signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def motif_tree_plot ( outfile , tree , data , circle = True , vmin = None , vmax = None , dpi = 300 ) :
"""Plot a " phylogenetic " tree""" | try :
from ete3 import Tree , faces , AttrFace , TreeStyle , NodeStyle
except ImportError :
print ( "Please install ete3 to use this functionality" )
sys . exit ( 1 )
# Define the tree
t , ts = _get_motif_tree ( tree , data , circle , vmin , vmax )
# Save image
t . render ( outfile , tree_style = ts , w = 1... |
def resize_for_flows ( self ) :
"""Extend ` unamey ` and ` fnamey ` for bus injections and line flows""" | if self . system . config . dime_enable :
self . system . tds . config . compute_flows = True
if self . system . tds . config . compute_flows :
nflows = 2 * self . system . Bus . n + 8 * self . system . Line . n + 2 * self . system . Area . n_combination
self . unamey . extend ( [ '' ] * nflows )
self .... |
def assert_valid_schema ( schema : GraphQLSchema ) -> None :
"""Utility function which asserts a schema is valid .
Throws a TypeError if the schema is invalid .""" | errors = validate_schema ( schema )
if errors :
raise TypeError ( "\n\n" . join ( error . message for error in errors ) ) |
def minute_to_session_label ( self , dt , direction = "next" ) :
"""Given a minute , get the label of its containing session .
Parameters
dt : pd . Timestamp or nanosecond offset
The dt for which to get the containing session .
direction : str
" next " ( default ) means that if the given dt is not part of... | if direction == "next" :
try :
return self . _minute_to_session_label_cache [ dt ]
except KeyError :
pass
idx = searchsorted ( self . market_closes_nanos , dt )
current_or_next_session = self . schedule . index [ idx ]
self . _minute_to_session_label_cache [ dt ] = current_or_next_session
if dir... |
def remove ( self , type_name , entity ) :
"""Removes an entity using the API . Shortcut for using call ( ) with the ' Remove ' method .
: param type _ name : The type of entity .
: type type _ name : str
: param entity : The entity to remove .
: type entity : dict
: raise MyGeotabException : Raises when ... | return self . call ( 'Remove' , type_name = type_name , entity = entity ) |
def install_package ( package , wheels_path , venv = None , requirement_files = None , upgrade = False , install_args = None ) :
"""Install a Python package .
Can specify a specific version .
Can specify a prerelease .
Can specify a venv to install in .
Can specify a list of paths or urls to requirement txt... | requirement_files = requirement_files or [ ]
logger . info ( 'Installing %s...' , package )
if venv and not os . path . isdir ( venv ) :
raise WagonError ( 'virtualenv {0} does not exist' . format ( venv ) )
pip_command = _construct_pip_command ( package , wheels_path , venv , requirement_files , upgrade , install_... |
def _update_rs_no_primary_from_member ( sds , replica_set_name , server_description ) :
"""RS without known primary . Update from a non - primary ' s response .
Pass in a dict of ServerDescriptions , current replica set name , and the
ServerDescription we are processing .
Returns ( new topology type , new rep... | topology_type = TOPOLOGY_TYPE . ReplicaSetNoPrimary
if replica_set_name is None :
replica_set_name = server_description . replica_set_name
elif replica_set_name != server_description . replica_set_name :
sds . pop ( server_description . address )
return topology_type , replica_set_name
# This isn ' t the pr... |
def _normalize ( self , addr ) :
"""Take any format of address and turn it into a hex string .""" | normalize = None
if isinstance ( addr , Address ) :
normalize = addr . addr
self . _is_x10 = addr . is_x10
elif isinstance ( addr , bytearray ) :
normalize = binascii . unhexlify ( binascii . hexlify ( addr ) . decode ( ) )
elif isinstance ( addr , bytes ) :
normalize = addr
elif isinstance ( addr , str... |
def _call_vecfield_1 ( self , vf , out ) :
"""Implement ` ` self ( vf , out ) ` ` for exponent 1.""" | vf [ 0 ] . ufuncs . absolute ( out = out )
if self . is_weighted :
out *= self . weights [ 0 ]
if len ( self . domain ) == 1 :
return
tmp = self . range . element ( )
for fi , wi in zip ( vf [ 1 : ] , self . weights [ 1 : ] ) :
fi . ufuncs . absolute ( out = tmp )
if self . is_weighted :
tmp *= ... |
def _run ( self , url_path , headers = None , ** kwargs ) :
"""Requests API""" | url = self . _construct_url ( url_path )
payload = kwargs
payload . update ( { 'api_token' : self . api_token } )
return self . _make_request ( url , payload , headers ) |
def client_config ( path , env_var = 'SALT_CLIENT_CONFIG' , defaults = None ) :
'''Load Master configuration data
Usage :
. . code - block : : python
import salt . config
master _ opts = salt . config . client _ config ( ' / etc / salt / master ' )
Returns a dictionary of the Salt Master configuration fil... | if defaults is None :
defaults = DEFAULT_MASTER_OPTS . copy ( )
xdg_dir = salt . utils . xdg . xdg_config_dir ( )
if os . path . isdir ( xdg_dir ) :
client_config_dir = xdg_dir
saltrc_config_file = 'saltrc'
else :
client_config_dir = os . path . expanduser ( '~' )
saltrc_config_file = '.saltrc'
# Ge... |
def float_range ( value ) :
"""Ensure that the provided value is a float integer in the range [ 0 . , 1 . ] .
