signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def parse_conditional_derived_variable ( self , node ) :
"""Parses < ConditionalDerivedVariable >
@ param node : Node containing the < ConditionalDerivedVariable > element
@ type node : xml . etree . Element
@ raise ParseError : Raised when no name or value is specified for the conditional derived variable ."... | if 'name' in node . lattrib :
name = node . lattrib [ 'name' ]
elif 'exposure' in node . lattrib :
name = node . lattrib [ 'exposure' ]
else :
self . raise_error ( '<ConditionalDerivedVariable> must specify a name' )
if 'exposure' in node . lattrib :
exposure = node . lattrib [ 'exposure' ]
else :
e... |
async def addreaction ( self , ctx , * , reactor = "" ) :
"""Interactively adds a custom reaction""" | if not reactor :
await self . bot . say ( "What should I react to?" )
response = await self . bot . wait_for_message ( author = ctx . message . author )
reactor = response . content
data = self . config . get ( ctx . message . server . id , { } )
keyword = data . get ( reactor , { } )
if keyword :
await... |
def weighted_round_robin ( iterable ) :
'''Takes an iterable of tuples of < item > , < weight > and cycles around them ,
returning heavier ( integer ) weighted items more frequently .''' | cyclable_list = [ ]
assigned_weight = 0
still_to_process = [ ( item , weight ) for item , weight in sorted ( iterable , key = lambda tup : tup [ 1 ] , reverse = True ) ]
while still_to_process :
for i , ( item , weight ) in enumerate ( still_to_process ) :
if weight > assigned_weight :
cyclable_... |
def _decode_messages ( self , messages ) :
'''Take the zmq messages , decrypt / decode them into a payload
: param list messages : A list of messages to be decoded''' | messages_len = len ( messages )
# if it was one message , then its old style
if messages_len == 1 :
payload = self . serial . loads ( messages [ 0 ] )
# 2 includes a header which says who should do it
elif messages_len == 2 :
if ( self . opts . get ( '__role' ) != 'syndic' and messages [ 0 ] not in ( 'broadcast... |
def _call_variants ( example_dir , region_bed , data , out_file ) :
"""Call variants from prepared pileup examples , creating tensorflow record file .""" | tf_out_file = "%s-tfrecord.gz" % utils . splitext_plus ( out_file ) [ 0 ]
if not utils . file_exists ( tf_out_file ) :
with file_transaction ( data , tf_out_file ) as tx_out_file :
model = "wes" if strelka2 . coverage_interval_from_bed ( region_bed ) == "targeted" else "wgs"
cmd = [ "dv_call_variant... |
def load ( cls , filename , project = None ) :
r"""Loads data onto the given network from an appropriately formatted
' mat ' file ( i . e . MatLAB output ) .
Parameters
filename : string ( optional )
The name of the file containing the data to import . The formatting
of this file is outlined below .
pro... | filename = cls . _parse_filename ( filename = filename , ext = 'mat' )
data = spio . loadmat ( filename )
# Reinsert the ' . ' separator into the array names
for item in list ( data . keys ( ) ) :
if item in [ '__header__' , '__version__' , '__globals__' ] :
data . pop ( item )
continue
elif '_p... |
def error_log ( self , msg = '' , level = 20 , traceback = False ) :
"""Write error message to log .
Args :
msg ( str ) : error message
level ( int ) : logging level
traceback ( bool ) : add traceback to output or not""" | # Override this in subclasses as desired
sys . stderr . write ( msg + '\n' )
sys . stderr . flush ( )
if traceback :
tblines = traceback_ . format_exc ( )
sys . stderr . write ( tblines )
sys . stderr . flush ( ) |
def handle ( self ) :
"""Handles a request ignoring dropped connections .""" | rv = None
try :
rv = BaseHTTPRequestHandler . handle ( self )
except ( _ConnectionError , socket . timeout ) as e :
self . connection_dropped ( e )
except Exception as e :
if self . server . ssl_context is None or not is_ssl_error ( e ) :
raise
if self . server . shutdown_signal :
self . initiat... |
def expand_includes ( text , path = '.' ) :
"""Recursively expands includes in given text .""" | def read_and_expand ( match ) :
filename = match . group ( 'filename' )
filename = join ( path , filename )
text = read ( filename )
return expand_includes ( text , path = join ( path , dirname ( filename ) ) )
return re . sub ( r'^\.\. include:: (?P<filename>.*)$' , read_and_expand , text , flags = re ... |
def is_pdf ( document ) :
"""Check if a document is a PDF file and return True if is is .""" | if not executable_exists ( 'pdftotext' ) :
current_app . logger . warning ( "GNU file was not found on the system. " "Switching to a weak file extension test." )
if document . lower ( ) . endswith ( ".pdf" ) :
return True
return False
# Tested with file version > = 4.10 . First test is secure and wo... |
def get_crl ( self , expires = 86400 , encoding = None , algorithm = None , password = None , scope = None , ** kwargs ) :
"""Generate a Certificate Revocation List ( CRL ) .
