signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def terminate ( self , signal_chain = KILL_CHAIN , kill_wait = KILL_WAIT_SEC , purge = True ) :
"""Ensure a process is terminated by sending a chain of kill signals ( SIGTERM , SIGKILL ) .""" | alive = self . is_alive ( )
if alive :
logger . debug ( 'terminating {}' . format ( self . _name ) )
for signal_type in signal_chain :
pid = self . pid
try :
logger . debug ( 'sending signal {} to pid {}' . format ( signal_type , pid ) )
self . _kill ( signal_type )
... |
def get_sub_electrodes ( self , adjacent_only = True ) :
"""If this electrode contains multiple voltage steps , then it is possible
to use only a subset of the voltage steps to define other electrodes .
For example , an LiTiO2 electrode might contain three subelectrodes :
[ LiTiO2 - - > TiO2 , LiTiO2 - - > Li... | if adjacent_only :
return [ self . __class__ ( self . _vpairs [ i : i + 1 ] , self . _working_ion_entry , self . _composition ) for i in range ( len ( self . _vpairs ) ) ]
sub_electrodes = [ ]
for i in range ( len ( self . _vpairs ) ) :
for j in range ( i , len ( self . _vpairs ) ) :
sub_electrodes . ap... |
def run_kernel ( self , func , gpu_args , threads , grid ) :
"""runs the CUDA kernel passed as ' func '
: param func : A PyCuda kernel compiled for this specific kernel configuration
: type func : pycuda . driver . Function
: param gpu _ args : A list of arguments to the kernel , order should match the
orde... | func ( * gpu_args , block = threads , grid = grid , texrefs = self . texrefs ) |
async def dist ( self , mesg ) :
'''Distribute an existing event tuple .
Args :
mesg ( ( str , dict ) ) : An event tuple .
Example :
await base . dist ( ( ' foo ' , { ' bar ' : ' baz ' } ) )''' | if self . isfini :
return ( )
ret = [ ]
for func in self . _syn_funcs . get ( mesg [ 0 ] , ( ) ) :
try :
ret . append ( await s_coro . ornot ( func , mesg ) )
except asyncio . CancelledError :
raise
except Exception :
logger . exception ( 'base %s error with mesg %s' , self , mes... |
def get_torrent_download_limit ( self , infohash_list ) :
"""Get download speed limit of the supplied torrents .
: param infohash _ list : Single or list ( ) of infohashes .""" | data = self . _process_infohash_list ( infohash_list )
return self . _post ( 'command/getTorrentsDlLimit' , data = data ) |
def get_event_data ( self , section , time_in_seconds = False ) :
"""Get the template or complement event data .
: param section : Either template , complement , or both .
: param time _ in _ seconds : Return the start and length fields
in seconds , rather than samples .
: return : The event dataset for the... | if section not in [ 'template' , 'complement' , 'both' ] :
raise Exception ( 'Unrecognized section: {} Expected: "template", "complement" or "both"' . format ( section ) )
results = self . get_results ( )
if results is None :
return None , None if section is 'both' else None
if section == 'both' :
sections ... |
def documents_upload ( ctx , max_threads , files ) :
"""Upload a document file ( of any type ) to One Codex""" | if len ( files ) == 0 :
click . echo ( ctx . get_help ( ) )
return
files = list ( files )
bar = click . progressbar ( length = sum ( [ _file_size ( x ) for x in files ] ) , label = "Uploading... " )
run_via_threadpool ( ctx . obj [ "API" ] . Documents . upload , files , { "progressbar" : bar } , max_threads = m... |
def instruction_DEC_register ( self , opcode , register ) :
"""Decrement accumulator""" | a = register . value
r = self . DEC ( a )
# log . debug ( " $ % x DEC % s value $ % x - 1 = $ % x " % (
# self . program _ counter ,
# register . name , a , r
register . set ( r ) |
def _Open ( self , path_spec = None , mode = 'rb' ) :
"""Opens the file - like object defined by path specification .
Args :
path _ spec ( PathSpec ) : path specification .
mode ( Optional [ str ] ) : file access mode .
Raises :
AccessError : if the access to open the file was denied .
IOError : if the ... | if not path_spec :
raise ValueError ( 'Missing path specification.' )
if path_spec . HasParent ( ) :
raise errors . PathSpecError ( 'Unsupported path specification with parent.' )
location = getattr ( path_spec , 'location' , None )
if location is None :
raise errors . PathSpecError ( 'Path specification mi... |
def subvol_snapshot ( self , source , destination , read_only = False ) :
"""Take a snapshot
: param source : source path of subvol
: param destination : destination path of snapshot
: param read _ only : Set read - only on the snapshot
: return :""" | args = { "source" : source , "destination" : destination , "read_only" : read_only , }
self . _subvol_snapshot_chk . check ( args )
self . _client . sync ( 'btrfs.subvol_snapshot' , args ) |
def close ( self ) :
"""Subprocess cleanup .""" | # Give time to flush data if debug was on
if self . debug :
time . sleep ( 10 )
# Terminate workers
for host in self . workers :
host . close ( )
# Terminate the brokers
for broker in self . brokers :
try :
broker . close ( )
except AttributeError : # Broker was not started ( probably mislaunche... |
def map_statistic ( self , plot ) :
"""Mapping aesthetics to computed statistics""" | data = self . data
if not len ( data ) :
return type ( data ) ( )
# Assemble aesthetics from layer , plot and stat mappings
aesthetics = deepcopy ( self . mapping )
if self . inherit_aes :
aesthetics = defaults ( aesthetics , plot . mapping )
aesthetics = defaults ( aesthetics , self . stat . DEFAULT_AES )
# Th... |
def trigger_show_by_id ( self , id , ** kwargs ) :
"https : / / developer . zendesk . com / rest _ api / docs / core / triggers # getting - triggers" | api_path = "/api/v2/triggers/{id}.json"
api_path = api_path . format ( id = id )
return self . call ( api_path , ** kwargs ) |
def marker_gene_overlap ( adata : AnnData , reference_markers : Union [ Dict [ str , set ] , Dict [ str , list ] ] , * , key : str = 'rank_genes_groups' , method : Optional [ str ] = 'overlap_count' , normalize : Union [ str , None ] = None , top_n_markers : Optional [ int ] = None , adj_pval_threshold : Optional [ flo... | # Test user inputs
if inplace :
raise NotImplementedError ( 'Writing Pandas dataframes to h5ad is ' 'currently under development.\n' 'Please use `inplace=False`.' )
if key not in adata . uns :
raise ValueError ( 'Could not find marker gene data. ' 'Please run `sc.tl.rank_genes_groups()` first.' )
avail_methods ... |
def rhombohedral ( a : float , alpha : float ) :
"""Convenience constructor for a rhombohedral lattice .
