
list of terms of n similarity .
: rtype : list""" | try :
from cltk . vector . word2vec import get_sims
except ImportError as imp_err :
print ( imp_err )
raise
similar_vectors = get_sims ( word , language , lemmatized = lemmatized , threshold = threshold )
return similar_vectors |
def get_catalog_metadata ( catalog , exclude_meta_fields = None ) :
"""Devuelve sólo la metadata de nivel catálogo .""" | exclude_meta_fields = exclude_meta_fields or [ ]
catalog_dict_copy = catalog . copy ( )
del catalog_dict_copy [ "dataset" ]
for excluded_meta_field in exclude_meta_fields :
catalog_dict_copy . pop ( excluded_meta_field , None )
return catalog_dict_copy |
def setdefault ( self , sid , value , dtype = F64 ) :
"""Works like ` dict . setdefault ` : if the ` sid ` key is missing , it fills
it with an array and returns the associate ProbabilityCurve
: param sid : site ID
: param value : value used to fill the returned ProbabilityCurve
: param dtype : dtype used i... | try :
return self [ sid ]
except KeyError :
array = numpy . empty ( ( self . shape_y , self . shape_z ) , dtype )
array . fill ( value )
pc = ProbabilityCurve ( array )
self [ sid ] = pc
return pc |
def compiled_init_func ( self ) :
"""Returns compiled init function""" | def get_column_assignment ( column_name ) :
return ALCHEMY_TEMPLATES . col_assignment . safe_substitute ( col_name = column_name )
def get_compiled_args ( arg_name ) :
return ALCHEMY_TEMPLATES . func_arg . safe_substitute ( arg_name = arg_name )
join_string = "\n" + self . tab + self . tab
column_assignments = ... |
def process_entries ( self , omimids , transform , included_fields = None , graph = None , limit = None , globaltt = None ) :
"""Given a list of omim ids ,
this will use the omim API to fetch the entries , according to the
` ` ` included _ fields ` ` ` passed as a parameter .
If a transformation function is s... | omimparams = { }
# add the included _ fields as parameters
if included_fields is not None and included_fields :
omimparams [ 'include' ] = ',' . join ( included_fields )
processed_entries = list ( )
# scrub any omim prefixes from the omimids before processing
# cleanomimids = set ( )
# for omimid in omimids :
# scr... |
def weighted_random ( sample , embedding ) :
"""Determines the sample values by weighed random choice .
Args :
sample ( dict ) : A sample of the form { v : val , . . . } where v is
a variable in the target graph and val is the associated value as
determined by a binary quadratic model sampler .
embedding ... | unembeded = { }
for v , chain in iteritems ( embedding ) :
vals = [ sample [ u ] for u in chain ]
# pick a random element uniformly from all vals , this weights them by
# the proportion of each
unembeded [ v ] = random . choice ( vals )
yield unembeded |
def insertFile ( self , qInserts = False ) :
"""API to insert a list of file into DBS in DBS . Up to 10 files can be inserted in one request .
: param qInserts : True means that inserts will be queued instead of done immediately . INSERT QUEUE Manager will perform the inserts , within few minutes .
: type qInse... | if qInserts in ( False , 'False' ) :
qInserts = False
try :
body = request . body . read ( )
indata = cjson . decode ( body ) [ "files" ]
if not isinstance ( indata , ( list , dict ) ) :
dbsExceptionHandler ( "dbsException-invalid-input" , "Invalid Input DataType" , self . logger . exception , "... |
def parse_cstring ( stream , offset ) :
"""parse _ cstring will parse a null - terminated string in a bytestream .
The string will be decoded with UTF - 8 decoder , of course since we are
doing this byte - a - byte , it won ' t really work for all Unicode strings .
