signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def _get_deltas ( self , sites ) :
"""Return delta ' s for equation 4
delta _ C = 1 for site class C , 0 otherwise
delta _ D = 1 for site class D , 0 otherwise""" | siteclass = sites . siteclass
delta_C = np . zeros_like ( siteclass , dtype = np . float )
delta_C [ siteclass == b'C' ] = 1
delta_D = np . zeros_like ( siteclass , dtype = np . float )
delta_D [ siteclass == b'D' ] = 1
return delta_C , delta_D |
def get_branch ( self , repository_id , name , project = None , base_version_descriptor = None ) :
"""GetBranch .
Retrieve statistics about a single branch .
: param str repository _ id : The name or ID of the repository .
: param str name : Name of the branch .
: param str project : Project ID or project n... | route_values = { }
if project is not None :
route_values [ 'project' ] = self . _serialize . url ( 'project' , project , 'str' )
if repository_id is not None :
route_values [ 'repositoryId' ] = self . _serialize . url ( 'repository_id' , repository_id , 'str' )
query_parameters = { }
if name is not None :
q... |
def get_bbox ( self ) :
"""Returns ( ( top , left ) , ( bottom , right ) ) of bounding box
A bounding box is the smallest rectangle that contains all selections .
Non - specified boundaries are None .""" | bb_top , bb_left , bb_bottom , bb_right = [ None ] * 4
# Block selections
for top_left , bottom_right in zip ( self . block_tl , self . block_br ) :
top , left = top_left
bottom , right = bottom_right
if bb_top is None or bb_top > top :
bb_top = top
if bb_left is None or bb_left > left :
... |
def put_manifest ( self , manifest ) :
"""Store the manifest .""" | logger . debug ( "Putting manifest" )
text = json . dumps ( manifest , indent = 2 , sort_keys = True )
key = self . get_manifest_key ( )
self . put_text ( key , text ) |
def updateTargetState ( self , newState ) :
"""Updates the system target state and propagates that to all devices .
: param newState :
: return :""" | self . _targetStateProvider . state = loadTargetState ( newState , self . _targetStateProvider . state )
for device in self . deviceController . getDevices ( ) :
self . updateDeviceState ( device . payload ) |
def _closest_location ( self , location_map , target ) :
"""Return path of font whose location is closest to target .""" | def dist ( a , b ) :
return math . sqrt ( sum ( ( a [ k ] - b [ k ] ) ** 2 for k in a . keys ( ) ) )
paths = iter ( location_map . keys ( ) )
closest = next ( paths )
closest_dist = dist ( target , location_map [ closest ] )
for path in paths :
cur_dist = dist ( target , location_map [ path ] )
if cur_dist ... |
def get_configuration ( self , uri ) :
'''get the configuration of a PartStudio
Args :
- uri ( dict ) : points to a particular element
Returns :
- requests . Response : Onshape response data''' | req_headers = { 'Accept' : 'application/vnd.onshape.v1+json' , 'Content-Type' : 'application/json' }
return self . _api . request ( 'get' , '/api/partstudios/d/' + uri [ "did" ] + '/' + uri [ "wvm_type" ] + '/' + uri [ "wvm" ] + '/e/' + uri [ "eid" ] + '/configuration' , headers = req_headers ) |
def save_as_cytoscape_html ( tree , out_html , column2states , layout = 'dagre' , name_feature = 'name' , name2colour = None , n2tooltip = None , years = None , is_compressed = True , n2date = None , date_column = 'Dist. to root' ) :
"""Converts a tree to an html representation using Cytoscape . js .
If categorie... | graph_name = os . path . splitext ( os . path . basename ( out_html ) ) [ 0 ]
json_dict , clazzes = _tree2json ( tree , column2states , name_feature = name_feature , node2tooltip = n2tooltip , years = years , is_compressed = is_compressed , n2date = n2date )
env = Environment ( loader = PackageLoader ( 'pastml' ) )
tem... |
def _python_to_mod_modify ( changes : Changeset ) -> Dict [ str , List [ Tuple [ Operation , List [ bytes ] ] ] ] :
"""Convert a LdapChanges object to a modlist for a modify operation .""" | table : LdapObjectClass = type ( changes . src )
changes = changes . changes
result : Dict [ str , List [ Tuple [ Operation , List [ bytes ] ] ] ] = { }
for key , l in changes . items ( ) :
field = _get_field_by_name ( table , key )
if field . db_field :
try :
new_list = [ ( operation , fiel... |
def get_spontaneous_environment ( * args ) :
"""Return a new spontaneous environment . A spontaneous environment is an
unnamed and unaccessible ( in theory ) environment that is used for
templates generated from a string and not from the file system .""" | try :
env = _spontaneous_environments . get ( args )
except TypeError :
return Environment ( * args )
if env is not None :
return env
_spontaneous_environments [ args ] = env = Environment ( * args )
env . shared = True
return env |
def view ( azimuth = None , elevation = None , distance = None ) :
"""Set camera angles and distance and return the current .
: param float azimuth : rotation around the axis pointing up in degrees
: param float elevation : rotation where + 90 means ' up ' , - 90 means ' down ' , in degrees
: param float dist... | fig = gcf ( )
# first calculate the current values
x , y , z = fig . camera . position
r = np . sqrt ( x ** 2 + y ** 2 + z ** 2 )
az = np . degrees ( np . arctan2 ( x , z ) )
el = np . degrees ( np . arcsin ( y / r ) )
if azimuth is None :
azimuth = az
if elevation is None :
elevation = el
if distance is None :... |
def filter_regex ( names , regex ) :
"""Return a tuple of strings that match the regular expression pattern .""" | return tuple ( name for name in names if regex . search ( name ) is not None ) |
def get_context ( self ) :
"""Add mails to the context""" | context = super ( MailListView , self ) . get_context ( )
mail_list = registered_mails_names ( )
context [ 'mail_map' ] = mail_list
return context |
def get_machine_usage ( machine , start , end ) :
"""Return a tuple of cpu hours and number of jobs for a machine
for a given period
Keyword arguments :
machine - -
start - - start date
end - - end date""" | try :
cache = MachineCache . objects . get ( machine = machine , date = datetime . date . today ( ) , start = start , end = end )
return cache . cpu_time , cache . no_jobs
except MachineCache . DoesNotExist :
return 0 , 0 |
def _get_numdiff_hessian_steps_func ( objective_func , nmr_steps , step_ratio ) :
"""Get a function to compute the multiple step sizes for a single element of the Hessian .""" | return SimpleCLFunction . from_string ( '''
/**
* Compute one element of the Hessian for a number of steps.
