signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def url_param ( param , default = None ) :
"""Read a url or post parameter and use it in your SQL Lab query
When in SQL Lab , it ' s possible to add arbitrary URL " query string "
parameters , and use those in your SQL code . For instance you can
alter your url and add ` ? foo = bar ` , as in
` { domain } /... | if request . args . get ( param ) :
return request . args . get ( param , default )
# Supporting POST as well as get
if request . form . get ( 'form_data' ) :
form_data = json . loads ( request . form . get ( 'form_data' ) )
url_params = form_data . get ( 'url_params' ) or { }
return url_params . get ( ... |
def tobool ( obj , default = False ) :
'''Returns a bool representation of ` obj ` : if ` obj ` is not a string ,
it is returned cast to a boolean by calling ` bool ( ) ` . Otherwise , it
is checked for " truthy " or " falsy " values , and that is returned . If
it is not truthy or falsy , ` default ` is retur... | if isinstance ( obj , bool ) :
return obj
if not isstr ( obj ) :
return bool ( obj )
lobj = obj . lower ( )
if lobj in truthy :
return True
if lobj in falsy :
return False
if default is ValueError :
raise ValueError ( 'invalid literal for tobool(): %r' % ( obj , ) )
return default |
def get_conf_d_files ( path ) :
"""Return alphabetical ordered : class : ` list ` of the * . conf * files
placed in the path . * path * is a directory path .
> > > get _ conf _ d _ files ( ' conf / conf . d / ' )
[ ' conf / conf . d / 10 - base . conf ' , ' conf / conf . d / 99 - dev . conf ' ]""" | if not os . path . isdir ( path ) :
raise ValueError ( "'%s' is not a directory" % path )
files_mask = os . path . join ( path , "*.conf" )
return [ f for f in sorted ( glob . glob ( files_mask ) ) if os . path . isfile ( f ) ] |
def set_icc_profile ( self , profile = None , name = 'ICC Profile' ) :
"""Add ICC Profile .
Prefered way is tuple ( ` profile _ name ` , ` profile _ bytes ` ) , but only
bytes with name as separate argument is also supported .""" | if isinstance ( profile , ( basestring , bytes ) ) :
icc_profile = [ name , profile ]
# TODO : more check
else :
icc_profile = profile
if not icc_profile [ 0 ] :
raise Error ( "ICC profile should have a name" )
elif not isinstance ( icc_profile [ 0 ] , bytes ) :
icc_profile [ 0 ] = strtobytes ( icc_prof... |
def from_array ( array ) :
"""Deserialize a new MediaGroupMessage from a given dictionary .
: return : new MediaGroupMessage instance .
: rtype : MediaGroupMessage""" | if array is None or not array :
return None
# end if
assert_type_or_raise ( array , dict , parameter_name = "array" )
from pytgbot . api_types . sendable . input_media import InputMediaPhoto
from pytgbot . api_types . sendable . input_media import InputMediaVideo
data = { }
if isinstance ( array . get ( 'media' ) ,... |
def f1 ( y , z ) :
"""F1 score : ` 2 * ( p * r ) / ( p + r ) ` , where p = precision and r = recall .""" | _recall = recall ( y , z )
_prec = precision ( y , z )
return 2 * ( _prec * _recall ) / ( _prec + _recall ) |
def prepare_axes ( wave , flux , fig = None , ax_lower = ( 0.1 , 0.1 ) , ax_dim = ( 0.85 , 0.65 ) ) :
"""Create fig and axes if needed and layout axes in fig .""" | # Axes location in figure .
if not fig :
fig = plt . figure ( )
ax = fig . add_axes ( [ ax_lower [ 0 ] , ax_lower [ 1 ] , ax_dim [ 0 ] , ax_dim [ 1 ] ] )
ax . plot ( wave , flux )
return fig , ax |
def hybrid_forward ( self , F , scores , offset ) :
"""Get the single lowest element per sentence from a ` scores ` matrix . Expects that
beam size is 1 , for greedy decoding .
: param scores : Vocabulary scores for the next beam step . ( batch _ size * beam _ size , target _ vocabulary _ size )
: param offse... | best_word_indices = F . cast ( F . argmin ( scores , axis = 1 ) , dtype = 'int32' )
values = F . pick ( scores , best_word_indices , axis = 1 )
values = F . reshape ( values , shape = ( - 1 , 1 ) )
# for top1 , the best hyp indices are equal to the plain offset
best_hyp_indices = offset
return best_hyp_indices , best_w... |
def find_mappable ( * axes ) :
"""Find the most recently added mappable layer in the given axes
Parameters
* axes : ` ~ matplotlib . axes . Axes `
one or more axes to search for a mappable""" | for ax in axes :
for aset in ( 'collections' , 'images' ) :
try :
return getattr ( ax , aset ) [ - 1 ]
except ( AttributeError , IndexError ) :
continue
raise ValueError ( "Cannot determine mappable layer on any axes " "for this colorbar" ) |
def create_network_interface ( SubnetId = None , Description = None , PrivateIpAddress = None , Groups = None , PrivateIpAddresses = None , SecondaryPrivateIpAddressCount = None , Ipv6Addresses = None , Ipv6AddressCount = None , DryRun = None ) :
"""Creates a network interface in the specified subnet .
For more i... | pass |
def generate_id ( cls , prefix = "pelix-" ) :
"""Generates a random MQTT client ID
: param prefix : Client ID prefix ( truncated to 8 chars )
: return : A client ID of 22 or 23 characters""" | if not prefix : # Normalize string
prefix = ""
else : # Truncate long prefixes
prefix = prefix [ : 8 ]
# Prepare the missing part
nb_bytes = ( 23 - len ( prefix ) ) // 2
random_bytes = os . urandom ( nb_bytes )
if sys . version_info [ 0 ] >= 3 :
random_ints = [ char for char in random_bytes ]
else :
ran... |
def _MaybePurgeOrphanedData ( self , event ) :
"""Maybe purge orphaned data due to a TensorFlow crash .
When TensorFlow crashes at step T + O and restarts at step T , any events
written after step T are now " orphaned " and will be at best misleading if
they are included in TensorBoard .
