signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def symmetrify ( A , upper = False ) :
"""Take the square matrix A and make it symmetrical by copting elements from
the lower half to the upper
works IN PLACE .
note : tries to use cython , falls back to a slower numpy version""" | if use_linalg_cython :
_symmetrify_cython ( A , upper )
else :
_symmetrify_numpy ( A , upper ) |
def _writeString ( self , obj , use_reference = True ) :
"""Appends a string to the serialization stream
: param obj : String to serialize
: param use _ reference : If True , allow writing a reference""" | # TODO : Convert to " modified UTF - 8"
# http : / / docs . oracle . com / javase / 7 / docs / api / java / io / DataInput . html # modified - utf - 8
string = to_bytes ( obj , "utf-8" )
if use_reference and isinstance ( obj , JavaString ) :
try :
idx = self . references . index ( obj )
except ValueErro... |
def fnmatch_pathname_to_regex ( pattern ) :
"""Implements fnmatch style - behavior , as though with FNM _ PATHNAME flagged ;
the path seperator will not match shell - style ' * ' and ' . ' wildcards .""" | i , n = 0 , len ( pattern )
nonsep = '' . join ( [ '[^' , os . sep , ']' ] )
res = [ ]
while i < n :
c = pattern [ i ]
i = i + 1
if c == '*' :
try :
if pattern [ i ] == '*' :
i = i + 1
res . append ( '.*' )
if pattern [ i ] == '/' :
... |
def installShlibLinks ( dest , source , env ) :
"""If we are installing a versioned shared library create the required links .""" | Verbose = False
symlinks = listShlibLinksToInstall ( dest , source , env )
if Verbose :
print ( 'installShlibLinks: symlinks={:r}' . format ( SCons . Tool . StringizeLibSymlinks ( symlinks ) ) )
if symlinks :
SCons . Tool . CreateLibSymlinks ( env , symlinks )
return |
def _ensure_opened ( self ) :
"""Start monitors , or restart after a fork .
Hold the lock when calling this .""" | if not self . _opened :
self . _opened = True
self . _update_servers ( )
# Start or restart the events publishing thread .
if self . _publish_tp or self . _publish_server :
self . __events_executor . open ( )
# Ensure that the monitors are open .
for server in itervalues ( self . _servers ) :
... |
def makeQ ( r1 , r2 , r3 , r4 = 0 ) :
"""matrix involved in quaternion rotation""" | Q = np . asarray ( [ [ r4 , - r3 , r2 , r1 ] , [ r3 , r4 , - r1 , r2 ] , [ - r2 , r1 , r4 , r3 ] , [ - r1 , - r2 , - r3 , r4 ] ] )
return Q |
def comment ( self , format , * args ) :
"""Add a comment to hash table before saving to disk . You can add as many
comment lines as you like . These comment lines are discarded when loading
the file . If you use a null format , all comments are deleted .""" | return lib . zhashx_comment ( self . _as_parameter_ , format , * args ) |
def refine_MIDDLEWARE_CLASSES ( original ) :
"""Django docs say that the LocaleMiddleware should come after the SessionMiddleware .
Here , we make sure that the SessionMiddleware is enabled and then place the
LocaleMiddleware at the correct position .
Be careful with the order when refining the MiddlewareClas... | try :
session_middleware_index = original . index ( 'django.contrib.sessions.middleware.SessionMiddleware' )
original . insert ( session_middleware_index + 1 , 'django.middleware.locale.LocaleMiddleware' )
return original
except ValueError :
raise LookupError ( 'SessionMiddleware not found! Please make ... |
def nvp2pl ( normal , point ) :
"""Make a plane from a normal vector and a point .
http : / / naif . jpl . nasa . gov / pub / naif / toolkit _ docs / C / cspice / nvp2pl _ c . html
: param normal : A normal vector defining a plane .
: type normal : 3 - Element Array of floats
: param point : A point definin... | normal = stypes . toDoubleVector ( normal )
point = stypes . toDoubleVector ( point )
plane = stypes . Plane ( )
libspice . nvp2pl_c ( normal , point , ctypes . byref ( plane ) )
return plane |
def _prefix_from_ip_int ( self , ip_int ) :
"""Return prefix length from the bitwise netmask .
Args :
ip _ int : An integer , the netmask in expanded bitwise format
Returns :
An integer , the prefix length .
Raises :
ValueError : If the input intermingles zeroes & ones""" | trailing_zeroes = _count_righthand_zero_bits ( ip_int , self . _max_prefixlen )
prefixlen = self . _max_prefixlen - trailing_zeroes
leading_ones = ip_int >> trailing_zeroes
all_ones = ( 1 << prefixlen ) - 1
if leading_ones != all_ones :
byteslen = self . _max_prefixlen // 8
details = _int_to_bytes ( ip_int , by... |
def cublasZhpr2 ( handle , uplo , n , alpha , x , inx , y , incy , AP ) :
"""Rank - 2 operation on Hermitian - packed matrix .""" | status = _libcublas . cublasZhpr2_v2 ( handle , _CUBLAS_FILL_MODE [ uplo ] , n , ctypes . byref ( cuda . cuDoubleComplex ( alpha . real , alpha . imag ) ) , int ( x ) , incx , int ( y ) , incy , int ( AP ) )
cublasCheckStatus ( status ) |
def evrs ( self ) :
"""Getter EVRs dictionary""" | if self . _evrs is None :
import ait . core . evr as evr
self . _evrs = evr . getDefaultDict ( )
return self . _evrs |
def simple_tpl_from_pars ( parnames , tplfilename = 'model.input.tpl' ) :
"""Make a template file just assuming a list of parameter names the values of which should be
listed in order in a model input file
Args :
parnames : list of names from which to make a template file
tplfilename : filename for TPL file... | with open ( tplfilename , 'w' ) as ofp :
ofp . write ( 'ptf ~\n' )
[ ofp . write ( '~{0:^12}~\n' . format ( cname ) ) for cname in parnames ] |
def normalizeCoordinateTuple ( value ) :
"""Normalizes coordinate tuple .