The ` ` full _ name ` ` and ` ` relative _ name ` ` parameters describe how to retrieve the CRL and are used in
the ` Issuing Distributio... | if scope is not None and scope not in [ 'ca' , 'user' , 'attribute' ] :
raise ValueError ( 'Scope must be either None, "ca", "user" or "attribute"' )
encoding = parse_encoding ( encoding )
now = now_builder = timezone . now ( )
algorithm = parse_hash_algorithm ( algorithm )
if timezone . is_aware ( now_builder ) :
... |
def returnOneIndex ( self , last = False ) :
'''Return the first origin index ( integer ) of the current list . That
index refers to it ' s placement in the original list of dictionaries .
This is very useful when one wants to reference the original entry by
index .
Example of use :
> > > test = [
. . .... | if len ( self . table ) == 0 :
return None
else :
if last :
return self . index_track . pop ( )
else :
return self . index_track [ 0 ] |
def rpm ( state , host , source , present = True ) :
'''Add / remove ` ` . rpm ` ` file packages .
+ source : filename or URL of the ` ` . rpm ` ` package
+ present : whether ore not the package should exist on the system
URL sources with ` ` present = False ` ` :
If the ` ` . rpm ` ` file isn ' t downloade... | # If source is a url
if urlparse ( source ) . scheme : # Generate a temp filename ( with . rpm extension to please yum )
temp_filename = '{0}.rpm' . format ( state . get_temp_filename ( source ) )
# Ensure it ' s downloaded
yield files . download ( state , host , source , temp_filename )
# Override the ... |
def _linear_seaborn_ ( self , label = None , style = None , opts = None ) :
"""Returns a Seaborn linear regression plot""" | xticks , yticks = self . _get_ticks ( opts )
try :
fig = sns . lmplot ( self . x , self . y , data = self . df )
fig = self . _set_with_height ( fig , opts )
return fig
except Exception as e :
self . err ( e , self . linear_ , "Can not draw linear regression chart" ) |
def delete_objective ( self , objective_id ) :
"""Deletes the ` ` Objective ` ` identified by the given ` ` Id ` ` .
arg : objective _ id ( osid . id . Id ) : the ` ` Id ` ` of the
` ` Objective ` ` to delete
raise : NotFound - an ` ` Objective ` ` was not found identified by
the given ` ` Id ` `
raise : ... | # Implemented from template for
# osid . learning . ObjectiveAdminSession . delete _ objective _ template
if not isinstance ( objective_id , ABCId ) :
raise errors . InvalidArgument ( 'the argument is not a valid OSID Id' )
collection = JSONClientValidated ( 'learning' , collection = 'Activity' , runtime = self . _... |
def get_new_term_doc_mat ( self , doc_domains ) :
'''Combines documents together that are in the same domain
Parameters
doc _ domains : array - like
Returns
scipy . sparse . csr _ matrix''' | assert len ( doc_domains ) == self . term_doc_matrix . get_num_docs ( )
doc_domain_set = set ( doc_domains )
num_terms = self . term_doc_matrix . get_num_terms ( )
num_domains = len ( doc_domain_set )
domain_mat = lil_matrix ( ( num_domains , num_terms ) , dtype = int )
X = self . term_doc_matrix . get_term_doc_mat ( )... |
def _cleanup ( self ) :
'''Cleanup all the local data .''' | self . _declare_cb = None
self . _bind_cb = None
self . _unbind_cb = None
self . _delete_cb = None
self . _purge_cb = None
super ( QueueClass , self ) . _cleanup ( ) |
def max ( self , axis = None , skipna = True , * args , ** kwargs ) :
"""Return the maximum value of the Index or maximum along
an axis .