This logic attempts... | if not self . purge_orphaned_data :
return
# # Check if the event happened after a crash , and purge expired tags .
if self . file_version and self . file_version >= 2 : # # If the file _ version is recent enough , use the SessionLog enum
# # to check for restarts .
self . _CheckForRestartAndMaybePurge ( event ... |
def resize ( self , width = None ) :
"""Resizes image to fit inside terminal
Called by the constructor automatically .""" | ( iw , ih ) = self . size
if width is None :
width = min ( iw , utils . term . width )
elif isinstance ( width , basestring ) :
percents = dict ( [ ( pct , '%s%%' % ( pct ) ) for pct in range ( 101 ) ] )
width = percents [ width ]
height = int ( float ( ih ) * ( float ( width ) / float ( iw ) ) )
height //=... |
def cli ( ctx , organism = "" , sequence = "" ) :
"""Get the features for an organism / sequence
Output :
A standard apollo feature dictionary ( { " features " : [ { . . . } ] } )""" | return ctx . gi . annotations . get_features ( organism = organism , sequence = sequence ) |
def _pull_assemble_error_status ( logs ) :
'''Given input in this form : :
u ' { " status " : " Pulling repository foo / ubuntubox " } :
" image ( latest ) from foo / . . .
rogress " : " complete " , " id " : " 2c80228370c9 " } '
construct something like that ( load JSON data is possible ) : :
[ u ' { " s... | comment = 'An error occurred pulling your image'
try :
for err_log in logs :
if isinstance ( err_log , dict ) :
if 'errorDetail' in err_log :
if 'code' in err_log [ 'errorDetail' ] :
msg = '\n{0}\n{1}: {2}' . format ( err_log [ 'error' ] , err_log [ 'errorDeta... |
def use ( node ) :
"Set the fabric environment for the specifed node" | try :
role = node . tags . get ( "Name" ) . split ( '-' ) [ 1 ]
env . roledefs [ role ] += [ ip ( node ) ]
except IndexError :
pass
env . nodes += [ node ]
env . hosts += [ ip ( node ) ] |
def get_all_spaces ( self , start = 0 , limit = 500 ) :
"""Get all spaces with provided limit
: param start : OPTIONAL : The start point of the collection to return . Default : None ( 0 ) .
: param limit : OPTIONAL : The limit of the number of pages to return , this may be restricted by
fixed system limits . ... | url = 'rest/api/space'
params = { }
if limit :
params [ 'limit' ] = limit
if start :
params [ 'start' ] = start
return ( self . get ( url , params = params ) or { } ) . get ( 'results' ) |
def _get_triplet_value ( self , graph , identity , rdf_type ) :
"""Get a value from an RDF triple""" | value = graph . value ( subject = identity , predicate = rdf_type )
return value . toPython ( ) if value is not None else value |
def gdcsreporter ( self , analysistype = 'GDCS' ) :
"""Creates a report of the GDCS results
: param analysistype : The variable to use when accessing attributes in the metadata object""" | logging . info ( 'Creating {} report' . format ( analysistype ) )
# Initialise list to store all the GDCS genes , and genera in the analysis
gdcs = list ( )
genera = list ( )
for sample in self . runmetadata . samples :
if sample . general . bestassemblyfile != 'NA' :
if os . path . isdir ( sample [ analysi... |
def getAllKws ( self ) :
"""extract all keywords into two categories
kws _ ele : magnetic elements
kws _ bl : beamline elements
return ( kws _ ele , kws _ bl )""" | kws_ele = [ ]
kws_bl = [ ]
for ele in self . all_elements :
if ele == '_prefixstr' or ele == '_epics' :
continue
elif self . getElementType ( ele ) . lower ( ) == u'beamline' :
kws_bl . append ( ele )
else :
kws_ele . append ( ele )
return tuple ( ( kws_ele , kws_bl ) ) |
def detect_worktree ( cls , binary = 'git' , subdir = None ) :
"""Detect the git working tree above cwd and return it ; else , return None .
: param string binary : The path to the git binary to use , ' git ' by default .
: param string subdir : The path to start searching for a git repo .
: returns : path to... | # TODO ( John Sirois ) : This is only used as a factory for a Git instance in
# pants . base . build _ environment . get _ scm , encapsulate in a true factory method .
cmd = [ binary , 'rev-parse' , '--show-toplevel' ]
try :
if subdir :
with pushd ( subdir ) :
process , out = cls . _invoke ( cmd... |
def _retry ( self , context , backoff ) :
'''A function which determines whether and how to retry .
: param ~ azure . storage . models . RetryContext context :
The retry context . This contains the request , response , and other data
which can be used to determine whether or not to retry .
: param function ... | # If the context does not contain a count parameter , this request has not
# been retried yet . Add the count parameter to track the number of retries .
if not hasattr ( context , 'count' ) :
context . count = 0
# Determine whether to retry , and if so increment the count , modify the
# request as desired , and ret... |
def nse ( sim = None , obs = None , node = None , skip_nan = False ) :
"""Calculate the efficiency criteria after Nash & Sutcliffe .
If the simulated values predict the observed values as well
as the average observed value ( regarding the the mean square
error ) , the NSE value is zero :
> > > from hydpy im... | sim , obs = prepare_arrays ( sim , obs , node , skip_nan )
return 1. - numpy . sum ( ( sim - obs ) ** 2 ) / numpy . sum ( ( obs - numpy . mean ( obs ) ) ** 2 ) |
def move_back ( columns = 1 , file = sys . stdout ) :
"""Move the cursor back a number of columns .
Esc [ < columns > D :
Moves the cursor back by the specified number of columns without
changing lines . If the cursor is already in the leftmost column ,
ANSI . SYS ignores this sequence .""" | move . back ( columns ) . write ( file = file ) |
def read_pestpp_runstorage ( filename , irun = 0 , with_metadata = False ) :
"""read pars and obs from a specific run in a pest + + serialized run storage file into
pandas . DataFrame ( s )
Parameters
filename : str
the name of the run storage file
irun : int
the run id to process . If ' all ' , then al... | header_dtype = np . dtype ( [ ( "n_runs" , np . int64 ) , ( "run_size" , np . int64 ) , ( "p_name_size" , np . int64 ) , ( "o_name_size" , np . int64 ) ] )
try :
irun = int ( irun )
except :
if irun . lower ( ) == "all" :
irun = irun . lower ( )
else :
raise Exception ( "unrecognized 'irun':... |
def filepaths ( self ) -> List [ str ] :
"""Absolute path names of the files contained in the current
working directory .