TODO : add proper Unicode support""" | stream . seek ( offset )
string = ""
while True :
char = struct . unpack ( 'c' , stream . read ( 1 ) ) [ 0 ]
if char == b'\x00' :
return string
else :
string += char . decode ( ) |
def earth_orientation ( date ) :
"""Earth orientation as a rotating matrix""" | x_p , y_p , s_prime = np . deg2rad ( _earth_orientation ( date ) )
return rot3 ( - s_prime ) @ rot2 ( x_p ) @ rot1 ( y_p ) |
def validate ( self , body , params = None ) :
""": arg body : The job config""" | if body in SKIP_IN_PATH :
raise ValueError ( "Empty value passed for a required argument 'body'." )
return self . transport . perform_request ( "POST" , "/_ml/anomaly_detectors/_validate" , params = params , body = body ) |
def _process_info ( raw_info : VideoInfo ) -> VideoInfo :
"""Process raw information about the video ( parse date , etc . ) .""" | raw_date = raw_info . date
date = datetime . strptime ( raw_date , '%Y-%m-%d %H:%M' )
# 2018-04-05 17:00
video_info = raw_info . _replace ( date = date )
return video_info |
def unpack_nested_exception ( error ) :
"""If exception are stacked , return the first one
: param error : A python exception with possible exception embeded within
: return : A python exception with no exception embeded within""" | i = 0
while True :
if error . args [ i : ] :
if isinstance ( error . args [ i ] , Exception ) :
error = error . args [ i ]
i = 0
else :
i += 1
else :
break
return error |
def set_result ( self , msg , valid = True , overwrite = False ) :
"""Set result string and validity .""" | if self . has_result and not overwrite :
log . warn ( LOG_CHECK , "Double result %r (previous %r) for %s" , msg , self . result , self )
else :
self . has_result = True
if not isinstance ( msg , unicode ) :
log . warn ( LOG_CHECK , "Non-unicode result for %s: %r" , self , msg )
elif not msg :
log . warn... |
def load_dataset ( date ) :
"""Load the dataset for a single date
Parameters
date : the date ( string ) for which to load the data & dataset
Returns
ds : the dataset object""" | LAB_DIR = "/home/annaho/TheCannon/data/lamost"
WL_DIR = "/home/annaho/TheCannon/code/lamost/mass_age/cn"
SPEC_DIR = "/home/annaho/TheCannon/code/apogee_lamost/xcalib_4labels/output"
wl = np . load ( WL_DIR + "/wl_cols.npz" ) [ 'arr_0' ] [ 0 : 3626 ]
# no cols
ds = dataset . Dataset ( wl , [ ] , [ ] , [ ] , [ ] , [ ] , ... |
def power_modulo_p ( n : int , p : int ) -> int :
"""Return 2 ^ n modulo p .
This function computes the value of 2 ^ n modulo p .
Args :
n ( int ) : The exponent to which 2 should be raised .
p ( int ) : The modulus against which the resulting value should be determined .
Returns :
int : The result of t... | if p == 0 :
raise ValueError ( "Modulo by zero is undefined." )
return pow ( 2 , n , p ) |
def set_field_value ( self , field_name , value ) :
"""Set value of response field named ` field _ name ` .
If response contains single item , its field is set .
If response contains multiple items , all the items in response
are edited .
To edit response meta ( e . g . ' count ' ) edit response directly at... | if self . response is None :
return
if 'data' in self . response :
items = self . response [ 'data' ]
else :
items = [ self . response ]
for item in items :
item [ field_name ] = value |
def modify_symbol ( sym : ast . Symbol , scope : ast . InstanceClass ) -> None :
"""Apply a modification to a symbol if the scope matches ( or is None )
: param sym : symbol to apply modifications for
: param scope : scope of modification""" | # We assume that we do not screw up the order of applying modifications
# when " moving up " with the scope .
apply_args = [ x for x in sym . class_modification . arguments if x . scope is None or x . scope . full_reference ( ) . to_tuple ( ) == scope . full_reference ( ) . to_tuple ( ) ]
skip_args = [ x for x in sym .... |
def set_selected_pair ( self , component , local_foundation , remote_foundation ) :
"""Force the selected candidate pair .