Parameters
value : float
The number to evaluate
Returns
value : float
Returns a float in the range ( 0 . , 1 . )""" | try :
value = float ( value )
except Exception :
raise argparse . ArgumentTypeError ( 'Invalid float value: \'{}\'' . format ( value ) )
if value < 0.0 or value > 1.0 :
raise argparse . ArgumentTypeError ( 'Invalid float value: \'{}\'' . format ( value ) )
return value |
def parseAnchorName ( anchorName , markPrefix = MARK_PREFIX , ligaSeparator = LIGA_SEPARATOR , ligaNumRE = LIGA_NUM_RE , ignoreRE = None , ) :
"""Parse anchor name and return a tuple that specifies :
1 ) whether the anchor is a " mark " anchor ( bool ) ;
2 ) the " key " name of the anchor , i . e . the name aft... | number = None
if ignoreRE is not None :
anchorName = re . sub ( ignoreRE , "" , anchorName )
m = ligaNumRE . match ( anchorName )
if not m :
key = anchorName
else :
number = m . group ( 1 )
key = anchorName . rstrip ( number )
separator = ligaSeparator
if key . endswith ( separator ) :
a... |
def _set_adj_type ( self , v , load = False ) :
"""Setter method for adj _ type , mapped from YANG variable / adj _ neighbor _ entries _ state / adj _ neighbor / adj _ type ( isis - adj - type )
If this variable is read - only ( config : false ) in the
source YANG file , then _ set _ adj _ type is considered as... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = RestrictedClassType ( base_type = unicode , restriction_type = "dict_key" , restriction_arg = { u'is-adj-ptpt' : { 'value' : 8 } , u'is-adj-l1' : { 'value' : 2 } , u'is-adj-l2' : { 'value' : 4 } , u'is-adj-es' : { 'value' : 1... |
def get_condition_value ( self , operator , value ) :
"""Gets the condition value based on the operator and value
: param operator : the condition operator name
: type operator : str
: param value : the value to be formatted based on the condition operator
: type value : object
: return : the comparison o... | if operator in ( 'contains' , 'icontains' ) :
value = '%{0}%' . format ( value )
elif operator == 'startswith' :
value = '{0}%' . format ( value )
return value |
def fromtif ( path , ext = 'tif' , start = None , stop = None , recursive = False , nplanes = None , npartitions = None , labels = None , engine = None , credentials = None , discard_extra = False ) :
"""Loads images from single or multi - page TIF files .
Parameters
path : str
Path to data files or directory... | from tifffile import TiffFile
if nplanes is not None and nplanes <= 0 :
raise ValueError ( 'nplanes must be positive if passed, got %d' % nplanes )
def getarray ( idx_buffer_filename ) :
idx , buf , fname = idx_buffer_filename
fbuf = BytesIO ( buf )
tfh = TiffFile ( fbuf )
ary = tfh . asarray ( )
... |
def flowspec_prefix_add ( self , flowspec_family , rules , route_dist = None , actions = None ) :
"""This method adds a new Flow Specification prefix to be advertised .
` ` flowspec _ family ` ` specifies one of the flowspec family name .
This parameter must be one of the following .
- FLOWSPEC _ FAMILY _ IPV... | func_name = 'flowspec.add'
# Set required arguments
kwargs = { FLOWSPEC_FAMILY : flowspec_family , FLOWSPEC_RULES : rules , FLOWSPEC_ACTIONS : actions or { } , }
if flowspec_family in [ FLOWSPEC_FAMILY_VPNV4 , FLOWSPEC_FAMILY_VPNV6 , FLOWSPEC_FAMILY_L2VPN ] :
func_name = 'flowspec.add_local'
kwargs . update ( {... |
def srfxpt ( method , target , et , abcorr , obsrvr , dref , dvec ) :
"""Deprecated : This routine has been superseded by the CSPICE
routine : func : ` sincpt ` . This routine is supported for purposes of
backward compatibility only .
Given an observer and a direction vector defining a ray , compute the
sur... | method = stypes . stringToCharP ( method )
target = stypes . stringToCharP ( target )
abcorr = stypes . stringToCharP ( abcorr )
obsrvr = stypes . stringToCharP ( obsrvr )
dref = stypes . stringToCharP ( dref )
dvec = stypes . toDoubleVector ( dvec )
spoint = stypes . emptyDoubleVector ( 3 )
trgepc = ctypes . c_double ... |
def zipsafe ( dist ) :
"""Returns whether or not we determine a distribution is zip - safe .""" | # zip - safety is only an attribute of eggs . wheels are considered never
# zip safe per implications of PEP 427.
if hasattr ( dist , 'egg_info' ) and dist . egg_info . endswith ( 'EGG-INFO' ) :
egg_metadata = dist . metadata_listdir ( '' )
return 'zip-safe' in egg_metadata and 'native_libs.txt' not in egg_meta... |
def uninstall ( ** kwargs ) :
"""Uninstall the current pre - commit hook .""" | force = kwargs . get ( 'force' )
restore_legacy = kwargs . get ( 'restore_legacy' )
colorama . init ( strip = kwargs . get ( 'no_color' ) )
git_dir = current_git_dir ( )
if git_dir is None :
output ( NOT_GIT_REPO_MSG )
exit ( 1 )
hook_path = os . path . join ( git_dir , 'hooks' , 'pre-commit' )
if not os . path... |
def set_host ( self , host ) :
"""Set the host for a lightning server .
Host can be local ( e . g . http : / / localhost : 3000 ) , a heroku
instance ( e . g . http : / / lightning - test . herokuapp . com ) , or
a independently hosted lightning server .""" | if host [ - 1 ] == '/' :
host = host [ : - 1 ]
self . host = host
return self |
def Extract ( self , components ) :
"""Extracts interesting paths from a given path .
Args :
components : Source string represented as a list of components .
Returns :
A list of extracted paths ( as strings ) .""" | for index , component in enumerate ( components ) :
if component . lower ( ) . endswith ( self . EXECUTABLE_EXTENSIONS ) :
extracted_path = " " . join ( components [ 0 : index + 1 ] )
return [ extracted_path ]
return [ ] |
def directory_values_generator ( self , key ) :
'''Retrieve directory values for given key .''' | directory = self . directory ( key )
for key in directory :
yield self . get ( Key ( key ) ) |
async def create_role ( self , * , reason = None , ** fields ) :
"""| coro |
Creates a : class : ` Role ` for the guild .