See Also
numpy . ndarray . max
Series . max : Return the maximum value in a Series .""" | nv . validate_max ( args , kwargs )
nv . validate_minmax_axis ( axis )
if not len ( self ) :
return self . _na_value
i8 = self . asi8
try : # quick check
if len ( i8 ) and self . is_monotonic :
if i8 [ - 1 ] != iNaT :
return self . _box_func ( i8 [ - 1 ] )
if self . hasnans :
if ... |
def read_input ( self , filename , has_header = True ) :
"""filename is any filename , or something on which open ( ) can be called
for example :
csv _ input = CSVInput ( )
csv _ input . read _ input ( " csvfile . csv " )""" | stream = open ( filename )
reader = csv . reader ( stream )
csv_data = [ ]
for ( i , row ) in enumerate ( reader ) :
if i == 0 :
if not has_header :
csv_data . append ( [ str ( i ) for i in xrange ( 0 , len ( row ) ) ] )
csv_data . append ( row )
self . data = csv_data |
def constant ( self , val , ty ) :
"""Creates a constant as a VexValue
: param val : The value , as an integer
: param ty : The type of the resulting VexValue
: return : a VexValue""" | if isinstance ( val , VexValue ) and not isinstance ( val , IRExpr ) :
raise Exception ( 'Constant cannot be made from VexValue or IRExpr' )
rdt = self . irsb_c . mkconst ( val , ty )
return VexValue ( self . irsb_c , rdt ) |
def bind ( self , study , ** kwargs ) : # @ UnusedVariable
"""Returns a copy of the Spec bound to the given study
Parameters
study : Study
A study to bind the fileset spec to ( should happen in the
study _ _ init _ _ )""" | if self . _study is not None : # Avoid rebinding specs in sub - studies that have already
# been bound to MultiStudy
bound = self
else :
bound = copy ( self )
bound . _study = study
if not hasattr ( study , self . pipeline_getter ) :
raise ArcanaError ( "{} does not have a method named '{}' requ... |
def runner ( ) :
'''Return all inline documentation for runner modules
CLI Example :
. . code - block : : bash
salt - run doc . runner''' | client = salt . runner . RunnerClient ( __opts__ )
ret = client . get_docs ( )
return ret |
def serialize_op ( cls , opcode , opdata , opfields , verbose = True ) :
"""Given an opcode ( byte ) , associated data ( dict ) , and the operation
fields to serialize ( opfields ) , convert it
into its canonical serialized form ( i . e . in order to
generate a consensus hash .
opdata is allowed to have ext... | fields = opfields . get ( opcode , None )
if fields is None :
log . error ( "BUG: unrecongnized opcode '%s'" % opcode )
return None
all_values = [ ]
debug_all_values = [ ]
missing = [ ]
for field in fields :
if not opdata . has_key ( field ) :
missing . append ( field )
field_value = opdata . ge... |
def to_bytes ( s ) :
"""Convert string ` s ` to an integer number of bytes . Suffixes like
' KB ' , ' MB ' , ' GB ' ( up to ' YB ' ) , with or without the trailing ' B ' ,
are allowed and properly accounted for . Case is ignored in
suffixes .
Examples : :
> > > to _ bytes ( ' 12 ' )
12
> > > to _ byte... | last = - 1
unit = s [ last ] . lower ( )
if unit . isdigit ( ) : # ` s ` is a integral number
return int ( s )
if unit == 'b' : # ignore the the ' b ' or ' B ' suffix
last -= 1
unit = s [ last ] . lower ( )
if unit == 'i' :
k = 1024
last -= 1
unit = s [ last ] . lower ( )
else :
k = 1000
# c... |
def handle_block ( mediator_state : MediatorTransferState , state_change : Block , channelidentifiers_to_channels : ChannelMap , pseudo_random_generator : random . Random , ) -> TransitionResult [ MediatorTransferState ] :
"""After Raiden learns about a new block this function must be called to
handle expiration ... | expired_locks_events = events_to_remove_expired_locks ( mediator_state , channelidentifiers_to_channels , state_change . block_number , pseudo_random_generator , )
secret_reveal_events = events_for_onchain_secretreveal_if_dangerzone ( channelmap = channelidentifiers_to_channels , secrethash = mediator_state . secrethas... |
def ordered_load ( self , stream , Loader = yaml . Loader , object_pairs_hook = OrderedDict ) :
"""Allows you to use ` pyyaml ` to load as OrderedDict .