If the remote party does not support ICE , you should using this
instead of calling : meth : ` connect ` .""" | # find local candidate
protocol = None
for p in self . _protocols :
if ( p . local_candidate . component == component and p . local_candidate . foundation == local_foundation ) :
protocol = p
break
# find remote candidate
remote_candidate = None
for c in self . _remote_candidates :
if c . compon... |
async def async_get_api_key ( session , host , port , username = None , password = None , ** kwargs ) :
"""Get a new API key for devicetype .""" | url = 'http://{host}:{port}/api' . format ( host = host , port = str ( port ) )
auth = None
if username and password :
auth = aiohttp . BasicAuth ( username , password = password )
data = b'{"devicetype": "pydeconz"}'
response = await async_request ( session . post , url , auth = auth , data = data )
api_key = resp... |
def _unload ( self , ) :
"""Unloads the plugin
: raises : errors . PluginUninitError""" | super ( JB_MayaPlugin , self ) . _unload ( )
try :
if not jukeboxmaya . STANDALONE_INITIALIZED :
self . uninit_ui ( )
except Exception :
log . exception ( "Unload Ui failed!" ) |
def send ( self , soapenv ) :
"""Send SOAP message .
Depending on how the ` ` nosend ` ` & ` ` retxml ` ` options are set , may do
one of the following :
* Return a constructed web service operation request without sending
it to the web service .
* Invoke the web service operation and return its SOAP repl... | location = self . __location ( )
log . debug ( "sending to (%s)\nmessage:\n%s" , location , soapenv )
plugins = PluginContainer ( self . options . plugins )
plugins . message . marshalled ( envelope = soapenv . root ( ) )
if self . options . prettyxml :
soapenv = soapenv . str ( )
else :
soapenv = soapenv . pla... |
def delete ( self , constraint ) :
"""Delete a record from the repository""" | results = self . _get_repo_filter ( Service . objects ) . extra ( where = [ constraint [ 'where' ] ] , params = constraint [ 'values' ] ) . all ( )
deleted = len ( results )
results . delete ( )
return deleted |
def _invite ( self , name , method , email , uuid , event , password = "" ) :
"""Actually invite a given user""" | props = { 'uuid' : std_uuid ( ) , 'status' : 'Open' , 'name' : name , 'method' : method , 'email' : email , 'password' : password , 'timestamp' : std_now ( ) }
enrollment = objectmodels [ 'enrollment' ] ( props )
enrollment . save ( )
self . log ( 'Enrollment stored' , lvl = debug )
self . _send_invitation ( enrollment... |
def resource_string ( package_or_requirement , resource_name ) :
"""Similar to pkg _ resources . resource _ string but if the resource it not found via pkg _ resources
it also looks in a predefined list of paths in order to find the resource
: param package _ or _ requirement : the module in which the resource ... | with open ( resource_filename ( package_or_requirement , resource_name ) , 'r' ) as resource_file :
return resource_file . read ( ) |
def find_related ( self , fullname ) :
"""Return a list of non - stdlib modules that are imported directly or
indirectly by ` fullname ` , plus their parents .
This method is like : py : meth : ` find _ related _ imports ` , but also
recursively searches any modules which are imported by ` fullname ` .
: pa... | stack = [ fullname ]
found = set ( )
while stack :
name = stack . pop ( 0 )
names = self . find_related_imports ( name )
stack . extend ( set ( names ) . difference ( set ( found ) . union ( stack ) ) )
found . update ( names )
found . discard ( fullname )
return sorted ( found ) |
def scatterAlign ( seq1 , seq2 , window = 7 ) :
"""Visually align two sequences .""" | d1 = defaultdict ( list )
d2 = defaultdict ( list )
for ( seq , section_dict ) in [ ( seq1 , d1 ) , ( seq2 , d2 ) ] :
for i in range ( len ( seq ) - window ) :
section = seq [ i : i + window ]
section_dict [ section ] . append ( i )
matches = set ( d1 ) . intersection ( d2 )
print ( '%i unique match... |
def local_asn ( self , ** kwargs ) :
"""Set BGP local ASN .