All fields are optional .
You must have the : attr : ` ~ Permissions . manage _ roles ` permission to
do this .
Parameters
name : : class : ` str `
The role name . Defaults to ' ne... | try :
perms = fields . pop ( 'permissions' )
except KeyError :
fields [ 'permissions' ] = 0
else :
fields [ 'permissions' ] = perms . value
try :
colour = fields . pop ( 'colour' )
except KeyError :
colour = fields . get ( 'color' , Colour . default ( ) )
finally :
fields [ 'color' ] = colour . ... |
def process_default ( self , raw_event , to_append = None ) :
"""Commons handling for the followings events :
IN _ ACCESS , IN _ MODIFY , IN _ ATTRIB , IN _ CLOSE _ WRITE , IN _ CLOSE _ NOWRITE ,
IN _ OPEN , IN _ DELETE , IN _ DELETE _ SELF , IN _ UNMOUNT .""" | watch_ = self . _watch_manager . get_watch ( raw_event . wd )
if raw_event . mask & ( IN_DELETE_SELF | IN_MOVE_SELF ) : # Unfornulately this information is not provided by the kernel
dir_ = watch_ . dir
else :
dir_ = bool ( raw_event . mask & IN_ISDIR )
dict_ = { 'wd' : raw_event . wd , 'mask' : raw_event . mas... |
def unsub ( feednames , delete , dontask ) :
"""Unsubscribe from the specified feed ( s ) .""" | ecode = 0
try :
for feed in feednames :
rc , msg = anchore_feeds . unsubscribe_anchore_feed ( feed )
if not rc :
ecode = 1
anchore_print_err ( msg )
else :
anchore_print ( msg )
if delete :
dodelete = False
if do... |
def publish_queue_length ( self , redis_client , port , db ) :
""": param redis _ client : Redis client
: param db : Redis Database index
: param port : Redis port
: return : Redis queue length""" | for queue in redis_client . smembers ( 'queues' ) :
queue_length = redis_client . llen ( 'queue:%s' % queue )
self . __publish ( port , db , queue , queue_length ) |
def current ( cls ) :
"""Helper method for getting the current peer of whichever host we ' re
running on .""" | name = socket . getfqdn ( )
ip = socket . gethostbyname ( name )
return cls ( name , ip ) |
def plot_events_in_signal ( signal , events_onsets , color = "red" , marker = None ) :
"""Plot events in signal .
Parameters
signal : array or DataFrame
Signal array ( can be a dataframe with many signals ) .
events _ onsets : list or ndarray
Events location .
color : int or list
Marker color .
mark... | df = pd . DataFrame ( signal )
ax = df . plot ( )
def plotOnSignal ( x , color , marker = None ) :
if ( marker is None ) :
plt . axvline ( x = event , color = color )
else :
plt . plot ( x , signal [ x ] , marker , color = color )
events_onsets = np . array ( events_onsets )
try :
len ( even... |
def free_symbols ( self ) :
"""Set of all symbols occcuring in S , L , or H""" | return set . union ( self . S . free_symbols , self . L . free_symbols , self . H . free_symbols ) |
def get_nnsoap ( obj , first_shell , alphas , betas , rcut = 6 , nmax = 10 , lmax = 9 , all_atomtypes = [ ] ) :
"""Takes cluster structure and nearest neighbour information of a datapoint ,
Returns concatenated soap vectors for each nearest
neighbour ( up to 3 ) . Top , bridge , hollow fill the initial
zero s... | soap_vector = [ ]
nnn = len ( first_shell )
for tbh in range ( 0 , 3 ) :
try :
atom_idx = first_shell [ tbh ]
except :
soap_vector . append ( soap_zero )
else :
Hpos = [ ]
print ( atom_idx )
pos = obj . get_positions ( ) [ atom_idx ]
Hpos . append ( pos )
... |
def to_python ( self ) :
"""Returns a plain python list and converts to plain python objects all
this object ' s descendants .""" | result = list ( self )
for index , value in enumerate ( result ) :
if isinstance ( value , DottedCollection ) :
result [ index ] = value . to_python ( )
return result |
def var_unset ( session , name ) :
"""Unsets the given variable""" | name = name . strip ( )
try :
session . unset ( name )
except KeyError :
session . write_line ( "Unknown variable: {0}" , name )
return False
else :
session . write_line ( "Variable {0} unset." , name )
return None |
def _get_best_min_account ( self , cluster , adj_list , counts ) :
'''return the min UMI ( s ) need to account for cluster''' | if len ( cluster ) == 1 :
return list ( cluster )
sorted_nodes = sorted ( cluster , key = lambda x : counts [ x ] , reverse = True )
for i in range ( len ( sorted_nodes ) - 1 ) :
if len ( remove_umis ( adj_list , cluster , sorted_nodes [ : i + 1 ] ) ) == 0 :
return sorted_nodes [ : i + 1 ] |
def get_objects ( self ) :
"""Returns the list of objects passed as this parameter""" | return rope . base . oi . soi . get_passed_objects ( self . pyfunction , self . index ) |
def validate_capacity ( capacity ) :
"""Validate ScalingConfiguration capacity for serverless DBCluster""" | if capacity not in VALID_SCALING_CONFIGURATION_CAPACITIES :
raise ValueError ( "ScalingConfiguration capacity must be one of: {}" . format ( ", " . join ( map ( str , VALID_SCALING_CONFIGURATION_CAPACITIES ) ) ) )
return capacity |
def create_datastore ( self , schema = None , primary_key = None , delete_first = 0 , path = None ) : # type : ( Optional [ List [ Dict ] ] , Optional [ str ] , int , Optional [ str ] ) - > None
"""For tabular data , create a resource in the HDX datastore which enables data preview in HDX . If no schema is provided... | if delete_first == 0 :
pass
elif delete_first == 1 :
self . delete_datastore ( )
elif delete_first == 2 :
if primary_key is None :
self . delete_datastore ( )
else :
raise HDXError ( 'delete_first must be 0, 1 or 2! (0 = No, 1 = Yes, 2 = Delete if no primary key)' )
if path is None : # Download ... |
def wait ( self , timeout = None ) :
"""Wait for the job to complete , or a timeout to happen .