Files names starting with underscores are ignored :
> > > from hydpy . core . filetools import FileManager
> > > filemanager = FileManager ( )
> > > filemanager . BASEDIR = ' basename ... | path = self . currentpath
return [ os . path . join ( path , name ) for name in self . filenames ] |
def initialize ( self , symbolic_vm : LaserEVM ) :
"""Initializes the mutation pruner
Introduces hooks for SSTORE operations
: param symbolic _ vm :
: return :""" | @ symbolic_vm . pre_hook ( "SSTORE" )
def mutator_hook ( global_state : GlobalState ) :
global_state . annotate ( MutationAnnotation ( ) )
@ symbolic_vm . laser_hook ( "add_world_state" )
def world_state_filter_hook ( global_state : GlobalState ) :
if And ( * global_state . mstate . constraints [ : ] + [ global... |
def register ( self , plugin ) :
"""Make a plugin known to the CMS .
: param plugin : The plugin class , deriving from : class : ` ContentPlugin ` .
: type plugin : : class : ` ContentPlugin `
The plugin will be instantiated once , just like Django does this with : class : ` ~ django . contrib . admin . Model... | # Duck - Typing does not suffice here , avoid hard to debug problems by upfront checks .
assert issubclass ( plugin , ContentPlugin ) , "The plugin must inherit from `ContentPlugin`"
assert plugin . model , "The plugin has no model defined"
assert issubclass ( plugin . model , ContentItem ) , "The plugin model must inh... |
def remove_all_timers ( self ) :
"""Remove all waiting timers and terminate any blocking threads .""" | with self . lock :
if self . rtimer is not None :
self . rtimer . cancel ( )
self . timers = { }
self . heap = [ ]
self . rtimer = None
self . expiring = False |
def lockToColumn ( self , index ) :
"""Sets the column that the tree view will lock to . If None is supplied ,
then locking will be removed .
: param index | < int > | | None""" | self . _lockColumn = index
if index is None :
self . __destroyLockedView ( )
return
else :
if not self . _lockedView :
view = QtGui . QTreeView ( self . parent ( ) )
view . setModel ( self . model ( ) )
view . setSelectionModel ( self . selectionModel ( ) )
view . setItemDele... |
def indentation ( node ) :
"""Returns the indentation for this node
Iff a node is in a suite , then it has indentation .""" | while node . parent is not None and node . parent . type != syms . suite :
node = node . parent
if node . parent is None :
return u""
# The first three children of a suite are NEWLINE , INDENT , ( some other node )
# INDENT . value contains the indentation for this suite
# anything after ( some other node ) has... |
def select_coins ( target , fee , output_size , min_change , * , absolute_fee = False , consolidate = False , unspents ) :
'''Implementation of Branch - and - Bound coin selection defined in Erhart ' s
Master ' s thesis An Evaluation of Coin Selection Strategies here :
http : / / murch . one / wp - content / up... | # The maximum number of tries for Branch - and - Bound :
BNB_TRIES = 1000000
# COST _ OF _ OVERHEAD excludes the return address of output _ size ( last element ) .
COST_OF_OVERHEAD = ( 8 + sum ( output_size [ : - 1 ] ) + 1 ) * fee
def branch_and_bound ( d , selected_coins , effective_value , target , fee , sorted_unspe... |
def load_tool ( tool , tooldir = None ) :
'''load _ tool : import a Python module , optionally using several directories .
@ param tool [ string ] : name of tool to import .
@ param tooldir [ list ] : directories to look for the tool .
@ return : the loaded module .
Warning : this function is not thread - s... | if tooldir :
assert isinstance ( tooldir , list )
sys . path = tooldir + sys . path
else :
tooldir = [ ]
try :
return __import__ ( tool )
finally :
for dt in tooldir :
sys . path . remove ( dt ) |
def setCurrentSchema ( self , schema ) :
"""Sets the index for this combobox to the inputed schema instance .
: param schema < orb . TableSchema >
: return < bool > success""" | if ( not schema in self . _schemas ) :
return False
index = self . _schemas . index ( schema )
self . setCurrentIndex ( index )
return True |
def highPassFilter ( self , threshold ) :
'''remove all low frequencies by setting a square in the middle of the
Fourier transformation of the size ( 2 * threshold ) ^ 2 to zero
threshold = 0 . . . 1''' | if not threshold :
return
rows , cols = self . img . shape
tx = int ( cols * threshold )
ty = int ( rows * threshold )
# middle :
crow , ccol = rows // 2 , cols // 2
# square in the middle to zero
self . fshift [ crow - tx : crow + tx , ccol - ty : ccol + ty ] = 0 |
def run ( self , change ) :
"""runs the report format instances in this reporter . Will call setup
if it hasn ' t been called already""" | if self . _formats is None :
self . setup ( )
entry = self . entry
for fmt in self . _formats :
fmt . run ( change , entry )
self . clear ( ) |
def energy_minimize ( self , forcefield = 'UFF' , steps = 1000 , ** kwargs ) :
"""Perform an energy minimization on a Compound
Default beahvior utilizes Open Babel ( http : / / openbabel . org / docs / dev / )
to perform an energy minimization / geometry optimization on a
Compound by applying a generic force ... | tmp_dir = tempfile . mkdtemp ( )
original = clone ( self )
self . _kick ( )
self . save ( os . path . join ( tmp_dir , 'un-minimized.mol2' ) )
extension = os . path . splitext ( forcefield ) [ - 1 ]
openbabel_ffs = [ 'MMFF94' , 'MMFF94s' , 'UFF' , 'GAFF' , 'Ghemical' ]
if forcefield in openbabel_ffs :
self . _energ... |
def list_to_raw_list ( poselist ) :
"""Flatten a normal pose list into a raw list
: param poselist : a formatted list [ [ x , y , z ] , [ x , y , z , w ] ]
: return : a raw list [ x , y , z , x , y , z , w ]""" | if not ( isinstance ( poselist , list ) or isinstance ( poselist , tuple ) ) :
raise TypeError ( "flatten_pose({}) does not accept this type of argument" . format ( str ( type ( poselist ) ) ) )
return [ field for pose in poselist for field in pose ] |
def finish_commit ( self , commit ) :
"""Ends the process of committing data to a Repo and persists the
Commit . Once a Commit is finished the data becomes immutable and
future attempts to write to it with PutFile will error .