* * * value * * must be a ` ` tuple ` ` or ` ` list ` ` .
* * * value * * must have exactly two items .
* * * value * * items must be an : ref : ` type - int - float ` .
* Returned value is a ` ` tuple ` ` of two values of the same ty... | if not isinstance ( value , ( tuple , list ) ) :
raise TypeError ( "Coordinates must be tuple instances, not %s." % type ( value ) . __name__ )
if len ( value ) != 2 :
raise ValueError ( "Coordinates must be tuples containing two items, " "not %d." % len ( value ) )
x , y = value
x = normalizeX ( x )
y = normal... |
def get_secret ( self , handle , contributor ) :
"""Retrieve an existing secret ' s value .
: param handle : Secret handle
: param contributor : User instance to perform contributor validation ,
which means that only secrets for the given contributor will be
looked up .""" | queryset = self . all ( )
if contributor is not None :
queryset = queryset . filter ( contributor = contributor )
secret = queryset . get ( handle = handle )
return secret . value |
def update_hosts_file ( ip , entry ) :
"""Updates the / etc / hosts file for the specified ip
This method updates the / etc / hosts file for the specified IP
address with the specified entry .
: param ip : ( str ) IP address to be added or updated
: param entry : ( str ) Hosts file entry to be added
: ret... | log = logging . getLogger ( mod_logger + '.update_hosts_file' )
# Validate args
if not isinstance ( ip , basestring ) :
msg = 'ip argument must be a string'
log . error ( msg )
raise CommandError ( msg )
if not isinstance ( entry , basestring ) :
msg = 'entry argument must be a string'
log . error (... |
def add ( self , directory , path = None ) -> None :
"""Add a directory and optionally its path .""" | objecttools . valid_variable_identifier ( directory )
if path is None :
path = directory
setattr ( self , directory , path ) |
def delete_all_events ( self , calendar_ids = ( ) ) :
"""Deletes all events managed through Cronofy from the all of the user ' s calendars .
: param tuple calendar _ ids : List of calendar ids to delete events for . ( Optional . Default empty tuple )""" | params = { 'delete_all' : True }
if calendar_ids :
params = { 'calendar_ids[]' : calendar_ids }
self . request_handler . delete ( endpoint = 'events' , params = params ) |
def _get_anns_to_remove ( in_file ) :
"""Find larger annotations , if present in VCF , that slow down processing .""" | to_remove = [ "ANN" , "LOF" ]
to_remove_str = tuple ( [ "##INFO=<ID=%s" % x for x in to_remove ] )
cur_remove = [ ]
with utils . open_gzipsafe ( in_file ) as in_handle :
for line in in_handle :
if not line . startswith ( "#" ) :
break
elif line . startswith ( to_remove_str ) :
... |
def add_execution_data ( self , context_id , data ) :
"""Within a context , append data to the execution result .
Args :
context _ id ( str ) : the context id returned by create _ context
data ( bytes ) : data to append
Returns :
( bool ) : True if the operation is successful , False if
the context _ id... | if context_id not in self . _contexts :
LOGGER . warning ( "Context_id not in contexts, %s" , context_id )
return False
context = self . _contexts . get ( context_id )
context . add_execution_data ( data )
return True |
def partition ( pred , iterable ) :
"""Partition an iterable .
Arguments
pred : function
A function that takes an element of the iterable and returns
a boolen indicating to which partition it belongs
iterable : iterable
Returns
A two - tuple of lists with the first list containing the elements on whic... | pos , neg = [ ] , [ ]
pos_append , neg_append = pos . append , neg . append
for elem in iterable :
if pred ( elem ) :
pos_append ( elem )
else :
neg_append ( elem )
return neg , pos |
def upload ( self , url = None , filepath = None , multipart = True , params = None , upload_processes = None , intelligent = False ) :
"""Uploads a file either through a local filepath or external _ url .
Uses multipart by default and Intelligent Ingestion by default ( if enabled ) .
You can specify the number... | if params : # Check the structure of parameters
STORE_SCHEMA . check ( params )
if filepath and url : # Raise an error for using both filepath and external url
raise ValueError ( "Cannot upload file and external url at the same time" )
if filepath : # Uploading from local drive
if intelligent :
resp... |
def _connectToFB ( self ) :
"""Establish the actual TCP connection to FB""" | if self . connected_to_fb :
logger . debug ( "Already connected to fb" )
return True
logger . debug ( "Connecting to fb" )
token = facebook_login . get_fb_token ( )
try :
self . fb = facebook . GraphAPI ( token )
except :
print ( "Couldn't connect to fb" )
return False
self . connected_to_fb = True
... |
def F_oneway ( * lists ) :
"""Performs a 1 - way ANOVA , returning an F - value and probability given
any number of groups . From Heiman , pp . 394-7.