Taken from https : / / stackoverflow . com / a / 21912744/1927102""" | class OrderedLoader ( Loader ) :
pass
def construct_mapping ( loader , node ) :
loader . flatten_mapping ( node )
return object_pairs_hook ( loader . construct_pairs ( node ) )
OrderedLoader . add_constructor ( yaml . resolver . BaseResolver . DEFAULT_MAPPING_TAG , construct_mapping )
try :
try :
... |
def create_alarm ( panel_json , abode , area = '1' ) :
"""Create a new alarm device from a panel response .""" | panel_json [ 'name' ] = CONST . ALARM_NAME
panel_json [ 'id' ] = CONST . ALARM_DEVICE_ID + area
panel_json [ 'type' ] = CONST . ALARM_TYPE
panel_json [ 'type_tag' ] = CONST . DEVICE_ALARM
panel_json [ 'generic_type' ] = CONST . TYPE_ALARM
return AbodeAlarm ( panel_json , abode , area ) |
def matchesOneOf ( cntxt : Context , T : RDFGraph , expr : ShExJ . OneOf , _ : DebugContext ) -> bool :
"""expr is a OneOf and there is some shape expression se2 in shapeExprs such that a matches ( T , se2 , m ) .""" | return any ( matches ( cntxt , T , e ) for e in expr . expressions ) |
def serviceManifest ( self , fileType = "json" ) :
"""The service manifest resource documents the data and other
resources that define the service origins and power the service .
This resource will tell you underlying databases and their location
along with other supplementary files that make up the service .... | url = self . _url + "/iteminfo/manifest/manifest.%s" % fileType
params = { }
f = self . _get ( url = url , param_dict = params , securityHandler = self . _securityHandler , proxy_url = self . _proxy_url , proxy_port = self . _proxy_port , out_folder = tempfile . gettempdir ( ) , file_name = os . path . basename ( url )... |
def removeRef ( self , doc ) :
"""Remove the given attribute from the Ref table maintained
internally .""" | if doc is None :
doc__o = None
else :
doc__o = doc . _o
ret = libxml2mod . xmlRemoveRef ( doc__o , self . _o )
return ret |
def delete_value ( hive , key , vname = None , use_32bit_registry = False ) :
'''Delete a registry value entry or the default value for a key .
Args :
hive ( str ) :
The name of the hive . Can be one of the following
- HKEY _ LOCAL _ MACHINE or HKLM
- HKEY _ CURRENT _ USER or HKCU
- HKEY _ USER or HKU
... | local_hive = _to_unicode ( hive )
local_key = _to_unicode ( key )
local_vname = _to_unicode ( vname )
registry = Registry ( )
try :
hkey = registry . hkeys [ local_hive ]
except KeyError :
raise CommandExecutionError ( 'Invalid Hive: {0}' . format ( local_hive ) )
access_mask = registry . registry_32 [ use_32bi... |
def get_patient_vcf ( job , patient_dict ) :
"""Convenience function to get the vcf from the patient dict
: param dict patient _ dict : dict of patient info
: return : The vcf
: rtype : toil . fileStore . FileID""" | temp = job . fileStore . readGlobalFile ( patient_dict [ 'mutation_vcf' ] , os . path . join ( os . getcwd ( ) , 'temp.gz' ) )
if is_gzipfile ( temp ) :
outfile = job . fileStore . writeGlobalFile ( gunzip ( temp ) )
job . fileStore . deleteGlobalFile ( patient_dict [ 'mutation_vcf' ] )
else :
outfile = pat... |
def describe_features ( self , traj ) :
"""Return a list of dictionaries describing the dihderal features .
