signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def match_similar ( base , items ) :
"""Get the most similar matching item from a list of items .
@ param base : base item to locate best match
@ param items : list of items for comparison
@ return : most similar matching item or None""" | finds = list ( find_similar ( base , items ) )
if finds :
return max ( finds , key = base . similarity )
# TODO : make O ( n )
return None |
def _valid_table_name ( self , table_name ) :
"""Check if the table name is obviously invalid .""" | if table_name is None or not len ( table_name . strip ( ) ) :
raise ValueError ( "Invalid table name: %r" % table_name )
return table_name . strip ( ) |
def add_all ( application , project_id , control_client , loader = service . Loaders . FROM_SERVICE_MANAGEMENT ) :
"""Adds all endpoints middleware to a wsgi application .
Sets up application to use all default endpoints middleware .
Example :
> > > application = MyWsgiApp ( ) # an existing WSGI application
... | return ConfigFetchWrapper ( application , project_id , control_client , loader ) |
def split ( expr , frac , seed = None ) :
"""Split the current column into two column objects with certain ratio .
: param float frac : Split ratio
: return : two split DataFrame objects""" | if hasattr ( expr , '_xflow_split' ) :
return expr . _xflow_split ( frac , seed = seed )
else :
return _split ( expr , frac , seed = seed ) |
def make_fcn ( filename ) :
"""Return the fit - test function corresponding to file ` ` filename ` ` .""" | # collect lines and parse first several lines for fit info
with open ( filename , 'r' ) as ifile :
lines = ifile . readlines ( )
name = filename . split ( '.' ) [ 0 ]
_certified_values = re . compile ( '.*Certified Values\s*\(lines\s*([0-9]*)\s*to\s*([0-9]*)\)' )
_data = re . compile ( '.*Data\s*\(lines\s*([0-9]*)\... |
def book_hotel ( intent_request ) :
"""Performs dialog management and fulfillment for booking a hotel .
Beyond fulfillment , the implementation for this intent demonstrates the following :
1 ) Use of elicitSlot in slot validation and re - prompting
2 ) Use of sessionAttributes to pass information that can be ... | location = try_ex ( lambda : intent_request [ 'currentIntent' ] [ 'slots' ] [ 'Location' ] )
checkin_date = try_ex ( lambda : intent_request [ 'currentIntent' ] [ 'slots' ] [ 'CheckInDate' ] )
nights = safe_int ( try_ex ( lambda : intent_request [ 'currentIntent' ] [ 'slots' ] [ 'Nights' ] ) )
room_type = try_ex ( lamb... |
def bam_to_bigwig ( self , input_bam , output_bigwig , genome_sizes , genome , tagmented = False , normalize = False , norm_factor = 1000 ) :
"""Convert a BAM file to a bigWig file .
: param str input _ bam : path to BAM file to convert
: param str output _ bigwig : path to which to write file in bigwig format ... | # TODO :
# addjust fragment length dependent on read size and real fragment size
# ( right now it asssumes 50bp reads with 180bp fragments )
cmds = list ( )
transient_file = os . path . abspath ( re . sub ( "\.bigWig" , "" , output_bigwig ) )
cmd1 = self . tools . bedtools + " bamtobed -i {0} |" . format ( input_bam )
... |
def delete_item ( self , item , expected_value = None , return_values = None ) :
"""Delete the item from Amazon DynamoDB .
: type item : : class : ` boto . dynamodb . item . Item `
: param item : The Item to delete from Amazon DynamoDB .
: type expected _ value : dict
: param expected _ value : A dictionary... | expected_value = self . dynamize_expected_value ( expected_value )
key = self . build_key_from_values ( item . table . schema , item . hash_key , item . range_key )
return self . layer1 . delete_item ( item . table . name , key , expected = expected_value , return_values = return_values , object_hook = item_object_hook... |
def diff_packages ( pkg1 , pkg2 = None ) :
"""Invoke a diff editor to show the difference between the source of two
packages .
Args :
pkg1 ( ` Package ` ) : Package to diff .
pkg2 ( ` Package ` ) : Package to diff against . If None , the next most recent
package version is used .""" | if pkg2 is None :
it = iter_packages ( pkg1 . name )
pkgs = [ x for x in it if x . version < pkg1 . version ]
if not pkgs :
raise RezError ( "No package to diff with - %s is the earliest " "package version" % pkg1 . qualified_name )
pkgs = sorted ( pkgs , key = lambda x : x . version )
pkg2 ... |
def get_obj_subcmds ( obj ) :
"""Fetch action in callable attributes which and commands
Callable must have their attribute ' command ' set to True to
be recognised by this lookup .
Please consider using the decorator ` ` @ cmd ` ` to declare your
subcommands in classes for instance .""" | subcmds = [ ]
for label in dir ( obj . __class__ ) :
if label . startswith ( "_" ) :
continue
if isinstance ( getattr ( obj . __class__ , label , False ) , property ) :
continue
rvalue = getattr ( obj , label )
if not callable ( rvalue ) or not is_cmd ( rvalue ) :
continue
if... |
def set_name_with_model ( self , model ) :
"""Sets an unique generated name for the index .
PartialIndex would like to only override " hash _ data = . . . " , but the entire method must be duplicated for that .""" | table_name = model . _meta . db_table
column_names = [ model . _meta . get_field ( field_name ) . column for field_name , order in self . fields_orders ]
column_names_with_order = [ ( ( '-%s' if order else '%s' ) % column_name ) for column_name , ( field_name , order ) in zip ( column_names , self . fields_orders ) ]
#... |
def is_by_step ( raw ) :
"""If the password is alphabet step by step .""" | # make sure it is unicode
delta = ord ( raw [ 1 ] ) - ord ( raw [ 0 ] )
for i in range ( 2 , len ( raw ) ) :
if ord ( raw [ i ] ) - ord ( raw [ i - 1 ] ) != delta :
return False
return True |
def fit_transform ( self , X , y = None ) :
"""Fits the imputer on X and return the transformed X .