Params :
* commit : A tuple , string , or Commit object representing the commit .... | req = proto . FinishCommitRequest ( commit = commit_from ( commit ) )
res = self . stub . FinishCommit ( req , metadata = self . metadata )
return res |
def selection ( self ) :
"""Return a datetime representing the current selected date .""" | if not self . _selection :
return None
year , month = self . _date . year , self . _date . month
return self . datetime ( year , month , int ( self . _selection [ 0 ] ) ) |
def process_command ( self , command ) :
'''Processes a user command using aliases
Arguments :
command A user command list ( e . g . argv )
Returns : A ScubaContext object with the following attributes :
script : a list of command line strings
image : the docker image name to use''' | result = ScubaContext ( )
result . script = None
result . image = self . image
result . entrypoint = self . entrypoint
result . environment = self . environment . copy ( )
if command :
alias = self . aliases . get ( command [ 0 ] )
if not alias : # Command is not an alias ; use it as - is .
result . scr... |
def channels_replies ( self , * , channel : str , thread_ts : str , ** kwargs ) -> SlackResponse :
"""Retrieve a thread of messages posted to a channel
Args :
channel ( str ) : The channel id . e . g . ' C1234567890'
thread _ ts ( str ) : The timestamp of an existing message with 0 or more replies .
e . g .... | kwargs . update ( { "channel" : channel , "thread_ts" : thread_ts } )
return self . api_call ( "channels.replies" , http_verb = "GET" , params = kwargs ) |
def stop_listener_thread ( self ) :
"""Kills sync _ thread greenlet before joining it""" | # when stopping , ` kill ` will cause the ` self . api . sync ` call in _ sync
# to raise a connection error . This flag will ensure it exits gracefully then
self . should_listen = False
if self . sync_thread :
self . sync_thread . kill ( )
self . sync_thread . get ( )
if self . _handle_thread is not None :
... |
def find_n50 ( self ) :
"""Calculate the N50 for each strain . N50 is defined as the largest contig such that at least half of the total
genome size is contained in contigs equal to or larger than this contig""" | for sample in self . metadata : # Initialise the N50 attribute in case there is no assembly , and the attribute is not created in the loop
sample [ self . analysistype ] . n50 = '-'
# Initialise a variable to store a running total of contig lengths
currentlength = 0
for contig_length in sample [ self . ... |
def _update_docstrings ( self ) :
"""Runs through the operation methods & updates their docstrings if
necessary .
If the method has the default placeholder docstring , this will replace
it with the docstring from the underlying connection .""" | ops = self . _details . resource_data [ 'operations' ]
for method_name in ops . keys ( ) :
meth = getattr ( self . __class__ , method_name , None )
if not meth :
continue
if meth . __doc__ != DEFAULT_DOCSTRING : # It already has a custom docstring . Leave it alone .
continue
# Needs upda... |
def date_totals ( entries , by ) :
"""Yield a user ' s name and a dictionary of their hours""" | date_dict = { }
for date , date_entries in groupby ( entries , lambda x : x [ 'date' ] ) :
if isinstance ( date , datetime . datetime ) :
date = date . date ( )
d_entries = list ( date_entries )
if by == 'user' :
name = ' ' . join ( ( d_entries [ 0 ] [ 'user__first_name' ] , d_entries [ 0 ] ... |
def save_experiment ( self , name , variants ) :
"""Persist an experiment and its variants ( unless they already exist ) .
: param name a unique string name for the experiment
: param variants a list of strings , each with a unique variant name""" | try :
model . Experiment ( name = name , started_on = datetime . utcnow ( ) , variants = [ model . Variant ( name = v , order = i ) for i , v in enumerate ( variants ) ] )
self . Session . commit ( )
finally :
self . Session . close ( ) |
def load_shortcuts ( self ) :
"""Load shortcuts and assign to table model .""" | shortcuts = [ ]
for context , name , keystr in iter_shortcuts ( ) :
shortcut = Shortcut ( context , name , keystr )
shortcuts . append ( shortcut )
shortcuts = sorted ( shortcuts , key = lambda x : x . context + x . name )
# Store the original order of shortcuts
for i , shortcut in enumerate ( shortcuts ) :
... |
def to_ ( self , attrvals ) :
"""Create a list of Attribute instances .
: param attrvals : A dictionary of attributes and values
: return : A list of Attribute instances""" | attributes = [ ]
for key , value in attrvals . items ( ) :
key = key . lower ( )
attributes . append ( factory ( saml . Attribute , name = key , name_format = self . name_format , attribute_value = do_ava ( value ) ) )
return attributes |
def aes_kdf ( key , rounds , password = None , keyfile = None ) :
"""Set up a context for AES128 - ECB encryption to find transformed _ key""" | cipher = AES . new ( key , AES . MODE_ECB )
key_composite = compute_key_composite ( password = password , keyfile = keyfile )
# get the number of rounds from the header and transform the key _ composite
transformed_key = key_composite
for _ in range ( 0 , rounds ) :
transformed_key = cipher . encrypt ( transformed_... |
def parse_phone ( parts , allow_multiple = False ) :
"""Parse the phone number from the ad ' s parts
parts - > The backpage ad ' s posting _ body , separated into substrings
allow _ multiple - > If false , arbitrarily chooses the most commonly occurring phone""" | # Get text substitutions ( ex : ' three ' - > ' 3 ' )
text_subs = misc . phone_text_subs ( )
Small = text_subs [ 'Small' ]
Magnitude = text_subs [ 'Magnitude' ]
Others = text_subs [ 'Others' ]
phone_pattern = r'1?(?:[2-9][0-8][0-9])\s?(?:[2-9][0-9]{2})\s?(?:[0-9]{2})\s?(?:[0-9]{2})'
phone_pattern_spaces = r'1?\W?[2-9]\... |
def img_encode ( arr , ** kwargs ) :
"""Encode ndarray to base64 string image data
Parameters
arr : ndarray ( rows , cols , depth )
kwargs : passed directly to matplotlib . image . imsave""" | sio = BytesIO ( )
imsave ( sio , arr , ** kwargs )
sio . seek ( 0 )
img_format = kwargs [ 'format' ] if kwargs . get ( 'format' ) else 'png'
img_str = base64 . b64encode ( sio . getvalue ( ) ) . decode ( )
return 'data:image/{};base64,{}' . format ( img_format , img_str ) |
def xmlstring ( self , pretty_print = False ) :
"""Serialises this FoLiA element and all its contents to XML .