This is more efficient than the version in the base Job class , in that we can
use a call that blocks for the poll duration rather than a sleep . That means we
shouldn ' t block unnecessarily long and can also poll... | poll = 30
while not self . _is_complete :
try :
query_result = self . _api . jobs_query_results ( self . _job_id , project_id = self . _context . project_id , page_size = 0 , timeout = poll * 1000 )
except Exception as e :
raise e
if query_result [ 'jobComplete' ] :
if 'totalBytesPro... |
def gridfs_namespace ( self , plain_src_ns ) :
"""Given a plain source namespace , return the corresponding plain
target namespace if this namespace is a gridfs collection .""" | namespace = self . lookup ( plain_src_ns )
if namespace and namespace . gridfs :
return namespace . dest_name
return None |
def setting ( key , default = None , expected_type = None , qsettings = None ) :
"""Helper function to get a value from settings under InaSAFE scope .
: param key : Unique key for setting .
: type key : basestring
: param default : The default value in case of the key is not found or there
is an error .
:... | if default is None :
default = inasafe_default_settings . get ( key , None )
full_key = '%s/%s' % ( APPLICATION_NAME , key )
return general_setting ( full_key , default , expected_type , qsettings ) |
def create_experiment ( self , workflow_type , microscope_type , plate_format , plate_acquisition_mode ) :
'''Creates the experiment .
Parameters
workflow _ type : str
workflow type
microscope _ type : str
microscope type
plate _ format : int
well - plate format , i . e . total number of wells per pla... | logger . info ( 'create experiment "%s"' , self . experiment_name )
content = { 'name' : self . experiment_name , 'workflow_type' : workflow_type , 'microscope_type' : microscope_type , 'plate_format' : plate_format , 'plate_acquisition_mode' : plate_acquisition_mode }
url = self . _build_api_url ( '/experiments' )
res... |
def files_sharedPublicURL ( self , * , id : str , ** kwargs ) -> SlackResponse :
"""Enables a file for public / external sharing .
Args :
id ( str ) : The file id . e . g . ' F1234467890'""" | self . _validate_xoxp_token ( )
kwargs . update ( { "id" : id } )
return self . api_call ( "files.sharedPublicURL" , json = kwargs ) |
def _make_matchers ( self , crontab ) :
'''This constructs the full matcher struct .''' | crontab = _aliases . get ( crontab , crontab )
ct = crontab . split ( )
if len ( ct ) == 5 :
ct . insert ( 0 , '0' )
ct . append ( '*' )
elif len ( ct ) == 6 :
ct . insert ( 0 , '0' )
_assert ( len ( ct ) == 7 , "improper number of cron entries specified; got %i need 5 to 7" % ( len ( ct , ) ) )
matchers = ... |
def write_to_ndef_service ( self , data , * blocks ) :
"""Write block data to an NDEF compatible tag .
This is a convinience method to write block data to a tag that
has system code 0x12FC ( NDEF ) . For other tags this method
simply does nothing . The * data * to write must be a string or
bytearray with le... | if self . sys == 0x12FC :
sc_list = [ ServiceCode ( 0 , 0b001001 ) ]
bc_list = [ BlockCode ( n ) for n in blocks ]
self . write_without_encryption ( sc_list , bc_list , data ) |
def local_imports ( remote_base , local_base , ontologies , local_versions = tuple ( ) , readonly = False , dobig = False , revert = False ) :
"""Read the import closure and use the local versions of the files .""" | done = [ ]
triples = set ( )
imported_iri_vs_ontology_iri = { }
p = owl . imports
oi = b'owl:imports'
oo = b'owl:Ontology'
def inner ( local_filepath , remote = False ) :
if noneMembers ( local_filepath , * bigleaves ) or dobig :
ext = os . path . splitext ( local_filepath ) [ - 1 ]
if ext == '.ttl'... |
def add_override ( self , symbol , ind , val , dt_log = None , user = None , comment = None ) :
"""Appends a single indexed - value pair , to a symbol object , to be
used during the final steps of the aggregation of the datatable .
With default settings Overrides , get applied with highest priority .
Paramete... | self . _add_orfs ( 'override' , symbol , ind , val , dt_log , user , comment ) |
def validate_session ( self , session , latest_only = False ) :
"""Check that a session is present in the metadata dictionary .
raises : exc : ` ~ billy . scrape . NoDataForPeriod ` if session is invalid
: param session : string representing session to check""" | if latest_only :
if session != self . metadata [ 'terms' ] [ - 1 ] [ 'sessions' ] [ - 1 ] :
raise NoDataForPeriod ( session )
for t in self . metadata [ 'terms' ] :
if session in t [ 'sessions' ] :
return True
raise NoDataForPeriod ( session ) |
def dispatch_request ( self ) :
"""Handle redirect back from provider""" | if current_user . is_authenticated :
return redirect ( self . next )
# clear previous !
if 'social_data' in session :
del session [ 'social_data' ]
res = self . app . authorized_response ( )
if res is None :
if self . flash :
flash ( self . auth_failed_msg , 'danger' )
return redirect ( self . n... |
def api_config ( path ) :
'''Read in the Salt Master config file and add additional configs that
need to be stubbed out for salt - api''' | # Let ' s grab a copy of salt - api ' s required defaults
opts = DEFAULT_API_OPTS . copy ( )
# Let ' s override them with salt ' s master opts
opts . update ( client_config ( path , defaults = DEFAULT_MASTER_OPTS . copy ( ) ) )
# Let ' s set the pidfile and log _ file values in opts to api settings
opts . update ( { 'p... |
def _Connect ( self , banner = None , ** kwargs ) :
"""Connect to the device .
Args :
banner : See protocol _ handler . Connect .