Args :
a ( float ) : * a * lattice parameter of the rhombohedral cell .
alpha ( float ) : Angle for the rhombohedral lattice in degrees .
Returns :
Rhombohedral lattice of dimensions a x a x a .""" | return Lattice . from_parameters ( a , a , a , alpha , alpha , alpha ) |
def bin2hex ( fin , fout , offset = 0 ) :
"""Simple bin - to - hex convertor .
@ return 0 if all OK
@ param fin input bin file ( filename or file - like object )
@ param fout output hex file ( filename or file - like object )
@ param offset starting address offset for loading bin""" | h = IntelHex ( )
try :
h . loadbin ( fin , offset )
except IOError :
e = sys . exc_info ( ) [ 1 ]
# current exception
txt = 'ERROR: unable to load bin file:' , str ( e )
print ( txt )
return 1
try :
h . tofile ( fout , format = 'hex' )
except IOError :
e = sys . exc_info ( ) [ 1 ]
# ... |
def attributes ( self ) :
"""Returns a list of attributes""" | overridden_attrs = self . _attributes
sortmap = { "neutral" : 1 , "positive" : 2 , "negative" : 3 }
sortedattrs = list ( overridden_attrs . values ( ) )
sortedattrs . sort ( key = operator . itemgetter ( "defindex" ) )
sortedattrs . sort ( key = lambda t : sortmap . get ( t . get ( "effect_type" , "neutral" ) , 99 ) )
... |
def post ( self , page , payload , parms = None ) :
'''Posts a string payload to the server - used to make new Redmine items . Returns an JSON string or error .''' | if self . readonlytest :
print 'Redmine read only test: Pretending to create: ' + page
return payload
else :
return self . open ( page , parms , payload ) |
def trigger_staged_cg_hook ( self , name , g , * args , ** kwargs ) :
"""Calls a three - staged hook :
1 . ` ` " pre _ " + name ` `
2 . ` ` " in _ " + name ` `
3 . ` ` " post _ " + name ` `""" | print_hooks = self . _print_hooks
# TODO : document name lookup business
# TODO : refactor this context stuff , its confusing
hook_name = "pre_" + name
printed_name = hook_name if print_hooks else None
self . trigger_cg_hook ( hook_name , g , printed_name , * args , ** kwargs )
# TODO : avoid copies
hook_name = "in_" +... |
def xrandr ( self ) :
"""This is the main py3status method , it will orchestrate what ' s being
displayed on the bar .""" | self . layout = self . _get_layout ( )
self . _set_available_combinations ( )
self . _choose_what_to_display ( )
if len ( self . available_combinations ) < 2 and self . hide_if_single_combination :
full_text = self . py3 . safe_format ( self . format , { "output" : "" } )
else :
if self . fixed_width is True :
... |
def run_edisgo_pool ( ding0_file_list , run_args_opt , workers = mp . cpu_count ( ) , worker_lifetime = 1 ) :
"""Use python multiprocessing toolbox for parallelization
Several grids are analyzed in parallel .
Parameters
ding0 _ file _ list : list
Ding0 grid data file names
run _ args _ opt : list
eDisGo... | def collect_pool_results ( result ) :
results . append ( result )
results = [ ]
pool = mp . Pool ( workers , maxtasksperchild = worker_lifetime )
for file in ding0_file_list :
edisgo_args = [ file ] + run_args_opt
pool . apply_async ( func = run_edisgo_twice , args = ( edisgo_args , ) , callback = collect_p... |
def directory_remove ( self , path ) :
"""Removes a guest directory if empty .
Symbolic links in the final component will not be followed ,
instead an not - a - directory error is reported .
in path of type str
Path to the directory that should be removed . Guest path style .""" | if not isinstance ( path , basestring ) :
raise TypeError ( "path can only be an instance of type basestring" )
self . _call ( "directoryRemove" , in_p = [ path ] ) |
def mkpartfs ( device , part_type , fs_type , start , end ) :
'''Make a < part _ type > partition with a new filesystem of < fs _ type > , beginning
at < start > and ending at < end > ( by default in megabytes ) .
< part _ type > should be one of " primary " , " logical " , or " extended " . < fs _ type >
mus... | _validate_device ( device )
if part_type not in set ( [ 'primary' , 'logical' , 'extended' ] ) :
raise CommandExecutionError ( 'Invalid part_type passed to partition.mkpartfs' )
if not _is_fstype ( fs_type ) :
raise CommandExecutionError ( 'Invalid fs_type passed to partition.mkpartfs' )
_validate_partition_bou... |
def check_model ( self ) :
"""Check the model for various errors . This method checks for the following
errors . In the same time also updates the cardinalities of all the random
variables .
* Checks if clique potentials are defined for all the cliques or not .
* Check for running intersection property is n... | if not nx . is_connected ( self ) :
raise ValueError ( 'The Junction Tree defined is not fully connected.' )
return super ( JunctionTree , self ) . check_model ( ) |
def _check_dir ( self ) :
"""Makes sure that the working directory for the wrapper modules exists .""" | from os import path , mkdir
if not path . isdir ( self . dirpath ) :
mkdir ( self . dirpath )
# Copy the ftypes . py module shipped with fortpy to the local directory .
ftypes = path . join ( get_fortpy_templates ( ) , "ftypes.py" )
from shutil import copy
copy ( ftypes , self . dirpath )
# Crea... |
def _write2 ( self , data , multithread = True , ** kwargs ) :
''': param data : Data to be written
: type data : str or mmap object
: param multithread : If True , sends multiple write requests asynchronously
: type multithread : boolean
Writes the data * data * to the file .
