signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def _zforce ( self , R , z , phi = 0. , t = 0. ) :
"""NAME :
zforce
PURPOSE :
evaluate vertical force K _ z ( R , z )
INPUT :
R - Cylindrical Galactocentric radius
z - vertical height
phi - azimuth
t - time
OUTPUT :
K _ z ( R , z )
HISTORY :
2012-12-27 - Written - Bovy ( IAS )""" | if self . _new : # if R > 6 . : return self . _ kp ( R , z )
if nu . fabs ( z ) < 10. ** - 6. :
return 0.
kalphamax1 = R
ks1 = kalphamax1 * 0.5 * ( self . _glx + 1. )
weights1 = kalphamax1 * self . _glw
sqrtp = nu . sqrt ( z ** 2. + ( ks1 + R ) ** 2. )
sqrtm = nu . sqrt ( z ** 2. + ( ks1... |
def list ( self , * args , ** kwargs ) :
"""List networks . Similar to the ` ` docker networks ls ` ` command .
Args :
names ( : py : class : ` list ` ) : List of names to filter by .
ids ( : py : class : ` list ` ) : List of ids to filter by .
filters ( dict ) : Filters to be processed on the network list ... | greedy = kwargs . pop ( 'greedy' , False )
resp = self . client . api . networks ( * args , ** kwargs )
networks = [ self . prepare_model ( item ) for item in resp ]
if greedy and version_gte ( self . client . api . _version , '1.28' ) :
for net in networks :
net . reload ( )
return networks |
def generate_host_passthrough ( self , vcpu_num ) :
"""Generate host - passthrough XML cpu node
Args :
vcpu _ num ( str ) : number of virtual CPUs
Returns :
lxml . etree . Element : CPU XML node""" | cpu = ET . Element ( 'cpu' , mode = 'host-passthrough' )
cpu . append ( self . generate_topology ( vcpu_num ) )
if vcpu_num > 1 :
cpu . append ( self . generate_numa ( vcpu_num ) )
return cpu |
def ExamineEvent ( self , mediator , event ) :
"""Analyzes an event and creates Windows Services as required .
At present , this method only handles events extracted from the Registry .
Args :
mediator ( AnalysisMediator ) : mediates interactions between analysis
plugins and other components , such as stora... | # TODO : Handle event log entries here also ( ie , event id 4697 ) .
event_data_type = getattr ( event , 'data_type' , '' )
if event_data_type == 'windows:registry:service' : # Create and store the service .
service = WindowsService . FromEvent ( event )
self . _service_collection . AddService ( service ) |
def pipe_numberinput ( context = None , _INPUT = None , conf = None , ** kwargs ) :
"""An input that prompts the user for a number and yields it forever .
Not loopable .
Parameters
context : pipe2py . Context object
_ INPUT : not used
conf : {
' name ' : { ' value ' : ' parameter name ' } ,
' prompt '... | value = utils . get_input ( context , conf )
try :
value = int ( value )
except :
value = 0
while True :
yield value |
def superscript ( self ) :
"""| True | if ` w : vertAlign / @ w : val ` is ' superscript ' . | False | if
` w : vertAlign / @ w : val ` contains any other value . | None | if
` w : vertAlign ` is not present .""" | vertAlign = self . vertAlign
if vertAlign is None :
return None
if vertAlign . val == ST_VerticalAlignRun . SUPERSCRIPT :
return True
return False |
def from_array ( array ) :
"""Deserialize a new EncryptedPassportElement from a given dictionary .
: return : new EncryptedPassportElement instance .
: rtype : EncryptedPassportElement""" | if array is None or not array :
return None
# end if
assert_type_or_raise ( array , dict , parameter_name = "array" )
from pytgbot . api_types . receivable . passport import PassportFile
data = { }
data [ 'type' ] = u ( array . get ( 'type' ) )
data [ 'hash' ] = u ( array . get ( 'hash' ) )
data [ 'data' ] = u ( ar... |
def wrapped_request ( self , request , * args , ** kwargs ) :
"""Create and send a request to the server .
This method implements a very small subset of the options
possible to send an request . It is provided as a shortcut to
sending a simple wrapped request .
Parameters
request : str
The request to ca... | f = tornado_Future ( )
try :
use_mid = kwargs . get ( 'use_mid' )
timeout = kwargs . get ( 'timeout' )
mid = kwargs . get ( 'mid' )
msg = Message . request ( request , * args , mid = mid )
except Exception :
f . set_exc_info ( sys . exc_info ( ) )
return f
return transform_future ( self . reply_... |
def to_dict ( self ) :
'''Save this wait _ time condition into a dictionary .''' | d = super ( WaitTime , self ) . to_dict ( )
d [ 'condition' ] = { 'waitTime' : { 'waitTime' : self . wait_time } }
return d |
def remove_out_of_bounds_bins ( df , chromosome_size ) : # type : ( pd . DataFrame , int ) - > pd . DataFrame
"""Remove all reads that were shifted outside of the genome endpoints .""" | # The dataframe is empty and contains no bins out of bounds
if "Bin" not in df :
return df
df = df . drop ( df [ df . Bin > chromosome_size ] . index )
return df . drop ( df [ df . Bin < 0 ] . index ) |
def reverse_query ( self ) :
'''Changes the coordinates as if the query sequence has been reverse complemented''' | self . qry_start = self . qry_length - self . qry_start - 1
self . qry_end = self . qry_length - self . qry_end - 1 |
def to_si ( self , values , from_unit ) :
"""Return values in SI and the units to which the values have been converted .""" | if from_unit in self . si_units :
return values , from_unit
elif from_unit == 'ton' :
return self . to_unit ( values , 'tonne' , from_unit ) , 'tonne'
else :
return self . to_unit ( values , 'kg' , from_unit ) , 'kg' |
def create_selection ( ) :
"""Create a selection expression""" | operation = Forward ( )
nested = Group ( Suppress ( "(" ) + operation + Suppress ( ")" ) ) . setResultsName ( "nested" )
select_expr = Forward ( )
functions = select_functions ( select_expr )
maybe_nested = functions | nested | Group ( var_val )
operation <<= maybe_nested + OneOrMore ( oneOf ( "+ - * /" ) + maybe_neste... |
def sp_rand ( m , n , a ) :
"""Generates an mxn sparse ' d ' matrix with round ( a * m * n ) nonzeros .""" | if m == 0 or n == 0 :
return spmatrix ( [ ] , [ ] , [ ] , ( m , n ) )
nnz = min ( max ( 0 , int ( round ( a * m * n ) ) ) , m * n )
nz = matrix ( random . sample ( range ( m * n ) , nnz ) , tc = 'i' )
return spmatrix ( normal ( nnz , 1 ) , nz % m , matrix ( [ int ( ii ) for ii in nz / m ] ) , ( m , n ) ) |
def init_UI ( self ) :
"""Set display variables ( font , resolution of GUI , sizer proportions )
then builds the Side bar panel , Top bar panel , and Plots scrolleing
panel which are then placed placed together in a sizer and fit to
the GUI wx . Frame""" | # Setup ScrolledPanel Ctrls - - - - -
# set ctrl size and style variables
dw , dh = wx . DisplaySize ( )
r1 = dw / 1210.