Returns :
str : a string with XML representation for this element and all its children""" | s = ElementTree . tostring ( self . xml ( ) , xml_declaration = False , pretty_print = pretty_print , encoding = 'utf-8' )
if sys . version < '3' :
if isinstance ( s , str ) :
s = unicode ( s , 'utf-8' )
# pylint : disable = undefined - variable
else :
if isinstance ( s , bytes ) :
s = s... |
def write_csv ( filename , data , delimiter = CSV_DELIMITER ) :
"""Write image data to CSV file
: param filename : name of CSV file to write data to
: type filename : str
: param data : image data to write to CSV file
: type data : numpy array
: param delimiter : delimiter used in CSV file . Default is ` ... | with open ( filename , 'w' ) as file :
csv_writer = csv . writer ( file , delimiter = delimiter )
for line in data :
csv_writer . writerow ( line ) |
def add_ref ( self , wordlist ) :
"""Adds a reference .""" | refname = wordlist [ 0 ] [ : - 1 ]
if ( refname in self . refs ) :
raise ReferenceError ( "[line {}]:{} already defined here (word) {} (line) {}" . format ( self . line_count , refname , self . refs [ refname ] [ 0 ] , self . refs [ refname ] [ 1 ] ) )
self . refs [ refname ] = ( self . word_count , self . line_cou... |
def run_checks ( collector ) :
"""Just run the checks for our modules""" | artifact = collector . configuration [ "dashmat" ] . artifact
chosen = artifact
if chosen in ( None , "" , NotSpecified ) :
chosen = None
dashmat = collector . configuration [ "dashmat" ]
modules = collector . configuration [ "__active_modules__" ]
config_root = collector . configuration [ "config_root" ]
module_op... |
def normalize_value ( value ) :
"""Convert value to string and make it lower cased .""" | cast = str
if six . PY2 :
cast = unicode
# noqa
return cast ( value ) . lower ( ) |
def _wiggle_interval ( value , wiggle = 0.5 ** 44 ) :
r"""Check if ` ` value ` ` is in : math : ` \ left [ 0 , 1 \ right ] ` .
Allows a little bit of wiggle room outside the interval . Any value
within ` ` wiggle ` ` of ` ` 0.0 ` will be converted to ` ` 0.0 ` and similar
for ` ` 1.0 ` ` .
. . note : :
Th... | if - wiggle < value < wiggle :
return 0.0 , True
elif wiggle <= value <= 1.0 - wiggle :
return value , True
elif 1.0 - wiggle < value < 1.0 + wiggle :
return 1.0 , True
else :
return np . nan , False |
def sendFuture ( self , future ) :
"""Send a Future to be executed remotely .""" | try :
if shared . getConst ( hash ( future . callable ) , timeout = 0 ) : # Enforce name reference passing if already shared
future . callable = SharedElementEncapsulation ( hash ( future . callable ) )
self . socket . send_multipart ( [ b"TASK" , pickle . dumps ( future , pickle . HIGHEST_PROTOCOL ) ] ... |
def _get_instance_attributes ( self ) :
"""Return a generator for instance attributes ' name and value .
. . code - block : : python3
for _ name , _ value in self . _ get _ instance _ attributes ( ) :
print ( " attribute name : { } " . format ( _ name ) )
print ( " attribute value : { } " . format ( _ value... | for name , value in self . __dict__ . items ( ) :
if name in map ( ( lambda x : x [ 0 ] ) , self . get_class_attributes ( ) ) :
yield ( name , value ) |
def to_json ( self ) :
"""Write Wea to json file
" location " : { } , / / ladybug location schema
" direct _ normal _ irradiance " : ( ) , / / Tuple of hourly direct normal
irradiance
" diffuse _ horizontal _ irradiance " : ( ) , / / Tuple of hourly diffuse
horizontal irradiance
" timestep " : float / /... | return { 'location' : self . location . to_json ( ) , 'direct_normal_irradiance' : self . direct_normal_irradiance . to_json ( ) , 'diffuse_horizontal_irradiance' : self . diffuse_horizontal_irradiance . to_json ( ) , 'timestep' : self . timestep , 'is_leap_year' : self . is_leap_year } |
def mktmpenv_cmd ( argv ) :
"""Create a temporary virtualenv .""" | parser = mkvirtualenv_argparser ( )
env = '.'
while ( workon_home / env ) . exists ( ) :
env = hex ( random . getrandbits ( 64 ) ) [ 2 : - 1 ]
args , rest = parser . parse_known_args ( argv )
mkvirtualenv ( env , args . python , args . packages , requirements = args . requirements , rest = rest )
print ( 'This is a... |
def default_capture_file_name ( self ) :
""": returns : File name for a capture on this link""" | capture_file_name = "{}_{}-{}_to_{}_{}-{}" . format ( self . _nodes [ 0 ] [ "node" ] . name , self . _nodes [ 0 ] [ "adapter_number" ] , self . _nodes [ 0 ] [ "port_number" ] , self . _nodes [ 1 ] [ "node" ] . name , self . _nodes [ 1 ] [ "adapter_number" ] , self . _nodes [ 1 ] [ "port_number" ] )
return re . sub ( "[... |
def support_support_param_password ( self , ** kwargs ) :
"""Auto Generated Code""" | config = ET . Element ( "config" )
support = ET . SubElement ( config , "support" , xmlns = "urn:brocade.com:mgmt:brocade-ras" )
support_param = ET . SubElement ( support , "support-param" )
password = ET . SubElement ( support_param , "password" )
password . text = kwargs . pop ( 'password' )
callback = kwargs . pop (... |
def _get_index ( self ) :
"""Get the guideline ' s index .