. . note : :
Writing to re... | if not USING_PYTHON2 :
assert ( isinstance ( data , bytes ) )
self . _ensure_write_bufsize ( ** kwargs )
def write_request ( data_for_write_req ) :
if multithread :
self . _async_upload_part_request ( data_for_write_req , index = self . _cur_part , ** kwargs )
else :
self . upload_part ( dat... |
def discard ( self , key ) :
"""Banana banana""" | if key in self . map :
key , prev , nxt = self . map . pop ( key )
prev [ 2 ] = nxt
nxt [ 1 ] = prev |
def millRule ( self , aLvlNow , pLvlNow , MPCnow , TranShkNow , EmpNow , t_age , LorenzBool , ManyStatsBool ) :
'''The millRule for this class simply calls the method calcStats .''' | self . calcStats ( aLvlNow , pLvlNow , MPCnow , TranShkNow , EmpNow , t_age , LorenzBool , ManyStatsBool )
if self . AggShockBool :
return self . calcRandW ( aLvlNow , pLvlNow )
else : # These variables are tracked but not created in no - agg - shocks specifications
self . MaggNow = 0.0
self . AaggNow = 0.0 |
def to_jd ( year , month , day ) :
'''Determine Julian day from Persian date''' | if year >= 0 :
y = 474
else :
y = 473
epbase = year - y
epyear = 474 + ( epbase % 2820 )
if month <= 7 :
m = ( month - 1 ) * 31
else :
m = ( month - 1 ) * 30 + 6
return day + m + trunc ( ( ( epyear * 682 ) - 110 ) / 2816 ) + ( epyear - 1 ) * 365 + trunc ( epbase / 2820 ) * 1029983 + ( EPOCH - 1 ) |
def send_chat_messages ( self , messages ) :
"""Useful for logging messages into the replay .""" | self . _parallel . run ( ( c . chat , message ) for c , message in zip ( self . _controllers , messages ) ) |
async def deserialize ( data : dict ) :
"""Create the object from a previously serialized object .
: param data : The output of the " serialize " call
Example :
source _ id = ' foobar123'
name = ' Address Schema '
version = ' 1.0'
attrs = [ ' address ' , ' city ' , ' state ' ]
payment _ handle = 0
s... | try : # Todo : Find better way to access attr _ names . Potential for issues .
schema = await Schema . _deserialize ( "vcx_schema_deserialize" , json . dumps ( data ) , data [ 'data' ] [ 'source_id' ] , data [ 'data' ] [ 'name' ] , data [ 'data' ] [ 'version' ] , data [ 'data' ] [ 'data' ] )
schema . schema_id ... |
def version_jar ( self ) :
"""Special case of version ( ) when the executable is a JAR file .""" | cmd = config . get_command ( 'java' )
cmd . append ( '-jar' )
cmd += self . cmd
self . version ( cmd = cmd , path = self . cmd [ 0 ] ) |
def trigger ( self , event : str , ** kwargs : Any ) -> None :
"""Trigger all handlers for an event to ( asynchronously ) execute""" | event = event . upper ( )
for func in self . _event_handlers [ event ] :
self . loop . create_task ( func ( ** kwargs ) )
# This will unblock anyone that is awaiting on the next loop update ,
# while still ensuring the next ` await client . wait ( event ) ` doesn ' t
# immediately fire .
async_event = self . _event... |
def _get_all_filtered_channels ( self , topics_without_signature ) :
"""get all filtered chanels from blockchain logs""" | mpe_address = self . get_mpe_address ( )
event_signature = self . ident . w3 . sha3 ( text = "ChannelOpen(uint256,uint256,address,address,address,bytes32,uint256,uint256)" ) . hex ( )
topics = [ event_signature ] + topics_without_signature
logs = self . ident . w3 . eth . getLogs ( { "fromBlock" : self . args . from_bl... |
def _next_image_partname ( self , ext ) :
"""The next available image partname , starting from
` ` / word / media / image1 . { ext } ` ` where unused numbers are reused . The
partname is unique by number , without regard to the extension . * ext *
does not include the leading period .""" | def image_partname ( n ) :
return PackURI ( '/word/media/image%d.%s' % ( n , ext ) )
used_numbers = [ image_part . partname . idx for image_part in self ]
for n in range ( 1 , len ( self ) + 1 ) :
if n not in used_numbers :
return image_partname ( n )
return image_partname ( len ( self ) + 1 ) |
def get_first_view ( self , fmt = 'json' ) :
"""Get a first view model as dict
: return :""" | url = self . __url + 'views/first'
return self . session . get ( url ) . json ( ) |
def insert ( self , index , value ) :
'''Insert a node in - place . It is highly suggested that you do not
use this method . Use assoc instead''' | newnode = LookupTreeNode ( index , value )
level = 0
node = self . root
while True :
ind = _getbits ( newnode . index , level )
level += 1
child = node . children [ ind ]
if child is None or child . index == newnode . index :
if child :
assert child . value == newnode . value
... |
def get_toolbar_buttons ( self ) :
"""Return toolbar buttons list .""" | buttons = [ ]
# Code to add the stop button
if self . stop_button is None :
self . stop_button = create_toolbutton ( self , text = _ ( "Stop" ) , icon = self . stop_icon , tip = _ ( "Stop the current command" ) )
self . disable_stop_button ( )
# set click event handler
self . stop_button . clicked . con... |
def flatten_and_batch_shift_indices ( indices : torch . Tensor , sequence_length : int ) -> torch . Tensor :
"""This is a subroutine for : func : ` ~ batched _ index _ select ` . The given ` ` indices ` ` of size
` ` ( batch _ size , d _ 1 , . . . , d _ n ) ` ` indexes into dimension 2 of a target tensor , which ... | # Shape : ( batch _ size )
offsets = get_range_vector ( indices . size ( 0 ) , get_device_of ( indices ) ) * sequence_length
for _ in range ( len ( indices . size ( ) ) - 1 ) :
offsets = offsets . unsqueeze ( 1 )
# Shape : ( batch _ size , d _ 1 , . . . , d _ n )
offset_indices = indices + offsets
# Shape : ( batch... |
def to_neo4j ( graph , neo_connection , use_tqdm = False ) :
"""Upload a BEL graph to a Neo4j graph database using : mod : ` py2neo ` .