r2 = dw / 640.
self . GUI_RESOLUTION = min ( r1 , r2 , 1 )
top_bar_2v_space = 5
top_bar_h_space = 10
spec_button_space = 10
side_bar_v_space = 10
# set font size and style
FONT_WEIGHT = 1
if sys . pl... |
def league_scores ( self , total_data , time , show_upcoming , use_12_hour_format ) :
"""Store output of fixtures based on league and time to a CSV file""" | headers = [ 'League' , 'Home Team Name' , 'Home Team Goals' , 'Away Team Goals' , 'Away Team Name' ]
result = [ headers ]
league = total_data [ 'competition' ] [ 'name' ]
result . extend ( [ league , score [ 'homeTeam' ] [ 'name' ] , score [ 'score' ] [ 'fullTime' ] [ 'homeTeam' ] , score [ 'score' ] [ 'fullTime' ] [ '... |
def load_hdf ( cls , filename , path = '' ) :
"""Loads OrbitPopulation from HDF file .
: param filename :
HDF file
: param path :
Path within HDF file store where : class : ` OrbitPopulation ` is saved .""" | df = pd . read_hdf ( filename , '{}/df' . format ( path ) )
return cls . from_df ( df ) |
def is_univariate_ca ( self ) :
"""True if cube only contains a CA dimension - pair , in either order .""" | return self . ndim == 2 and set ( self . dim_types ) == { DT . CA_SUBVAR , DT . CA_CAT } |
def on_assign ( self , node ) : # ( ' targets ' , ' value ' )
"""Simple assignment .""" | val = self . run ( node . value )
for tnode in node . targets :
self . node_assign ( tnode , val )
return |
def discover_satellite ( cli , deploy = True , timeout = 5 ) :
"""Looks to make sure a satellite exists , returns endpoint
First makes sure we have dotcloud account credentials . Then it looks
up the environment for the satellite app . This will contain host and
port to construct an endpoint . However , if ap... | if not cli . global_config . loaded :
cli . die ( "Please setup skypipe by running `skypipe --setup`" )
try :
endpoint = lookup_endpoint ( cli )
ok = client . check_skypipe_endpoint ( endpoint , timeout )
if ok :
return endpoint
else :
return launch_satellite ( cli ) if deploy else N... |
def __perform_unsolicited_callbacks ( self , msg ) :
"""Callbacks for which a client reference is either optional or does not apply at all""" | type_ = msg [ M_TYPE ]
payload = msg [ M_PAYLOAD ]
# callbacks for responses which might be unsolicited ( e . g . created or deleted )
if type_ in _RSP_PAYLOAD_CB_MAPPING :
self . __fire_callback ( _RSP_PAYLOAD_CB_MAPPING [ type_ ] , msg )
# Perform callbacks for feed data
elif type_ == E_FEEDDATA :
self . __si... |
def restore ( self ) :
"""Restore the main dataframe""" | if self . backup_df is None :
self . warning ( "No dataframe is backed up: nothing restore" )
return
self . df = self . backup_df
self . ok ( "Dataframe is restored" ) |
def _set_pyqtgraph_title ( layout ) :
"""Private function to add a title to the first row of the window .
Returns True if a Title is set . Else , returns False .""" | if 'title_size' in pytplot . tplot_opt_glob :
size = pytplot . tplot_opt_glob [ 'title_size' ]
if 'title_text' in pytplot . tplot_opt_glob :
if pytplot . tplot_opt_glob [ 'title_text' ] != '' :
layout . addItem ( LabelItem ( pytplot . tplot_opt_glob [ 'title_text' ] , size = size , color = 'k' ) , row =... |
def _example_order_book ( quote_ctx ) :
"""获取摆盘数据 , 输出 买价 , 买量 , 买盘经纪个数 , 卖价 , 卖量 , 卖盘经纪个数""" | stock_code_list = [ "US.AAPL" , "HK.00700" ]
# subscribe " ORDER _ BOOK "
ret_status , ret_data = quote_ctx . subscribe ( stock_code_list , ft . SubType . ORDER_BOOK )
if ret_status != ft . RET_OK :
print ( ret_data )
exit ( )
for stk_code in stock_code_list :
ret_status , ret_data = quote_ctx . get_order_b... |
def _outfp_write_with_check ( self , outfp , data , enable_overwrite_check = True ) : # type : ( BinaryIO , bytes , bool ) - > None
'''Internal method to write data out to the output file descriptor ,
ensuring that it doesn ' t go beyond the bounds of the ISO .