Parameters
traj : mdtraj . Trajectory
The trajectory to describe
Returns
feature _ descs : list of dict
Dictionary describing each feature with the following information
about the atoms particip... | feature_descs = [ ]
for dihed_type in self . types : # TODO : Don ' t recompute dihedrals , just get the indices
func = getattr ( md , 'compute_%s' % dihed_type )
# ainds is a list of four - tuples of atoms participating
# in each dihedral
aind_tuples , _ = func ( traj )
top = traj . topology
bi... |
def clean_out_dir ( directory ) :
"""Delete all the files and subdirectories in a directory .""" | if not isinstance ( directory , path ) :
directory = path ( directory )
for file_path in directory . files ( ) :
file_path . remove ( )
for dir_path in directory . dirs ( ) :
dir_path . rmtree ( ) |
def _l_cv_weight ( self , donor_catchment ) :
"""Return L - CV weighting for a donor catchment .
Methodology source : Science Report SC050050 , eqn . 6.18 and 6.22a""" | try :
dist = donor_catchment . similarity_dist
except AttributeError :
dist = self . _similarity_distance ( self . catchment , donor_catchment )
b = 0.0047 * sqrt ( dist ) + 0.0023 / 2
c = 0.02609 / ( donor_catchment . record_length - 1 )
return 1 / ( b + c ) |
def _seconds_or_timedelta ( duration ) :
"""Returns ` datetime . timedelta ` object for the passed duration .
Keyword Arguments :
duration - - ` datetime . timedelta ` object or seconds in ` int ` format .""" | if isinstance ( duration , int ) :
dt_timedelta = timedelta ( seconds = duration )
elif isinstance ( duration , timedelta ) :
dt_timedelta = duration
else :
raise TypeError ( 'Expects argument as `datetime.timedelta` object ' 'or seconds in `int` format' )
return dt_timedelta |
def train ( cls , data , iterations = 100 , step = 1.0 , miniBatchFraction = 1.0 , initialWeights = None , regParam = 0.0 , regType = None , intercept = False , validateData = True , convergenceTol = 0.001 ) :
"""Train a linear regression model using Stochastic Gradient
Descent ( SGD ) . This solves the least squ... | warnings . warn ( "Deprecated in 2.0.0. Use ml.regression.LinearRegression." , DeprecationWarning )
def train ( rdd , i ) :
return callMLlibFunc ( "trainLinearRegressionModelWithSGD" , rdd , int ( iterations ) , float ( step ) , float ( miniBatchFraction ) , i , float ( regParam ) , regType , bool ( intercept ) , b... |
def watch_crc ( params , ctxt , scope , stream , coord ) :
"""WatchCrc32 - Watch the total crc32 of the params .
Example :
The code below uses the ` ` WatchCrc32 ` ` update function to update
the ` ` crc ` ` field to the crc of the ` ` length ` ` and ` ` data ` ` fields : :
char length ;
char data [ lengt... | if len ( params ) <= 1 :
raise errors . InvalidArguments ( coord , "{} args" . format ( len ( params ) ) , "at least two arguments" )
to_update = params [ 0 ]
total_data = utils . binary ( "" )
for param in params [ 1 : ] :
total_data += param . _pfp__build ( )
to_update . _pfp__set_value ( binascii . crc32 ( t... |
def gf_poly_div ( dividend , divisor ) :
'''Fast polynomial division by using Extended Synthetic Division and optimized for GF ( 2 ^ p ) computations ( doesn ' t work with standard polynomials outside of this galois field ) .''' | # CAUTION : this function expects polynomials to follow the opposite convention at decoding : the terms must go from the biggest to lowest degree ( while most other functions here expect a list from lowest to biggest degree ) . eg : 1 + 2x + 5x ^ 2 = [ 5 , 2 , 1 ] , NOT [ 1 , 2 , 5]
msg_out = bytearray ( dividend )
# C... |
def with_vtk ( plot = True ) :
"""Tests VTK interface and mesh repair of Stanford Bunny Mesh""" | mesh = vtki . PolyData ( bunny_scan )
meshfix = pymeshfix . MeshFix ( mesh )
if plot :
print ( 'Plotting input mesh' )
meshfix . plot ( )
meshfix . repair ( )
if plot :
print ( 'Plotting repaired mesh' )
meshfix . plot ( )
return meshfix . mesh |
def get_qword_from_data ( self , data , offset ) :
"""Convert eight bytes of data to a word ( little endian )
' offset ' is assumed to index into a word array . So setting it to
N will return a dword out of the data starting at offset N * 8.