Parameters
X : array - like , shape ( n _ samples , n _ features )
Input data , where " n _ samples " is the number of samples and
" n _ features " is the number of features .
y : ignored .
Returns
Xt :... | self . random_state_ = getattr ( self , "random_state_" , check_random_state ( self . random_state ) )
if self . n_iter < 0 :
raise ValueError ( "'n_iter' should be a positive integer. Got {} instead." . format ( self . n_iter ) )
if self . predictor is None :
if self . sample_posterior :
from sklearn .... |
def create_folder_manage_actions ( self , fnames ) :
"""Return folder management actions""" | actions = [ ]
if os . name == 'nt' :
_title = _ ( "Open command prompt here" )
else :
_title = _ ( "Open terminal here" )
_title = _ ( "Open IPython console here" )
action = create_action ( self , _title , triggered = lambda : self . open_interpreter ( fnames ) )
actions . append ( action )
return actions |
def parse_iterable ( self , stream , start , end ) :
"""Sequence : : = SequenceStart WSC SequenceValue ? WSC SequenceEnd
Set : = SetStart WSC SequenceValue ? WSC SetEnd
SequenceValue : : = Value ( WSC SeparatorSymbol WSC Value ) *""" | values = [ ]
self . expect ( stream , start )
self . skip_whitespace_or_comment ( stream )
if self . has_next ( end , stream ) :
self . expect ( stream , end )
return values
while 1 :
self . skip_whitespace_or_comment ( stream )
values . append ( self . parse_value ( stream ) )
self . skip_whitespac... |
def select_fds ( read_fds , timeout , selector = AutoSelector ) :
"""Wait for a list of file descriptors ( ` read _ fds ` ) to become ready for
reading . This chooses the most appropriate select - tool for use in
prompt - toolkit .""" | # Map to ensure that we return the objects that were passed in originally .
# Whether they are a fd integer or an object that has a fileno ( ) .
# ( The ' poll ' implementation for instance , returns always integers . )
fd_map = dict ( ( fd_to_int ( fd ) , fd ) for fd in read_fds )
# Wait , using selector .
sel = selec... |
def __parse_tostr ( self , text , ** kwargs ) :
'''Builds and returns the MeCab function for parsing Unicode text .
Args :
fn _ name : MeCab function name that determines the function
behavior , either ' mecab _ sparse _ tostr ' or
' mecab _ nbest _ sparse _ tostr ' .
Returns :
A function definition , t... | n = self . options . get ( 'nbest' , 1 )
if self . _KW_BOUNDARY in kwargs :
patt = kwargs . get ( self . _KW_BOUNDARY , '.' )
tokens = list ( self . __split_pattern ( text , patt ) )
text = '' . join ( [ t [ 0 ] for t in tokens ] )
btext = self . __str2bytes ( text )
self . __mecab . mecab_lattice_s... |
def get_last_response_xml ( self , pretty_print_if_possible = False ) :
"""Retrieves the raw XML ( decrypted ) of the last SAML response ,
or the last Logout Response generated or processed
: returns : SAML response XML
: rtype : string | None""" | response = None
if self . __last_response is not None :
if isinstance ( self . __last_response , compat . str_type ) :
response = self . __last_response
else :
response = tostring ( self . __last_response , encoding = 'unicode' , pretty_print = pretty_print_if_possible )
return response |
def translate ( dnaseq , host = 'human' , fmtout = str , tax_id = None ) :
"""Translates a DNA seqeunce
: param dnaseq : DNA sequence
: param host : host organism
: param fmtout : format of output sequence""" | if isinstance ( dnaseq , str ) :
dnaseq = Seq . Seq ( dnaseq , Alphabet . generic_dna )
if tax_id is None :
tax_id = 1
# stanndard codon table . ref http : / / biopython . org / DIST / docs / tutorial / Tutorial . html # htoc25
prtseq = dnaseq . translate ( table = tax_id )
if fmtout is str :
return str... |
def setCenterLineColor ( self , color ) :
"""Sets the color for the center line .
: return < QColor >""" | palette = self . palette ( )
palette . setColor ( palette . GridCenterline , QColor ( color ) ) |
def iterator ( self ) :
"""Returns an iterator over all entity states held by this Unit Of Work .""" | # FIXME : There is no dependency tracking ; objects are iterated in
# random order .
for ent_cls in list ( self . __entity_set_map . keys ( ) ) :
for ent in self . __entity_set_map [ ent_cls ] :
yield EntityState . get_state ( ent ) |
def _find_no_duplicates ( self , name , domain = None , path = None ) :
"""Both ` ` _ _ get _ item _ _ ` ` and ` ` get ` ` call this function : it ' s never
used elsewhere in Requests .
: param name : a string containing name of cookie
: param domain : ( optional ) string containing domain of cookie
: param... | toReturn = None
for cookie in iter ( self ) :
if cookie . name == name :
if domain is None or cookie . domain == domain :
if path is None or cookie . path == path :
if toReturn is not None : # if there are multiple cookies that meet passed in criteria
raise Co... |
def _exec_loop_moving_window ( self , a_all , bd_all , mask , bd_idx ) :
"""Solves the kriging system by looping over all specified points .
Uses only a certain number of closest points . Not very memory intensive ,
but the loop is done in pure Python .""" | import scipy . linalg . lapack
npt = bd_all . shape [ 0 ]
n = bd_idx . shape [ 1 ]
kvalues = np . zeros ( npt )
sigmasq = np . zeros ( npt )
for i in np . nonzero ( ~ mask ) [ 0 ] :
b_selector = bd_idx [ i ]
bd = bd_all [ i ]
a_selector = np . concatenate ( ( b_selector , np . array ( [ a_all . shape [ 0 ] ... |
async def addMachines ( self , params = None ) :
""": param params dict :
Dictionary specifying the machine to add . All keys are optional .