Parameters :
outfp - The file object to write to... | start = outfp . tell ( )
outfp . write ( data )
if self . _track_writes : # After the write , double check that we didn ' t write beyond the
# boundary of the PVD , and raise a PyCdlibException if we do .
end = outfp . tell ( )
if end > self . pvd . space_size * self . pvd . logical_block_size ( ) :
rai... |
def Box ( pos = ( 0 , 0 , 0 ) , length = 1 , width = 2 , height = 3 , normal = ( 0 , 0 , 1 ) , c = "g" , alpha = 1 , texture = None ) :
"""Build a box of dimensions ` x = length , y = width and z = height ` oriented along vector ` normal ` .
. . hint : : | aspring | | aspring . py | _""" | src = vtk . vtkCubeSource ( )
src . SetXLength ( length )
src . SetYLength ( width )
src . SetZLength ( height )
src . Update ( )
poly = src . GetOutput ( )
axis = np . array ( normal ) / np . linalg . norm ( normal )
theta = np . arccos ( axis [ 2 ] )
phi = np . arctan2 ( axis [ 1 ] , axis [ 0 ] )
t = vtk . vtkTransfo... |
def get ( key , service = None , profile = None ) : # pylint : disable = W0613
'''Get a decrypted secret from the tISMd API''' | if not profile . get ( 'url' ) or not profile . get ( 'token' ) :
raise SaltConfigurationError ( "url and/or token missing from the tism sdb profile" )
request = { "token" : profile [ 'token' ] , "encsecret" : key }
result = http . query ( profile [ 'url' ] , method = 'POST' , data = salt . utils . json . dumps ( r... |
def make_heap ( n_points , size ) :
"""Constructor for the numba enabled heap objects . The heaps are used
for approximate nearest neighbor search , maintaining a list of potential
neighbors sorted by their distance . We also flag if potential neighbors
are newly added to the list or not . Internally this is ... | result = np . zeros ( ( 3 , int ( n_points ) , int ( size ) ) , dtype = np . float64 )
result [ 0 ] = - 1
result [ 1 ] = np . infty
result [ 2 ] = 0
return result |
def peek_step ( self , val : ArrayValue , sn : "DataNode" ) -> Tuple [ ObjectValue , "DataNode" ] :
"""Return the entry addressed by the receiver + its schema node .
Args :
val : Current value ( array ) .
sn : Current schema node .""" | keys = self . parse_keys ( sn )
for en in val :
flag = True
try :
for k in keys :
if en [ k ] != keys [ k ] :
flag = False
break
except KeyError :
continue
if flag :
return ( en , sn )
return ( None , sn ) |
def _less_or_close ( a , value , ** kwargs ) :
r"""Compare values for less or close to boolean masks .
Returns a boolean mask for values less than or equal to a target within a specified
absolute or relative tolerance ( as in : func : ` numpy . isclose ` ) .
Parameters
a : array - like
Array of values to ... | return ( a < value ) | np . isclose ( a , value , ** kwargs ) |
def _get_s3_key ( ) :
'''Get AWS keys from pillar or config''' | key = __opts__ [ 's3.key' ] if 's3.key' in __opts__ else None
keyid = __opts__ [ 's3.keyid' ] if 's3.keyid' in __opts__ else None
service_url = __opts__ [ 's3.service_url' ] if 's3.service_url' in __opts__ else None
verify_ssl = __opts__ [ 's3.verify_ssl' ] if 's3.verify_ssl' in __opts__ else None
kms_keyid = __opts__ ... |
def get_stored_files ( self ) :
"""Check which files are in your temporary storage .""" | method = 'GET'
endpoint = '/rest/v1/storage/{}' . format ( self . client . sauce_username )
return self . client . request ( method , endpoint ) |
def _get ( self , action , show , proxy , timeout ) :
"""make HTTP request and cache response""" | silent = self . flags [ 'silent' ]
if action in self . cache :
if action != 'imageinfo' and action != 'labels' :
utils . stderr ( "+ %s results in cache" % action , silent )
return
else :
self . cache [ action ] = { }
if self . flags . get ( 'skip' ) and action in self . flags [ 'skip' ] :
i... |
def make_time_series ( x , t = pd . Timestamp ( datetime . datetime ( 1970 , 1 , 1 ) ) , freq = None ) :
"""Convert a 2 - D array of time / value pairs ( or pair of time / value vectors ) into a pd . Series time - series
> > > make _ time _ series ( range ( 3 ) , freq = ' 15min ' ) # doctest : + NORMALIZE _ WHITE... | if isinstance ( x , pd . DataFrame ) :
x = pd . Series ( x [ x . columns [ 0 ] ] )
elif not isinstance ( x , pd . Series ) and ( not isinstance ( t , ( pd . Series , pd . Index , list , tuple ) ) or not len ( t ) ) : # warnings . warn ( " Coercing a non - Series " )
if len ( x ) == 2 :
t , x = listify (... |
def ReadFlowProcessingRequests ( self , cursor = None ) :
"""Reads all flow processing requests from the database .""" | query = ( "SELECT request, UNIX_TIMESTAMP(timestamp) " "FROM flow_processing_requests" )
cursor . execute ( query )
res = [ ]
for serialized_request , ts in cursor . fetchall ( ) :
req = rdf_flows . FlowProcessingRequest . FromSerializedString ( serialized_request )
req . timestamp = mysql_utils . TimestampToRD... |
def create_long ( self , value : int ) -> Long :
"""Creates a new : class : ` ConstantLong ` , adding it to the pool and
returning it .
: param value : The value of the new long .""" | self . append ( ( 5 , value ) )
self . append ( None )
return self . get ( self . raw_count - 2 ) |
def keyPressEvent ( self , evt ) :
"""This handles Ctrl + PageUp , Ctrl + PageDown , Ctrl + Tab , Ctrl + Shift + Tab""" | incr = 0
if evt . modifiers ( ) == Qt . ControlModifier :
n = self . tabWidget . count ( )
if evt . key ( ) in [ Qt . Key_PageUp , Qt . Key_Backtab ] :
incr = - 1
elif evt . key ( ) in [ Qt . Key_PageDown , Qt . Key_Tab ] :
incr = 1
if incr != 0 :
new_index = self . _get_tab_inde... |
def create_model ( self , parent , name , multiplicity = Multiplicity . ZERO_MANY ) :
"""Create a single part model in this scope .