Usage : F _ oneway ( * lists ) where * lists is any number of lists , one per
treatment group
Returns : F value , one - tailed p - value""" | a = len ( lists )
# ANOVA on ' a ' groups , each in it ' s own list
means = [ 0 ] * a
vars = [ 0 ] * a
ns = [ 0 ] * a
alldata = [ ]
tmp = lists
means = map ( mean , tmp )
vars = map ( var , tmp )
ns = map ( len , lists )
for i in range ( len ( lists ) ) :
alldata = alldata + lists [ i ]
bign = len ( alldata )
sstot... |
def target_to_hostname ( target ) :
"""Attempt to return a single hostname list from a target string .""" | if len ( target ) == 0 or len ( target ) > 255 :
return None
if not re . match ( r'^[\w.-]+$' , target ) :
return None
return [ target ] |
def parse_collection ( location : str , base_item_type : Type [ T ] , item_name_for_log : str = None , file_mapping_conf : FileMappingConfiguration = None , logger : Logger = default_logger , lazy_mfcollection_parsing : bool = False ) -> Dict [ str , T ] :
"""Utility method to create a RootParser ( ) with default c... | rp = _create_parser_from_default ( logger )
opts = create_parser_options ( lazy_mfcollection_parsing = lazy_mfcollection_parsing )
return rp . parse_collection ( location , base_item_type , item_name_for_log = item_name_for_log , file_mapping_conf = file_mapping_conf , options = opts ) |
def touch2screen ( w , h , o , x , y ) :
'''convert touch position''' | if o == 0 :
return x , y
elif o == 1 : # landscape - right
return y , w - x
elif o == 2 : # upsidedown
return w - x , h - y
elif o == 3 : # landscape - left
return h - y , x
return x , y |
def impulse_deltav_plummerstream ( v , y , b , w , GSigma , rs , tmin = None , tmax = None ) :
"""NAME :
impulse _ deltav _ plummerstream
PURPOSE :
calculate the delta velocity to due an encounter with a Plummer - softened stream in the impulse approximation ; allows for arbitrary velocity vectors , but y is ... | if len ( v . shape ) == 1 :
v = numpy . reshape ( v , ( 1 , 3 ) )
y = numpy . reshape ( y , ( 1 , 1 ) )
if tmax is None or tmax is None :
raise ValueError ( "tmin= and tmax= need to be set" )
nv = v . shape [ 0 ]
vmag = numpy . sqrt ( numpy . sum ( v ** 2. , axis = 1 ) )
# Build the rotation matrices and th... |
def run_analysis ( self , argv ) :
"""Run this analysis""" | args = self . _parser . parse_args ( argv )
name_keys = dict ( target_type = args . ttype , target_name = args . target , sim_name = args . sim , fullpath = True )
orig_dir = NAME_FACTORY . targetdir ( ** name_keys )
dest_dir = NAME_FACTORY . sim_targetdir ( ** name_keys )
self . copy_target_dir ( orig_dir , dest_dir ,... |
def delete ( gandi , resource ) :
"""Delete DNSSEC key .""" | result = gandi . dnssec . delete ( resource )
gandi . echo ( 'Delete successful.' )
return result |
def fcoe_fcoe_fabric_map_fcoe_fabric_mode ( self , ** kwargs ) :
"""Auto Generated Code""" | config = ET . Element ( "config" )
fcoe = ET . SubElement ( config , "fcoe" , xmlns = "urn:brocade.com:mgmt:brocade-fcoe" )
fcoe_fabric_map = ET . SubElement ( fcoe , "fcoe-fabric-map" )
fcoe_fabric_map_name_key = ET . SubElement ( fcoe_fabric_map , "fcoe-fabric-map-name" )
fcoe_fabric_map_name_key . text = kwargs . po... |
def _plunge ( tasks , pausing , finish ) :
"""( internal ) calls the next method of weaved tasks until they are finished
or The ` ` Plumber ` ` instance is stopped see : ` ` Dagger . chinkup ` ` .""" | # If no result received either not started or start & stop
# could have been called before the plunger thread
while True :
if pausing ( ) :
tasks . stop ( )
try :
tasks . next ( )
except StopIteration :
finish ( pausing ( ) )
break |
def PointCollection ( mode = "raw" , * args , ** kwargs ) :
"""mode : string
- " raw " ( speed : fastest , size : small , output : ugly )
- " agg " ( speed : fast , size : small , output : beautiful )""" | if mode == "raw" :
return RawPointCollection ( * args , ** kwargs )
return AggPointCollection ( * args , ** kwargs ) |
def set_flowcontrol_receive ( self , name , value = None , default = False , disable = False ) :
"""Configures the interface flowcontrol receive value
Args :
name ( string ) : The interface identifier . It must be a full
interface name ( ie Ethernet , not Et )
value ( boolean ) : True if the interface shoul... | return self . set_flowcontrol ( name , 'receive' , value , default , disable ) |
def get_product_url ( self , force_http = False ) :
"""Creates base url of product location on AWS .
: param force _ http : True if HTTP base URL should be used and False otherwise
: type force _ http : str
: return : url of product location
: rtype : str""" | base_url = self . base_http_url if force_http else self . base_url
return '{}products/{}/{}' . format ( base_url , self . date . replace ( '-' , '/' ) , self . product_id ) |
def update_session_variables ( self , variables_mapping ) :
"""update session with extracted variables mapping .
these variables are valid in the whole running session .""" | variables_mapping = utils . ensure_mapping_format ( variables_mapping )
self . session_variables_mapping . update ( variables_mapping )
self . test_variables_mapping . update ( self . session_variables_mapping ) |
def create_rt_extended_community ( value , subtype = 2 ) :
"""Creates an instance of the BGP Route Target Community ( if " subtype = 2 " )
or Route Origin Community ( " subtype = 3 " ) .
: param value : String of Route Target or Route Origin value .
: param subtype : Subtype of Extended Community .
: return... | global_admin , local_admin = value . split ( ':' )
local_admin = int ( local_admin )
if global_admin . isdigit ( ) and 0 <= int ( global_admin ) <= 0xffff :
ext_com = BGPTwoOctetAsSpecificExtendedCommunity ( subtype = subtype , as_number = int ( global_admin ) , local_administrator = local_admin )
elif global_admin... |
def spreadsheet2gradebook ( self , csv_file , email_field = None , approve_grades = False , use_max_points_column = False , max_points_column = None , normalize_column = None ) :
"""Upload grade spreadsheet to gradebook .