Keys include :
series : string specifying the machine OS series .
constraints : string holding machine constraints , if any . We ' ll
parse this into the json friend... | params = params or { }
# Normalize keys
params = { normalize_key ( k ) : params [ k ] for k in params . keys ( ) }
# Fix up values , as necessary .
if 'parent_id' in params :
if params [ 'parent_id' ] . startswith ( '$addUnit' ) :
unit = self . resolve ( params [ 'parent_id' ] ) [ 0 ]
params [ 'pare... |
def load ( path ) :
"""Load pickled object from the specified file path .
Parameters
path : string
File path
Returns
unpickled : type of object stored in file""" | f = open ( path , 'rb' )
try :
return pickle . load ( f )
finally :
f . close ( ) |
def get_api_url ( self , api_resource , auth_token_ticket , authenticator , private_key , service_url = None , ** kwargs ) :
'''Build an auth - token - protected CAS API url .''' | auth_token , auth_token_signature = self . _build_auth_token_data ( auth_token_ticket , authenticator , private_key , ** kwargs )
params = { 'at' : auth_token , 'ats' : auth_token_signature , }
if service_url is not None :
params [ 'service' ] = service_url
url = '{}?{}' . format ( self . _get_api_url ( api_resourc... |
def wait_socks ( sock_events , inmask = 1 , outmask = 2 , timeout = None ) :
"""wait on a combination of zeromq sockets , normal sockets , and fds
. . note : : this method can block
it will return once there is relevant activity on any of the
descriptors or sockets , or the timeout expires
: param sock _ ev... | results = [ ]
for sock , mask in sock_events :
if isinstance ( sock , zmq . backend . Socket ) :
mask = _check_events ( sock , mask , inmask , outmask )
if mask :
results . append ( ( sock , mask ) )
if results :
return results
fd_map = { }
fd_events = [ ]
for sock , mask in sock_eve... |
def get_config ( self ) :
"""Returns pickle - serializable configuration struct for storage .""" | # Fill this dict with config data
return { 'hash_name' : self . hash_name , 'dim' : self . dim , 'bin_width' : self . bin_width , 'projection_count' : self . projection_count , 'components' : self . components } |
def draw_normal ( self ) :
"""Draw parameters from a mean - field normal family""" | means , scale = self . get_means_and_scales ( )
return np . random . normal ( means , scale , size = [ self . sims , means . shape [ 0 ] ] ) . T |
def get_review_history_for ( brain_or_object ) :
"""Returns the review history list for the given object . If there is no
review history for the object , it returns a default review history""" | workflow_history = api . get_object ( brain_or_object ) . workflow_history
if not workflow_history : # No review _ history for this object ! . This object was probably
# migrated to 1.3.0 before review _ history was handled in this
# upgrade step .
# https : / / github . com / senaite / senaite . core / issues / 1270
... |
def _handle_eio_disconnect ( self ) :
"""Handle the Engine . IO disconnection event .""" | self . logger . info ( 'Engine.IO connection dropped' )
for n in self . namespaces :
self . _trigger_event ( 'disconnect' , namespace = n )
self . _trigger_event ( 'disconnect' , namespace = '/' )
self . callbacks = { }
self . _binary_packet = None
if self . eio . state == 'connected' and self . reconnection :
... |
def _file_prefix ( self ) :
"""* Generate a file prefix based on the type of search for saving files to disk *
* * Return : * *
- ` ` prefix ` ` - - the file prefix""" | self . log . info ( 'starting the ``_file_prefix`` method' )
if self . ra :
now = datetime . now ( )
prefix = now . strftime ( "%Y%m%dt%H%M%S%f_tns_conesearch_" )
elif self . name :
prefix = self . name + "_tns_conesearch_"
elif self . internal_name :
prefix = self . internal_name + "_tns_conesearch_"
e... |
def _encode_buffer ( string , f ) :
"""Writes the bencoded form of the input string or bytes""" | if isinstance ( string , str ) :
string = string . encode ( )
f . write ( str ( len ( string ) ) . encode ( ) )
f . write ( _TYPE_SEP )
f . write ( string ) |
def netconf_state_sessions_session_source_host ( self , ** kwargs ) :
"""Auto Generated Code""" | config = ET . Element ( "config" )
netconf_state = ET . SubElement ( config , "netconf-state" , xmlns = "urn:ietf:params:xml:ns:yang:ietf-netconf-monitoring" )
sessions = ET . SubElement ( netconf_state , "sessions" )
session = ET . SubElement ( sessions , "session" )
session_id_key = ET . SubElement ( session , "sessi... |
def vmstats ( ) :
'''Return information about the virtual memory on the machine
Returns :
dict : A dictionary of virtual memory stats
CLI Example :
. . code - block : : bash
salt * status . vmstats''' | # Setup the SPI Structure
spi = SYSTEM_PERFORMANCE_INFORMATION ( )
retlen = ctypes . c_ulong ( )
# 2 means to query System Performance Information and return it in a
# SYSTEM _ PERFORMANCE _ INFORMATION Structure
ctypes . windll . ntdll . NtQuerySystemInformation ( 2 , ctypes . byref ( spi ) , ctypes . sizeof ( spi ) ,... |
def def_attrs ( cls , ** kw ) :
'''set attributes for class .
@ param cls [ any class ] : the class to update the given attributes in .
@ param kw [ dictionary ] : dictionary of attributes names and values .
if the given class hasn ' t one ( or more ) of these attributes , add the attribute with its value to ... | for k , v in kw . iteritems ( ) :
if not hasattr ( cls , k ) :
setattr ( cls , k , v ) |
def from_rdata_list ( ttl , rdatas ) :
"""Create an rdataset with the specified TTL , and with
the specified list of rdata objects .