See : class : ` pykechain . Client . create _ model ` for available parameters .""" | return self . _client . create_model ( parent , name , multiplicity = multiplicity ) |
def check_status ( self , job_id ) :
"""Check status of a job .""" | response , http_response = self . _client . jobs . get_job ( job_id = job_id ) . result ( )
if http_response . status_code == 404 :
raise HTTPNotFound ( 'The given job ID was not found. Error: {}' . format ( http_response . data ) )
return response |
def get_course_video_image_url ( course_id , edx_video_id ) :
"""Returns course video image url or None if no image found""" | try :
video_image = CourseVideo . objects . select_related ( 'video_image' ) . get ( course_id = course_id , video__edx_video_id = edx_video_id ) . video_image
return video_image . image_url ( )
except ObjectDoesNotExist :
return None |
def main ( args = None ) :
"""Main entry point""" | # parse args
if args is None :
args = parse_args ( sys . argv [ 1 : ] )
# set logging level
if args . verbose > 1 :
set_log_debug ( )
elif args . verbose == 1 :
set_log_info ( )
outpath = os . path . abspath ( os . path . expanduser ( args . out_dir ) )
cachepath = os . path . abspath ( os . path . expandus... |
def _Dielectric ( rho , T ) :
"""Equation for the Dielectric constant
Parameters
rho : float
Density , [ kg / m3]
T : float
Temperature , [ K ]
Returns
epsilon : float
Dielectric constant , [ - ]
Notes
Raise : class : ` NotImplementedError ` if input isn ' t in limit :
* 238 ≤ T ≤ 1200
Examp... | # Check input parameters
if T < 238 or T > 1200 :
raise NotImplementedError ( "Incoming out of bound" )
k = 1.380658e-23
Na = 6.0221367e23
alfa = 1.636e-40
epsilon0 = 8.854187817e-12
mu = 6.138e-30
d = rho / rhoc
Tr = Tc / T
I = [ 1 , 1 , 1 , 2 , 3 , 3 , 4 , 5 , 6 , 7 , 10 , None ]
J = [ 0.25 , 1 , 2.5 , 1.5 , 1.5 ... |
def _to_torch ( Z , dtype = None ) :
"""Converts a None , list , np . ndarray , or torch . Tensor to torch . Tensor ;
also handles converting sparse input to dense .""" | if Z is None :
return None
elif issparse ( Z ) :
Z = torch . from_numpy ( Z . toarray ( ) )
elif isinstance ( Z , torch . Tensor ) :
pass
elif isinstance ( Z , list ) :
Z = torch . from_numpy ( np . array ( Z ) )
elif isinstance ( Z , np . ndarray ) :
Z = torch . from_numpy ( Z )
else :
msg = ( ... |
def as_slice ( slice_ ) :
"""Convert an object to a slice , if possible""" | if isinstance ( slice_ , ( Integral , numpy . integer , type ( None ) ) ) :
return slice ( 0 , None , 1 )
if isinstance ( slice_ , ( slice , numpy . ndarray ) ) :
return slice_
if isinstance ( slice_ , ( list , tuple ) ) :
return tuple ( map ( as_slice , slice_ ) )
raise TypeError ( "Cannot format {!r} as s... |
def _compute_mean ( self , C , mag , rhypo , hypo_depth , mean , idx ) :
"""Compute mean value according to equations 10 and 11 page 226.""" | mean [ idx ] = ( C [ 'C1' ] + C [ 'C2' ] * mag + C [ 'C3' ] * np . log ( rhypo [ idx ] + C [ 'C4' ] * np . exp ( C [ 'C5' ] * mag ) ) + C [ 'C6' ] * hypo_depth ) |
def create ( cls , service = Service ( ) , private = False ) :
"""create a bin instance on the server""" | response = service . send ( SRequest ( 'POST' , cls . path , data = { 'private' : private } ) )
return cls . from_response ( response , service = service ) |
def plunge_bearing2pole ( plunge , bearing ) :
"""Converts the given ` plunge ` and ` bearing ` in degrees to a strike and dip
of the plane whose pole would be parallel to the line specified . ( i . e . The
pole to the plane returned would plot at the same point as the specified
plunge and bearing . )
Param... | plunge , bearing = np . atleast_1d ( plunge , bearing )
strike = bearing + 90
dip = 90 - plunge
strike [ strike >= 360 ] -= 360
return strike , dip |
def delete ( self ) :
"""Destructor .""" | if self . maplesat :
pysolvers . maplechrono_del ( self . maplesat )
self . maplesat = None
if self . prfile :
self . prfile . close ( ) |
def accept ( self ) :
"""Send a response disposition to the service to indicate that
a received message has been accepted . If the client is running in PeekLock
mode , the service will wait on this disposition . Otherwise it will
be ignored . Returns ` True ` is message was accepted , or ` False ` if the mess... | if self . _can_settle_message ( ) :
self . _response = errors . MessageAccepted ( )
self . _settler ( self . _response )
self . state = constants . MessageState . ReceivedSettled
return True
return False |
def deprecated ( replacement_description ) :
"""States that method is deprecated .
: param replacement _ description : Describes what must be used instead .