Args :
local _ as ( str ) : Local ASN of NOS deice .
vrf ( str ) : The VRF for this BGP process .
rbridge _ id ( str ) : The rbridge ID of the device on which BGP will be
configured in a VCS fabric .
get ( bool ) : Get config instead of editing... | vrf = kwargs . pop ( 'vrf' , 'default' )
is_get_config = kwargs . pop ( 'get' , False )
if not is_get_config :
local_as = kwargs . pop ( 'local_as' )
else :
local_as = ''
rbridge_id = kwargs . pop ( 'rbridge_id' , '1' )
callback = kwargs . pop ( 'callback' , self . _callback )
bgp_args = dict ( vrf_name = vrf ,... |
def _add_node ( self , idx , unique_idx , frac_coords ) :
"""Add information about a node describing a critical point .
: param idx : unique index
: param unique _ idx : index of unique CriticalPoint ,
used to look up more information of point ( field etc . )
: param frac _ coord : fractional co - ordinates... | self . nodes [ idx ] = { 'unique_idx' : unique_idx , 'frac_coords' : frac_coords } |
def extend_partial ( self , times , obs_times , obs_losses , config = None ) :
"""extends a partially observed curve
Parameters :
times : numpy array
times where to predict the loss
obs _ times : numpy array
times where the curve has already been observed
obs _ losses : numpy array
corresponding obser... | return self . predict_unseen ( times , config ) |
def indent ( self , space = 4 ) :
'''Return an indented Newick string , just like ` ` nw _ indent ` ` in Newick Utilities
Args :
` ` space ` ` ( ` ` int ` ` ) : The number of spaces a tab should equal
Returns :
` ` str ` ` : An indented Newick string''' | if not isinstance ( space , int ) :
raise TypeError ( "space must be an int" )
if space < 0 :
raise ValueError ( "space must be a non-negative integer" )
space = ' ' * space ;
o = [ ] ;
l = 0
for c in self . newick ( ) :
if c == '(' :
o . append ( '(\n' ) ;
l += 1 ;
o . append ( spac... |
def list_plugins ( ) :
'''List all the munin plugins
CLI Example :
. . code - block : : bash
salt ' * ' munin . list _ plugins''' | pluginlist = os . listdir ( PLUGINDIR )
ret = [ ]
for plugin in pluginlist : # Check if execute bit
statf = os . path . join ( PLUGINDIR , plugin )
try :
executebit = stat . S_IXUSR & os . stat ( statf ) [ stat . ST_MODE ]
except OSError :
pass
if executebit :
ret . append ( plug... |
def map_permissions_check ( view_func ) :
"""Used for URLs dealing with the map .""" | @ wraps ( view_func )
def wrapper ( request , * args , ** kwargs ) :
map_inst = get_object_or_404 ( Map , pk = kwargs [ 'map_id' ] )
user = request . user
kwargs [ 'map_inst' ] = map_inst
# Avoid rerequesting the map in the view
if map_inst . edit_status >= map_inst . EDITORS :
can_edit = ma... |
def get_all_chunks_for_term ( self , termid ) :
"""Returns all the chunks in which the term is contained
@ type termid : string
@ param termid : the term identifier
@ rtype : list
@ return : list of chunks""" | terminal_id = self . terminal_for_term . get ( termid )
paths = self . paths_for_terminal [ terminal_id ]
for path in paths :
for node in path :
this_type = self . label_for_nonter [ node ]
subsumed = self . terms_subsumed_by_nonter . get ( node )
if subsumed is not None :
yield ... |
def _batch_load ( project , workspace , headerline , entity_data , chunk_size = 500 ) :
"""Submit a large number of entity updates in batches of chunk _ size""" | if fcconfig . verbosity :
print ( "Batching " + str ( len ( entity_data ) ) + " updates to Firecloud..." )
# Parse the entity type from the first cell , e . g . " entity : sample _ id "
# First check that the header is valid
if not _valid_headerline ( headerline ) :
eprint ( "Invalid loadfile header:\n" + heade... |
def filter_tasks ( self , task_names , keep_dependencies = False ) :
"""If filter is applied only tasks with given name and its dependencies ( if keep _ keep _ dependencies = True ) are kept in the list of tasks .""" | new_tasks = { }
for task_name in task_names :
task = self . get_task ( task_name )
if task not in new_tasks :
new_tasks [ task . name ] = task
if keep_dependencies :
for dependency in task . ordered_dependencies ( ) :
if dependency not in new_tasks :
new_tasks [ d... |
def extract_subject_info_extension ( cert_obj ) :
"""Extract DataONE SubjectInfo XML doc from certificate .