* * kwargs : See protocol _ handler . Connect and adb _ commands . ConnectDevice for kwargs .
Includes handle , rsa _ keys , and auth _ timeout _ ms .
Returns :
An instance o... | if not banner :
banner = socket . gethostname ( ) . encode ( )
conn_str = self . protocol_handler . Connect ( self . _handle , banner = banner , ** kwargs )
# Remove banner and colons after device state ( state : : banner )
parts = conn_str . split ( b'::' )
self . _device_state = parts [ 0 ]
# Break out the build ... |
def get_trigger_data ( value , mode = 0 ) :
'''Returns 31bit trigger counter ( mode = 0 ) , 31bit timestamp ( mode = 1 ) , 15bit timestamp and 16bit trigger counter ( mode = 2)''' | if mode == 2 :
return np . right_shift ( np . bitwise_and ( value , 0x7FFF0000 ) , 16 ) , np . bitwise_and ( value , 0x0000FFFF )
else :
return np . bitwise_and ( value , 0x7FFFFFFF ) |
def parse_solr_geo_range_as_pair ( geo_box_str ) :
""": param geo _ box _ str : [ - 90 , - 180 TO 90,180]
: return : ( " - 90 , - 180 " , " 90,180 " )""" | pattern = "\\[(.*) TO (.*)\\]"
matcher = re . search ( pattern , geo_box_str )
if matcher :
return matcher . group ( 1 ) , matcher . group ( 2 )
else :
raise Exception ( "Regex {0} could not parse {1}" . format ( pattern , geo_box_str ) ) |
def rank ( values , axis = 0 , method = 'average' , na_option = 'keep' , ascending = True , pct = False ) :
"""Rank the values along a given axis .
Parameters
values : array - like
Array whose values will be ranked . The number of dimensions in this
array must not exceed 2.
axis : int , default 0
Axis o... | if values . ndim == 1 :
f , values = _get_data_algo ( values , _rank1d_functions )
ranks = f ( values , ties_method = method , ascending = ascending , na_option = na_option , pct = pct )
elif values . ndim == 2 :
f , values = _get_data_algo ( values , _rank2d_functions )
ranks = f ( values , axis = axis... |
def shapes_match ( a , b ) :
"""Recursively check if shapes of object ` a ` and ` b ` match .
Will walk lists , tuples and dicts .
Args :
a : object of type ( numpy . ndarray , tf . Tensor , list , tuple , dict )
to check for matching shapes against ` b ` .
b : object to check for matching shape against `... | if isinstance ( a , ( tuple , list ) ) and isinstance ( b , ( tuple , list ) ) :
if len ( a ) != len ( b ) :
return False
return all ( [ shapes_match ( ia , ib ) for ia , ib in zip ( a , b ) ] )
elif isinstance ( a , dict ) and isinstance ( b , dict ) :
if len ( a ) != len ( b ) :
return Fal... |
def get_region ( self , ip ) :
'''Get region''' | rec = self . get_all ( ip )
return rec and rec . region |
def Package ( env , target = None , source = None , ** kw ) :
"""Entry point for the package tool .""" | # check if we need to find the source files ourself
if not source :
source = env . FindInstalledFiles ( )
if len ( source ) == 0 :
raise UserError ( "No source for Package() given" )
# decide which types of packages shall be built . Can be defined through
# four mechanisms : command line argument , keyword argu... |
def register ( event = None ) :
"""Decorator method to * register * event handlers . This is the client - less
` add _ event _ handler
< telethon . client . updates . UpdateMethods . add _ event _ handler > ` variant .
Note that this method only registers callbacks as handlers ,
and does not attach them to ... | if isinstance ( event , type ) :
event = event ( )
elif not event :
event = Raw ( )
def decorator ( callback ) :
handlers = getattr ( callback , _HANDLERS_ATTRIBUTE , [ ] )
handlers . append ( event )
setattr ( callback , _HANDLERS_ATTRIBUTE , handlers )
return callback
return decorator |
def move_in ( self , space , offset , length , width , extended = False ) :
"""Moves a block of data to local memory from the specified address space and offset .
: param space : Specifies the address space . ( Constants . * SPACE * )
: param offset : Offset ( in bytes ) of the address or register from which to... | return self . visalib . move_in ( self . session , space , offset , length , width , extended ) |
def print_maps_by_type ( map_type , number = None ) :
"""Print all available maps of a given type .
Parameters
map _ type : { ' Sequential ' , ' Diverging ' , ' Qualitative ' }
Select map type to print .
number : int , optional
Filter output by number of defined colors . By default there is
no numeric f... | map_type = map_type . lower ( ) . capitalize ( )
if map_type not in MAP_TYPES :
s = 'Invalid map type, must be one of {0}' . format ( MAP_TYPES )
raise ValueError ( s )
print ( map_type )
map_keys = sorted ( COLOR_MAPS [ map_type ] . keys ( ) )
format_str = '{0:8} : {1}'
for mk in map_keys :
num_keys = so... |
def restricted_brands ( self ) :
"""| Comment : ids of all brands that this ticket form is restricted to""" | if self . api and self . restricted_brand_ids :
return self . api . _get_restricted_brands ( self . restricted_brand_ids ) |
def print_all_param_defaults ( ) :
"""Print the default values for all imported Parameters .""" | print ( "_______________________________________________________________________________" )
print ( "" )
print ( " Parameter Default Values" )
print ( "" )
classes = descendents ( Parameterized )
classes . sort ( key = lambda x : x . __name__ )
for c in classes :
c . print_param_defaults (... |
def DeserializeMessage ( self , response_type , data ) :
"""Deserialize the given data as method _ config . response _ type .""" | try :
message = encoding . JsonToMessage ( response_type , data )
except ( exceptions . InvalidDataFromServerError , messages . ValidationError , ValueError ) as e :
raise exceptions . InvalidDataFromServerError ( 'Error decoding response "%s" as type %s: %s' % ( data , response_type . __name__ , e ) )
return m... |
def get_analysis_data_for ( self , ar ) :
"""Return the Analysis data for this AR""" | # Exclude analyses from children ( partitions )
analyses = ar . objectValues ( "Analysis" )
out = [ ]
for an in analyses :
info = self . get_base_info ( an )
info . update ( { "service_uid" : an . getServiceUID ( ) , } )
out . append ( info )
return out |
def plot_pnlmoney ( self ) :
"""画出pnl盈亏额散点图""" | plt . scatter ( x = self . pnl . sell_date . apply ( str ) , y = self . pnl . pnl_money )
plt . gcf ( ) . autofmt_xdate ( )
return plt |
def xlsx_part ( self ) :
"""Return the related | EmbeddedXlsxPart | object having its rId at
` c : chartSpace / c : externalData / @ rId ` or | None | if there is no
` < c : externalData > ` element .""" | xlsx_part_rId = self . _chartSpace . xlsx_part_rId
if xlsx_part_rId is None :
return None
return self . _chart_part . related_parts [ xlsx_part_rId ] |
def proxy_manager_for ( self , proxy , ** proxy_kwargs ) :
"""Return urllib3 ProxyManager for the given proxy .