: return : the original method with modified docstring .""" | def decorate ( fn_or_class ) :
if isinstance ( fn_or_class , type ) :
pass
# Can ' t change _ _ doc _ _ of type objects
else :
try :
fn_or_class . __doc__ = "This API point is obsolete. %s\n\n%s" % ( replacement_description , fn_or_class . __doc__ , )
except Attribute... |
def _get_foundation_pos ( self , i ) :
"""Private . Get the absolute coordinates to use for a deck ' s
foundation , based on the ` ` starting _ pos _ hint ` ` , the
` ` deck _ hint _ step ` ` , ` ` deck _ x _ hint _ offsets ` ` , and
` ` deck _ y _ hint _ offsets ` ` .""" | ( phx , phy ) = get_pos_hint ( self . starting_pos_hint , * self . card_size_hint )
phx += self . deck_x_hint_step * i + self . deck_x_hint_offsets [ i ]
phy += self . deck_y_hint_step * i + self . deck_y_hint_offsets [ i ]
x = phx * self . width + self . x
y = phy * self . height + self . y
return ( x , y ) |
def read ( self , entity = None , attrs = None , ignore = None , params = None ) :
"""Provide a default value for ` ` entity ` ` .
By default , ` ` nailgun . entity _ mixins . EntityReadMixin . read ` ` provides a
default value for ` ` entity ` ` like so : :
entity = type ( self ) ( )
However , : class : ` ... | # read ( ) should not change the state of the object it ' s called on , but
# super ( ) alters the attributes of any entity passed in . Creating a new
# object and passing it to super ( ) lets this one avoid changing state .
if entity is None :
entity = type ( self ) ( self . _server_config , repository = self . re... |
def set_row ( x , row ) :
"""We use db 1 , use offset 4 , we replace row x . To find the correct
start _ index we mulitpy by row _ size by x and we put the
byte array representation of row in the PLC""" | row_size = 126
set_db_row ( 1 , 4 + x * row_size , row_size , row . _bytearray ) |
def data_properties ( data , mask = None , background = None ) :
"""Calculate the morphological properties ( and centroid ) of a 2D array
( e . g . an image cutout of an object ) using image moments .
Parameters
data : array _ like or ` ~ astropy . units . Quantity `
The 2D array of the image .
mask : arr... | from . . segmentation import SourceProperties
# prevent circular imports
segment_image = np . ones ( data . shape , dtype = np . int )
return SourceProperties ( data , segment_image , label = 1 , mask = mask , background = background ) |
def bootstrap_salt ( name , config = None , approve_key = True , install = True , pub_key = None , priv_key = None , bootstrap_url = None , force_install = False , unconditional_install = False , bootstrap_delay = None , bootstrap_args = None , bootstrap_shell = None ) :
'''Bootstrap a container from package server... | if bootstrap_delay is not None :
try :
time . sleep ( bootstrap_delay )
except TypeError : # Bad input , but assume since a value was passed that
# a delay was desired , and sleep for 5 seconds
time . sleep ( 5 )
c_info = info ( name )
if not c_info :
return None
# default set here as we... |
def run ( self ) :
"""Run charge balance command""" | # Load compound information
def compound_name ( id ) :
if id not in self . _model . compounds :
return id
return self . _model . compounds [ id ] . properties . get ( 'name' , id )
# Create a set of excluded reactions
exclude = set ( self . _args . exclude )
count = 0
unbalanced = 0
unchecked = 0
for re... |
def get_group_instance ( self , parent ) :
"""Create an instance object""" | o = copy . copy ( self )
o . init_instance ( parent )
return o |
def validate_key ( key , sign = False , encrypt = False ) :
"""Assert that a key is valide and optionally that it can be used for
signing or encrypting . Raise GPGProblem otherwise .
: param key : the GPG key to check
: type key : gpg . gpgme . _ gpgme _ key
: param sign : whether the key should be able to ... | if key . revoked :
raise GPGProblem ( 'The key "{}" is revoked.' . format ( key . uids [ 0 ] . uid ) , code = GPGCode . KEY_REVOKED )
elif key . expired :
raise GPGProblem ( 'The key "{}" is expired.' . format ( key . uids [ 0 ] . uid ) , code = GPGCode . KEY_EXPIRED )
elif key . invalid :
raise GPGProblem ... |
def flag_time_err ( phase_err , time_thresh = 0.02 ) :
"""Find large time errors in list .
Scan through a list of tuples of time stamps and phase errors
and return a list of time stamps with timing errors above a threshold .
. . note : :
This becomes important for networks cross - correlations , where
if ... | time_err = [ ]
for stamp in phase_err :
if abs ( stamp [ 1 ] ) > time_thresh :
time_err . append ( stamp [ 0 ] )
return time_err |
def get_builds ( galaxy_base ) :
"""Retrieve configured genome builds and reference files , using Galaxy configuration files .
Allows multiple dbkey specifications in the same file , using the most recently added .""" | name = "samtools"
galaxy_config = _get_galaxy_tool_info ( galaxy_base )
galaxy_dt = _get_galaxy_data_table ( name , galaxy_config [ "tool_data_table_config_path" ] )
loc_file , need_remap = _get_galaxy_loc_file ( name , galaxy_dt , galaxy_config [ "tool_data_path" ] , galaxy_base )
assert not need_remap , "Should not n... |
def main ( ) :
'''Main function .''' | usage = ( '\n\n %prog [options] XML_PATH\n\nArguments:\n\n ' 'XML_PATH the directory containing the ' 'GermaNet .xml files' )
parser = optparse . OptionParser ( usage = usage )
parser . add_option ( '--host' , default = None , help = 'hostname or IP address of the MongoDB instance ' 'where the GermaNet d... |
def ls ( params = "" , directory = "." , printed = True ) :
"""Know the best python implantation of ls ? It ' s just to subprocess ls . . .
( uses dir on windows ) .
: param params : options to pass to ls or dir
: param directory : if not this directory
: param printed : If you ' re using this , you probabl... | command = "{0} {1} {2}" . format ( "ls" if not win_based else "dir" , params , directory )
response = run ( command , shell = True )
# Shell required for windows
response . check_returncode ( )
if printed :
print ( response . stdout . decode ( "utf-8" ) )
else :
return response . stdout |
def request_ligodotorg ( url , debug = False ) :
"""Request the given URL using LIGO . ORG SAML authentication .