Certificates issued by DataONE may include an embedded XML doc containing
additional information about the subject specified in the certificate DN . If
present , the doc is stored as an extension with a... | try :
subject_info_der = cert_obj . extensions . get_extension_for_oid ( cryptography . x509 . oid . ObjectIdentifier ( DATAONE_SUBJECT_INFO_OID ) ) . value . value
return str ( pyasn1 . codec . der . decoder . decode ( subject_info_der ) [ 0 ] )
except Exception as e :
logging . debug ( 'SubjectInfo not ex... |
def validate_user_threaded_json ( pjson ) :
"""Takes a parsed JSON dict representing a set of tests in the user - threaded
format and validates it .""" | tests = pjson [ "tests" ]
# Verify that ' tests ' is a two dimensional list
is_2d_list = lambda ls : len ( ls ) == len ( filter ( lambda l : type ( l ) is list , ls ) )
if type ( tests ) is not list or not is_2d_list ( tests ) :
raise ParseError ( "'tests' should be a two-dimensional list of strings when '--user-de... |
def urlfetch_async ( self , url , method = 'GET' , headers = None , payload = None , deadline = None , callback = None , follow_redirects = False ) :
"""Make an async urlfetch ( ) call .
This is an async wrapper around urlfetch ( ) . It adds an authentication
header .
Args :
url : the url to fetch .
metho... | headers = { } if headers is None else dict ( headers )
headers . update ( self . user_agent )
try :
self . token = yield self . get_token_async ( )
except app_identity . InternalError , e :
if os . environ . get ( 'DATACENTER' , '' ) . endswith ( 'sandman' ) :
self . token = None
logging . warni... |
def _get_json ( endpoint , params , referer = 'scores' ) :
"""Internal method to streamline our requests / json getting
Args :
endpoint ( str ) : endpoint to be called from the API
params ( dict ) : parameters to be passed to the API
Raises :
HTTPError : if requests hits a status code ! = 200
Returns : ... | h = dict ( HEADERS )
h [ 'referer' ] = 'http://stats.nba.com/{ref}/' . format ( ref = referer )
_get = get ( BASE_URL . format ( endpoint = endpoint ) , params = params , headers = h )
# print _ get . url
_get . raise_for_status ( )
return _get . json ( ) |
def parse_cache_url ( url ) :
"""Parses a cache URL .""" | config = { }
url = urlparse . urlparse ( url )
# Update with environment configuration .
config [ 'BACKEND' ] = CACHE_SCHEMES [ url . scheme ]
if url . scheme in ( 'file' , 'uwsgi' ) :
config [ 'LOCATION' ] = url . path
return config
elif url . scheme in ( 'redis' , 'hiredis' ) :
if url . netloc == 'unix' :... |
def annotate ( g , fname , tables , feature_strand = False , in_memory = False , header = None , out = sys . stdout , _chrom = None , parallel = False ) :
"""annotate bed file in fname with tables .