@ rtype : dns . rdataset . Rdataset object""" | if len ( rdatas ) == 0 :
raise ValueError ( "rdata list must not be empty" )
r = None
for rd in rdatas :
if r is None :
r = Rdataset ( rd . rdclass , rd . rdtype )
r . update_ttl ( ttl )
first_time = False
r . add ( rd )
return r |
def _set_ldp_gr ( self , v , load = False ) :
"""Setter method for ldp _ gr , mapped from YANG variable / mpls _ config / router / mpls / mpls _ cmds _ holder / ldp / ldp _ holder / ldp _ gr ( container )
If this variable is read - only ( config : false ) in the
source YANG file , then _ set _ ldp _ gr is consi... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = ldp_gr . ldp_gr , is_container = 'container' , presence = True , yang_name = "ldp-gr" , rest_name = "graceful-restart" , parent = self , path_helper = self . _path_helper , extmethods = self . _extmethods , register_paths = T... |
def ls_dir ( base_dir ) :
"""List files recursively .""" | return [ os . path . join ( dirpath . replace ( base_dir , '' , 1 ) , f ) for ( dirpath , dirnames , files ) in os . walk ( base_dir ) for f in files ] |
def find_callback ( args , kw = None ) :
'Return callback whether passed as a last argument or as a keyword' | if args and callable ( args [ - 1 ] ) :
return args [ - 1 ] , args [ : - 1 ]
try :
return kw [ 'callback' ] , args
except ( KeyError , TypeError ) :
return None , args |
def get_var_properties ( self ) :
"""Get some properties of the variables in the current
namespace""" | from spyder_kernels . utils . nsview import get_remote_data
settings = self . namespace_view_settings
if settings :
ns = self . _get_current_namespace ( )
data = get_remote_data ( ns , settings , mode = 'editable' , more_excluded_names = EXCLUDED_NAMES )
properties = { }
for name , value in list ( data ... |
def make_step_lcont ( transition ) :
"""Return a ufunc - like step function that is left - continuous . Returns 1 if
x > transition , 0 otherwise .""" | if not np . isfinite ( transition ) :
raise ValueError ( '"transition" argument must be finite number; got %r' % transition )
def step_lcont ( x ) :
x = np . asarray ( x )
x1 = np . atleast_1d ( x )
r = ( x1 > transition ) . astype ( x . dtype )
if x . ndim == 0 :
return np . asscalar ( r )
... |
def _encrypt_queue_message ( message , key_encryption_key ) :
'''Encrypts the given plain text message using AES256 in CBC mode with 128 bit padding .
Wraps the generated content - encryption - key using the user - provided key - encryption - key ( kek ) .
Returns a json - formatted string containing the encryp... | _validate_not_none ( 'message' , message )
_validate_not_none ( 'key_encryption_key' , key_encryption_key )
_validate_key_encryption_key_wrap ( key_encryption_key )
# AES256 uses 256 bit ( 32 byte ) keys and always with 16 byte blocks
content_encryption_key = os . urandom ( 32 )
initialization_vector = os . urandom ( 1... |
def authenticate_admin ( self , transport , account_name , password ) :
"""Authenticates administrator using username and password .""" | Authenticator . authenticate_admin ( self , transport , account_name , password )
auth_token = AuthToken ( )
auth_token . account_name = account_name
params = { sconstant . E_NAME : account_name , sconstant . E_PASSWORD : password }
self . log . debug ( 'Authenticating admin %s' % account_name )
try :
res = transpo... |
def _normalize_field_name ( value ) :
"""Normalizing value string used as key and field name .
: param value : String to normalize
: type value : str
: return : normalized string
: rtype : str""" | # Replace non word / letter character
return_value = re . sub ( r'[^\w\s-]+' , '' , value )
# Replaces whitespace with underscores
return_value = re . sub ( r'\s+' , '_' , return_value )
return return_value . lower ( ) |
def get_plat_operator ( auth , url ) :
"""Funtion takes no inputs and returns a list of dictionaties of all of the operators currently
configured on the HPE IMC system
: param auth : requests auth object # usually auth . creds from auth pyhpeimc . auth . class
: param url : base url of IMC RS interface # usua... | f_url = url + '/imcrs/plat/operator?start=0&size=1000&orderBy=id&desc=false&total=false'
try :
response = requests . get ( f_url , auth = auth , headers = HEADERS )
plat_oper_list = json . loads ( response . text ) [ 'operator' ]
if isinstance ( plat_oper_list , dict ) :
oper_list = [ plat_oper_list... |
def _pys2col_widths ( self , line ) :
"""Updates col _ widths in code _ array""" | # Split with maxsplit 3
split_line = self . _split_tidy ( line )
key = col , tab = self . _get_key ( * split_line [ : 2 ] )
width = float ( split_line [ 2 ] )
shape = self . code_array . shape
try :
if col < shape [ 1 ] and tab < shape [ 2 ] :
self . code_array . col_widths [ key ] = width
except ValueError... |
def lookup_ips ( ips ) :
"""Return set of host names that resolve to given ips .""" | hosts = set ( )
for ip in ips :
try :
hosts . add ( socket . gethostbyaddr ( ip ) [ 0 ] )
except socket . error :
hosts . add ( ip )
return hosts |
def bulkImport_json ( self , filename , onDuplicate = "error" , formatType = "auto" , ** params ) :
"""bulk import from a file repecting arango ' s key / value format""" | url = "%s/import" % self . database . URL
params [ "onDuplicate" ] = onDuplicate
params [ "collection" ] = self . name
params [ "type" ] = formatType
with open ( filename ) as f :
data = f . read ( )
r = self . connection . session . post ( URL , params = params , data = data )
try :
errorMessage = ... |
def add_osm_layer ( self ) :
"""Add OSM tile layer to the map .
This uses a gdal wrapper around the OSM tile service - see the
WorldOSM . gdal file for how it is constructed .""" | path = resources_path ( 'osm' , 'WorldOSM.gdal' )
layer = QgsRasterLayer ( path , self . tr ( 'OpenStreetMap' ) )
project = QgsProject . instance ( )
# Try to add it as the last layer in the list
# False flag prevents layer being added to legend
project . addMapLayer ( layer , False )
root = QgsProject . instance ( ) .... |
def dpt_timeseries ( adata , color_map = None , show = None , save = None , as_heatmap = True ) :
"""Heatmap of pseudotime series .