*
* This uses the initial steps in the data structure, indexed by the parameters to change (px, py).
*
* Args:
* data: the data container
*... |
def subunits ( self ) :
"""DictList : Subunits represented as a DictList of Protein objects""" | # TODO : [ VizRecon ]
# TODO : will need to adapt this to allow for input of previously created Protein objects
subunits = DictList ( )
for s in self . subunit_dict :
subunits . append ( Protein ( ident = s , description = 'Subunit of complex {}' . format ( self . id ) , root_dir = self . complex_dir , pdb_file_typ... |
def Target_setAutoAttach ( self , autoAttach , waitForDebuggerOnStart ) :
"""Function path : Target . setAutoAttach
Domain : Target
Method name : setAutoAttach
Parameters :
Required arguments :
' autoAttach ' ( type : boolean ) - > Whether to auto - attach to related targets .
' waitForDebuggerOnStart '... | assert isinstance ( autoAttach , ( bool , ) ) , "Argument 'autoAttach' must be of type '['bool']'. Received type: '%s'" % type ( autoAttach )
assert isinstance ( waitForDebuggerOnStart , ( bool , ) ) , "Argument 'waitForDebuggerOnStart' must be of type '['bool']'. Received type: '%s'" % type ( waitForDebuggerOnStart )
... |
def connect ( host = "localhost" , port = 1113 , discovery_host = None , discovery_port = 2113 , username = None , password = None , loop = None , name = None , selector = select_random , ) -> Client :
"""Create a new client .
Examples :
Since the Client is an async context manager , we can use it in a
with b... | discovery = get_discoverer ( host , port , discovery_host , discovery_port , selector )
dispatcher = MessageDispatcher ( name = name , loop = loop )
connector = Connector ( discovery , dispatcher , name = name )
credential = msg . Credential ( username , password ) if username and password else None
return Client ( con... |
def percentAt ( self , value ) :
"""Returns the percentage where the given value lies between this rulers
minimum and maximum values . If the value equals the minimum , then the
percent is 0 , if it equals the maximum , then the percent is 1 - any
value between will be a floating point . If the ruler is a cus... | if value is None :
return 0.0
values = self . values ( )
try :
return float ( values . index ( value ) ) / ( len ( values ) - 1 )
except ValueError :
return 0.0
except ZeroDivisionError :
return 1.0 |
def convert ( files , ** kwargs ) :
"""Wrap directory to pif as a dice extension
: param files : a list of files , which must be non - empty
: param kwargs : any additional keyword arguments
: return : the created pif""" | if len ( files ) < 1 :
raise ValueError ( "Files needs to be a non-empty list" )
if len ( files ) == 1 :
if os . path . isfile ( files [ 0 ] ) :
return files_to_pif ( files , ** kwargs )
else :
return directory_to_pif ( files [ 0 ] , ** kwargs )
else :
return files_to_pif ( [ x for x in ... |
def create_port_binding ( self , port , host ) :
"""Enqueue port binding create""" | if not self . get_instance_type ( port ) :
return
for pb_key in self . _get_binding_keys ( port , host ) :
pb_res = MechResource ( pb_key , a_const . PORT_BINDING_RESOURCE , a_const . CREATE )
self . provision_queue . put ( pb_res ) |
def spkpds ( body , center , framestr , typenum , first , last ) :
"""Perform routine error checks and if all check pass , pack the
descriptor for an SPK segment
http : / / naif . jpl . nasa . gov / pub / naif / toolkit _ docs / C / cspice / spkpds _ c . html
: param body : The NAIF ID code for the body of th... | body = ctypes . c_int ( body )
center = ctypes . c_int ( center )
framestr = stypes . stringToCharP ( framestr )
typenum = ctypes . c_int ( typenum )
first = ctypes . c_double ( first )
last = ctypes . c_double ( last )
descr = stypes . emptyDoubleVector ( 5 )
libspice . spkpds_c ( body , center , framestr , typenum , ... |
def train ( self , env_fn , hparams , simulated , save_continuously , epoch , sampling_temp = 1.0 , num_env_steps = None , env_step_multiplier = 1 , eval_env_fn = None , report_fn = None ) :
"""Train .""" | raise NotImplementedError ( ) |
def X_length ( self , new_window_length ) :
"""Use presets for length of the window .""" | self . parent . value ( 'window_length' , new_window_length )
self . parent . overview . update_position ( ) |
def get_all_accounts ( self ) :
"""iterates through trie to and yields non - blank leafs as accounts .""" | for address_hash , rlpdata in self . secure_trie . trie . iter_branch ( ) :
if rlpdata != trie . BLANK_NODE :
yield rlp . decode ( rlpdata , Account , db = self . db , addr = address_hash ) |
def _request_get_helper ( self , url , params = None ) :
'''API GET request helper''' | if not isinstance ( params , dict ) :
params = dict ( )
if self . api_key :
params [ 'api_key' ] = self . api_key
return requests . get ( url , params = params , timeout = 60 ) |
def _write_tfrecords_from_generator ( generator , output_files , shuffle = True ) :
"""Writes generated str records to output _ files in round - robin order .""" | if do_files_exist ( output_files ) :
raise ValueError ( "Pre-processed files already exists: {}." . format ( output_files ) )
with _incomplete_files ( output_files ) as tmp_files : # Write all shards
writers = [ tf . io . TFRecordWriter ( fname ) for fname in tmp_files ]
with _close_on_exit ( writers ) as w... |
def _get_LMv2_response ( user_name , password , domain_name , server_challenge , client_challenge ) :
"""[ MS - NLMP ] v28.0 2016-07-14
2.2.2.4 LMv2 _ RESPONSE
The LMv2 _ RESPONSE structure defines the NTLM v2 authentication LmChallengeResponse
in the AUTHENTICATE _ MESSAGE . This response is used only when N... | nt_hash = comphash . _ntowfv2 ( user_name , password , domain_name )
lm_hash = hmac . new ( nt_hash , ( server_challenge + client_challenge ) ) . digest ( )
response = lm_hash + client_challenge
return response |
def replay_block ( self , block_to_replay , limit = 5 ) :
"""Replay all transactions in parent currency to passed in " source " currency .