This must return an ` ` int ` ` .
Subclasses may override this method .""" | glyph = self . glyph
if glyph is not None :
parent = glyph
else :
parent = self . font
if parent is None :
return None
return parent . guidelines . index ( self ) |
def age ( * paths ) :
'''Return the minimum age of a set of files .
Returns 0 if no paths are given .
Returns time . time ( ) if a path does not exist .''' | if not paths :
return 0
for path in paths :
if not os . path . exists ( path ) :
return time . time ( )
return min ( [ ( time . time ( ) - os . path . getmtime ( path ) ) for path in paths ] ) |
def download ( self , url , location , ** kwargs ) :
"""Fetch document located at ` ` url ` ` and save to to ` ` location ` ` .""" | doc = self . go ( url , ** kwargs )
with open ( location , 'wb' ) as out :
out . write ( doc . body )
return len ( doc . body ) |
def diff_for_humans ( self , other = None , absolute = False , locale = None ) :
"""Get the difference in a human readable format in the current locale .
When comparing a value in the past to default now :
1 day ago
5 months ago
When comparing a value in the future to default now :
1 day from now
5 mont... | is_now = other is None
if is_now :
other = self . today ( )
diff = self . diff ( other )
return pendulum . format_diff ( diff , is_now , absolute , locale ) |
def _get_frdata ( stream , num , name , ctype = None ) :
"""Brute force - ish method to return the FrData structure for a channel
This saves on pulling the channel type from the TOC""" | ctypes = ( ctype , ) if ctype else ( 'adc' , 'proc' , 'sim' )
for ctype in ctypes :
_reader = getattr ( stream , 'ReadFr{0}Data' . format ( ctype . title ( ) ) )
try :
return _reader ( num , name )
except IndexError as exc :
if FRERR_NO_CHANNEL_OF_TYPE . match ( str ( exc ) ) :
c... |
def get_metrics ( predicted : Union [ str , List [ str ] , Tuple [ str , ... ] ] , gold : Union [ str , List [ str ] , Tuple [ str , ... ] ] ) -> Tuple [ float , float ] :
"""Takes a predicted answer and a gold answer ( that are both either a string or a list of
strings ) , and returns exact match and the DROP F1... | predicted_bags = _answer_to_bags ( predicted )
gold_bags = _answer_to_bags ( gold )
exact_match = 1.0 if predicted_bags [ 0 ] == gold_bags [ 0 ] else 0
f1_per_bag = _align_bags ( predicted_bags [ 1 ] , gold_bags [ 1 ] )
f1 = np . mean ( f1_per_bag )
f1 = round ( f1 , 2 )
return exact_match , f1 |
def load ( cls , build_file , name , target_aliases ) :
"""A BuildFileManipulator factory class method .
Note that BuildFileManipulator requires a very strict formatting of target declaration .
In particular , it wants to see a newline after ` target _ type ( ` , ` dependencies = [ ` , and
the last param to t... | with open ( build_file . full_path , 'r' ) as f :
source = f . read ( )
source_lines = source . split ( '\n' )
tree = ast . parse ( source )
# Since we ' re not told what the last line of an expression is , we have
# to figure it out based on the start of the expression after it .
# The interval that we consider oc... |
def get_share_metadata ( self , share_name , timeout = None ) :
'''Returns all user - defined metadata for the specified share .
: param str share _ name :
Name of existing share .
: param int timeout :
The timeout parameter is expressed in seconds .
: return :
A dictionary representing the share metada... | _validate_not_none ( 'share_name' , share_name )
request = HTTPRequest ( )
request . method = 'GET'
request . host = self . _get_host ( )
request . path = _get_path ( share_name )
request . query = [ ( 'restype' , 'share' ) , ( 'comp' , 'metadata' ) , ( 'timeout' , _int_to_str ( timeout ) ) , ]
response = self . _perfo... |
def readcbf ( name , load_header = False , load_data = True , for_nexus = False ) :
"""Read a cbf ( crystallographic binary format ) file from a Dectris PILATUS
detector .
Inputs
name : string
the file name
load _ header : bool
if the header data is to be loaded .
load _ data : bool
if the binary da... | with open ( name , 'rb' ) as f :
cbfbin = f . read ( )
datastart = cbfbin . find ( b'\x0c\x1a\x04\xd5' ) + 4
hed = [ x . strip ( ) for x in cbfbin [ : datastart ] . split ( b'\n' ) ]
header = { }
readingmode = None
for i in range ( len ( hed ) ) :
if not hed [ i ] : # skip empty header lines
continue
... |
def send_image ( self , user_id , media_id , account = None ) :
"""发送图片消息
详情请参考
http : / / mp . weixin . qq . com / wiki / 7/12a5a320ae96fecdf0e15cb06123de9f . html
: param user _ id : 用户 ID 。 就是你收到的 ` Message ` 的 source
: param media _ id : 图片的媒体ID 。 可以通过 : func : ` upload _ media ` 上传 。
: param account ... | data = { 'touser' : user_id , 'msgtype' : 'image' , 'image' : { 'media_id' : media_id } }
return self . _send_custom_message ( data , account = account ) |
def callOrder ( cls , * args ) : # pylint : disable = invalid - name
"""Checking the inspector is called with given priority
Args : SinonSpy , list of inspectors
eg .
[ spy1 , spy2 , spy3 ] = > spy1 is called before spy2 , spy2 is called before spy3
[ spy1 , spy2 , spy1 ] = > spy1 is called before and after... | for spy in args :
cls . __is_spy ( spy )
for idx , val in enumerate ( args ) :
if val != args [ 0 ] :
if not ( val . calledAfter ( args [ idx - 1 ] ) ) :
raise cls . failException ( cls . message )
if val != args [ - 1 ] :
if not ( val . calledBefore ( args [ idx + 1 ] ) ) :
... |
def clear_input_field ( self , locator , method = 0 ) :
"""Clears the text field identified by ` locator `
The element . clear ( ) method doesn ' t seem to work properly on
all browsers , so this keyword was created to offer alternatives .