Returns None if the data can ' t be turned into a quad word .""" | if ( offset + 1 ) * 8 > len ( data ) :
return None
return struct . unpack ( '<Q' , data [ offset * 8 : ( offset + 1 ) * 8 ] ) [ 0 ] |
def _PrintEventLabelsCounter ( self , event_labels_counter , session_identifier = None ) :
"""Prints the event labels counter .
Args :
event _ labels _ counter ( collections . Counter ) : number of event tags per
label .
session _ identifier ( Optional [ str ] ) : session identifier .""" | if not event_labels_counter :
return
title = 'Event tags generated per label'
if session_identifier :
title = '{0:s}: {1:s}' . format ( title , session_identifier )
table_view = views . ViewsFactory . GetTableView ( self . _views_format_type , column_names = [ 'Label' , 'Number of event tags' ] , title = title ... |
def highlight_canvas ( self , highlight ) :
"""Set a colored frame around the FigureCanvas if highlight is True .""" | colorname = self . canvas . palette ( ) . highlight ( ) . color ( ) . name ( )
if highlight :
self . canvas . setStyleSheet ( "FigureCanvas{border: 1px solid %s;}" % colorname )
else :
self . canvas . setStyleSheet ( "FigureCanvas{}" ) |
def project_delete_event ( self , proj_info ) :
"""Process project delete event .""" | LOG . debug ( "Processing project_delete_event..." )
proj_id = proj_info . get ( 'resource_info' )
proj_name = self . get_project_name ( proj_id )
if proj_name :
try :
self . dcnm_client . delete_project ( proj_name , self . cfg . dcnm . default_partition_name )
except dexc . DfaClientRequestFailed : # ... |
def _find_parent ( self , path_elements ) :
"""Recurse up the tree of FileSetStates until we find a parent , i . e .
one whose path _ elements member is the start of the path _ element
argument""" | if not self . path_elements : # Automatically terminate on root
return self
elif self . path_elements == path_elements [ 0 : len ( self . path_elements ) ] :
return self
else :
return self . parent . _find_parent ( path_elements ) |
def backward ( self , loss ) :
"""backward propagation with loss""" | with mx . autograd . record ( ) :
if isinstance ( loss , ( tuple , list ) ) :
ls = [ l * self . _scaler . loss_scale for l in loss ]
else :
ls = loss * self . _scaler . loss_scale
mx . autograd . backward ( ls ) |
def _setter ( self , attr , value , bottom , top , to_step ) :
"""Set a value .
: param attr : Attribute to set .
: param value : Value to use .
: param bottom : Get to bottom value .
: param top : Get to top value .
: param to _ step : Get to intermediary value .""" | if value < 0 or value > 1 :
raise ValueError ( "out of range" )
if value == 0.0 :
bottom ( )
elif value == 1.0 :
top ( )
else :
to_step ( value )
setattr ( self , attr , value ) |
def parse_cgn_postag ( rawtag , raisefeatureexceptions = False ) :
global subsets , constraints
"""decodes PoS features like " N ( soort , ev , basis , onz , stan ) " into a PosAnnotation data structure
based on CGN tag overview compiled by Matje van de Camp""" | begin = rawtag . find ( '(' )
if rawtag [ - 1 ] == ')' and begin > 0 :
tag = folia . PosAnnotation ( None , cls = rawtag , set = 'http://ilk.uvt.nl/folia/sets/cgn' )
head = rawtag [ 0 : begin ]
tag . append ( folia . Feature , subset = 'head' , cls = head )
rawfeatures = rawtag [ begin + 1 : - 1 ] . spl... |
def init_config ( cls ) :
"""Initialize Gandi CLI configuration .