: param pybel . BELGraph graph : A BEL Graph
: param neo _ connection : A : mod : ` py2neo ` connection object . Refer to the
` py2neo documentation < http : / / py2neo . org... | import py2neo
if isinstance ( neo_connection , str ) :
neo_connection = py2neo . Graph ( neo_connection )
tx = neo_connection . begin ( )
node_map = { }
nodes = list ( graph )
if use_tqdm :
nodes = tqdm ( nodes , desc = 'nodes' )
for node in nodes :
if NAMESPACE not in node or VARIANTS in node or MEMBERS in... |
def SerializeExclusiveData ( self , writer ) :
"""Serialize object .
Args :
writer ( neo . IO . BinaryWriter ) :""" | writer . WriteVarBytes ( self . Script )
if self . Version >= 1 :
writer . WriteFixed8 ( self . Gas ) |
def search_song ( self , song_name , quiet = False , limit = 9 ) :
"""Search song by song name .
: params song _ name : song name .
: params quiet : automatically select the best one .
: params limit : song count returned by weapi .
: return : a Song object .""" | result = self . search ( song_name , search_type = 1 , limit = limit )
if result [ 'result' ] [ 'songCount' ] <= 0 :
LOG . warning ( 'Song %s not existed!' , song_name )
raise SearchNotFound ( 'Song {} not existed.' . format ( song_name ) )
else :
songs = result [ 'result' ] [ 'songs' ]
if quiet :
... |
def _set_detail ( self , v , load = False ) :
"""Setter method for detail , mapped from YANG variable / openflow _ state / detail ( container )
If this variable is read - only ( config : false ) in the
source YANG file , then _ set _ detail is considered as a private
method . Backends looking to populate this... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = detail . detail , is_container = 'container' , presence = False , yang_name = "detail" , rest_name = "detail" , parent = self , path_helper = self . _path_helper , extmethods = self . _extmethods , register_paths = True , ext... |
def execute ( self ) :
"""Execute the search and return an instance of ` ` Response ` ` wrapping all
the data .""" | es = connections . get_connection ( self . _using )
self . _response = self . _response_class ( self , es . update_by_query ( index = self . _index , body = self . to_dict ( ) , ** self . _params ) )
return self . _response |
def update ( self , defaults = values . unset ) :
"""Update the DefaultsInstance
: param dict defaults : A JSON string that describes the default task links .
: returns : Updated DefaultsInstance
: rtype : twilio . rest . autopilot . v1 . assistant . defaults . DefaultsInstance""" | data = values . of ( { 'Defaults' : serialize . object ( defaults ) , } )
payload = self . _version . update ( 'POST' , self . _uri , data = data , )
return DefaultsInstance ( self . _version , payload , assistant_sid = self . _solution [ 'assistant_sid' ] , ) |
def help_center_section_subscription_show ( self , section_id , id , locale = None , ** kwargs ) :
"https : / / developer . zendesk . com / rest _ api / docs / help _ center / subscriptions # show - section - subscription" | api_path = "/api/v2/help_center/sections/{section_id}/subscriptions/{id}.json"
api_path = api_path . format ( section_id = section_id , id = id )
if locale :
api_opt_path = "/api/v2/help_center/{locale}/sections/{section_id}/subscriptions/{id}.json"
api_path = api_opt_path . format ( section_id = section_id , i... |
def _set_path ( self , v , load = False ) :
"""Setter method for path , mapped from YANG variable / mpls _ config / router / mpls / mpls _ cmds _ holder / path ( list )
If this variable is read - only ( config : false ) in the
source YANG file , then _ set _ path is considered as a private
method . Backends l... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = YANGListType ( "path_name" , path . path , yang_name = "path" , rest_name = "path" , parent = self , is_container = 'list' , user_ordered = False , path_helper = self . _path_helper , yang_keys = 'path-name' , extensions = { ... |
def _create_event_listeners ( self ) :
"""Create and bind the event listeners .""" | LOG . debug ( "Create the event listeners." )
for event_type , callback in self . _event_callback_pairs :
LOG . debug ( "Create listener for %r event" , event_type )
listener = self . _utils . get_vnic_event_listener ( event_type )
eventlet . spawn_n ( listener , callback ) |
def project_process ( index , start , end ) :
"""Compute the metrics for the project process section of the enriched
github issues index .
Returns a dictionary containing " bmi _ metrics " , " time _ to _ close _ metrics " ,
" time _ to _ close _ review _ metrics " and patchsets _ metrics as the keys and
th... | results = { "bmi_metrics" : [ BMI ( index , start , end ) ] , "time_to_close_metrics" : [ DaysToCloseAverage ( index , start , end ) , DaysToCloseMedian ( index , start , end ) ] , "time_to_close_review_metrics" : [ ] , "patchsets_metrics" : [ ] }
return results |
def _parse_welcome ( client , command , actor , args ) :
"""Parse a WELCOME and update user state , then dispatch a WELCOME event .""" | _ , _ , hostmask = args . rpartition ( ' ' )
client . user . update_from_hostmask ( hostmask )
client . dispatch_event ( "WELCOME" , hostmask ) |
def det_refpoint ( self , angle ) :
"""Return the detector reference point position at ` ` angle ` ` .