This method should not be called from user code , and is only
exposed for use when subclassing the
: class : ` HTTPAdapter < requests . adapters . HTTPAdapter > ` .
: param proxy : The proxy to re... | if not proxy in self . proxy_manager :
proxy_headers = self . proxy_headers ( proxy )
self . proxy_manager [ proxy ] = proxy_from_url ( proxy , proxy_headers = proxy_headers , num_pools = self . _pool_connections , maxsize = self . _pool_maxsize , block = self . _pool_block , ** proxy_kwargs )
return self . pro... |
def amplification_type ( self , channels = None ) :
"""Get the amplification type used for the specified channel ( s ) .
Each channel uses one of two amplification types : linear or
logarithmic . This function returns , for each channel , a tuple of
two numbers , in which the first number indicates the number... | # Check default
if channels is None :
channels = self . _channels
# Get numerical indices of channels
channels = self . _name_to_index ( channels )
# Get detector type of the specified channels
if hasattr ( channels , '__iter__' ) and not isinstance ( channels , six . string_types ) :
return [ self . _amplifica... |
def stage_tc ( self , owner , staging_data , variable ) :
"""Stage data using ThreatConnect API .
. . code - block : : javascript
" data " : {
" id " : 116,
" value " : " adversary001 - build - testing " ,
" type " : " Adversary " ,
" ownerName " : " qa - build " ,
" dateAdded " : " 2017-08-16T18:35:0... | # parse resource _ data
resource_type = staging_data . pop ( 'type' )
if resource_type in self . tcex . indicator_types or resource_type in self . tcex . group_types :
try :
attributes = staging_data . pop ( 'attribute' )
except KeyError :
attributes = [ ]
try :
security_labels = sta... |
def encrypt ( message , keyPath ) :
"""Encrypts a message given a path to a local file containing a key .
: param message : The message to be encrypted .
: param keyPath : A path to a file containing a 256 - bit key ( and nothing else ) .
: type message : bytes
: type keyPath : str
: rtype : bytes
A con... | with open ( keyPath , 'rb' ) as f :
key = f . read ( )
if len ( key ) != SecretBox . KEY_SIZE :
raise ValueError ( "Key is %d bytes, but must be exactly %d bytes" % ( len ( key ) , SecretBox . KEY_SIZE ) )
sb = SecretBox ( key )
# We generate the nonce using secure random bits . For long enough
# nonce size , t... |
def next_frame_basic_stochastic_discrete ( ) :
"""Basic 2 - frame conv model with stochastic discrete latent .""" | hparams = basic_deterministic_params . next_frame_sampling ( )
hparams . batch_size = 4
hparams . video_num_target_frames = 6
hparams . scheduled_sampling_mode = "prob_inverse_lin"
hparams . scheduled_sampling_decay_steps = 40000
hparams . scheduled_sampling_max_prob = 1.0
hparams . dropout = 0.15
hparams . filter_doub... |
def start ( self , tag , attrib ) :
"""On start of element tag""" | if tag == E_CLINICAL_DATA :
self . ref_state = AUDIT_REF_STATE
self . context = Context ( attrib [ A_STUDY_OID ] , attrib [ A_AUDIT_SUBCATEGORY_NAME ] , int ( attrib [ A_METADATA_VERSION_OID ] ) )
elif tag == E_SUBJECT_DATA :
self . context . subject = Subject ( attrib . get ( A_SUBJECT_KEY ) , attrib . get... |
def _basic_auth_str ( username , password ) :
"""Returns a Basic Auth string .""" | # " I want us to put a big - ol ' comment on top of it that
# says that this behaviour is dumb but we need to preserve
# it because people are relying on it . "
# - Lukasa
# These are here solely to maintain backwards compatibility
# for things like ints . This will be removed in 3.0.0.
if not isinstance ( username , b... |
def recipe ( package , repository = None , depends_on = None , release = False , output_path = None , auto = False , overwrite = False , name = None ) :
"""Create a new upgrade recipe , for developers .""" | upgrader = InvenioUpgrader ( )
logger = upgrader . get_logger ( )
try :
path , found_repository = _upgrade_recipe_find_path ( package )
if output_path :
path = output_path
if not repository :
repository = found_repository
if not os . path . exists ( path ) :
raise RuntimeError ( ... |
def _get_distance_segment_coefficients ( self , rval ) :
"""Returns the coefficients describing the distance attenuation shape
for three different distance bins , equations 12a - 12c""" | # Get distance segment ends
nsites = len ( rval )
# Equation 12a
f_0 = np . log10 ( self . CONSTS [ "r0" ] / rval )
f_0 [ rval > self . CONSTS [ "r0" ] ] = 0.0
# Equation 12b
f_1 = np . log10 ( rval )
f_1 [ rval > self . CONSTS [ "r1" ] ] = np . log10 ( self . CONSTS [ "r1" ] )
# Equation 12c
f_2 = np . log10 ( rval / ... |
def has_comic ( name ) :
"""Check if comic name already exists .""" | names = [ ( "Creators/%s" % name ) . lower ( ) , ( "GoComics/%s" % name ) . lower ( ) , ]
for scraperclass in get_scraperclasses ( ) :
lname = scraperclass . getName ( ) . lower ( )
if lname in names :
return True
return False |
def disable ( self ) :
"""Disable the Cloud .