Upload grades from CSV format spreadsheet file into the
Learning Modules gradebook . The s... | non_assignment_fields = [ 'ID' , 'Username' , 'Full Name' , 'edX email' , 'External email' ]
if max_points_column is not None :
non_assignment_fields . append ( max_points_column )
if normalize_column is not None :
non_assignment_fields . append ( normalize_column )
if email_field is not None :
non_assignme... |
def get_include ( ) :
'''return a list of include directories .''' | dirname = os . path . abspath ( os . path . join ( os . path . dirname ( __file__ ) ) )
# Header files may be stored in different relative locations
# depending on installation mode ( e . g . , ` python setup . py install ` ,
# ` python setup . py develop ` . The first entry in each list is
# where develop - mode heade... |
def _get_blkid_type ( self ) :
"""Retrieves the FS type from the blkid command .""" | try :
result = _util . check_output_ ( [ 'blkid' , '-p' , '-O' , str ( self . offset ) , self . get_raw_path ( ) ] )
if not result :
return None
# noinspection PyTypeChecker
blkid_result = dict ( re . findall ( r'([A-Z]+)="(.+?)"' , result ) )
self . info [ 'blkid_data' ] = blkid_result
... |
def logs ( awsclient , function_name , start_dt , end_dt = None , tail = False ) :
"""Send a ping request to a lambda function .
: param awsclient :
: param function _ name :
: param start _ dt :
: param end _ dt :
: param tail :
: return :""" | log . debug ( 'Getting cloudwatch logs for: %s' , function_name )
log_group_name = '/aws/lambda/%s' % function_name
current_date = None
start_ts = datetime_to_timestamp ( start_dt )
if end_dt :
end_ts = datetime_to_timestamp ( end_dt )
else :
end_ts = None
# tail mode
# we assume that logs can arrive late but n... |
def waverange ( self ) :
"""Range of ` waveset ` .""" | if self . waveset is None :
x = [ None , None ]
else :
x = u . Quantity ( [ self . waveset . min ( ) , self . waveset . max ( ) ] )
return x |
def _iter ( root , term ) :
'''Checks for python2.6 or python2.7''' | if sys . version_info < ( 2 , 7 ) :
return root . getiterator ( term )
else :
return root . iter ( term ) |
def namedb_is_name_zonefile_hash ( cur , name , zonefile_hash ) :
"""Determine if a zone file hash was sent by a name .
Return True if so , false if not""" | select_query = 'SELECT COUNT(value_hash) FROM history WHERE history_id = ? AND value_hash = ?'
select_args = ( name , zonefile_hash )
rows = namedb_query_execute ( cur , select_query , select_args )
count = None
for r in rows :
count = r [ 'COUNT(value_hash)' ]
break
return count > 0 |
def has_column ( self , table , column ) :
"""Determine if the given table has a given column .
: param table : The table
: type table : str
: type column : str
: rtype : bool""" | column = column . lower ( )
return column in list ( map ( lambda x : x . lower ( ) , self . get_column_listing ( table ) ) ) |
def fit_candidates ( AggOp , B , tol = 1e-10 ) :
"""Fit near - nullspace candidates to form the tentative prolongator .
Parameters
AggOp : csr _ matrix
Describes the sparsity pattern of the tentative prolongator .
Has dimension ( # blocks , # aggregates )
B : array
The near - nullspace candidates stored... | if not isspmatrix_csr ( AggOp ) :
raise TypeError ( 'expected csr_matrix for argument AggOp' )
B = np . asarray ( B )
if B . dtype not in [ 'float32' , 'float64' , 'complex64' , 'complex128' ] :
B = np . asarray ( B , dtype = 'float64' )
if len ( B . shape ) != 2 :
raise ValueError ( 'expected 2d array for ... |
def potential ( __func__ = None , ** kwds ) :
"""Decorator function instantiating potentials . Usage :
@ potential
def B ( parent _ name = . , . . . )
return baz ( parent _ name , . . . )
where baz returns the deterministic B ' s value conditional
on its parents .
: SeeAlso :
Deterministic , determini... | def instantiate_pot ( __func__ ) :
junk , parents = _extract ( __func__ , kwds , keys , 'Potential' , probe = False )
return Potential ( parents = parents , ** kwds )
keys = [ 'logp' ]
instantiate_pot . kwds = kwds
if __func__ :
return instantiate_pot ( __func__ )
return instantiate_pot |
def outline_segments ( self , mask_background = False ) :
"""Outline the labeled segments .
The " outlines " represent the pixels * just inside * the segments ,
leaving the background pixels unmodified .
Parameters
mask _ background : bool , optional
Set to ` True ` to mask the background pixels ( labels ... | from scipy . ndimage import grey_erosion , grey_dilation
# mode = ' constant ' ensures outline is included on the image borders
selem = np . array ( [ [ 0 , 1 , 0 ] , [ 1 , 1 , 1 ] , [ 0 , 1 , 0 ] ] )
eroded = grey_erosion ( self . data , footprint = selem , mode = 'constant' , cval = 0. )
dilated = grey_dilation ( sel... |
def convert ( model , input_features , output_features ) :
"""Convert a normalizer model to the protobuf spec .
Parameters
model : Normalizer
A Normalizer .
input _ features : str
Name of the input column .
output _ features : str
Name of the output column .