Block _ to _ replay can either be an integer or a block object .""" | if block_to_replay == 'latest' :
if self . verbose :
print ( "Getting latest %s block header" % source . upper ( ) )
block = get_block ( self . source , latest = True , verbose = self . verbose )
if self . verbose :
print ( "Latest %s block is #%s" % ( self . source . upper ( ) , block [ 'bl... |
def _upcase_word ( text , pos ) :
"""Uppercase the current ( or following ) word .""" | text , new_pos = _forward_word ( text , pos )
return text [ : pos ] + text [ pos : new_pos ] . upper ( ) + text [ new_pos : ] , new_pos |
def focusout ( self , event ) :
"""Change style on focus out events .""" | bc = self . style . lookup ( "TEntry" , "bordercolor" , ( "!focus" , ) )
dc = self . style . lookup ( "TEntry" , "darkcolor" , ( "!focus" , ) )
lc = self . style . lookup ( "TEntry" , "lightcolor" , ( "!focus" , ) )
self . style . configure ( "%s.spinbox.TFrame" % self . frame , bordercolor = bc , darkcolor = dc , ligh... |
def delete_forecast ( self , job_id , forecast_id = None , params = None ) :
"""` < http : / / www . elastic . co / guide / en / elasticsearch / reference / current / ml - delete - forecast . html > ` _
: arg job _ id : The ID of the job from which to delete forecasts
: arg forecast _ id : The ID of the forecas... | if job_id in SKIP_IN_PATH :
raise ValueError ( "Empty value passed for a required argument 'job_id'." )
return self . transport . perform_request ( "DELETE" , _make_path ( "_ml" , "anomaly_detectors" , job_id , "_forecast" , forecast_id ) , params = params , ) |
def describe ( id_or_link , ** kwargs ) :
''': param id _ or _ link : String containing an object ID or dict containing a DXLink ,
or a list of object IDs or dicts containing a DXLink .
Given an object ID , calls : meth : ` ~ dxpy . bindings . DXDataObject . describe ` on the object .
Example : :
describe (... | # If this is a list , extract the ids .
# TODO : modify the procedure to use project ID when possible
if isinstance ( id_or_link , basestring ) or is_dxlink ( id_or_link ) :
handler = get_handler ( id_or_link )
return handler . describe ( ** kwargs )
else :
links = [ ]
for link in id_or_link : # If this... |
def unpack_rsp ( cls , rsp_pb ) :
"""Convert from PLS response to user response""" | if rsp_pb . retType != RET_OK :
return RET_ERROR , rsp_pb . retMsg , None
raw_order_list = rsp_pb . s2c . orderList
order_list = [ OrderListQuery . parse_order ( rsp_pb , order ) for order in raw_order_list ]
return RET_OK , "" , order_list |
def _percent_match ( date_classes , tokens ) :
"""For each date class , return the percentage of tokens that the class matched ( floating point [ 0.0 - 1.0 ] ) . The
returned value is a tuple of length patterns . Tokens should be a list .""" | match_count = [ 0 ] * len ( date_classes )
for i , date_class in enumerate ( date_classes ) :
for token in tokens :
if date_class . is_match ( token ) :
match_count [ i ] += 1
percentages = tuple ( [ float ( m ) / len ( tokens ) for m in match_count ] )
return percentages |
def predict ( self , data , output_margin = False , ntree_limit = 0 , pred_leaf = False , pred_contribs = False , approx_contribs = False , pred_interactions = False , validate_features = True ) :
"""Predict with data .
. . note : : This function is not thread safe .
For each booster object , predict can only b... | option_mask = 0x00
if output_margin :
option_mask |= 0x01
if pred_leaf :
option_mask |= 0x02
if pred_contribs :
option_mask |= 0x04
if approx_contribs :
option_mask |= 0x08
if pred_interactions :
option_mask |= 0x10
if validate_features :
self . _validate_features ( data )
length = c_bst_ulong (... |
def itemsize_bits ( self ) :
"""Number of bits per element""" | if self . dtype is not None :
return self . dtype . itemsize * 8
else :
return sum ( x [ 1 ] for x in self . format ) |
def get_field_references ( ctx , field_names , simplify = False ) :
"""Create a mapping from fields to corresponding child indices
: param ctx : ANTLR node
: param field _ names : list of strings
: param simplify : if True , omits fields with empty lists or None
this makes it easy to detect nodes that only ... | field_dict = { }
for field_name in field_names :
field = get_field ( ctx , field_name )
if ( not simplify or field is not None and ( not isinstance ( field , list ) or len ( field ) > 0 ) ) :
if isinstance ( field , list ) :
value = [ ctx . children . index ( el ) for el in field ]
e... |
def ocrd_cli_options ( f ) :
"""Implement MP CLI .