Create global configuration directory with API credentials""" | try : # first load current conf and only overwrite needed params
# we don ' t want to reset everything
config_file = os . path . expanduser ( cls . home_config )
config = cls . load ( config_file , 'global' )
cls . _del ( 'global' , 'api.env' )
hidden_apikey = '%s...' % cls . get ( 'api.key' , '' ) [ : ... |
def all ( ctx , fetcher_num , processor_num , result_worker_num , run_in ) :
"""Run all the components in subprocess or thread""" | ctx . obj [ 'debug' ] = False
g = ctx . obj
# FIXME : py34 cannot run components with threads
if run_in == 'subprocess' and os . name != 'nt' :
run_in = utils . run_in_subprocess
else :
run_in = utils . run_in_thread
threads = [ ]
try : # phantomjs
if not g . get ( 'phantomjs_proxy' ) :
phantomjs_co... |
def switch_format ( self , gsr ) :
"""Convert the Wharton GSR format into the studyspaces API format .""" | if "error" in gsr :
return gsr
categories = { "cid" : 1 , "name" : "Huntsman Hall" , "rooms" : [ ] }
for time in gsr [ "times" ] :
for entry in time :
entry [ "name" ] = entry [ "room_number" ]
del entry [ "room_number" ]
start_time_str = entry [ "start_time" ]
end_time = datetim... |
def commit_msg_hook ( argv ) :
"""Hook : for checking commit message ( prevent commit ) .""" | with open ( argv [ 1 ] , "r" , "utf-8" ) as fh :
message = "\n" . join ( filter ( lambda x : not x . startswith ( "#" ) , fh . readlines ( ) ) )
options = { "allow_empty" : True }
if not _check_message ( message , options ) :
click . echo ( "Aborting commit due to commit message errors (override with " "'git co... |
def get_addon_name ( addonxml ) :
'''Parses an addon name from the given addon . xml filename .''' | xml = parse ( addonxml )
addon_node = xml . getElementsByTagName ( 'addon' ) [ 0 ]
return addon_node . getAttribute ( 'name' ) |
def newComic ( self , comic ) :
"""Start new comic list in HTML .""" | if self . lastUrl is not None :
self . html . write ( u'</li>\n' )
if self . lastComic is not None :
self . html . write ( u'</ul>\n' )
self . html . write ( u'<li>%s</li>\n' % comic . name )
self . html . write ( u'<ul>\n' ) |
def new_points ( factory : IterationPointFactory , solution , weights : List [ List [ float ] ] = None ) -> List [ Tuple [ np . ndarray , List [ float ] ] ] :
"""Generate approximate set of points
Generate set of Pareto optimal solutions projecting from the Pareto optimal solution
using weights to determine the... | from desdeo . preference . direct import DirectSpecification
points = [ ]
nof = factory . optimization_method . optimization_problem . problem . nof_objectives ( )
if not weights :
weights = random_weights ( nof , 50 * nof )
for pref in map ( lambda w : DirectSpecification ( factory . optimization_method , np . arr... |
def parse_template ( template_str ) :
"""Parse the SAM template .
: param template _ str : A packaged YAML or json CloudFormation template
: type template _ str : str
: return : Dictionary with keys defined in the template
: rtype : dict""" | try : # PyYAML doesn ' t support json as well as it should , so if the input
# is actually just json it is better to parse it with the standard
# json parser .
return json . loads ( template_str , object_pairs_hook = OrderedDict )
except ValueError :
yaml . SafeLoader . add_constructor ( yaml . resolver . BaseR... |
def make_close_message ( code = 1000 , message = b'' ) :
"""Close the websocket , sending the specified code and message .""" | return _make_frame ( struct . pack ( '!H%ds' % len ( message ) , code , message ) , opcode = OPCODE_CLOSE ) |
def main ( ) :
"""The main function .
These are the steps performed for the data clean up :
1 . Prints the version number .
2 . Reads the configuration file ( : py : func : ` read _ config _ file ` ) .
3 . Creates a new directory with ` ` data _ clean _ up ` ` as prefix and the date
and time as suffix .
... | # Getting and checking the options
args = parse_args ( )
check_args ( args )
# The directory name
dirname = "data_clean_up."
dirname += datetime . datetime . today ( ) . strftime ( "%Y-%m-%d_%H.%M.%S" )
while os . path . isdir ( dirname ) :
time . sleep ( 1 )
dirname = "data_clean_up."
dirname += datetime .... |
def display ( self , * arg ) :
"""For simple Demo
測試用顯示樣式 。""" | print self . stock_name , self . stock_no
print '%s %s %s(%+.2f%%)' % ( self . data_date [ - 1 ] , self . raw_data [ - 1 ] , self . stock_range [ - 1 ] , self . range_per )
for i in arg :
print ' - MA%02s %.2f %s(%s)' % ( i , self . MA ( i ) , self . MAC ( i ) , self . MA_serial ( i ) [ 0 ] )
print ' - Volume: %s ... |
def get_country ( _ , data ) :
"""http : / / git . kernel . org / cgit / linux / kernel / git / jberg / iw . git / tree / scan . c ? id = v3.17 # n267.