distances are integers for distance . and intron / exon / utr5 etc for gene - pred
tables . if the annotation fea... | close = False
if isinstance ( out , basestring ) :
out = nopen ( out , "w" )
close = True
if parallel :
import multiprocessing
import signal
p = multiprocessing . Pool ( initializer = lambda : signal . signal ( signal . SIGINT , signal . SIG_IGN ) )
chroms = _split_chroms ( fname )
def write... |
def new_dataset ( data , identifier = None ) :
"""Initialize a new RT - DC dataset
Parameters
data :
can be one of the following :
- dict
- . tdms file
- . rtdc file
- subclass of ` RTDCBase `
( will create a hierarchy child )
identifier : str
A unique identifier for this dataset . If set to ` N... | if isinstance ( data , dict ) :
return fmt_dict . RTDC_Dict ( data , identifier = identifier )
elif isinstance ( data , ( str_types ) ) or isinstance ( data , pathlib . Path ) :
return load_file ( data , identifier = identifier )
elif isinstance ( data , RTDCBase ) :
return fmt_hierarchy . RTDC_Hierarchy ( ... |
def main ( argv = None ) :
'''Command line options .''' | program_name = os . path . basename ( sys . argv [ 0 ] )
program_version = version
program_build_date = "%s" % __updated__
program_version_string = '%%prog %s (%s)' % ( program_version , program_build_date )
# program _ usage = ' ' ' usage : spam two eggs ' ' ' # optional - will be autogenerated by optparse
program_lon... |
def _norm ( self , x ) :
"""Return the norm of ` ` x ` ` .
This method is intended to be private . Public callers should
resort to ` norm ` which is type - checked .""" | return float ( np . sqrt ( self . inner ( x , x ) . real ) ) |
def keys ( self ) :
"""Return ids of all indexed documents .""" | result = [ ]
if self . fresh_index is not None :
result += self . fresh_index . keys ( )
if self . opt_index is not None :
result += self . opt_index . keys ( )
return result |
def get_directory_nodes ( self , path ) :
"""Returns the : class : ` umbra . components . factory . script _ editor . nodes . DirectoryNode ` class Nodes with given path .
: param path : Directory path .
: type path : unicode
: return : DirectoryNode nodes .
: rtype : list""" | return [ directory_node for directory_node in self . list_directory_nodes ( ) if directory_node . path == path ] |
def wrap ( self , message ) :
"""[ MS - NLMP ] v28.0 2016-07-14
3.4.6 GSS _ WrapEx ( )
Emulates the GSS _ Wrap ( ) implementation to sign and seal messages if the correct flags
are set .
@ param message : The message data that will be wrapped
@ return message : The message that has been sealed if flags ar... | if self . negotiate_flags & NegotiateFlags . NTLMSSP_NEGOTIATE_SEAL :
encrypted_message = self . _seal_message ( message )
signature = self . _get_signature ( message )
message = encrypted_message
elif self . negotiate_flags & NegotiateFlags . NTLMSSP_NEGOTIATE_SIGN :
signature = self . _get_signature (... |
def get_email_logs ( self ) :
'''Returns a string representation of logs .
Only displays errors and warnings in the email logs
to avoid being verbose''' | message = ""
for log in self . record :
if log [ "log_type" ] in [ ERROR , WARNING ] :
message += self . format_message ( ** log )
return message |
def packages ( self ) :
"""Show all packages""" | pattern = re . compile ( r'package:(/[^=]+\.apk)=([^\s]+)' )
packages = [ ]
for line in self . shell ( 'pm' , 'list' , 'packages' , '-f' ) . splitlines ( ) :
m = pattern . match ( line )
if not m :
continue
path , name = m . group ( 1 ) , m . group ( 2 )
packages . append ( self . Package ( name... |
def _loglr ( self ) :
r"""Computes the log likelihood ratio ,
. . math : :
\ log \ mathcal { L } ( \ Theta ) =
I _ 0 \ left ( \ left | \ sum _ i O ( h ^ 0 _ i , d _ i ) \ right | \ right ) -
\ frac { 1 } { 2 } \ left < h ^ 0 _ i , h ^ 0 _ i \ right > ,
at the current point in parameter space : math : ` \ ... | params = self . current_params
try :
wfs = self . _waveform_generator . generate ( ** params )
except NoWaveformError :
return self . _nowaveform_loglr ( )
hh = 0.