Usage : :
import ocrd _ click _ cli from ocrd . utils
@ click . command ( )
@ ocrd _ click _ cli
def cli ( mets _ url ) :
print ( mets _ url )""" | params = [ click . option ( '-m' , '--mets' , help = "METS URL to validate" ) , click . option ( '-w' , '--working-dir' , help = "Working Directory" ) , click . option ( '-I' , '--input-file-grp' , help = 'File group(s) used as input.' , default = 'INPUT' ) , click . option ( '-O' , '--output-file-grp' , help = 'File g... |
def __reorganize_chron_header ( line ) :
"""Reorganize the list of variables . If there are units given , log them .
: param str line :
: return dict : key : variable , val : units ( optional )""" | d = { }
# Header variables should be tab - delimited . Use regex to split by tabs
m = re . split ( re_tab_split , line )
# If there was an output match from the line , then keep going
if m : # Loop once for each variable in the line
for s in m : # Match the variable to the ' variable ( units ) ' regex to look for u... |
def scheduled ( ) :
'''List scheduled jobs .''' | for job in sorted ( schedulables ( ) , key = lambda s : s . name ) :
for task in PeriodicTask . objects ( task = job . name ) :
label = job_label ( task . task , task . args , task . kwargs )
echo ( SCHEDULE_LINE . format ( name = white ( task . name . encode ( 'utf8' ) ) , label = label , schedule ... |
def framewise ( self ) :
"""Property to determine whether the current frame should have
framewise normalization enabled . Required for bokeh plotting
classes to determine whether to send updated ranges for each
frame .""" | current_frames = [ el for f in self . traverse ( lambda x : x . current_frame ) for el in ( f . traverse ( lambda x : x , [ Element ] ) if f else [ ] ) ]
current_frames = util . unique_iterator ( current_frames )
return any ( self . lookup_options ( frame , 'norm' ) . options . get ( 'framewise' ) for frame in current_... |
def _get_repo_filter ( self , query ) :
"""Apply repository wide side filter / mask query""" | if self . filter is not None :
return query . extra ( where = [ self . filter ] )
return query |
def _get_attribute_dimension ( trait_name , mark_type = None ) :
"""Returns the dimension for the name of the trait for the specified mark .
If ` mark _ type ` is ` None ` , then the ` trait _ name ` is returned
as is .
Returns ` None ` if the ` trait _ name ` is not valid for ` mark _ type ` .""" | if ( mark_type is None ) :
return trait_name
scale_metadata = mark_type . class_traits ( ) [ 'scales_metadata' ] . default_args [ 0 ]
return scale_metadata . get ( trait_name , { } ) . get ( 'dimension' , None ) |
def update_objective ( self , objective_form ) :
"""Updates an existing objective .
arg : objective _ form ( osid . learning . ObjectiveForm ) : the form
containing the elements to be updated
raise : IllegalState - ` ` objective _ form ` ` already used in an
update transaction
raise : InvalidArgument - th... | # Implemented from template for
# osid . resource . ResourceAdminSession . update _ resource _ template
collection = JSONClientValidated ( 'learning' , collection = 'Objective' , runtime = self . _runtime )
if not isinstance ( objective_form , ABCObjectiveForm ) :
raise errors . InvalidArgument ( 'argument type is ... |
def qualifier_encoded ( self ) :
"""Union [ str , bytes ] : The qualifier encoded in binary .
The type is ` ` str ` ` ( Python 2 . x ) or ` ` bytes ` ` ( Python 3 . x ) . The module
will handle base64 encoding for you .
See
https : / / cloud . google . com / bigquery / docs / reference / rest / v2 / jobs # ... | prop = self . _properties . get ( "qualifierEncoded" )
if prop is None :
return None
return base64 . standard_b64decode ( _to_bytes ( prop ) ) |
def fetch ( self ) :
"""Fetch a FeedbackInstance
: returns : Fetched FeedbackInstance
: rtype : twilio . rest . api . v2010 . account . call . feedback . FeedbackInstance""" | params = values . of ( { } )
payload = self . _version . fetch ( 'GET' , self . _uri , params = params , )
return FeedbackInstance ( self . _version , payload , account_sid = self . _solution [ 'account_sid' ] , call_sid = self . _solution [ 'call_sid' ] , ) |
def propagate ( cls , date ) :
"""Compute the position of the sun at a given date
Args :
date ( ~ beyond . utils . date . Date )
Return :
~ beyond . orbits . orbit . Orbit : Position of the sun in MOD frame
Example :
. . code - block : : python
from beyond . utils . date import Date
SunPropagator . ... | date = date . change_scale ( 'UT1' )
t_ut1 = date . julian_century
lambda_M = 280.460 + 36000.771 * t_ut1
M = np . radians ( 357.5291092 + 35999.05034 * t_ut1 )
lambda_el = np . radians ( lambda_M + 1.914666471 * np . sin ( M ) + 0.019994643 * np . sin ( 2 * M ) )
r = 1.000140612 - 0.016708617 * np . cos ( M ) - 0.0001... |
def update_asset ( self , asset_form = None ) :
"""Updates an existing asset .
: param asset _ form : the form containing the elements to be updated
: type asset _ form : ` ` osid . repository . AssetForm ` `
: raise : ` ` IllegalState ` ` - - ` ` asset _ form ` ` already used in anupdate transaction
: rais... | if asset_form is None :
raise NullArgument ( )
if not isinstance ( asset_form , abc_repository_objects . AssetForm ) :
raise InvalidArgument ( 'argument type is not an AssetForm' )
if not asset_form . is_for_update ( ) :
raise InvalidArgument ( 'form is for create only, not update' )
try :
if self . _fo... |
def _send_request ( self ) :
"""Sends the request to the backend .""" | if isinstance ( self . _worker , str ) :
classname = self . _worker
else :
classname = '%s.%s' % ( self . _worker . __module__ , self . _worker . __name__ )
self . request_id = str ( uuid . uuid4 ( ) )
self . send ( { 'request_id' : self . request_id , 'worker' : classname , 'data' : self . _args } ) |
def print_plugin_list ( plugins : Dict [ str , pkg_resources . EntryPoint ] ) :
"""Prints all registered plugins and checks if they can be loaded or not .