The ` method ` argument defines the method it should use in order
to... | element = self . _element_find ( locator , True , True )
if ( int ( method ) == 0 ) :
self . _info ( "Clearing input on element '%s'" % ( locator ) )
element . clear ( )
elif ( int ( method ) == 1 ) :
self . _info ( "Clearing input on element '%s' by pressing 'CTRL + A + DELETE'" % ( locator ) )
element... |
def collect_variables ( self , variables : MultisetOfVariables ) -> None :
"""Recursively adds all variables occuring in the expression to the given multiset .
This is used internally by ` variables ` . Needs to be overwritten by inheriting container expression classes .
This method can be used when gathering t... | if self . variable_name is not None :
variables . add ( self . variable_name ) |
def assert_raises_regex ( expected_exception , expected_regex , extras = None , * args , ** kwargs ) :
"""Assert that an exception is raised when a function is called .
If no exception is raised , test fail . If an exception is raised but not
of the expected type , the exception is let through . If an exception... | context = _AssertRaisesContext ( expected_exception , expected_regex , extras = extras )
return context |
def parse_from_dict ( json_dict ) :
"""Given a Unified Uploader message , parse the contents and return a
MarketOrderList .
: param dict json _ dict : A Unified Uploader message as a JSON dict .
: rtype : MarketOrderList
: returns : An instance of MarketOrderList , containing the orders
within .""" | order_columns = json_dict [ 'columns' ]
order_list = MarketOrderList ( upload_keys = json_dict [ 'uploadKeys' ] , order_generator = json_dict [ 'generator' ] , )
for rowset in json_dict [ 'rowsets' ] :
generated_at = parse_datetime ( rowset [ 'generatedAt' ] )
region_id = rowset [ 'regionID' ]
type_id = row... |
def run ( self , run_fit_model = True ) :
"""Run the Graph Cut segmentation according to preset parameters .
: param run _ fit _ model : Allow to skip model fit when the model is prepared before
: return :""" | if run_fit_model :
self . fit_model ( self . img , self . voxelsize , self . seeds )
self . _start_time = time . time ( )
if self . segparams [ "method" ] . lower ( ) in ( "graphcut" , "gc" ) :
self . __single_scale_gc_run ( )
elif self . segparams [ "method" ] . lower ( ) in ( "multiscale_graphcut" , "multisca... |
def excel_key ( index ) :
"""create a key for index by converting index into a base - 26 number , using A - Z as the characters .""" | X = lambda n : ~ n and X ( ( n // 26 ) - 1 ) + chr ( 65 + ( n % 26 ) ) or ''
return X ( int ( index ) ) |
def blast ( self , blastfile = None , outfile = None ) :
"""convert anchor file to 12 col blast file""" | from jcvi . formats . blast import BlastSlow , BlastLineByConversion
if not outfile :
outfile = self . filename + ".blast"
if blastfile is not None :
blasts = BlastSlow ( blastfile ) . to_dict ( )
else :
blasts = None
fw = must_open ( outfile , "w" , checkexists = True )
nlines = 0
for a , b , id in self . ... |
def _build_line ( colwidths , colaligns , linefmt ) :
"Return a string which represents a horizontal line ." | if not linefmt :
return None
if hasattr ( linefmt , "__call__" ) :
return linefmt ( colwidths , colaligns )
else :
begin , fill , sep , end = linefmt
cells = [ fill * w for w in colwidths ]
return _build_simple_row ( cells , ( begin , sep , end ) ) |
def package_files ( directory ) :
"""Get list of data files to add to the package .""" | paths = [ ]
for ( path , _ , file_names ) in walk ( directory ) :
for filename in file_names :
paths . append ( join ( '..' , path , filename ) )
return paths |
def iter_decode ( input , fallback_encoding , errors = 'replace' ) :
"""" Pull " - based decoder .
: param input :
An iterable of byte strings .
The input is first consumed just enough to determine the encoding
based on the precense of a BOM ,
then consumed on demand when the return value is .
: param f... | decoder = IncrementalDecoder ( fallback_encoding , errors )
generator = _iter_decode_generator ( input , decoder )
encoding = next ( generator )
return generator , encoding |
def _GetAttributeNames ( self , data_type_definition ) :
"""Determines the attribute ( or field ) names of the members .
Args :
data _ type _ definition ( DataTypeDefinition ) : data type definition .
Returns :
list [ str ] : attribute names .
Raises :
FormatError : if the attribute names cannot be dete... | if not data_type_definition :
raise errors . FormatError ( 'Missing data type definition' )
attribute_names = [ ]
for member_definition in data_type_definition . members :
attribute_names . append ( member_definition . name )
return attribute_names |
def print_device_list ( self , device_list = None ) :
"""Optional parameter is a list of device objects . If omitted , will
just print all portal devices objects .""" | dev_list = device_list if device_list is not None else self . get_all_devices_in_portal ( )
for dev in dev_list :
print ( '{0}\t\t{1}\t\t{2}' . format ( dev [ 'info' ] [ 'description' ] [ 'name' ] , dev [ 'sn' ] , dev [ 'portals_aliases' ] if len ( dev [ 'portals_aliases' ] ) != 1 else dev [ 'portals_aliases' ] [ 0... |
def add_batch ( self , nlive = 500 , wt_function = None , wt_kwargs = None , maxiter = None , maxcall = None , save_bounds = True , print_progress = True , print_func = None , stop_val = None ) :
"""Allocate an additional batch of ( nested ) samples based on
the combined set of previous samples using the specifie... | # Initialize values .
if maxcall is None :
maxcall = sys . maxsize
if maxiter is None :
maxiter = sys . maxsize
if wt_function is None :
wt_function = weight_function
if wt_kwargs is None :
wt_kwargs = dict ( )
if print_func is None :
print_func = print_fn
# If we have either likelihood calls or ite... |
def _add_escape_character_for_quote_prime_character ( self , text ) :
"""Fix for https : / / github . com / openatx / facebook - wda / issues / 33
Returns :
string with properly formated quotes , or non changed text""" | if text is not None :
if "'" in text :
return text . replace ( "'" , "\\'" )
elif '"' in text :
return text . replace ( '"' , '\\"' )
else :
return text
else :
return text |
def inter ( a , b ) :
"""Intersect two sets of any data type to form a third set .
http : / / naif . jpl . nasa . gov / pub / naif / toolkit _ docs / C / cspice / inter _ c . html
: param a : First input set .