Returns
model _ spec : An object of typ... | if not ( _HAS_SKLEARN ) :
raise RuntimeError ( 'scikit-learn not found. scikit-learn conversion API is disabled.' )
# Test the scikit - learn model
_sklearn_util . check_expected_type ( model , Normalizer )
_sklearn_util . check_fitted ( model , lambda m : hasattr ( m , 'norm' ) )
# Set the interface params .
spec ... |
def get_application ( * args ) :
'''Returns a WSGI application function . If you supply the WSGI app and config
it will use that , otherwise it will try to obtain them from a local Salt
installation''' | opts_tuple = args
def wsgi_app ( environ , start_response ) :
root , _ , conf = opts_tuple or bootstrap_app ( )
cherrypy . config . update ( { 'environment' : 'embedded' } )
cherrypy . tree . mount ( root , '/' , conf )
return cherrypy . tree ( environ , start_response )
return wsgi_app |
def run ( self ) :
"""Runs the scanner
: return : self""" | # Normalize path
self . path = os . path . expanduser ( self . path )
# Start scanning
if os . path . isdir ( self . path ) :
self . search_script_directory ( self . path )
return self
else :
raise ScannerException ( "Unknown directory: %s" % self . path ) |
def os_version ( self , value ) :
"""The os _ version property .
Args :
value ( string ) . the property value .""" | if value == self . _defaults [ 'ai.device.osVersion' ] and 'ai.device.osVersion' in self . _values :
del self . _values [ 'ai.device.osVersion' ]
else :
self . _values [ 'ai.device.osVersion' ] = value |
def webui_schematics_panels_panel_components_component_id ( self , ** kwargs ) :
"""Auto Generated Code""" | config = ET . Element ( "config" )
webui = ET . SubElement ( config , "webui" , xmlns = "http://tail-f.com/ns/webui" )
schematics = ET . SubElement ( webui , "schematics" )
panels = ET . SubElement ( schematics , "panels" )
panel = ET . SubElement ( panels , "panel" )
name_key = ET . SubElement ( panel , "name" )
name_... |
def format_search_results ( self , search_results ) :
"""Format search results .
Args :
search _ results ( list of ` ResourceSearchResult ` ) : Search to format .
Returns :
List of 2 - tuple : Text and color to print in .""" | formatted_lines = [ ]
for search_result in search_results :
lines = self . _format_search_result ( search_result )
formatted_lines . extend ( lines )
return formatted_lines |
def add_consumer ( self , consumer ) :
"""Add another consumer from a : class : ` Consumer ` instance .""" | consumer . backend = self . backend
self . consumers . append ( consumer ) |
def _to_dict ( self ) :
"""Return a json dictionary representing this model .""" | _dict = { }
if hasattr ( self , 'document_id' ) and self . document_id is not None :
_dict [ 'document_id' ] = self . document_id
if hasattr ( self , 'passage_score' ) and self . passage_score is not None :
_dict [ 'passage_score' ] = self . passage_score
if hasattr ( self , 'passage_text' ) and self . passage_... |
def del_doc ( self , doc ) :
"""Delete a document""" | logger . info ( "Removing doc from the index: %s" % doc )
doc = doc . clone ( )
# make sure it can be serialized safely
self . docsearch . index . del_doc ( doc ) |
def light_to_gl ( light , transform , lightN ) :
"""Convert trimesh . scene . lighting . Light objects into
args for gl . glLightFv calls
Parameters
light : trimesh . scene . lighting . Light
Light object to be converted to GL
transform : ( 4 , 4 ) float
Transformation matrix of light
lightN : int
R... | # convert color to opengl
gl_color = vector_to_gl ( light . color . astype ( np . float64 ) / 255.0 )
assert len ( gl_color ) == 4
# cartesian translation from matrix
gl_position = vector_to_gl ( transform [ : 3 , 3 ] )
# create the different position and color arguments
args = [ ( lightN , gl . GL_POSITION , gl_positi... |
def set ( self , x , y , value ) :
"""Set the data at ( x , y ) to value .""" | xBase = int ( x ) * self . xScale
yBase = int ( y ) * self . yScale
for xOffset in range ( self . xScale ) :
for yOffset in range ( self . yScale ) :
self . data [ yBase + yOffset , xBase + xOffset ] = value |
def extra_hosts ( self , value ) :
""": param value :
: return None :""" | if value is None :
self . _extra_hosts = value
elif isinstance ( value , list ) : # TODO : better validation
self . _extra_hosts = value
elif isinstance ( value , dict ) :
converted_extra_hosts = [ ]
for k , v in sorted ( six . iteritems ( value ) ) :
if not is_valid_hostname ( k ) :
... |
def exit ( self , status = 0 , message = None ) :
"""Delegates to ` ArgumentParser . exit `""" | if status :
self . logger . error ( message )
if self . __parser__ : # pylint : disable - msg = E1101
self . __parser__ . exit ( status , message )
# pylint : disable - msg = E1101
else :
sys . exit ( status ) |
def get_attached_instruments ( self , expected : Dict [ Mount , str ] ) -> Dict [ Mount , Dict [ str , Optional [ str ] ] ] :
"""Find the instruments attached to our mounts .
: param expected : A dict that may contain a mapping from mount to
strings that should prefix instrument model names .