: param plugins : plugins
: type plugins : Dict [ str , ~ pkg _ resources . EntryPoint ]""" | for trigger , entry_point in plugins . items ( ) :
try :
plugin_class = entry_point . load ( )
version = str ( plugin_class . _info . version )
print ( f"{trigger} (ok)\n" f" {version}" )
except Exception :
print ( f"{trigger} (failed)" ) |
def info ( context , keywords , x86 , x64 , x32 , common ) :
"""Find in the Linux system calls .""" | logging . info ( _ ( 'Current Mode: Find in Linux' ) )
database = context . obj [ 'database' ]
for one in keywords :
abis = [ 'i386' , 'x64' , 'common' , 'x32' ]
if x86 :
abis = [ 'i386' ]
if x64 :
abis = [ 'x64' , 'common' ]
if x32 :
abis = [ 'x32' , 'common' ]
if common :
... |
def _update_property_keys ( cls ) :
"""Set unspecified property _ keys for each ConfigProperty to the name of the class attr""" | for attr_name , config_prop in cls . _iter_config_props ( ) :
if config_prop . property_key is None :
config_prop . property_key = attr_name |
def _validate_resource_dict ( cls , logical_id , resource_dict ) :
"""Validates that the provided resource dict contains the correct Type string , and the required Properties dict .
: param dict resource _ dict : the resource dict to validate
: returns : True if the resource dict has the expected format
: rty... | if 'Type' not in resource_dict :
raise InvalidResourceException ( logical_id , "Resource dict missing key 'Type'." )
if resource_dict [ 'Type' ] != cls . resource_type :
raise InvalidResourceException ( logical_id , "Resource has incorrect Type; expected '{expected}', " "got '{actual}'" . format ( expected = cl... |
def get_row_metadata ( gctx_file_path , convert_neg_666 = True ) :
"""Opens . gctx file and returns only row metadata
Input :
Mandatory :
- gctx _ file _ path ( str ) : full path to gctx file you want to parse .
Optional :
- convert _ neg _ 666 ( bool ) : whether to convert - 666 values to num
Output : ... | full_path = os . path . expanduser ( gctx_file_path )
# open file
gctx_file = h5py . File ( full_path , "r" )
row_dset = gctx_file [ row_meta_group_node ]
row_meta = parse_metadata_df ( "row" , row_dset , convert_neg_666 )
gctx_file . close ( )
return row_meta |
def _wrap ( text , wrap_max = 80 , indent = 4 ) :
"""Wrap text at given width using textwrap module .
text ( unicode ) : Text to wrap . If it ' s a Path , it ' s converted to string .
wrap _ max ( int ) : Maximum line length ( indent is deducted ) .
indent ( int ) : Number of spaces for indentation .
RETURN... | indent = indent * ' '
wrap_width = wrap_max - len ( indent )
if isinstance ( text , Path ) :
text = path2str ( text )
return textwrap . fill ( text , width = wrap_width , initial_indent = indent , subsequent_indent = indent , break_long_words = False , break_on_hyphens = False ) |
def POST ( self , ** kwargs ) :
r'''Easily generate keys for a minion and auto - accept the new key
Accepts all the same parameters as the : py : func : ` key . gen _ accept
< salt . wheel . key . gen _ accept > ` .
. . note : : A note about ` ` curl ` `
Avoid using the ` ` - i ` ` flag or HTTP headers will... | lowstate = cherrypy . request . lowstate
lowstate [ 0 ] . update ( { 'client' : 'wheel' , 'fun' : 'key.gen_accept' , } )
if 'mid' in lowstate [ 0 ] :
lowstate [ 0 ] [ 'id_' ] = lowstate [ 0 ] . pop ( 'mid' )
result = self . exec_lowstate ( )
ret = next ( result , { } ) . get ( 'data' , { } ) . get ( 'return' , { } ... |
def user_organization_memberships ( self , user_id , ** kwargs ) :
"https : / / developer . zendesk . com / rest _ api / docs / core / organization _ memberships # list - memberships" | api_path = "/api/v2/users/{user_id}/organization_memberships.json"
api_path = api_path . format ( user_id = user_id )
return self . call ( api_path , ** kwargs ) |
def download_dataset ( self , dataset_name , local_path , how = "stream" ) :
"""It downloads from the repository the specified dataset and puts it
in the specified local folder
: param dataset _ name : the name the dataset has in the repository
: param local _ path : where you want to save the dataset
: par... | if not os . path . isdir ( local_path ) :
os . makedirs ( local_path )
else :
raise ValueError ( "Path {} already exists!" . format ( local_path ) )
local_path = os . path . join ( local_path , FILES_FOLDER )
os . makedirs ( local_path )
if how == 'zip' :
return self . download_as_zip ( dataset_name , local... |
def setnil ( self , flag = True ) :
"""Set this node to I { nil } as defined by having an I { xsi : nil } = I { flag }
attribute .
@ param flag : A flag indicating how I { xsi : nil } will be set .
@ type flag : boolean
@ return : self
@ rtype : L { Element }""" | p , u = Namespace . xsins
name = ":" . join ( ( p , "nil" ) )
self . set ( name , str ( flag ) . lower ( ) )
self . addPrefix ( p , u )
if flag :
self . text = None
return self |
def _fadn_orth ( vec , geom ) :
"""First non - zero Atomic Displacement Non - Orthogonal to Vec
Utility function to identify the first atomic displacement in a geometry
that is ( a ) not the zero vector ; and ( b ) not normal to the reference vector .