Parameters
as _ heatmap : bool ( default : False )
Plot the timeseries as heatmap .""" | if adata . n_vars > 100 :
logg . warn ( 'Plotting more than 100 genes might take some while,' 'consider selecting only highly variable genes, for example.' )
# only if number of genes is not too high
if as_heatmap : # plot time series as heatmap , as in Haghverdi et al . ( 2016 ) , Fig . 1d
timeseries_as_heatma... |
def createEditor ( self , parent , column , op , value ) :
"""Creates a new editor for the parent based on the plugin parameters .
: param parent | < QWidget >
: return < QWidget > | | None""" | try :
cls = self . _operatorMap [ nativestring ( op ) ] . cls
except KeyError , AttributeError :
return None
# create the new editor
if cls :
widget = cls ( parent )
widget . setAttribute ( Qt . WA_DeleteOnClose )
projexui . setWidgetValue ( widget , value )
return widget
return None |
def covariance_matrix ( nums_with_uncert ) :
"""Calculate the covariance matrix of uncertain variables , oriented by the
order of the inputs
Parameters
nums _ with _ uncert : array - like
A list of variables that have an associated uncertainty
Returns
cov _ matrix : 2d - array - like
A nested list con... | ufuncs = list ( map ( to_uncertain_func , nums_with_uncert ) )
cov_matrix = [ ]
for ( i1 , expr1 ) in enumerate ( ufuncs ) :
coefs_expr1 = [ ]
mean1 = expr1 . mean
for ( i2 , expr2 ) in enumerate ( ufuncs [ : i1 + 1 ] ) :
mean2 = expr2 . mean
coef = np . mean ( ( expr1 . _mcpts - mean1 ) * (... |
def side_chain ( self ) :
"""List of the side - chain atoms ( R - group ) .
Notes
Returns empty list for glycine .
Returns
side _ chain _ atoms : list ( ` Atoms ` )""" | side_chain_atoms = [ ]
if self . mol_code != 'GLY' :
covalent_bond_graph = generate_covalent_bond_graph ( find_covalent_bonds ( self ) )
try :
subgraphs = generate_bond_subgraphs_from_break ( covalent_bond_graph , self [ 'CA' ] , self [ 'CB' ] )
if len ( subgraphs ) == 1 :
subgraphs ... |
def _check_error_response ( self , response , context ) :
"""Check if the response is an OAuth error response .
: param response : the OIDC response
: type response : oic . oic . message
: raise SATOSAAuthenticationError : if the response is an OAuth error response""" | if "error" in response :
satosa_logging ( logger , logging . DEBUG , "%s error: %s %s" % ( type ( response ) . __name__ , response [ "error" ] , response . get ( "error_description" , "" ) ) , context . state )
raise SATOSAAuthenticationError ( context . state , "Access denied" ) |
def __get_lowpoints ( node , dfs_data ) :
"""Calculates the lowpoints for a single node in a graph .""" | ordering_lookup = dfs_data [ 'ordering_lookup' ]
t_u = T ( node , dfs_data )
sorted_t_u = sorted ( t_u , key = lambda a : ordering_lookup [ a ] )
lowpoint_1 = sorted_t_u [ 0 ]
lowpoint_2 = sorted_t_u [ 1 ]
return lowpoint_1 , lowpoint_2 |
def _load_training_state ( self , train_iter : data_io . BaseParallelSampleIter ) :
"""Loads the full training state from disk .
: param train _ iter : training data iterator .""" | # (1 ) Parameters
params_fname = os . path . join ( self . training_state_dirname , C . TRAINING_STATE_PARAMS_NAME )
self . model . load_params_from_file ( params_fname )
# (2 ) Optimizer states
opt_state_fname = os . path . join ( self . training_state_dirname , C . OPT_STATES_LAST )
self . model . load_optimizer_stat... |
def quantile ( self , q = 0.5 , axis = 0 , numeric_only = True , interpolation = "linear" ) :
"""Return values at the given quantile over requested axis ,
a la numpy . percentile .
Args :
q ( float ) : 0 < = q < = 1 , the quantile ( s ) to compute
axis ( int ) : 0 or ' index ' for row - wise ,
1 or ' colu... | axis = self . _get_axis_number ( axis ) if axis is not None else 0
def check_dtype ( t ) :
return is_numeric_dtype ( t ) or is_datetime_or_timedelta_dtype ( t )
if not numeric_only : # If not numeric _ only and columns , then check all columns are either
# numeric , timestamp , or timedelta
if not axis and not ... |
def validate_uses_tls_for_glance ( audit_options ) :
"""Verify that TLS is used to communicate with Glance .""" | section = _config_section ( audit_options , 'glance' )
assert section is not None , "Missing section 'glance'"
assert not section . get ( 'insecure' ) and "https://" in section . get ( "api_servers" ) , "TLS is not used for Glance" |
def connection_made ( self , transport ) :
"""Used to signal ` asyncio . Protocol ` of a successful connection .""" | self . _transport = transport
self . _raw_transport = transport
if isinstance ( transport , asyncio . SubprocessTransport ) :
self . _transport = transport . get_pipe_transport ( 0 ) |
def environment_run ( up , down , sleep = None , endpoints = None , conditions = None , env_vars = None , wrapper = None ) :
"""This utility provides a convenient way to safely set up and tear down arbitrary types of environments .
: param up : A custom setup callable .