When instruments... | to_return : Dict [ Mount , Dict [ str , Optional [ str ] ] ] = { }
for mount in Mount :
found_model = self . _smoothie_driver . read_pipette_model ( mount . name . lower ( ) )
found_id = self . _smoothie_driver . read_pipette_id ( mount . name . lower ( ) )
expected_instr = expected . get ( mount , None )
... |
def indent_files ( arguments ) :
"""indent _ files ( fname : str )
1 . Creates a backup of the source file ( backup _ source _ file ( ) )
2 . Reads the files contents ( read _ file ( ) )
3 . Indents the code ( indent _ code ( ) )
4 . Writes the file or print the indented code ( _ after _ indentation ( ) )""... | opts = parse_options ( arguments )
if not opts . files : # Indent from stdin
code = sys . stdin . read ( )
indent_result = indent_code ( code , opts )
_after_indentation ( indent_result )
for fname in opts . files :
code = read_file ( fname )
if not opts . dialect : # Guess dialect from the file ext... |
def settlement_date ( self , value ) :
"""Force the settlement _ date to always be a date
: param value :
: return :""" | if value :
self . _settlement_date = parse ( value ) . date ( ) if isinstance ( value , type_check ) else value |
def _get_instance ( project_id , instance_zone , name , service ) :
'''Get instance details''' | return service . instances ( ) . get ( project = project_id , zone = instance_zone , instance = name ) . execute ( ) |
def delete ( self ) :
"""Delete the cloud from the list of added clouds in mist . io service .
: returns : A list of mist . clients ' updated clouds .""" | req = self . request ( self . mist_client . uri + '/clouds/' + self . id )
req . delete ( )
self . mist_client . update_clouds ( ) |
def covariance ( self , param_1 , param_2 ) :
"""Return the covariance between param _ 1 and param _ 2.
: param param _ 1 : ` ` Parameter ` ` Instance .
: param param _ 2 : ` ` Parameter ` ` Instance .
: return : Covariance of the two params .""" | param_1_number = self . model . params . index ( param_1 )
param_2_number = self . model . params . index ( param_2 )
return self . covariance_matrix [ param_1_number , param_2_number ] |
def rewriteFasta ( sequence , sequence_name , fasta_in , fasta_out ) :
"""Rewrites a specific sequence in a multifasta file while keeping the sequence header .
: param sequence : a string with the sequence to be written
: param sequence _ name : the name of the sequence to be retrieved eg . for ' > 2 dna : chro... | f = open ( fasta_in , 'r+' )
f2 = open ( fasta_out , 'w' )
lines = f . readlines ( )
i = 0
while i < len ( lines ) :
line = lines [ i ]
if line [ 0 ] == ">" :
f2 . write ( line )
fChr = line . split ( " " ) [ 0 ]
fChr = fChr [ 1 : ]
if fChr == sequence_name :
code = [... |
def Logs ( loggername , echo = True , debug = False , chatty = False , loglevel = logging . INFO , logfile = None , logpath = None , fileHandler = None ) :
"""Initialize logging""" | log = logging . getLogger ( loggername )
if fileHandler is None :
if logfile is None :
logFilename = _ourName
else :
logFilename = logfile
if '.log' not in logFilename :
logFilename = '%s.log' % logFilename
if logpath is not None :
logFilename = os . path . join ( logpath... |
def imbalance_metrics ( data ) :
"""Computes imbalance metric for a given dataset .
Imbalance metric is equal to 0 when a dataset is perfectly balanced ( i . e . number of in each class is exact ) .
: param data : pandas . DataFrame
A dataset in a panda ' s data frame
: returns int
A value of imbalance me... | if not data :
return 0
# imb - shows measure of inbalance within a dataset
imb = 0
num_classes = float ( len ( Counter ( data ) ) )
for x in Counter ( data ) . values ( ) :
p_x = float ( x ) / len ( data )
if p_x > 0 :
imb += ( p_x - 1 / num_classes ) * ( p_x - 1 / num_classes )
# worst case scenari... |
def base_list_parser ( ) :
"""Creates a parser with arguments specific to formatting lists
of resources .
Returns :
{ ArgumentParser } : Base parser with defaul list args""" | base_parser = ArgumentParser ( add_help = False )
base_parser . add_argument ( '-F' , '--format' , action = 'store' , default = 'default' , choices = [ 'csv' , 'json' , 'yaml' , 'default' ] , help = 'choose the output format' )
return base_parser |
def iter_filth_clss ( ) :
"""Iterate over all of the filths that are included in this sub - package .
This is a convenience method for capturing all new Filth that are added
over time .""" | return iter_subclasses ( os . path . dirname ( os . path . abspath ( __file__ ) ) , Filth , _is_abstract_filth , ) |
def bootstrap_buttons ( parser , token ) :
"""Render buttons for form
* * Tag name * * : :
buttons
* * Parameters * * :
submit
Text for a submit button
reset
Text for a reset button
* * Usage * * : :
{ % buttons % } { % endbuttons % }
* * Example * * : :
{ % buttons submit = ' OK ' reset = " C... | kwargs = parse_token_contents ( parser , token )
kwargs [ "nodelist" ] = parser . parse ( ( "endbuttons" , ) )
parser . delete_first_token ( )
return ButtonsNode ( ** kwargs ) |
def bulk_load ( self , ** kwargs ) :
"""Uploads data to the Blazegraph Triplestore that is stored in files
that are in a local directory
kwargs :
file _ directory : a string path to the file directory
file _ extensions : a list of file extensions to filter
example [ ' xml ' , ' rdf ' ] . If none include a... | namespace = kwargs . get ( 'namespace' , self . namespace )
graph = kwargs . get ( 'graph' , self . graph )
if kwargs . get ( 'reset' ) == True :
self . reset_namespace ( )
file_directory = kwargs . get ( 'file_directory' , self . local_directory )
file_extensions = kwargs . get ( 'file_extensions' , self . rdf_for... |
def stats_send ( self , template , start_date , end_date , options = None ) :
"""Retrieve information about a particular transactional or aggregated information
from transactionals from that template over a specified date range .
http : / / docs . sailthru . com / api / stat""" | options = options or { }
data = options . copy ( )
data = { 'template' : template , 'start_date' : start_date , 'end_date' : end_date }
data [ 'stat' ] = 'send'
return self . _stats ( data ) |
def link_connection_to_account ( app ) :
"""Link the connection to your Heroku user account .