Parameters
vec
length - 3 | npfloat _ | - -
Referenc... | # Imports
import numpy as np
from scipy import linalg as spla
from . . const import PRM
from . . error import InertiaError
from . vector import orthonorm_check as onchk
# Geom and vec must both be the right shape
if not ( len ( geom . shape ) == 1 and geom . shape [ 0 ] % 3 == 0 ) :
raise ValueError ( "Geometry is ... |
def find ( self , * params ) :
"""按照简单 、 一般 、 特殊的顺序寻找新闻发布时间
Keyword * params :
params - - 可以接收多个含有时间的文本 , str类型""" | for string in params :
self . easy_time_extrator ( string )
if self . check_time_extrator ( ) :
log ( 'debug' , '通过简单模式找到时间信息' )
return self . check_time_extrator ( )
for string in params :
self . common_time_extrator ( string )
if self . check_time_extrator ( ) :
log ( 'debug' ,... |
def p_field_expr ( p ) :
"""expr : expr FIELD""" | p [ 0 ] = node . expr ( op = "." , args = node . expr_list ( [ p [ 1 ] , node . ident ( name = p [ 2 ] , lineno = p . lineno ( 2 ) , lexpos = p . lexpos ( 2 ) ) ] ) ) |
def md5 ( filename ) :
'''Return MD5 hex digest of local file , or None if file is not present .''' | if not os . path . exists ( filename ) :
return None
digest = _md5 ( )
blocksize = 64 * 1024
infile = open ( filename , 'rb' )
block = infile . read ( blocksize )
while block :
digest . update ( block )
block = infile . read ( blocksize )
infile . close ( )
return digest . hexdigest ( ) |
def log_init ( ) :
"""Function that sets log levels and format strings . Checks for the
OT _ API _ LOG _ LEVEL environment variable otherwise defaults to DEBUG .""" | fallback_log_level = 'INFO'
ot_log_level = hardware . config . log_level
if ot_log_level not in logging . _nameToLevel :
log . info ( "OT Log Level {} not found. Defaulting to {}" . format ( ot_log_level , fallback_log_level ) )
ot_log_level = fallback_log_level
level_value = logging . _nameToLevel [ ot_log_lev... |
def get_token ( self , token ) :
'''Request a token from the master''' | load = { }
load [ 'token' ] = token
load [ 'cmd' ] = 'get_token'
tdata = self . _send_token_request ( load )
return tdata |
def _get_item ( self , question_id ) :
"""we need a middle - man method to convert the unique " assessment - session "
authority question _ ids into " real " itemIds
BUT this also has to return the " magic " item , so we can ' t rely
on
question = self . get _ question ( question _ id )
ils = self . _ get... | question_map = self . _get_question_map ( question_id )
# Throws NotFound ( )
real_question_id = Id ( question_map [ 'questionId' ] )
return self . _get_item_lookup_session ( ) . get_item ( real_question_id ) |
def replace_braces ( s , env ) :
"""Makes tox substitutions to s , with respect to environment env .
Example
> > > replace _ braces ( " echo { posargs : { env : USER : } passed no posargs } " )
" echo andy passed no posargs "
Note : first " { env : USER : } " is replaced with os . environ . get ( " USER " ,... | def replace ( m ) :
return _replace_match ( m , env )
for _ in range ( DEPTH ) :
s = re . sub ( r"{[^{}]*}" , replace , s )
return s |
def iter_links_object_element ( cls , element ) :
'''Iterate ` ` object ` ` and ` ` embed ` ` elements .
This function also looks at ` ` codebase ` ` and ` ` archive ` ` attributes .''' | base_link = element . attrib . get ( 'codebase' , None )
if base_link : # lxml returns codebase as inline
link_type = element . attrib . get ( base_link )
yield LinkInfo ( element = element , tag = element . tag , attrib = 'codebase' , link = base_link , inline = True , linked = False , base_link = None , value... |
def publishAsync ( self , topic , payload , QoS , ackCallback = None ) :
"""* * Description * *
Publish a new message asynchronously to the desired topic with QoS and PUBACK callback . Note that the ack
callback configuration for a QoS0 publish request will be ignored as there are no PUBACK reception .
* * Sy... | return self . _mqtt_core . publish_async ( topic , payload , QoS , False , ackCallback ) |
def get_room_info ( self , room_id , ** kwargs ) :
"""Get various information about a specific channel / room
: param room _ id :
: param kwargs :
: return :""" | return GetRoomInfo ( settings = self . settings , ** kwargs ) . call ( room_id = room_id , ** kwargs ) |
def restrict ( self , point ) :
"""Apply the ` ` restrict ` ` method to all functions .
Returns a new farray .""" | items = [ f . restrict ( point ) for f in self . _items ]
return self . __class__ ( items , self . shape , self . ftype ) |
def clean ( mapping , bind , values ) :
"""Perform several types of string cleaning for titles etc . .""" | categories = { 'C' : ' ' }
for value in values :
if isinstance ( value , six . string_types ) :
value = normality . normalize ( value , lowercase = False , collapse = True , decompose = False , replace_categories = categories )
yield value |
def _get_diff ( environ , label , pop = False ) :
"""Get previously frozen key - value pairs .
: param str label : The name for the frozen environment .
: param bool pop : Destroy the freeze after use ; only allow application once .
: returns : ` ` dict ` ` of frozen values .""" | if pop :
blob = environ . pop ( _variable_name ( label ) , None )
else :
blob = environ . get ( _variable_name ( label ) )
return _loads ( blob ) if blob else { } |
def tox_get_python_executable ( envconfig ) :
"""Return a python executable for the given python base name .
The first plugin / hook which returns an executable path will determine it .
` ` envconfig ` ` is the testenv configuration which contains
per - testenv configuration , notably the ` ` . envname ` ` an... | try : # pylint : disable = no - member
pyenv = ( getattr ( py . path . local . sysfind ( 'pyenv' ) , 'strpath' , 'pyenv' ) or 'pyenv' )
cmd = [ pyenv , 'which' , envconfig . basepython ]
pipe = subprocess . Popen ( cmd , stdout = subprocess . PIPE , stderr = subprocess . PIPE , universal_newlines = True )
... |
def _persist ( self ) :
"""Run the command inside a thread so that we can catch output for each
line as it comes in and display it .""" | # run the block / command
for command in self . commands :
try :
process = Popen ( [ command ] , stdout = PIPE , stderr = PIPE , universal_newlines = True , env = self . env , shell = True , )
except Exception as e :
retcode = process . poll ( )
msg = "Command '{cmd}' {error} retcode {re... |
def export ( self , filename = 'element.zip' ) :
"""Export this element .