For an angle ` ` phi ` ` , the detector position is given by : :
det _ ref ( phi ) = translation +
rot _ matrix ( phi ) * ( det _ rad * src _ to _ det _ init )
where ` ` src _ to _ det _ init ` ` is the in... | squeeze_out = ( np . shape ( angle ) == ( ) )
angle = np . array ( angle , dtype = float , copy = False , ndmin = 1 )
# Initial vector from the rotation center to the detector . It can be
# computed this way since source and detector are at maximum distance ,
# i . e . the connecting line passes the origin .
center_to_... |
def agent ( ) :
"""Run the agent , connecting to a ( remote ) host started independently .""" | agent_module , agent_name = FLAGS . agent . rsplit ( "." , 1 )
agent_cls = getattr ( importlib . import_module ( agent_module ) , agent_name )
logging . info ( "Starting agent:" )
with lan_sc2_env . LanSC2Env ( host = FLAGS . host , config_port = FLAGS . config_port , race = sc2_env . Race [ FLAGS . agent_race ] , step... |
def setup ( cli ) :
"""Everything to make skypipe ready to use""" | if not cli . global_config . loaded :
setup_dotcloud_account ( cli )
discover_satellite ( cli )
cli . success ( "Skypipe is ready for action" ) |
def urljoin ( netloc , port , ssl ) :
"""Basically the counter - part of : func : ` urlsplit ` .""" | rv = ( "https" if ssl else "http" ) + "://" + netloc
if ssl and port != 443 or not ssl and port != 80 :
rv += ":%i" % port
return rv |
def get_dir ( self , scope , class_ ) :
"""Return the callable function from appdirs , but with the
result wrapped in self . path _ class""" | prop_name = '{scope}_{class_}_dir' . format ( ** locals ( ) )
value = getattr ( self . wrapper , prop_name )
MultiPath = Multi . for_class ( self . path_class )
return MultiPath . detect ( value ) |
def create_hook ( self , auth , repo_name , hook_type , config , events = None , organization = None , active = False ) :
"""Creates a new hook , and returns the created hook .
: param auth . Authentication auth : authentication object , must be admin - level
: param str repo _ name : the name of the repo for w... | if events is None :
events = [ "push" ]
# default value is mutable , so assign inside body
data = { "type" : hook_type , "config" : config , "events" : events , "active" : active }
url = "/repos/{o}/{r}/hooks" . format ( o = organization , r = repo_name ) if organization is not None else "/repos/{r}/hooks" . format... |
def update_context ( self , context , update_mask = None , retry = google . api_core . gapic_v1 . method . DEFAULT , timeout = google . api_core . gapic_v1 . method . DEFAULT , metadata = None ) :
"""Updates the specified context .
Example :
> > > import dialogflow _ v2
> > > client = dialogflow _ v2 . Contex... | # Wrap the transport method to add retry and timeout logic .
if 'update_context' not in self . _inner_api_calls :
self . _inner_api_calls [ 'update_context' ] = google . api_core . gapic_v1 . method . wrap_method ( self . transport . update_context , default_retry = self . _method_configs [ 'UpdateContext' ] . retr... |
def export ( self ) :
"""Serializes to JSON .""" | fields = [ 'id' , 'host' , 'port' , 'user' ]
out = { }
for field in fields :
out [ field ] = getattr ( self , field , None )
out [ 'mountOptions' ] = self . mount_opts
out [ 'mountPoint' ] = self . mount_point
out [ 'beforeMount' ] = self . cmd_before_mount
out [ 'authType' ] = self . auth_method
out [ 'sshKey' ] =... |
def printAllElements ( self ) :
"""print out all modeled elements""" | cnt = 1
print ( "{id:<3s}: {name:<12s} {type:<10s} {classname:<10s}" . format ( id = 'ID' , name = 'Name' , type = 'Type' , classname = 'Class Name' ) )
for e in self . _lattice_eleobjlist :
print ( "{cnt:>03d}: {name:<12s} {type:<10s} {classname:<10s}" . format ( cnt = cnt , name = e . name , type = e . typename ,... |
def on_finish ( self ) :
"""Invoked once the request has been finished . Increment a counter
created in the format :
package [ . module ] . Class . METHOD . STATUS
tornado . web . RequestHandler . GET . 200""" | super ( StatsdMixin , self ) . on_finish ( )
key = '%s.%s.%s.%s' % ( self . __module__ , self . __class__ . __name__ , self . request . method , self . _status_code )
LOGGER . info ( 'Processing %s' , key )
self . statsd_incr ( key )
self . statsd_add_timing ( key , self . request . request_time ( ) * 1000 ) |
def summary_status ( call , data ) :
"""Retrieve status in regions of interest , along with heterogeneity metrics .
Provides output with overall purity and ploidy , along with region
specific calls .""" | out_file = None
if call . get ( "vrn_file" ) and os . path . exists ( call . get ( "vrn_file" ) ) :
out_file = os . path . join ( os . path . dirname ( call [ "vrn_file" ] ) , "%s-%s-lohsummary.yaml" % ( dd . get_sample_name ( data ) , call [ "variantcaller" ] ) )
if not utils . file_uptodate ( out_file , call ... |
def _config_logic ( napalm_device , loaded_result , test = False , debug = False , replace = False , commit_config = True , loaded_config = None , commit_in = None , commit_at = None , revert_in = None , revert_at = None , commit_jid = None , ** kwargs ) :
'''Builds the config logic for ` load _ config ` and ` load... | # As the Salt logic is built around independent events
# when it comes to configuration changes in the
# candidate DB on the network devices , we need to
# make sure we ' re using the same session .
# Hence , we need to pass the same object around .
# the napalm _ device object is inherited from
# the load _ config or ... |
def removeRandomLenPadding ( str , blocksize = AES_blocksize ) :
'ISO 10126 Padding ( withdrawn , 2007 ) : Remove Padding with random bytes + last byte equal to the number of padding bytes' | pad_len = ord ( str [ - 1 ] )
# last byte contains number of padding bytes
assert pad_len < blocksize , 'padding error'
assert pad_len < len ( str ) , 'padding error'
return str [ : - pad_len ] |
def _add_debugging_fields ( gelf_dict , record ) :
"""Add debugging fields to the given ` ` gelf _ dict ` `
: param gelf _ dict : dictionary representation of a GELF log .