https : / / devcenter . heroku . com / articles / heroku - connect - api # step - 3 - link - the - connection - to - your - heroku - user - account""" | url = os . path . join ( settings . HEROKU_CONNECT_API_ENDPOINT , 'users' , 'me' , 'apps' , app , 'auth' )
response = requests . post ( url = url , headers = _get_authorization_headers ( ) )
response . raise_for_status ( ) |
def sum ( self ) :
"""Evaluate the integral over the given interval using
Clenshaw - Curtis quadrature .""" | ak = self . coefficients ( )
ak2 = ak [ : : 2 ]
n = len ( ak2 )
Tints = 2 / ( 1 - ( 2 * np . arange ( n ) ) ** 2 )
val = np . sum ( ( Tints * ak2 . T ) . T , axis = 0 )
a_ , b_ = self . domain ( )
return 0.5 * ( b_ - a_ ) * val |
def chromaticity_to_XYZ ( white , red , green , blue ) :
"""From the " CalRGB Color Spaces " section of " PDF Reference " , 6th ed .""" | xW , yW = white
xR , yR = red
xG , yG = green
xB , yB = blue
R = G = B = 1.0
z = yW * ( ( xG - xB ) * yR - ( xR - xB ) * yG + ( xR - xG ) * yB )
YA = yR / R * ( ( xG - xB ) * yW - ( xW - xB ) * yG + ( xW - xG ) * yB ) / z
XA = YA * xR / yR
ZA = YA * ( ( 1 - xR ) / yR - 1 )
YB = - yG / G * ( ( xR - xB ) * yW - ( xW - xB... |
def main ( argv ) :
"""Main .""" | del argv
# Unused .
if flags . FLAGS . version :
print ( "GRR frontend {}" . format ( config_server . VERSION [ "packageversion" ] ) )
return
config . CONFIG . AddContext ( "HTTPServer Context" )
server_startup . Init ( )
httpd = CreateServer ( )
server_startup . DropPrivileges ( )
try :
httpd . serve_forev... |
def add_perm ( self , subj_str , perm_str ) :
"""Add a permission for a subject .
Args :
subj _ str : str
Subject for which to add permission ( s )
perm _ str : str
Permission to add . Implicitly adds all lower permissions . E . g . , ` ` write ` `
will also add ` ` read ` ` .""" | self . _assert_valid_permission ( perm_str )
self . _perm_dict . setdefault ( perm_str , set ( ) ) . add ( subj_str ) |
def get_configs ( self ) :
""": return : overall index , agent config , loadout config in that order""" | loadout_config = self . loadout_preset . config . copy ( )
config_path = None
if self . agent_preset . config_path is not None : # Might be none if preset was never saved to disk .
config_path = os . path . dirname ( self . agent_preset . config_path )
config = self . agent_preset . config . copy ( )
config . set_v... |
def _validate_freq ( self ) :
"""Validate & return window frequency .""" | from pandas . tseries . frequencies import to_offset
try :
return to_offset ( self . window )
except ( TypeError , ValueError ) :
raise ValueError ( "passed window {0} is not " "compatible with a datetimelike " "index" . format ( self . window ) ) |
def gopro_set_request_encode ( self , target_system , target_component , cmd_id , value ) :
'''Request to set a GOPRO _ COMMAND with a desired
target _ system : System ID ( uint8 _ t )
target _ component : Component ID ( uint8 _ t )
cmd _ id : Command ID ( uint8 _ t )
value : Value ( uint8 _ t )''' | return MAVLink_gopro_set_request_message ( target_system , target_component , cmd_id , value ) |
def remove_host ( self , host ) :
"""Called when the control connection observes that a node has left the
ring . Intended for internal use only .""" | if host and self . metadata . remove_host ( host ) :
log . info ( "Cassandra host %s removed" , host )
self . on_remove ( host ) |
def create ( self , file_or_path = None , data = None , obj_name = None , content_type = None , etag = None , content_encoding = None , content_length = None , ttl = None , chunked = False , metadata = None , chunk_size = None , headers = None , return_none = False ) :
"""Creates or replaces a storage object in thi... | return self . object_manager . create ( file_or_path = file_or_path , data = data , obj_name = obj_name , content_type = content_type , etag = etag , content_encoding = content_encoding , content_length = content_length , ttl = ttl , chunked = chunked , metadata = metadata , chunk_size = chunk_size , headers = headers ... |
def configuration_callback ( cmd_name , option_name , config_file_name , saved_callback , provider , implicit , ctx , param , value ) :
"""Callback for reading the config file .
Also takes care of calling user specified custom callback afterwards .
cmd _ name : str
The command name . This is used to determine... | ctx . default_map = ctx . default_map or { }
cmd_name = cmd_name or ctx . info_name
if implicit :
default_value = os . path . join ( click . get_app_dir ( cmd_name ) , config_file_name )
param . default = default_value
value = value or default_value
if value :
try :
config = provider ( value , c... |
def solve_potts_approx ( y , w , gamma = None , min_size = 1 , ** kw ) :
"""Fit penalized stepwise constant function ( Potts model ) to data
approximatively , in linear time .