hd = 0j
for det , h in wfs . items ( ) : # the kmax of the waveforms may be different than internal kmax
kmax = min ( len ( h ) , self . _kmax )... |
def select ( self , table , fields = [ '*' ] , where = None , orderby = None , limit = None , offset = None ) :
"""Query and return list of records .
> > > import getpass
> > > s = DB ( dbname = ' test ' , user = getpass . getuser ( ) , host = ' localhost ' ,
. . . password = ' ' )
> > > s . execute ( ' dro... | ( sql , values ) = sqlselect ( table , fields , where , orderby , limit , offset )
self . execute ( sql , values )
return self . fetchall ( ) |
def cleanup ( self , cluster ) :
"""Deletes the inventory file used last recently used .
: param cluster : cluster to clear up inventory file for
: type cluster : : py : class : ` elasticluster . cluster . Cluster `""" | if self . _storage_path and os . path . exists ( self . _storage_path ) :
fname = '%s.%s' % ( AnsibleSetupProvider . inventory_file_ending , cluster . name )
inventory_path = os . path . join ( self . _storage_path , fname )
if os . path . exists ( inventory_path ) :
try :
os . unlink ( ... |
def select ( self , axis : AxisIdentifier , index , force_copy : bool = False ) -> HistogramBase :
"""Select in an axis .
Parameters
axis : int or str
Axis , in which we select .
index : int or slice
Index of bin ( as in numpy ) .
force _ copy : bool
If True , identity slice force a copy to be made ."... | if index == slice ( None ) and not force_copy :
return self
axis_id = self . _get_axis ( axis )
array_index = [ slice ( None , None , None ) for i in range ( self . ndim ) ]
array_index [ axis_id ] = index
frequencies = self . _frequencies [ tuple ( array_index ) ] . copy ( )
errors2 = self . _errors2 [ tuple ( arr... |
def build ( self , builder ) :
"""Build XML by appending to builder""" | params = dict ( OID = self . oid , Name = self . name )
if self . field_number is not None :
params [ "FieldNumber" ] = str ( self . field_number )
builder . start ( "mdsol:LabelDef" , params )
for translation in self . translations :
translation . build ( builder )
for view_restriction in self . view_restricti... |
def type_check ( func_handle ) :
"""Ensure arguments have the type specified in the annotation signature .
Example : :
def foo ( a , b : str , c : int = 0 , d : ( int , list ) = None ) :
pass
This function accepts an arbitrary parameter for ` ` a ` ` , a string
for ` ` b ` ` , an integer for ` ` c ` ` whi... | def checkType ( var_name , var_val , annot ) : # Retrieve the annotation for this variable and determine
# if the type of that variable matches with the annotation .
# This annotation is stored in the dictionary ` ` annot ` `
# but contains only variables for such an annotation exists ,
# hence the if / else branch .
... |
def get_min_max_bounds ( self ) :
"""Return a dict of min - and max - values for the given column .
This is required to estimate the bounds of images .""" | bound = Bound ( 999999.0 , 0.0 )
for bp in Breakpoint :
bound . extend ( self . get_bound ( bp ) )
return { 'min' : bound . min , 'max' : bound . max } |
def _exception_gather_guard ( self , fn ) :
"""A higher order function to trap UserExceptions and then log them .
This is to present nicer output to the user when failures are
occuring in another thread of execution that may not end up at
the catch - all try / except in main ( ) .""" | @ functools . wraps ( fn )
def wrapper ( * args , ** kwargs ) :
try :
return fn ( * args , ** kwargs )
except UserException as e :
self . exceptions . append ( e )
return wrapper |
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