: type gelf _ dict : dict
: param record : : class : ` logging . LogRecord ` to extract debugging
fields from to insert into the given `... | gelf_dict . update ( { 'file' : record . pathname , 'line' : record . lineno , '_function' : record . funcName , '_pid' : record . process , '_thread_name' : record . threadName , } )
# record . processName was added in Python 2.6.2
pn = getattr ( record , 'processName' , None )
if pn is not None :
gelf_dict [ '_pr... |
def default_login_checker ( user ) :
"""user must be a dictionary here default is
checking username / password
if login is ok returns True else False
: param user : dict { ' username ' : ' ' , ' password ' : ' ' }""" | username = user . get ( 'username' )
password = user . get ( 'password' )
the_username = os . environ . get ( 'SIMPLELOGIN_USERNAME' , current_app . config . get ( 'SIMPLELOGIN_USERNAME' , 'admin' ) )
the_password = os . environ . get ( 'SIMPLELOGIN_PASSWORD' , current_app . config . get ( 'SIMPLELOGIN_PASSWORD' , 'sec... |
def from_bytes ( cls , xbytes : bytes ) -> 'BlsEntity' :
"""Creates and Bls entity from bytes representation .
: param xbytes : Bytes representation of Bls entity
: return : BLS entity intance""" | logger = logging . getLogger ( __name__ )
logger . debug ( "BlsEntity::from_bytes: >>>" )
c_instance = c_void_p ( )
do_call ( cls . from_bytes_handler , xbytes , len ( xbytes ) , byref ( c_instance ) )
res = cls ( c_instance )
logger . debug ( "BlsEntity::from_bytes: <<< res: %r" , res )
return res |
def get_child_vault_ids ( self , vault_id ) :
"""Gets the child ` ` Ids ` ` of the given vault .
arg : vault _ id ( osid . id . Id ) : the ` ` Id ` ` to query
return : ( osid . id . IdList ) - the children of the vault
raise : NotFound - ` ` vault _ id ` ` is not found
raise : NullArgument - ` ` vault _ id ... | # Implemented from template for
# osid . resource . BinHierarchySession . get _ child _ bin _ ids
if self . _catalog_session is not None :
return self . _catalog_session . get_child_catalog_ids ( catalog_id = vault_id )
return self . _hierarchy_session . get_children ( id_ = vault_id ) |
def decode ( self , name ) :
"""Translate a target name into its integer code .
> > > planets . decode ( ' Venus ' )
299
Raises ` ` ValueError ` ` if you supply an unknown name , or
` ` KeyError ` ` if the target is missing from this kernel . You can
supply an integer code if you already have one and just... | if isinstance ( name , int ) :
code = name
else :
name = name . upper ( )
code = _targets . get ( name )
if code is None :
raise ValueError ( 'unknown SPICE target {0!r}' . format ( name ) )
if code not in self . codes :
targets = ', ' . join ( _format_code_and_name ( c ) for c in self . cod... |
def ServiceWorker_deliverPushMessage ( self , origin , registrationId , data ) :
"""Function path : ServiceWorker . deliverPushMessage
Domain : ServiceWorker
Method name : deliverPushMessage
Parameters :
Required arguments :
' origin ' ( type : string ) - > No description
' registrationId ' ( type : str... | assert isinstance ( origin , ( str , ) ) , "Argument 'origin' must be of type '['str']'. Received type: '%s'" % type ( origin )
assert isinstance ( registrationId , ( str , ) ) , "Argument 'registrationId' must be of type '['str']'. Received type: '%s'" % type ( registrationId )
assert isinstance ( data , ( str , ) ) ,... |
def ipython_only ( option ) :
"""Mark that an option should only be exposed in IPython .
Parameters
option : decorator
A click . option decorator .
Returns
ipython _ only _ dec : decorator
A decorator that correctly applies the argument even when not
using IPython mode .""" | if __IPYTHON__ :
return option
argname = extract_option_object ( option ) . name
def d ( f ) :
@ wraps ( f )
def _ ( * args , ** kwargs ) :
kwargs [ argname ] = None
return f ( * args , ** kwargs )
return _
return d |
def make_nn_descent ( dist , dist_args ) :
"""Create a numba accelerated version of nearest neighbor descent
specialised for the given distance metric and metric arguments . Numba
doesn ' t support higher order functions directly , but we can instead JIT
compile the version of NN - descent for any given metri... | @ numba . njit ( parallel = True )
def nn_descent ( data , n_neighbors , rng_state , max_candidates = 50 , n_iters = 10 , delta = 0.001 , rho = 0.5 , rp_tree_init = True , leaf_array = None , verbose = False , ) :
n_vertices = data . shape [ 0 ]
current_graph = make_heap ( data . shape [ 0 ] , n_neighbors )
... |
def train ( self , ds ) :
"""Run training step : solve for best - fit spectral model""" | if self . useErrors :
self . coeffs , self . scatters , self . new_tr_labels , self . chisqs , self . pivots , self . scales = _train_model_new ( ds )
else :
self . coeffs , self . scatters , self . chisqs , self . pivots , self . scales = _train_model ( ds ) |
def is_in_schedule_mode ( self ) :
"""Returns True if base _ station is currently on a scheduled mode .""" | resource = "schedule"
mode_event = self . publish_and_get_event ( resource )
if mode_event and mode_event . get ( "resource" , None ) == "schedule" :
properties = mode_event . get ( 'properties' )
return properties . get ( "active" , False )
return False |
def distance_tt_point ( a , b ) :
"""Euclidean distance between two ( tracktotrip ) points
Args :
a ( : obj : ` Point ` )
b ( : obj : ` Point ` )
Returns :
float""" | return math . sqrt ( ( b . lat - a . lat ) ** 2 + ( b . lon - a . lon ) ** 2 ) |
def _prepare_encryption_table ( ) :
"""Prepare encryption table for MPQ hash function .""" | seed = 0x00100001
crypt_table = { }
for i in range ( 256 ) :
index = i
for j in range ( 5 ) :
seed = ( seed * 125 + 3 ) % 0x2AAAAB
temp1 = ( seed & 0xFFFF ) << 0x10
seed = ( seed * 125 + 3 ) % 0x2AAAAB
temp2 = ( seed & 0xFFFF )
crypt_table [ index ] = ( temp1 | temp2 )
... |
def _last_commit ( self ) :
"""Retrieve the most recent commit message ( with ` ` svn log - l1 ` ` )
Returns :
tuple : ( datestr , ( revno , user , None , desc ) )
$ svn log - l1
r25701 | bhendrix | 2010-08-02 12:14:25 - 0500 ( Mon , 02 Aug 2010 ) | 1 line
added selection range traits to make it possible ... | cmd = [ 'svn' , 'log' '-l1' ]
op = self . sh ( cmd , shell = False )
data , rest = op . split ( '\n' , 2 ) [ 1 : ]
revno , user , datestr , lc = data . split ( ' | ' , 3 )
desc = '\n' . join ( rest . split ( '\n' ) [ 1 : - 2 ] )
revno = revno [ 1 : ]
# lc = long ( lc . rstrip ( ' line ' ) )
return datestr , ( revno , u... |
def start ( self ) :
"""Initiate the session by starting to execute the command with the peer .