Do this by running the exact solver using a small maximum interval
size , and then combining consecutive intervals together if it
de... | n = len ( y )
if n == 0 :
return [ ] , [ ] , [ ]
mu_dist = kw . get ( 'mu_dist' )
if mu_dist is None :
mu_dist = get_mu_dist ( y , w )
kw [ 'mu_dist' ] = mu_dist
if gamma is None :
mu , dist = mu_dist . mu , mu_dist . dist
gamma = 3 * dist ( 0 , n - 1 ) * math . log ( n ) / n
if min_size < 10 :
... |
def to_api_repr ( self ) :
"""Generate a resource for : meth : ` _ begin ` .""" | configuration = self . _configuration . to_api_repr ( )
resource = { "jobReference" : self . _properties [ "jobReference" ] , "configuration" : configuration , }
configuration [ "query" ] [ "query" ] = self . query
return resource |
def _round_multiple ( x : int , mult : int = None ) -> int :
"Calc ` x ` to nearest multiple of ` mult ` ." | return ( int ( x / mult + 0.5 ) * mult ) if mult is not None else x |
def is_regex_type ( type_ ) :
"""Checks if the given type is a regex type .
: param type _ : The type to check
: return : True if the type is a regex type , otherwise False
: rtype : bool""" | return ( callable ( type_ ) and getattr ( type_ , "__name__" , None ) == REGEX_TYPE_NAME and hasattr ( type_ , "__supertype__" ) and is_compiled_pattern ( type_ . __supertype__ ) ) |
def get_chat_member ( self , chat_id , user_id ) :
"""Use this method to get information about a member of a chat . Returns a ChatMember object on success .
: param chat _ id :
: param user _ id :
: return :""" | result = apihelper . get_chat_member ( self . token , chat_id , user_id )
return types . ChatMember . de_json ( result ) |
def deploy_wsgi ( ) :
"""deploy python wsgi file ( s )""" | if 'libapache2-mod-wsgi' in get_packages ( ) :
remote_dir = '/' . join ( [ deployment_root ( ) , 'env' , env . project_fullname , 'wsgi' ] )
wsgi = 'apache2'
elif 'gunicorn' in get_packages ( ) :
remote_dir = '/etc/init'
wsgi = 'gunicorn'
deployed = [ ]
# ensure project apps path is also added to enviro... |
def count ( self , * , page_size = DEFAULT_BATCH_SIZE , ** options ) :
"""Counts the number of entities that match this query .
Note :
Since Datastore doesn ' t provide a native way to count
entities by query , this method paginates through all the
entities ' keys and counts them .
Parameters :
\**optio... | entities = 0
options = QueryOptions ( self ) . replace ( keys_only = True )
for page in self . paginate ( page_size = page_size , ** options ) :
entities += len ( list ( page ) )
return entities |
def set_modifier_mapping ( self , keycodes ) :
"""Set the keycodes for the eight modifiers X . Shift , X . Lock ,
X . Control , X . Mod1 , X . Mod2 , X . Mod3 , X . Mod4 and X . Mod5 . keycodes
should be a eight - element list where each entry is a list of the
keycodes that should be bound to that modifier . ... | r = request . SetModifierMapping ( display = self . display , keycodes = keycodes )
return r . status |
def prefetch_docker_image_on_private_agents ( image , timeout = timedelta ( minutes = 5 ) . total_seconds ( ) ) :
"""Given a docker image . An app with the image is scale across the private
agents to ensure that the image is prefetched to all nodes .
: param image : docker image name
: type image : str
: pa... | agents = len ( shakedown . get_private_agents ( ) )
app = { "id" : "/prefetch" , "instances" : agents , "container" : { "type" : "DOCKER" , "docker" : { "image" : image } } , "cpus" : 0.1 , "mem" : 128 }
client = marathon . create_client ( )
client . add_app ( app )
shakedown . deployment_wait ( timeout )
shakedown . d... |
def from_bytes ( cls , bitstream ) :
'''Parse the given record and update properties accordingly''' | record = cls ( )
# Convert to ConstBitStream ( if not already provided )
if not isinstance ( bitstream , ConstBitStream ) :
if isinstance ( bitstream , Bits ) :
bitstream = ConstBitStream ( auto = bitstream )
else :
bitstream = ConstBitStream ( bytes = bitstream )
# Read the priorities and weigh... |
def duplicate_nodes ( self ) :
"""Return a sequence of node keys of identical meshes .
Will combine meshes duplicated by copying in space with different keys in
self . geometry , as well as meshes repeated by self . nodes .
Returns
duplicates : ( m ) sequence of keys to self . nodes that represent
identic... | # if there is no geometry we can have no duplicate nodes
if len ( self . geometry ) == 0 :
return [ ]
# geometry name : md5 of mesh
mesh_hash = { k : int ( m . identifier_md5 , 16 ) for k , m in self . geometry . items ( ) }
# the name of nodes in the scene graph with geometry
node_names = np . array ( self . graph... |
def _build_command ( self ) :
"""Command to start the QEMU process .
( to be passed to subprocess . Popen ( ) )""" | additional_options = self . _options . strip ( )
additional_options = additional_options . replace ( "%vm-name%" , '"' + self . _name . replace ( '"' , '\\"' ) + '"' )
additional_options = additional_options . replace ( "%vm-id%" , self . _id )
additional_options = additional_options . replace ( "%project-id%" , self .... |
def source ( self , source ) :
"""When the source gets updated , update the select widget""" | if isinstance ( source , list ) : # if source is a list , get first item or None
source = source [ 0 ] if len ( source ) > 0 else None
self . _source = source |
def get_unused_list_annotation_values ( graph ) -> Mapping [ str , Set [ str ] ] :
"""Get all of the unused values for list annotations .
: param pybel . BELGraph graph : A BEL graph
: return : A dictionary of { str annotation : set of str values that aren ' t used }""" | result = { }
for annotation , values in graph . annotation_list . items ( ) :
used_values = get_annotation_values ( graph , annotation )
if len ( used_values ) == len ( values ) : # all values have been used
continue
result [ annotation ] = set ( values ) - used_values
return result |
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