Usage : :
engine = Engine ( ' myfirewall ' )
extask = engine . export ( filename = ' fooexport . zip ' )
while not extask . done ( ) :
extask . wait ( 3)
print ( " Finished download task : % s " % extask . message ( ) )
print ( ... | from smc . administration . tasks import Task
return Task . download ( self , 'export' , filename ) |
def filter_requires_grad ( pgroups ) :
"""Returns parameter groups where parameters
that don ' t require a gradient are filtered out .
Parameters
pgroups : dict
Parameter groups to be filtered""" | warnings . warn ( "For filtering gradients, please use skorch.callbacks.Freezer." , DeprecationWarning )
for pgroup in pgroups :
output = { k : v for k , v in pgroup . items ( ) if k != 'params' }
output [ 'params' ] = ( p for p in pgroup [ 'params' ] if p . requires_grad )
yield output |
def _get_column_names_in_altered_table ( self , diff ) :
""": param diff : The table diff
: type diff : orator . dbal . table _ diff . TableDiff
: rtype : dict""" | columns = OrderedDict ( )
for column_name , column in diff . from_table . get_columns ( ) . items ( ) :
columns [ column_name . lower ( ) ] = column . get_name ( )
for column_name , column in diff . removed_columns . items ( ) :
column_name = column_name . lower ( )
if column_name in columns :
del c... |
def get_tags_of_delivery_note_per_page ( self , delivery_note_id , per_page = 1000 , page = 1 ) :
"""Get tags of delivery note per page
: param delivery _ note _ id : the delivery note id
: param per _ page : How many objects per page . Default : 1000
: param page : Which page . Default : 1
: return : list"... | return self . _get_resource_per_page ( resource = DELIVERY_NOTE_TAGS , per_page = per_page , page = page , params = { 'delivery_note_id' : delivery_note_id } , ) |
def admm ( X , prox_f , step_f , prox_g = None , step_g = None , L = None , e_rel = 1e-6 , e_abs = 0 , max_iter = 1000 , traceback = None ) :
"""Alternating Direction Method of Multipliers
This method implements the linearized ADMM from Parikh & Boyd ( 2014 ) .
Args :
X : initial X will be updated
prox _ f ... | # use matrix adapter for convenient & fast notation
_L = utils . MatrixAdapter ( L )
# get / check compatible step size for g
if prox_g is not None and step_g is None :
step_g = utils . get_step_g ( step_f , _L . spectral_norm )
# init
Z , U = utils . initZU ( X , _L )
it = 0
if traceback is not None :
tracebac... |
def run ( self ) :
'''Runs the de - trending step .''' | try : # Load raw data
log . info ( "Loading target data..." )
self . load_tpf ( )
self . mask_planets ( )
self . plot_aperture ( [ self . dvs . top_right ( ) for i in range ( 4 ) ] )
self . init_kernel ( )
M = self . apply_mask ( np . arange ( len ( self . time ) ) )
self . cdppr_arr = self ... |
def read_constraints_from_config ( cp , transforms = None , constraint_section = 'constraint' ) :
"""Loads parameter constraints from a configuration file .
Parameters
cp : WorkflowConfigParser
An open config parser to read from .
transforms : list , optional
List of transforms to apply to parameters befo... | cons = [ ]
for subsection in cp . get_subsections ( constraint_section ) :
name = cp . get_opt_tag ( constraint_section , "name" , subsection )
constraint_arg = cp . get_opt_tag ( constraint_section , "constraint_arg" , subsection )
# get any other keyword arguments
kwargs = { }
section = constraint... |
def _set_traffic_eng ( self , v , load = False ) :
"""Setter method for traffic _ eng , mapped from YANG variable / mpls _ config / router / mpls / mpls _ cmds _ holder / mpls _ interface / interface _ dynamic _ bypass / mpls _ interface _ dynamic _ bypass _ sub _ cmds / traffic _ eng ( container )
If this variab... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = traffic_eng . traffic_eng , is_container = 'container' , presence = False , yang_name = "traffic-eng" , rest_name = "traffic-eng" , parent = self , path_helper = self . _path_helper , extmethods = self . _extmethods , registe... |
def sim ( sense1 : "wn.Synset" , sense2 : "wn.Synset" , option : str = "path" ) -> float :
"""Calculates similarity based on user ' s choice .
: param sense1 : A synset .
: param sense2 : A synset .
: param option : String , one of ( ' path ' , ' wup ' , ' lch ' , ' res ' , ' jcn ' , ' lin ' ) .
: return : ... | option = option . lower ( )
if option . lower ( ) in [ "path" , "path_similarity" , "wup" , "wupa" , "wu-palmer" , "wu-palmer" , 'lch' , "leacock-chordorow" ] :
return similarity_by_path ( sense1 , sense2 , option )
elif option . lower ( ) in [ "res" , "resnik" , "jcn" , "jiang-conrath" , "lin" ] :
return simil... |
def from_dict ( raw_data ) :
"""Create WordSet from raw dictionary data .""" | try :
set_id = raw_data [ 'id' ]
title = raw_data [ 'title' ]
terms = [ Term . from_dict ( term ) for term in raw_data [ 'terms' ] ]
return WordSet ( set_id , title , terms )
except KeyError :
raise ValueError ( 'Unexpected set json structure' ) |
def alter_database ( self , dbname , db ) :
"""Parameters :
- dbname
- db""" | self . send_alter_database ( dbname , db )
self . recv_alter_database ( ) |
def _make_input_file_list ( binnedfile , num_files ) :
"""Make the list of input files for a particular energy bin X psf type""" | outdir_base = os . path . abspath ( os . path . dirname ( binnedfile ) )
outbasename = os . path . basename ( binnedfile )
filelist = ""
for i in range ( num_files ) :
split_key = "%06i" % i
output_dir = os . path . join ( outdir_base , split_key )
filepath = os . path . join ( output_dir , outbasename . re... |
def _initialize_variogram_model ( X , y , variogram_model , variogram_model_parameters , variogram_function , nlags , weight , coordinates_type ) :
"""Initializes the variogram model for kriging . If user does not specify
parameters , calls automatic variogram estimation routine .