: return : The : attr : ` ~ . xso . Command . first _ payload ` of the response
This sends an empty command IQ request with the
: attr : ` ~ . ActionType . EXECUTE ` action .
The : attr : ` status ` , : attr : ` ... | if self . _response is not None :
raise RuntimeError ( "command execution already started" )
request = aioxmpp . IQ ( type_ = aioxmpp . IQType . SET , to = self . _peer_jid , payload = adhoc_xso . Command ( self . _command_name ) , )
self . _response = yield from self . _stream . send_iq_and_wait_for_reply ( reques... |
def validate_parameters ( self ) :
"""Validate that the parameters are correctly specified .""" | for p in self . params :
if p not in self . known_params :
raise errors . UnknownParameter ( p , self . known_params ) |
def p_flatten ( self , obj , ** kwargs ) :
"""Flatten a list of lists of lists . . . of strings into a string
This is usually used as the action for sequence expressions :
. . code - block : :
my _ rule < - ' a ' . ' c ' { p _ flatten }
With the input " abc " and no action , this rule returns [ ' a ' , ' b ... | if isinstance ( obj , six . string_types ) :
return obj
result = ""
for i in obj :
result += self . p_flatten ( i )
return result |
def open_sciobj_file_by_path ( abs_path , write = False ) :
"""Open a SciObj file for read or write . If opened for write , create any missing
directories . For a SciObj stored in the default SciObj store , the path includes the
PID hash based directory levels .
This is the only method in GMN that opens SciOb... | if write :
d1_common . utils . filesystem . create_missing_directories_for_file ( abs_path )
return open ( abs_path , 'wb' if write else 'rb' ) |
def apply_T1 ( word ) :
'''There is a syllable boundary in front of every CV - sequence .''' | # split consonants and vowels : ' balloon ' - > [ ' b ' , ' a ' , ' ll ' , ' oo ' , ' n ' ]
WORD = [ w for w in re . split ( '([ieAyOauo]+)' , word ) if w ]
count = 0
for i , v in enumerate ( WORD ) :
if i == 0 and is_consonant ( v [ 0 ] ) :
continue
elif is_consonant ( v [ 0 ] ) and i + 1 != len ( WORD... |
def assign ( self , ** kwargs ) :
r"""Assign new columns to a DataFrame .
Returns a new object with all original columns in addition to new ones .
Existing columns that are re - assigned will be overwritten .
Parameters
* * kwargs : dict of { str : callable or Series }
The column names are keywords . If t... | data = self . copy ( )
# > = 3.6 preserve order of kwargs
if PY36 :
for k , v in kwargs . items ( ) :
data [ k ] = com . apply_if_callable ( v , data )
else : # < = 3.5 : do all calculations first . . .
results = OrderedDict ( )
for k , v in kwargs . items ( ) :
results [ k ] = com . apply_i... |
async def variant ( self , elem = None , elem_type = None , params = None ) :
"""Loads / dumps variant type
: param elem :
: param elem _ type :
: param params :
: return :""" | elem_type = elem_type if elem_type else elem . __class__
version = await self . version ( elem_type , params , elem = elem )
if self . is_tracked ( ) :
return self . get_tracked ( )
if hasattr ( elem_type , 'boost_serialize' ) :
elem = elem_type ( ) if elem is None else elem
self . pop_track ( )
return ... |
def parse_document ( xmlcontent ) :
"""Parse document with content .
Content is placed in file ' document . xml ' .""" | document = etree . fromstring ( xmlcontent )
body = document . xpath ( './/w:body' , namespaces = NAMESPACES ) [ 0 ]
document = doc . Document ( )
for elem in body :
if elem . tag == _name ( '{{{w}}}p' ) :
document . elements . append ( parse_paragraph ( document , elem ) )
if elem . tag == _name ( '{{{... |
def exists ( self , document_or_id = None , session = None , ** kwargs ) :
"""Check if a file exists in this instance of : class : ` GridFS ` .
The file to check for can be specified by the value of its
` ` _ id ` ` key , or by passing in a query document . A query
document can be passed in as dictionary , or... | if kwargs :
f = self . __files . find_one ( kwargs , [ "_id" ] , session = session )
else :
f = self . __files . find_one ( document_or_id , [ "_id" ] , session = session )
return f is not None |
def set_menu_separator ( self , img ) :
"""Sets the menu separator .