: type up : ` ` callable ` `
: param do... | if not callable ( up ) :
raise TypeError ( 'The custom setup `{}` is not callable.' . format ( repr ( up ) ) )
elif not callable ( down ) :
raise TypeError ( 'The custom tear down `{}` is not callable.' . format ( repr ( down ) ) )
conditions = list ( conditions ) if conditions is not None else [ ]
if endpoints... |
def django_object_from_row ( row , model , field_names = None , ignore_fields = ( 'id' , 'pk' ) , ignore_related = True , strip = True , ignore_errors = True , verbosity = 0 ) :
"""Construct Django model instance from values provided in a python dict or Mapping
Args :
row ( list or dict ) : Data ( values of any... | field_dict , errors = field_dict_from_row ( row , model , field_names = field_names , ignore_fields = ignore_fields , strip = strip , ignore_errors = ignore_errors , ignore_related = ignore_related , verbosity = verbosity )
if verbosity >= 3 :
print 'field_dict = %r' % field_dict
try :
obj = model ( ** field_di... |
def run_sweep ( self , program : Union [ circuits . Circuit , schedules . Schedule ] , params : study . Sweepable , repetitions : int = 1 , ) -> List [ study . TrialResult ] :
"""Samples from the given Circuit or Schedule .
In contrast to run , this allows for sweeping over different parameter
values .
Args :... | |
def clear ( self ) :
"""calls clear on any report format instances created during setup
and drops the cache""" | if self . _formats :
for fmt in self . _formats :
fmt . clear ( )
self . _formats = None |
def mouseMoveEvent ( self , event ) :
"""Handle mouse over file link .""" | c = self . cursorForPosition ( event . pos ( ) )
block = c . block ( )
self . _link_match = None
self . viewport ( ) . setCursor ( QtCore . Qt . IBeamCursor )
for match in self . link_regex . finditer ( block . text ( ) ) :
if not match :
continue
start , end = match . span ( )
if start <= c . posit... |
def _is_text_file ( filename ) :
'''Checks if a file is a text file''' | type_of_file = os . popen ( 'file -bi {0}' . format ( filename ) , 'r' ) . read ( )
return type_of_file . startswith ( 'text' ) |
def label_saves ( name ) :
"""Labels plots and saves file""" | plt . legend ( loc = 0 )
plt . ylim ( [ 0 , 1.025 ] )
plt . xlabel ( '$U/D$' , fontsize = 20 )
plt . ylabel ( '$Z$' , fontsize = 20 )
plt . savefig ( name , dpi = 300 , format = 'png' , transparent = False , bbox_inches = 'tight' , pad_inches = 0.05 ) |
def tail ( filepath = "log.txt" , lines = 50 ) :
"""Return a specified number of last lines of a specified file . If there is an
error or the file does not exist , return False .""" | try :
filepath = os . path . expanduser ( os . path . expandvars ( filepath ) )
if os . path . isfile ( filepath ) :
text = subprocess . check_output ( [ "tail" , "-" + str ( lines ) , filepath ] )
if text :
return text
else :
return False
else :
retur... |
def set ( self , subname , value ) :
'''Set the data ignoring the sign , ie set ( " test " , - 1 ) will set " test "
exactly to - 1 ( not decrement it by 1)
See https : / / github . com / etsy / statsd / blob / master / docs / metric _ types . md
" Adding a sign to the gauge value will change the value , rath... | assert isinstance ( value , compat . NUM_TYPES )
if value < 0 :
self . _send ( subname , 0 )
return self . _send ( subname , value ) |
def create_hipersocket ( self , properties ) :
"""Create and configure a HiperSockets Adapter in this CPC .
Authorization requirements :
* Object - access permission to the scoping CPC .
* Task permission to the " Create HiperSockets Adapter " task .
Parameters :
properties ( dict ) : Initial property val... | result = self . session . post ( self . cpc . uri + '/adapters' , body = properties )
# There should not be overlaps , but just in case there are , the
# returned props should overwrite the input props :
props = copy . deepcopy ( properties )
props . update ( result )
name = props . get ( self . _name_prop , None )
uri... |
def get_order_history ( self , market = None ) :
"""Used to retrieve order trade history of account
Endpoint :
1.1 / account / getorderhistory
2.0 / key / orders / getorderhistory or / key / market / GetOrderHistory
: param market : optional a string literal for the market ( ie . BTC - LTC ) .
If omitted ... | if market :
return self . _api_query ( path_dict = { API_V1_1 : '/account/getorderhistory' , API_V2_0 : '/key/market/GetOrderHistory' } , options = { 'market' : market , 'marketname' : market } , protection = PROTECTION_PRV )
else :
return self . _api_query ( path_dict = { API_V1_1 : '/account/getorderhistory' ... |
def get_case_lists ( study_id ) :
"""Return a list of the case set ids for a particular study .
TAKE NOTE the " case _ list _ id " are the same thing as " case _ set _ id "
Within the data , this string is referred to as a " case _ list _ id " .
Within API calls it is referred to as a ' case _ set _ id ' .
... | data = { 'cmd' : 'getCaseLists' , 'cancer_study_id' : study_id }
df = send_request ( ** data )
case_set_ids = df [ 'case_list_id' ] . tolist ( )
return case_set_ids |
def _recursive_work_resolver ( self , worker_name , md5 ) :
"""Internal : Input dependencies are recursively backtracked , invoked and then
passed down the pipeline until getting to the requested worker .""" | # Looking for the sample ?
if worker_name == 'sample' :
return self . get_sample ( md5 )
# Looking for info ?
if worker_name == 'info' :
return self . _get_work_results ( 'info' , md5 )
# Looking for tags ?
if worker_name == 'tags' :
return self . _get_work_results ( 'tags' , md5 )
# Do I actually have this... |
def add_hyperedge ( self , hyperedge ) :
"""Add given hyperedge to the hypergraph .
@ attention : While hyperedge - nodes can be of any type , it ' s strongly recommended to use only
numbers and single - line strings as node identifiers if you intend to use write ( ) .
@ type hyperedge : hyperedge
@ param h... | if ( not hyperedge in self . edge_links ) :
self . edge_links [ hyperedge ] = [ ]
self . graph . add_node ( ( hyperedge , 'h' ) ) |
def buttons ( self , master ) :
'''Add a standard button box .