: returns : A list of mist . clients ' updated clouds .""" | payload = { "new_state" : "0" }
data = json . dumps ( payload )
req = self . request ( self . mist_client . uri + '/clouds/' + self . id , data = data )
req . post ( )
self . enabled = False
self . mist_client . update_clouds ( ) |
def log_flush_for_obj_for_interval ( self , log_type , obj_id , interval ) :
"""Flush logs for an interval of time for a specific object .
Please note , log _ type is a variable according to the API docs ,
but acceptable values are not listed . Only " policies " is
demonstrated as an acceptable value .
Args... | if not log_type :
log_type = "policies"
# The XML for the / logflush basic endpoint allows spaces
# instead of " + " , so do a replace here just in case .
interval = interval . replace ( " " , "+" )
flush_url = "{}/{}/id/{}/interval/{}" . format ( self . url , log_type , obj_id , interval )
self . jss . delete ( fl... |
def callHook ( self , hookname , * args , ** kwargs ) :
'Call all functions registered with ` addHook ` for the given hookname .' | r = [ ]
for f in self . hooks [ hookname ] :
try :
r . append ( f ( * args , ** kwargs ) )
except Exception as e :
exceptionCaught ( e )
return r |
def get_custom_values ( self , key ) :
"""Return a set of values for the given customParameter name .""" | self . _handled . add ( key )
return self . _lookup [ key ] |
def get_scm_status ( config , read_modules = False , repo_url = None , mvn_repo_local = None , additional_params = None ) :
"""Gets the artifact status ( MavenArtifact instance ) from SCM defined by config . Only the top - level artifact is read by
default , although it can be requested to read the whole availabl... | global scm_status_cache
if config . artifact in scm_status_cache . keys ( ) :
result = scm_status_cache [ config . artifact ]
elif not read_modules and ( ( "%s|False" % config . artifact ) in scm_status_cache . keys ( ) ) :
result = scm_status_cache [ "%s|False" % config . artifact ]
else :
result = _get_sc... |
def schedule ( self , task ) :
"""Schedules a new Task in the PoolManager .""" | self . task_manager . register ( task )
self . worker_manager . dispatch ( task ) |
def getOutputDevice ( self , textureType ) :
"""* Returns platform - and texture - type specific adapter identification so that applications and the
compositor are creating textures and swap chains on the same GPU . If an error occurs the device
will be set to 0.
pInstance is an optional parameter that is req... | fn = self . function_table . getOutputDevice
pnDevice = c_uint64 ( )
pInstance = VkInstance_T ( )
fn ( byref ( pnDevice ) , textureType , byref ( pInstance ) )
return pnDevice . value , pInstance |
def productinfo ( self ) :
"""Return the productversion and channel of this MAR if present .""" | if not self . mardata . additional :
return None
for s in self . mardata . additional . sections :
if s . id == 1 :
return str ( s . productversion ) , str ( s . channel )
return None |
def startstop ( inst_id , cmdtodo ) :
"""Start or Stop the Specified Instance .
Args :
inst _ id ( str ) : instance - id to perform command against
cmdtodo ( str ) : command to perform ( start or stop )
Returns :
response ( dict ) : reponse returned from AWS after
performing specified action .""" | tar_inst = EC2R . Instance ( inst_id )
thecmd = getattr ( tar_inst , cmdtodo )
response = thecmd ( )
return response |
def __get_document ( self , content ) :
"""Returns a ` QTextDocument < http : / / doc . qt . nokia . com / qtextdocument . html > ` _ class instance
with given content .
: return : Document .
: rtype : QTextDocument""" | document = QTextDocument ( QString ( content ) )
document . clearUndoRedoStacks ( )
document . setModified ( False )
return document |
def local_expiring_lru ( obj ) :
"""Property that maps to a key in a local dict - like attribute .
self . _ cache must be an OrderedDict
self . _ cache _ size must be defined as LRU size
self . _ cache _ ttl is the expiration time in seconds
class Foo ( object ) :
def _ _ init _ _ ( self , cache _ size = ... | @ wraps ( obj )
def memoizer ( * args , ** kwargs ) :
instance = args [ 0 ]
lru_size = instance . _cache_size
cache_ttl = instance . _cache_ttl
if lru_size and cache_ttl :
cache = instance . _cache
kargs = list ( args )
kargs [ 0 ] = id ( instance )
key = str ( ( kargs , ... |
def _erase_in_line ( self , type_of = 0 ) :
"""Erases the row in a specific way , depending on the type _ of .""" | row = self . display [ self . y ]
attrs = self . attributes [ self . y ]
if type_of == 0 : # Erase from the cursor to the end of line , including the cursor
row = row [ : self . x ] + u" " * ( self . size [ 1 ] - self . x )
attrs = attrs [ : self . x ] + [ self . default_attributes ] * ( self . size [ 1 ] - sel... |
async def connect ( self , * args , ** kwargs ) :
"""Connect to a Juju controller .
This supports two calling conventions :
The controller and ( optionally ) authentication information can be
taken from the data files created by the Juju CLI . This convention
will be used if a ` ` controller _ name ` ` is s... | await self . disconnect ( )
if 'endpoint' not in kwargs and len ( args ) < 2 :
if args and 'model_name' in kwargs :
raise TypeError ( 'connect() got multiple values for ' 'controller_name' )
elif args :
controller_name = args [ 0 ]
else :
controller_name = kwargs . pop ( 'controller_... |
def MultiDelete ( self , urns , token = None ) :
"""Drop all the information about given objects .