Must be called before adding entries to the menu""" | if img :
self . menu_separator_tag = '<img src="{}" alt="/" />' . format ( self . _rel ( img ) )
else :
self . menu_separator_tag = None |
def imagetransformer_base_12l_8h_big ( ) :
"""big 1d model for conditional image generation .""" | hparams = imagetransformer_sep_channels_8l_8h ( )
hparams . filter_size = 1024
hparams . num_decoder_layers = 12
hparams . batch_size = 1
hparams . hidden_size = 512
hparams . learning_rate_warmup_steps = 4000
hparams . sampling_method = "random"
hparams . beam_size = 1
hparams . block_width = 256
return hparams |
def log_subtract ( loga , logb ) :
r"""Numerically stable method for avoiding overflow errors when calculating
: math : ` \ log ( a - b ) ` , given : math : ` \ log ( a ) ` , : math : ` \ log ( a ) ` and that
: math : ` a > b ` .
See https : / / hips . seas . harvard . edu / blog / 2013/01/09 / computing - lo... | return loga + np . log ( 1 - np . exp ( logb - loga ) ) |
def per_version_data ( self ) :
"""Return download data by version .
: return : dict of cache data ; keys are datetime objects , values are
dict of version ( str ) to count ( int )
: rtype : dict""" | ret = { }
for cache_date in self . cache_dates :
data = self . _cache_get ( cache_date )
if len ( data [ 'by_version' ] ) == 0 :
data [ 'by_version' ] = { 'other' : 0 }
ret [ cache_date ] = data [ 'by_version' ]
return ret |
def history ( self , currency , since = 0 , until = 9999999999 , limit = 500 , wallet = 'exchange' ) :
"""View you balance ledger entries
: param currency : currency to look for
: param since : Optional . Return only the history after this timestamp .
: param until : Optional . Return only the history before ... | payload = { "request" : "/v1/history" , "nonce" : self . _nonce , "currency" : currency , "since" : since , "until" : until , "limit" : limit , "wallet" : wallet }
signed_payload = self . _sign_payload ( payload )
r = requests . post ( self . URL + "/history" , headers = signed_payload , verify = True )
json_resp = r .... |
def simulated_annealing ( problem , schedule = _exp_schedule , iterations_limit = 0 , viewer = None ) :
'''Simulated annealing .
schedule is the scheduling function that decides the chance to choose worst
nodes depending on the time .
If iterations _ limit is specified , the algorithm will end after that
nu... | return _local_search ( problem , _create_simulated_annealing_expander ( schedule ) , iterations_limit = iterations_limit , fringe_size = 1 , stop_when_no_better = iterations_limit == 0 , viewer = viewer ) |
def convert_to_process_params_dict ( opt ) :
"""Takes the namespace object ( opt ) from the multi - detector interface and
returns a dictionary of command line options that will be handled correctly
by the register _ to _ process _ params ligolw function .""" | opt = copy . deepcopy ( opt )
for arg , val in vars ( opt ) . items ( ) :
if isinstance ( val , DictWithDefaultReturn ) :
new_val = [ ]
for key in val . keys ( ) :
if isinstance ( val [ key ] , list ) :
for item in val [ key ] :
if item is not None :
... |
def query ( self , query ) :
"""Sends a query to the Riemann server
> > > client . query ( ' true ' )
: returns : A list of event dictionaries taken from the response
: raises Exception : if used with a : py : class : ` . UDPTransport `""" | if isinstance ( self . transport , riemann_client . transport . UDPTransport ) :
raise Exception ( 'Cannot query the Riemann server over UDP' )
response = self . send_query ( query )
return [ self . create_dict ( e ) for e in response . events ] |
def _remove_buffers ( state ) :
"""Return ( state _ without _ buffers , buffer _ paths , buffers ) for binary message parts
A binary message part is a memoryview , bytearray , or python 3 bytes object .
As an example :
> > > state = { ' plain ' : [ 0 , ' text ' ] , ' x ' : { ' ar ' : memoryview ( ar1 ) } , ' ... | buffer_paths , buffers = [ ] , [ ]
state = _separate_buffers ( state , [ ] , buffer_paths , buffers )
return state , buffer_paths , buffers |
def display ( self ) :
"""dump operation""" | print ( "{}" . format ( self ) )
for task in self . tasks :
print ( " - {}" . format ( task ) ) |
def convert_ensembl_to_entrez ( self , ensembl ) :
"""Convert Ensembl Id to Entrez Gene Id""" | if 'ENST' in ensembl :
pass
else :
raise ( IndexError )
# Submit resquest to NCBI eutils / Gene database
server = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" + self . options + "&db=gene&term={0}" . format ( ensembl )
r = requests . get ( server , headers = { "Content-Type" : "text/xml" } )
if ... |
def loop ( self ) :
"""The actual infinite loop for this transformation .""" | logger . debug ( "Node loop starts for {!r}." . format ( self ) )
while self . should_loop :
try :
self . step ( )
except InactiveReadableError :
break
logger . debug ( "Node loop ends for {!r}." . format ( self ) ) |
def attention_lm_moe_memory_efficient ( ) :
"""Memory - efficient version .""" | hparams = attention_lm_moe_large ( )
hparams . diet_experts = True
hparams . layer_preprocess_sequence = "n"
hparams . layer_postprocess_sequence = "da"
hparams . layer_prepostprocess_dropout = 0.0
hparams . memory_efficient_ffn = True
hparams . attention_type = AttentionType . MEMORY_EFFICIENT
hparams . num_heads = 8
... |
def _get_preprocessed ( self , data ) :
"""Returns :
( DeveloperPackage , new _ data ) 2 - tuple IFF the preprocess function
changed the package ; otherwise None .""" | from rez . serialise import process_python_objects
from rez . utils . data_utils import get_dict_diff_str
from copy import deepcopy
with add_sys_paths ( config . package_definition_build_python_paths ) :
preprocess_func = getattr ( self , "preprocess" , None )
if preprocess_func :
print_info ( "Applying... |
def _remove_persistent_module ( mod , comment ) :
'''Remove module from loader . conf . If comment is true only comment line where
module is .''' | if not mod or mod not in mod_list ( True ) :
return set ( )
if comment :
__salt__ [ 'file.comment' ] ( _LOADER_CONF , _MODULE_RE . format ( mod ) )
else :
__salt__ [ 'file.sed' ] ( _LOADER_CONF , _MODULE_RE . format ( mod ) , '' )
return set ( [ mod ] ) |
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