Override if you do not want the standard buttons''' | box = tk . Frame ( master )
ttk . Button ( box , text = "Next" , width = 10 , command = self . next_day ) . pack ( side = tk . LEFT , padx = 5 , pady = 5 )
ttk . Button ( box , text = "OK" , width = 10 , command = self . ok , default = tk . ACTIVE ) . pack ( side = tk . LEFT , padx = 5 , pady = 5 )
ttk . Button ( box ,... |
def efficient_risk ( self , target_risk , risk_free_rate = 0.02 , market_neutral = False ) :
"""Calculate the Sharpe - maximising portfolio for a given volatility ( i . e max return
for a target risk ) .
: param target _ risk : the desired volatility of the resulting portfolio .
: type target _ risk : float
... | if not isinstance ( target_risk , float ) or target_risk < 0 :
raise ValueError ( "target_risk should be a positive float" )
if not isinstance ( risk_free_rate , ( int , float ) ) :
raise ValueError ( "risk_free_rate should be numeric" )
args = ( self . expected_returns , self . cov_matrix , self . gamma , risk... |
def _filter_rows ( self , rows ) :
"""Filter ` rows ` based on the visible columns .""" | filtered_rows = [ ]
for row in rows :
filtered_row = [ ]
for idx , name in enumerate ( self . columns . keys ( ) ) :
if name in self . visible_columns :
filtered_row . append ( row [ idx ] )
filtered_rows . append ( filtered_row )
return filtered_rows |
def form_valid ( self , form , formsets ) :
"""Response for valid form . In one transaction this will
save the current form and formsets , log the action
and message the user .
Returns the results of calling the ` success _ response ` method .""" | # check if it ' s a new object before it save the form
new_object = False
if not self . object :
new_object = True
instance = getattr ( form , 'instance' , None )
auto_tags , changed_tags , old_tags = tag_handler . get_tags_from_data ( form . data , self . get_tags ( instance ) )
tag_handler . set_auto_tags_for_for... |
def get_vip_settings ( vip ) :
"""Calculate which nic is on the correct network for the given vip .
If nic or netmask discovery fail then fallback to using charm supplied
config . If fallback is used this is indicated via the fallback variable .
@ param vip : VIP to lookup nic and cidr for .
@ returns ( str... | iface = get_iface_for_address ( vip )
netmask = get_netmask_for_address ( vip )
fallback = False
if iface is None :
iface = config ( 'vip_iface' )
fallback = True
if netmask is None :
netmask = config ( 'vip_cidr' )
fallback = True
return iface , netmask , fallback |
def describe ( cwd , rev = 'tip' , user = None ) :
'''Mimic git describe and return an identifier for the given revision
cwd
The path to the Mercurial repository
rev : tip
The path to the archive tarball
user : None
Run hg as a user other than what the minion runs as
CLI Example :
. . code - block :... | cmd = [ 'hg' , 'log' , '-r' , '{0}' . format ( rev ) , '--template' , "'{{latesttag}}-{{latesttagdistance}}-{{node|short}}'" ]
desc = __salt__ [ 'cmd.run_stdout' ] ( cmd , cwd = cwd , runas = user , python_shell = False )
return desc or revision ( cwd , rev , short = True ) |
def on_get ( resc , req , resp ) :
"""Get the models identified by query parameters
We return an empty list if no models are found .""" | signals . pre_req . send ( resc . model )
signals . pre_req_search . send ( resc . model )
models = goldman . sess . store . search ( resc . rtype , ** { 'filters' : req . filters , 'pages' : req . pages , 'sorts' : req . sorts , } )
props = to_rest_models ( models , includes = req . includes )
resp . serialize ( props... |
def query_total_cat_recent_no_label ( cat_id_arr , num = 8 , kind = '1' ) :
''': param cat _ id _ arr : list of categories . [ ' 0101 ' , ' 0102 ' ]''' | return TabPost . select ( ) . join ( TabPost2Tag , on = ( TabPost . uid == TabPost2Tag . post_id ) ) . where ( ( TabPost . kind == kind ) & ( TabPost2Tag . tag_id << cat_id_arr ) # the " < < " operator signifies an " IN " query
) . order_by ( TabPost . time_create . desc ( ) ) . limit ( num ) |
def add_to_object ( self , target : object , override : bool = False ) -> int :
"""Add the bindings to the target object
: param target : target to add to
: param override : override existing bindings if they are of type Namespace
: return : number of items actually added""" | nret = 0
for k , v in self :
key = k . upper ( )
exists = hasattr ( target , key )
if not exists or ( override and isinstance ( getattr ( target , k ) , ( Namespace , _RDFNamespace ) ) ) :
setattr ( target , k , v )
nret += 1
else :
print ( f"Warning: {key} is already defined in ... |
def get_assessment_part_item_session ( self , proxy ) :
"""Gets the ` ` OsidSession ` ` associated with the assessment part item service .
return : ( osid . assessment . authoring . AssessmentPartItemSession )
- an ` ` AssessmentPartItemSession ` `
raise : OperationFailed - unable to complete request
raise ... | if not self . supports_assessment_part_lookup ( ) : # This is kludgy , but only until Tom fixes spec
raise errors . Unimplemented ( )
# pylint : disable = no - member
return sessions . AssessmentPartItemSession ( proxy = proxy , runtime = self . _runtime ) |
def arc_center ( points ) :
"""Given three points on an arc find :
center , radius , normal , and angle .
This uses the fact that the intersection of the perp
bisectors of the segments between the control points
is the center of the arc .