This requires an active Kerberos ticket for the user , to get one :
$ kinit albert . einstein @ LIGO . ORG
Parameters
url : ` str `
URL path for request
debug : ` bool ` , optional
Query in... | # set debug to 1 to see all HTTP ( s ) traffic
debug = int ( debug )
# need an instance of HTTPS handler to do HTTPS
httpsHandler = urllib2 . HTTPSHandler ( debuglevel = debug )
# use a cookie jar to store session cookies
jar = cookielib . LWPCookieJar ( )
# if a cookier jar exists open it and read the cookies
# and ma... |
def _iterate_marginal_coef_slices ( self , i ) :
"""iterator of indices into tensor ' s coef vector for marginal term i ' s coefs
takes a tensor _ term and returns an iterator of indices
that chop up the tensor ' s coef vector into slices belonging to term i
Parameters
i : int ,
index of marginal term
Y... | dims = [ term_ . n_coefs for term_ in self ]
# make all linear indices
idxs = np . arange ( np . prod ( dims ) )
# reshape indices to a Nd matrix
idxs = idxs . reshape ( dims )
# reshape to a 2d matrix , where we can loop over rows
idxs = np . moveaxis ( idxs , i , 0 ) . reshape ( idxs . shape [ i ] , int ( idxs . size... |
def init_service_processes ( self ) :
"""Prepare processes defined in the * * settings . SERVICE _ PROCESSES * * .
Return : class : ` list ` of the : class : ` ProcessWrapper ` instances .""" | processes = [ ]
for process_struct in getattr ( self . context . config . settings , 'SERVICE_PROCESSES' , ( ) ) :
process_cls = import_object ( process_struct [ 0 ] )
wait_unless_ready , timeout = process_struct [ 1 ] , process_struct [ 2 ]
self . logger . info ( "Init service process '%s'" , process_cls .... |
def parse ( name , content , releases , get_head_fn ) :
"""Parses the given content for a valid changelog
: param name : str , package name
: param content : str , content
: param releases : list , releases
: param get _ head _ fn : function
: return : dict , changelog""" | changelog = { }
releases = frozenset ( releases )
head = False
for line in content . splitlines ( ) :
new_head = get_head_fn ( name = name , line = line , releases = releases )
if new_head :
head = new_head
changelog [ head ] = ""
continue
if not head :
continue
line = li... |
def iter_processes ( self , proc_filter = None ) :
"""Yields processes from psutil . process _ iter with an optional filter and swallows psutil errors .
If a psutil exception is raised during execution of the filter , that process will not be
yielded but subsequent processes will . On the other hand , if psutil... | with swallow_psutil_exceptions ( ) : # process _ iter may raise
for proc in psutil . process_iter ( ) :
with swallow_psutil_exceptions ( ) : # proc _ filter may raise
if ( proc_filter is None ) or proc_filter ( proc ) :
yield proc |
def create_tab ( self , location = None ) :
"""Create a new tab page .""" | eb = self . _get_or_create_editor_buffer ( location )
self . tab_pages . insert ( self . active_tab_index + 1 , TabPage ( Window ( eb ) ) )
self . active_tab_index += 1 |
def extend ( self , api , route = "" , base_url = "" , http = True , cli = True , ** kwargs ) :
"""Adds handlers from a different Hug API to this one - to create a single API""" | api = API ( api )
if http and hasattr ( api , '_http' ) :
self . http . extend ( api . http , route , base_url , ** kwargs )
if cli and hasattr ( api , '_cli' ) :
self . cli . extend ( api . cli , ** kwargs )
for directive in getattr ( api , '_directives' , { } ) . values ( ) :
self . add_directive ( direct... |
def _absent ( name , dataset_type , force = False , recursive = False , recursive_all = False ) :
'''internal shared function for * _ absent
name : string
name of dataset
dataset _ type : string [ filesystem , volume , snapshot , or bookmark ]
type of dataset to remove
force : boolean
try harder to dest... | ret = { 'name' : name , 'changes' : { } , 'result' : True , 'comment' : '' }
# # log configuration
dataset_type = dataset_type . lower ( )
log . debug ( 'zfs.%s_absent::%s::config::force = %s' , dataset_type , name , force )
log . debug ( 'zfs.%s_absent::%s::config::recursive = %s' , dataset_type , name , recursive )
#... |
def _parse_xml ( self , xml ) :
"""Extracts the attributes from the XMLElement instance .""" | from re import split
vms ( "Parsing <cron> XML child tag." , 2 )
self . frequency = get_attrib ( xml , "frequency" , default = 5 , cast = int )
self . emails = split ( ",\s*" , get_attrib ( xml , "emails" , default = "" ) )
self . notify = split ( ",\s*" , get_attrib ( xml , "notify" , default = "" ) ) |
def _handle_value ( self , value ) :
"""Given a value string , unquote , remove comment ,
handle lists . ( including empty and single member lists )""" | if self . _inspec : # Parsing a configspec so don ' t handle comments
return ( value , '' )
# do we look for lists in values ?
if not self . list_values :
mat = self . _nolistvalue . match ( value )
if mat is None :
raise SyntaxError ( )
# NOTE : we don ' t unquote here
return mat . groups (... |
def _enforceDataType ( self , data ) :
"""Converts to float so that this CTI always stores that type .
Replaces infinite with the maximum respresentable float .
Raises a ValueError if data is a NaN .""" | value = float ( data )
if math . isnan ( value ) :
raise ValueError ( "FloatCti can't store NaNs" )
if math . isinf ( value ) :
if value > 0 :
logger . warn ( "Replacing inf by the largest representable float" )
value = sys . float_info . max
else :
logger . warn ( "Replacing -inf by... |
def build_response ( self , req , resp ) :
"""Builds a : class : ` Response < requests . Response > ` object from a urllib3
response . This should not be called from user code , and is only exposed
for use when subclassing the
: class : ` HTTPAdapter < requests . adapters . HTTPAdapter > `
: param req : The... | response = Response ( )
# Fallback to None if there ' s no status _ code , for whatever reason .
response . status_code = getattr ( resp , 'status' , None )
# Make headers case - insensitive .
response . headers = CaseInsensitiveDict ( getattr ( resp , 'headers' , { } ) )
# Set encoding .
response . encoding = get_enco... |
def get_tree ( cls , parent = None ) :
""": returns :
A * queryset * of nodes ordered as DFS , including the parent .