Returns lags , semivariance , ... | # distance calculation for rectangular coords now leverages
# scipy . spatial . distance ' s pdist function , which gives pairwise distances
# in a condensed distance vector ( distance matrix flattened to a vector )
# to calculate semivariances . . .
if coordinates_type == 'euclidean' :
d = pdist ( X , metric = 'eu... |
def compute_membership_strengths ( knn_indices , knn_dists , sigmas , rhos ) :
"""Construct the membership strength data for the 1 - skeleton of each local
fuzzy simplicial set - - this is formed as a sparse matrix where each row is
a local fuzzy simplicial set , with a membership strength for the
1 - simplex... | n_samples = knn_indices . shape [ 0 ]
n_neighbors = knn_indices . shape [ 1 ]
rows = np . zeros ( ( n_samples * n_neighbors ) , dtype = np . int64 )
cols = np . zeros ( ( n_samples * n_neighbors ) , dtype = np . int64 )
vals = np . zeros ( ( n_samples * n_neighbors ) , dtype = np . float64 )
for i in range ( n_samples ... |
def internal2external_grad ( xi , bounds ) :
"""Calculate the internal to external gradiant
Calculates the partial of external over internal""" | ge = np . empty_like ( xi )
for i , ( v , bound ) in enumerate ( zip ( xi , bounds ) ) :
a = bound [ 0 ]
# minimum
b = bound [ 1 ]
# maximum
if a == None and b == None : # No constraints
ge [ i ] = 1.0
elif b == None : # only min
ge [ i ] = v / np . sqrt ( v ** 2 + 1 )
elif a... |
def y_select_cb ( self , w , index ) :
"""Callback to set Y - axis column .""" | try :
self . y_col = self . cols [ index ]
except IndexError as e :
self . logger . error ( str ( e ) )
else :
self . plot_two_columns ( reset_ylimits = True ) |
def file_logger ( app , level = None ) :
"""Get file logger
Returns configured fire logger ready to be attached to app
: param app : application instance
: param level : log this level
: return : RotatingFileHandler""" | path = os . path . join ( os . getcwd ( ) , 'var' , 'logs' , 'app.log' )
max_bytes = 1024 * 1024 * 2
file_handler = RotatingFileHandler ( filename = path , mode = 'a' , maxBytes = max_bytes , backupCount = 10 )
if level is None :
level = logging . INFO
file_handler . setLevel ( level )
log_format = '%(asctime)s %(l... |
def getSkeletalBoneData ( self , action , eTransformSpace , eMotionRange , unTransformArrayCount ) :
"""Reads the state of the skeletal bone data associated with this action and copies it into the given buffer .""" | fn = self . function_table . getSkeletalBoneData
pTransformArray = VRBoneTransform_t ( )
result = fn ( action , eTransformSpace , eMotionRange , byref ( pTransformArray ) , unTransformArrayCount )
return result , pTransformArray |
def with_context ( self , required_by ) :
"""If required _ by is non - empty , return a version of self that is a
ContextualVersionConflict .""" | if not required_by :
return self
args = self . args + ( required_by , )
return ContextualVersionConflict ( * args ) |
def add_event ( event_collection , body , timestamp = None ) :
"""Adds an event .
Depending on the persistence strategy of the client ,
this will either result in the event being uploaded to Keen
immediately or will result in saving the event to some local cache .
: param event _ collection : the name of th... | _initialize_client_from_environment ( )
_client . add_event ( event_collection , body , timestamp = timestamp ) |
def parse ( file_contents , file_name ) :
'''Takes a list of files which are assumed to be jinja2 templates and tries to
parse the contents of the files
Args :
file _ contents ( str ) : File contents of a jinja file
Raises :
Exception : An exception is raised if the contents of the file cannot be
parsed... | env = Environment ( )
result = ""
try :
env . parse ( file_contents )
except Exception :
_ , exc_value , _ = sys . exc_info ( )
result += "ERROR: Jinja2 Template File: {0}" . format ( file_name )
result += repr ( exc_value ) + '\n'
return result |
def run ( self ) :
"""Build extensions in build directory , then copy if - - inplace""" | old_inplace , self . inplace = self . inplace , 0
_build_ext . run ( self )
self . inplace = old_inplace
if old_inplace :
self . copy_extensions_to_source ( ) |
def dist_between ( h , seg1 , seg2 ) :
"""Calculates the distance between two segments . I stole this function from
a post by Michael Hines on the NEURON forum
( www . neuron . yale . edu / phpbb / viewtopic . php ? f = 2 & t = 2114)""" | h . distance ( 0 , seg1 . x , sec = seg1 . sec )
return h . distance ( seg2 . x , sec = seg2 . sec ) |
def _call_pyfftw ( self , x , out , ** kwargs ) :
"""Implement ` ` self ( x [ , out , * * kwargs ] ) ` ` using pyfftw .
Parameters
x : ` numpy . ndarray `
Input array to be transformed
out : ` numpy . ndarray `
Output array storing the result
flags : sequence of strings , optional
Flags for the transf... | assert isinstance ( x , np . ndarray )
assert isinstance ( out , np . ndarray )
kwargs . pop ( 'normalise_idft' , None )
# Using ` False ` here
kwargs . pop ( 'axes' , None )
kwargs . pop ( 'halfcomplex' , None )
flags = list ( _pyfftw_to_local ( flag ) for flag in kwargs . pop ( 'flags' , ( 'FFTW_MEASURE' , ) ) )
try ... |
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