Parameters
points : ( 3 , dimension ) float
Points in space , w... | # it ' s a lot easier to treat 2D as 3D with a zero Z value
points , is_2D = util . stack_3D ( points , return_2D = True )
# find the two edge vectors of the triangle
edge_direction = np . diff ( points , axis = 0 )
edge_midpoints = ( edge_direction * 0.5 ) + points [ : 2 ]
# three points define a plane , so we find it... |
def hpsplit ( self , data : [ 'SASdata' , str ] = None , cls : [ str , list ] = None , code : str = None , grow : str = None , id : str = None , input : [ str , list , dict ] = None , model : str = None , out : [ str , bool , 'SASdata' ] = None , partition : str = None , performance : str = None , prune : str = None , ... | |
def lt ( self , v , limit = None , offset = None ) :
"""Returns the list of the members of the set that have scores
less than v .""" | if limit is not None and offset is None :
offset = 0
return self . zrangebyscore ( self . _min_score , "(%f" % v , start = offset , num = limit ) |
def sh ( cmd , ignore_error = False , cwd = None , shell = False , ** kwargs ) :
"""Execute a command with subprocess . Popen and block until output
Args :
cmd ( tuple or str ) : same as subprocess . Popen args
Keyword Arguments :
ignore _ error ( bool ) : if False , raise an Exception if p . returncode is ... | kwargs . update ( { 'shell' : shell , 'cwd' : cwd , 'stderr' : subprocess . STDOUT , 'stdout' : subprocess . PIPE , } )
log . debug ( ( ( 'cmd' , cmd ) , ( 'kwargs' , kwargs ) ) )
p = subprocess . Popen ( cmd , universal_newlines = True , ** kwargs )
p_stdout = p . communicate ( ) [ 0 ]
if p . returncode and not ignore... |
def simToReg ( self , sim ) :
"""Convert simplified domain expression to regular expression""" | # remove initial slash if present
res = re . sub ( '^/' , '' , sim )
res = re . sub ( '/$' , '' , res )
return '^/?' + re . sub ( '\*' , '[^/]+' , res ) + '/?$' |
def parse ( self ) :
"""parse the data""" | wb = load_workbook ( self . getInputFile ( ) )
sheet = wb . worksheets [ 0 ]
sample_id = None
cnt = 0
for row in sheet . rows : # sampleid is only present in first row of each sample .
# any rows above the first sample id are ignored .
if row [ 1 ] . value :
sample_id = row [ 1 ] . value
if not sample_i... |
def response ( code , body = '' , etag = None , last_modified = None , expires = None , ** kw ) :
"""Helper to build an HTTP response .
Parameters :
code
: An integer status code .
body
: The response body . See ` Response . _ _ init _ _ ` for details .
etag
: A value for the ETag header . Double quot... | if etag is not None :
if not ( etag [ 0 ] == '"' and etag [ - 1 ] == '"' ) :
etag = '"%s"' % etag
kw [ 'etag' ] = etag
if last_modified is not None :
kw [ 'last_modified' ] = datetime_to_httpdate ( last_modified )
if expires is not None :
if isinstance ( expires , datetime ) :
kw [ 'expi... |
def clear_droppables ( self ) :
"""stub""" | if self . get_droppables_metadata ( ) . is_read_only ( ) :
raise NoAccess ( )
self . my_osid_object_form . _my_map [ 'droppables' ] = self . _droppables_metadata [ 'default_object_values' ] [ 0 ] |
def __parameter_default ( self , field ) :
"""Returns default value of field if it has one .
Args :
field : A simple field .
Returns :
The default value of the field , if any exists , with the exception of an
enum field , which will have its value cast to a string .""" | if field . default :
if isinstance ( field , messages . EnumField ) :
return field . default . name
elif isinstance ( field , messages . BooleanField ) : # The Python standard representation of a boolean value causes problems
# when generating client code .
return 'true' if field . default e... |
def extract_profiles ( self , pipeline_name , expose_data = True ) :
"""Extract all the profiles of a specific pipeline and exposes the data
in the namespace""" | compas_pipe = self . __profile_definition ( pipeline_name )
get_variable = compas_pipe . GEtUserVariable
if os . path . isdir ( self . path + 'profiles' ) is not True :
os . mkdir ( self . path + 'profiles' )
target_dir = self . path + 'profiles'
if expose_data is True :
self . profiles [ pipeline_name ] = { }
... |
def filter_events ( cls , client , event_data ) :
"""Filter registered events and yield them .""" | for event in cls . events : # try event filters
if event . matches ( client , event_data ) :
yield event |
def mulmod ( computation : BaseComputation ) -> None :
"""Modulo Multiplication""" | left , right , mod = computation . stack_pop ( num_items = 3 , type_hint = constants . UINT256 )
if mod == 0 :
result = 0
else :
result = ( left * right ) % mod
computation . stack_push ( result ) |
def CreateHttpHeader ( self ) :
"""Creates an OAuth2 HTTP header .
The OAuth2 credentials will be refreshed as necessary . In the event that
the credentials fail to refresh , a message is logged but no exception is
raised .
Returns :
A dictionary containing one entry : the OAuth2 Bearer header under the
... | oauth2_header = { }
if self . creds . expiry is None or self . creds . expired :
self . Refresh ( )
self . creds . apply ( oauth2_header )
return oauth2_header |
def read_jsonld ( ) :
"""Find jsonld file in the cwd ( or within a 2 levels below cwd ) , and load it in .
: return dict : Jsonld data""" | _d = { }
try : # Find a jsonld file in cwd . If none , fallback for a json file . If neither found , return empty .
_filename = [ file for file in os . listdir ( ) if file . endswith ( ".jsonld" ) ] [ 0 ]
if not _filename :
_filename = [ file for file in os . listdir ( ) if file . endswith ( ".json" ) ]... |
def parseStr ( self , html ) :
'''parseStr - Parses a string and creates the DOM tree and indexes .
@ param html < str > - valid HTML''' | self . reset ( )
if isinstance ( html , bytes ) :
self . feed ( html . decode ( self . encoding ) )
else :
self . feed ( html ) |
def sync_druid_source ( self ) :
"""Syncs the druid datasource in main db with the provided config .
The endpoint takes 3 arguments :
user - user name to perform the operation as
cluster - name of the druid cluster
config - configuration stored in json that contains :
name : druid datasource name
dimens... | payload = request . get_json ( force = True )
druid_config = payload [ 'config' ]
user_name = payload [ 'user' ]
cluster_name = payload [ 'cluster' ]
user = security_manager . find_user ( username = user_name )
DruidDatasource = ConnectorRegistry . sources [ 'druid' ]
DruidCluster = DruidDatasource . cluster_class
if n... |
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