If no parent is given , all trees are returned .""" | cls = get_result_class ( cls )
if parent is None : # return the entire tree
return cls . objects . all ( )
if parent . is_leaf ( ) :
return cls . objects . filter ( pk = parent . pk )
return cls . objects . filter ( tree_id = parent . tree_id , lft__range = ( parent . lft , parent . rgt - 1 ) ) |
def iter_links ( operations , page ) :
"""Generate links for an iterable of operations on a starting page .""" | for operation , ns , rule , func in operations :
yield Link . for_ ( operation = operation , ns = ns , type = ns . subject_name , qs = page . to_items ( ) , ) |
def get_platforms ( self , automation_api = 'all' ) :
"""Get a list of objects describing all the OS and browser platforms
currently supported on Sauce Labs .""" | method = 'GET'
endpoint = '/rest/v1/info/platforms/{}' . format ( automation_api )
return self . client . request ( method , endpoint ) |
def _renumber ( a : np . ndarray , keys : np . ndarray , values : np . ndarray ) -> np . ndarray :
"""Renumber ' a ' by replacing any occurrence of ' keys ' by the corresponding ' values '""" | ordering = np . argsort ( keys )
keys = keys [ ordering ]
values = keys [ ordering ]
index = np . digitize ( a . ravel ( ) , keys , right = True )
return ( values [ index ] . reshape ( a . shape ) ) |
async def disconnect_message ( self , message , context ) :
"""Handle a disconnect message .
See : meth : ` AbstractDeviceAdapter . disconnect ` .""" | conn_string = message . get ( 'connection_string' )
client_id = context . user_data
await self . disconnect ( client_id , conn_string ) |
def login_user ( user , remember = False , duration = None , force = False , fresh = True ) :
'''Logs a user in . You should pass the actual user object to this . If the
user ' s ` is _ active ` property is ` ` False ` ` , they will not be logged in
unless ` force ` is ` ` True ` ` .
This will return ` ` True... | if not force and not user . is_active :
return False
user_id = getattr ( user , current_app . login_manager . id_attribute ) ( )
session [ 'user_id' ] = user_id
session [ '_fresh' ] = fresh
session [ '_id' ] = current_app . login_manager . _session_identifier_generator ( )
if remember :
session [ 'remember' ] =... |
def get_pmids ( self ) :
"""Get list of all PMIDs associated with edges in the network .""" | pmids = [ ]
for ea in self . _edge_attributes . values ( ) :
edge_pmids = ea . get ( 'pmids' )
if edge_pmids :
pmids += edge_pmids
return list ( set ( pmids ) ) |
def wrap_list ( item ) :
"""Returns an object as a list .
If the object is a list , it is returned directly . If it is a tuple or set , it
is returned as a list . If it is another object , it is wrapped in a list and
returned .""" | if item is None :
return [ ]
elif isinstance ( item , list ) :
return item
elif isinstance ( item , ( tuple , set ) ) :
return list ( item )
else :
return [ item ] |
def alterar ( self , id_script_type , type , description ) :
"""Change Script Type from by the identifier .
: param id _ script _ type : Identifier of the Script Type . Integer value and greater than zero .
: param type : Script Type type . String with a minimum 3 and maximum of 40 characters
: param descript... | if not is_valid_int_param ( id_script_type ) :
raise InvalidParameterError ( u'The identifier of Script Type is invalid or was not informed.' )
script_type_map = dict ( )
script_type_map [ 'type' ] = type
script_type_map [ 'description' ] = description
url = 'scripttype/' + str ( id_script_type ) + '/'
code , xml =... |
def punchFile ( rh ) :
"""Punch a file to a virtual reader of the specified virtual machine .
Input :
Request Handle with the following properties :
function - ' CHANGEVM '
subfunction - ' PUNCHFILE '
userid - userid of the virtual machine
parms [ ' class ' ] - Spool class ( optional )
parms [ ' file ... | rh . printSysLog ( "Enter changeVM.punchFile" )
# Default spool class in " A " , if specified change to specified class
spoolClass = "A"
if 'class' in rh . parms :
spoolClass = str ( rh . parms [ 'class' ] )
punch2reader ( rh , rh . userid , rh . parms [ 'file' ] , spoolClass )
rh . printSysLog ( "Exit changeVM.pun... |
def _create_default_config_file ( self ) :
"""If config file does not exists create and set default values .""" | logger . info ( 'Initialize Maya launcher, creating config file...\n' )
self . add_section ( self . DEFAULTS )
self . add_section ( self . PATTERNS )
self . add_section ( self . ENVIRONMENTS )
self . add_section ( self . EXECUTABLES )
self . set ( self . DEFAULTS , 'executable' , None )
self . set ( self . DEFAULTS , '... |
def set_flag_bit ( self , x ) :
"""Function internally used in set _ flags . No multi - line lambdas in python : /
: param x :
: return :""" | x = bytes_to_byte ( x )
if KeyTypes . COMM_ENC in self . keys :
x &= ~ 0x8
if KeyTypes . APP_KEY in self . keys :
x &= ~ 0x10
return byte_to_bytes ( x ) |
def calculate_crop_list ( full_page_box_list , bounding_box_list , angle_list , page_nums_to_crop ) :
"""Given a list of full - page boxes ( media boxes ) and a list of tight
bounding boxes for each page , calculate and return another list giving the
list of bounding boxes to crop down to . The parameter ` angl... | # Definition : the deltas are the four differences , one for each margin ,
# between the original full page box and the final , cropped full - page box .
# In the usual case where margin sizes decrease these are the same as the
# four margin - reduction values ( in absolute points ) . The deltas are
# usually positive ... |
def _quote ( str , LegalChars = _LegalChars ) :
r"""Quote a string for use in a cookie header .