: type a : spiceypy . utils . support _ types . SpiceCell
: param b : Second input set .
: type ... | assert isinstance ( a , stypes . SpiceCell )
assert isinstance ( b , stypes . SpiceCell )
assert a . dtype == b . dtype
# Next line was redundant with [ raise NotImpImplementedError ] below
# assert a . dtype = = 0 or a . dtype = = 1 or a . dtype = = 2
if a . dtype is 0 :
c = stypes . SPICECHAR_CELL ( max ( a . siz... |
def absent ( name , tags = None , region = None , key = None , keyid = None , profile = None ) :
'''Ensure VPC with passed properties is absent .
name
Name of the VPC .
tags
A list of tags . All tags must match .
region
Region to connect to .
key
Secret key to be used .
keyid
Access key to be us... | ret = { 'name' : name , 'result' : True , 'comment' : '' , 'changes' : { } }
r = __salt__ [ 'boto_vpc.get_id' ] ( name = name , tags = tags , region = region , key = key , keyid = keyid , profile = profile )
if 'error' in r :
ret [ 'result' ] = False
ret [ 'comment' ] = 'Failed to delete VPC: {0}.' . format ( r... |
def get_or_generate_vocab_inner ( data_dir , vocab_filename , vocab_size , generator , max_subtoken_length = None , reserved_tokens = None ) :
"""Inner implementation for vocab generators .
Args :
data _ dir : The base directory where data and vocab files are stored . If None ,
then do not save the vocab even... | if data_dir and vocab_filename :
vocab_filepath = os . path . join ( data_dir , vocab_filename )
if tf . gfile . Exists ( vocab_filepath ) :
tf . logging . info ( "Found vocab file: %s" , vocab_filepath )
return text_encoder . SubwordTextEncoder ( vocab_filepath )
else :
vocab_filepath = Non... |
def get_neighbor_names ( self , node_name : str , order : int = 1 ) -> list :
"""Get the names of all neighbors of a node , and the node itself .
: param node _ name : Node whose neighbor names are requested .
: return : A list of names of all neighbors of a node , and the node itself .""" | logger . info ( "In get_neighbor_names()" )
node = self . graph . vs . find ( name = node_name )
neighbors = self . graph . neighborhood ( node , order = order )
names = self . graph . vs [ neighbors ] [ "name" ]
names . append ( node_name )
return list ( names ) |
def get_nova_endpoint ( cls , json_resp , nova_api_version = None ) :
"""Parse the service catalog returned by the Identity API for an endpoint matching
the Nova service with the requested version
Sends a CRITICAL service check when no viable candidates are found in the Catalog""" | nova_version = nova_api_version or DEFAULT_NOVA_API_VERSION
catalog = json_resp . get ( 'token' , { } ) . get ( 'catalog' , [ ] )
nova_match = 'novav21' if nova_version == V21_NOVA_API_VERSION else 'nova'
for entry in catalog :
if entry [ 'name' ] == nova_match or 'Compute' in entry [ 'name' ] : # Collect any endpo... |
def factor_cumulative_returns ( factor_data , period , long_short = True , group_neutral = False , equal_weight = False , quantiles = None , groups = None ) :
"""Simulate a portfolio using the factor in input and returns the cumulative
returns of the simulated portfolio
Parameters
factor _ data : pd . DataFra... | fwd_ret_cols = utils . get_forward_returns_columns ( factor_data . columns )
if period not in fwd_ret_cols :
raise ValueError ( "Period '%s' not found" % period )
todrop = list ( fwd_ret_cols )
todrop . remove ( period )
portfolio_data = factor_data . drop ( todrop , axis = 1 )
if quantiles is not None :
portfo... |
def transmit_metrics ( self ) :
"""Keep metrics updated about how long time ago each filetype was successfully uploaded .
Transmits max once per ten seconds , regardless of how many threads are running .""" | global _last_stats_transmit_time
# pylint : disable = global - statement
with _STATS_LOCK : # pylint : disable = not - context - manager
if time . monotonic ( ) - _last_stats_transmit_time < 10.0 :
return
for site in self . state :
for filetype , prop in self . state [ site ] [ "upload" ] . item... |
def shape_factors ( n , dim = 2 ) :
"""Returns a : obj : ` numpy . ndarray ` of factors : samp : ` f ` such
that : samp : ` ( len ( f ) = = { dim } ) and ( numpy . product ( f ) = = { n } ) ` .
The returned factors are as * square * ( * cubic * , etc ) as possible .
For example : :
> > > shape _ factors ( 2... | if dim <= 1 :
factors = [ n , ]
else :
for f in range ( int ( n ** ( 1.0 / float ( dim ) ) ) + 1 , 0 , - 1 ) :
if ( n % f ) == 0 :
factors = [ f , ] + list ( shape_factors ( n // f , dim = dim - 1 ) )
break
factors . sort ( )
return _np . array ( factors ) |
def bsp_resize ( node : tcod . bsp . BSP , x : int , y : int , w : int , h : int ) -> None :
""". . deprecated : : 2.0
Assign directly to : any : ` BSP ` attributes instead .""" | node . x = x
node . y = y
node . width = w
node . height = h |
def get_statements ( self , filter = False ) :
"""Return the combined list of statements from BEL and Pathway Commons .
Internally calls : py : meth : ` get _ biopax _ stmts ` and
: py : meth : ` get _ bel _ stmts ` .
Parameters
filter : bool
If True , includes only those statements that exclusively menti... | bp_stmts = self . get_biopax_stmts ( filter = filter )
bel_stmts = self . get_bel_stmts ( filter = filter )
return bp_stmts + bel_stmts |
def prune_dupes ( self ) :
"""Remove all but the last entry for a given resource URI .
Returns the number of entries removed . Also removes all entries for a
given URI where the first entry is a create and the last entry is a
delete .""" | n = 0
pruned1 = [ ]
seen = set ( )
deletes = { }
for r in reversed ( self . resources ) :
if ( r . uri in seen ) :
n += 1
if ( r . uri in deletes ) :
deletes [ r . uri ] = r . change
else :
pruned1 . append ( r )
seen . add ( r . uri )
if ( r . change == 'dele... |
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