DANGEROUS ! This recursively deletes all objects contained within the
specified URN .
Args :
urns : Urns of objects to remove .
token : The Security Token to use for opening this item .
Raises :
ValueErr... | urns = [ rdfvalue . RDFURN ( urn ) for urn in urns ]
if token is None :
token = data_store . default_token
for urn in urns :
if urn . Path ( ) == "/" :
raise ValueError ( "Can't delete root URN. Please enter a valid URN" )
deletion_pool = DeletionPool ( token = token )
deletion_pool . MultiMarkForDeleti... |
def dtdQElementDesc ( self , name , prefix ) :
"""Search the DTD for the description of this element""" | ret = libxml2mod . xmlGetDtdQElementDesc ( self . _o , name , prefix )
if ret is None :
raise treeError ( 'xmlGetDtdQElementDesc() failed' )
__tmp = xmlElement ( _obj = ret )
return __tmp |
def _get_time_stamp ( entry ) :
"""Return datetime object from a timex constraint start / end entry .
Example string format to convert : 2018-01-01T00:00""" | if not entry or entry == 'Undef' :
return None
try :
dt = datetime . datetime . strptime ( entry , '%Y-%m-%dT%H:%M' )
except Exception as e :
logger . debug ( 'Could not parse %s format' % entry )
return None
return dt |
def declare_api_routes ( config ) :
"""Declare routes , with a custom pregenerator .""" | # The pregenerator makes sure we can generate a path using
# request . route _ path even if we don ' t have all the variables .
# For example , instead of having to do this :
# request . route _ path ( ' resource ' , hash = hash , ignore = ' ' )
# it ' s possible to do this :
# request . route _ path ( ' resource ' , h... |
def generate_broadcast_to ( node_name , x , y , out_name , axis , base_name , func_counter ) :
"""Generate a BroadcastTo operator to brodcast specified buffer""" | bt = nnabla_pb2 . Function ( )
bt . type = "BroadcastTo"
set_function_name ( bt , node_name , base_name , func_counter )
bt . input . extend ( [ x , y ] )
bt . output . extend ( [ out_name ] )
btp = bt . broadcast_to_param
btp . axis = axis
return bt |
def continue_with ( self , continuation_func , * args ) :
"""Create a continuation that executes when the Future is completed .
: param continuation _ func : A function which takes the future as the only parameter . Return value of the function
will be set as the result of the continuation future .
: return :... | future = Future ( )
def callback ( f ) :
try :
future . set_result ( continuation_func ( f , * args ) )
except :
future . set_exception ( sys . exc_info ( ) [ 1 ] , sys . exc_info ( ) [ 2 ] )
self . add_done_callback ( callback )
return future |
def as_dash_instance ( self , cache_id = None ) :
'Return a dash application instance for this model instance' | dash_app = self . stateless_app . as_dash_app ( )
# pylint : disable = no - member
base = self . current_state ( )
return dash_app . do_form_dash_instance ( replacements = base , specific_identifier = self . slug , cache_id = cache_id ) |
def tn_mean ( tasmin , freq = 'YS' ) :
r"""Mean minimum temperature .
Mean of daily minimum temperature .
Parameters
tasmin : xarray . DataArray
Minimum daily temperature [ ° C ] or [ K ]
freq : str , optional
Resampling frequency
Returns
xarray . DataArray
Mean of daily minimum temperature .
No... | arr = tasmin . resample ( time = freq ) if freq else tasmin
return arr . mean ( dim = 'time' , keep_attrs = True ) |
def compare_words_lexicographic ( word_a , word_b ) :
"""compare words in Tamil lexicographic order""" | # sanity check for words to be all Tamil
if ( not all_tamil ( word_a ) ) or ( not all_tamil ( word_b ) ) : # print ( " # # " )
# print ( word _ a )
# print ( word _ b )
# print ( " Both operands need to be Tamil words " )
pass
La = len ( word_a )
Lb = len ( word_b )
all_TA_letters = u"" . join ( tamil_letters )
for... |
def generate_data_key ( self , name , key_type , context = "" , nonce = "" , bits = 256 , mount_point = DEFAULT_MOUNT_POINT ) :
"""Generates a new high - entropy key and the value encrypted with the named key .
Optionally return the plaintext of the key as well . Whether plaintext is returned depends on the path ... | if key_type not in transit_constants . ALLOWED_DATA_KEY_TYPES :
error_msg = 'invalid key_type argument provided "{arg}", supported types: "{allowed_types}"'
raise exceptions . ParamValidationError ( error_msg . format ( arg = key_type , allowed_types = ', ' . join ( transit_constants . ALLOWED_DATA_KEY_TYPES ) ... |
def get_maxcov_downsample_cl ( data , in_pipe = None ) :
"""Retrieve command line for max coverage downsampling , fitting into bamsormadup output .""" | max_cov = _get_maxcov_downsample ( data ) if dd . get_aligner ( data ) not in [ "snap" ] else None
if max_cov :
if in_pipe == "bamsormadup" :
prefix = "level=0"
elif in_pipe == "samtools" :
prefix = "-l 0"
else :
prefix = ""
# Swap over to multiple cores until after testing
#... |
def categorical_df_concat ( df_list , inplace = False ) :
"""Prepare list of pandas DataFrames to be used as input to pd . concat .
Ensure any columns of type ' category ' have the same categories across each
dataframe .
Parameters
df _ list : list
List of dataframes with same columns .
inplace : bool
... | if not inplace :
df_list = deepcopy ( df_list )
# Assert each dataframe has the same columns / dtypes
df = df_list [ 0 ]
if not all ( [ ( df . dtypes . equals ( df_i . dtypes ) ) for df_i in df_list [ 1 : ] ] ) :
raise ValueError ( "Input DataFrames must have the same columns/dtypes." )
categorical_columns = df... |
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