If the string does not need to be double - quoted , then just return the
string . Otherwise , surround the string in doublequotes and quote
( with a \ ) special characters .""" | if all ( c in LegalChars for c in str ) :
return str
else :
return '"' + _nulljoin ( _Translator . get ( s , s ) for s in str ) + '"' |
def add_params ( self , ** kw ) :
"""Add [ possibly many ] parameters to the track .
Parameters will be checked against known UCSC parameters and their
supported formats .
E . g . : :
add _ params ( color = ' 128,0,0 ' , visibility = ' dense ' )""" | for k , v in kw . items ( ) :
if ( k not in self . params ) and ( k not in self . specific_params ) :
raise ParameterError ( '"%s" is not a valid parameter for %s' % ( k , self . __class__ . __name__ ) )
try :
self . params [ k ] . validate ( v )
except KeyError :
self . specific_par... |
def createLabels2D ( self ) :
"""2D labeling at zmax""" | logger . debug ( " Creating 2D labels..." )
self . zmax = np . argmax ( self . values , axis = 1 )
self . vmax = self . values [ np . arange ( len ( self . pixels ) , dtype = int ) , self . zmax ]
kwargs = dict ( pixels = self . pixels , values = self . vmax , nside = self . nside , threshold = self . threshold , xsiz... |
def roles ( self ) :
"""Access the roles
: returns : twilio . rest . chat . v2 . service . role . RoleList
: rtype : twilio . rest . chat . v2 . service . role . RoleList""" | if self . _roles is None :
self . _roles = RoleList ( self . _version , service_sid = self . _solution [ 'sid' ] , )
return self . _roles |
def apply ( self , cls , originalMemberNameList , classNamingConvention ) :
""": type cls : type
: type originalMemberNameList : list ( str )
: type classNamingConvention : INamingConvention""" | self . _memberDelegate . apply ( cls = cls , originalMemberNameList = originalMemberNameList , memberName = self . _memberName , classNamingConvention = classNamingConvention , getter = self . _makeGetter ( ) , setter = self . _makeSetter ( ) ) |
def get_ecdh_key ( self , other ) :
'''other - - > Key25519 instance''' | if self . __secretkey is None :
raise KeyTypeError ( 'Wrong key type for operation' )
# Copy because curve25519 _ dh _ CreateSharedKey changes secretkey
tmp_secretkey = ffi . new ( C_SECRETKEY , self . secretkey )
ecdh_key = ffi . new ( C_SHAREDKEY )
lib . curve25519_dh_CreateSharedKey ( ecdh_key , other . pubkey ,... |
def K ( self , X , X2 = None , presliced = False ) :
"""Calculates the kernel matrix K ( X , X2 ) ( or K ( X , X ) if X2 is None ) .
Handles the slicing as well as scaling and computes k ( x , x ' ) = k ( r ) ,
where r2 = ( ( x - x ' ) / lengthscales ) 2.
Internally , this calls self . K _ r2 ( r2 ) , which i... | if not presliced :
X , X2 = self . _slice ( X , X2 )
return self . K_r2 ( self . scaled_square_dist ( X , X2 ) ) |
def setTargets ( self , targets ) :
"""Sets the targets .""" | if not self . verifyArguments ( targets ) and not self . patterned :
raise NetworkError ( 'setTargets() requires [[...],[...],...] or [{"layerName": [...]}, ...].' , targets )
self . targets = targets |
def open ( self , number = 0 ) :
"""Open the FaderPort and register a callback so we can send and
receive MIDI messages .
: param number : 0 unless you ' ve got more than one FaderPort attached .
In which case 0 is the first , 1 is the second etc
I only have access to a single device so I can ' t
actually... | self . inport = mido . open_input ( find_faderport_input_name ( number ) )
self . outport = mido . open_output ( find_faderport_output_name ( number ) )
self . outport . send ( mido . Message . from_bytes ( [ 0x91 , 0 , 0x64 ] ) )
# A reset message ? ? ?
time . sleep ( 0.01 )
self . inport . callback = self . _message_... |
def list_agents ( self ) :
'''List agents hosted by the agency .''' | t = text_helper . Table ( fields = ( "Agent ID" , "Agent class" , "State" ) , lengths = ( 40 , 25 , 15 ) )
return t . render ( ( a . _descriptor . doc_id , a . log_category , a . _get_machine_state ( ) . name ) for a in self . _agents ) |
def save_to_file ( self , path ) :
"""Dump all cookies to file .
Cookies are dumped as JSON - serialized dict of keys and values .""" | with open ( path , 'w' ) as out :
out . write ( json . dumps ( self . get_dict ( ) ) ) |
def add_device_items ( self , item , device ) :
"""Add the various items from the device to the node
: param str item : item key
: param dict device : dictionary containing items""" | if item in ( 'aux' , 'console' ) :
self . node [ 'properties' ] [ item ] = device [ item ]
elif item . startswith ( 'slot' ) : # if self . device _ info [ ' model ' ] = = ' c7200 ' :
# if item ! = ' slot0 ' :
# self . node [ ' properties ' ] [ item ] = device [ item ]
# else :
self . node [ 'properties' ] [ ite... |
def get_dataset_feature_statistics ( builder , split ) :
"""Calculate statistics for the specified split .""" | statistics = statistics_pb2 . DatasetFeatureStatistics ( )
# Make this to the best of our abilities .
schema = schema_pb2 . Schema ( )
dataset = builder . as_dataset ( split = split )
# Just computing the number of examples for now .
statistics . num_examples = 0
# Feature dictionaries .
feature_to_num_examples = colle... |
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