Positional arguments :
data - - bytearray data to read .
Returns :
Dict .""" | answers = { 'Environment' : country_env_str ( chr ( data [ 2 ] ) ) }
data = data [ 3 : ]
while len ( data ) >= 3 :
triplet = ieee80211_country_ie_triplet ( data )
if triplet . ext . reg_extension_id >= IEEE80211_COUNTRY_EXTENSION_ID :
answers [ 'Extension ID' ] = triplet . ext . reg_extension_id
... |
def get_list ( client , list_id ) :
'''Gets the given list''' | endpoint = '/' . join ( [ client . api . Endpoints . LISTS , str ( list_id ) ] )
response = client . authenticated_request ( endpoint )
return response . json ( ) |
def _name ( self ) :
"""Define object name .""" | return "{0} {1} {2}" . format ( self . _camera . name , pretty_timestamp ( self . created_at ) , self . _attrs . get ( 'mediaDuration' ) ) |
def md_report ( self , file_path ) :
"""Generate and save MD report""" | self . logger . debug ( 'Generating MD report' )
report = self . zap . core . mdreport ( )
self . _write_report ( report , file_path ) |
def ufo2glyphs ( options ) :
"""Convert one designspace file or one or more UFOs to a Glyphs . app source file .""" | import fontTools . designspaceLib
import defcon
sources = options . designspace_file_or_UFOs
designspace_file = None
if ( len ( sources ) == 1 and sources [ 0 ] . endswith ( ".designspace" ) and os . path . isfile ( sources [ 0 ] ) ) :
designspace_file = sources [ 0 ]
designspace = fontTools . designspaceLib . ... |
def get_available_devices ( self ) :
"""Gets available devices using mbedls and self . available _ edbg _ ports .
: return : List of connected devices as dictionaries .""" | connected_devices = self . mbeds . list_mbeds ( ) if self . mbeds else [ ]
# Check non mbedOS supported devices .
# Just for backward compatible reason - is obsolete . .
edbg_ports = self . available_edbg_ports ( )
for port in edbg_ports :
connected_devices . append ( { "platform_name" : "SAM4E" , "serial_port" : p... |
def docx_docx_gen_text ( doc : DOCX_DOCUMENT_TYPE , config : TextProcessingConfig ) -> Iterator [ str ] : # only called if docx loaded
"""Iterate through a DOCX file and yield text .
Args :
doc : DOCX document to process
config : : class : ` TextProcessingConfig ` control object
Yields :
pieces of text ( ... | if in_order :
for thing in docx_docx_iter_block_items ( doc ) :
if isinstance ( thing , docx . text . paragraph . Paragraph ) :
yield docx_process_simple_text ( thing . text , config . width )
elif isinstance ( thing , docx . table . Table ) :
yield docx_process_table ( thing... |
def detectRamPorts ( stm : IfContainer , current_en : RtlSignalBase ) :
"""Detect RAM ports in If statement
: param stm : statement to detect the ram ports in
: param current _ en : curent en / clk signal""" | if stm . ifFalse or stm . elIfs :
return
for _stm in stm . ifTrue :
if isinstance ( _stm , IfContainer ) :
yield from detectRamPorts ( _stm , _stm . cond & current_en )
elif isinstance ( _stm , Assignment ) :
if isinstance ( _stm . dst . _dtype , HArray ) :
assert len ( _stm . in... |
def _enforce_instance ( model_or_class ) :
"""It ' s a common mistake to not initialize a
schematics class . We should handle that by just
calling the default constructor .""" | if isinstance ( model_or_class , type ) and issubclass ( model_or_class , BaseType ) :
return model_or_class ( )
return model_or_class |
def prepare_mosaic ( self , image , fov_deg , name = None ) :
"""Prepare a new ( blank ) mosaic image based on the pointing of
the parameter image""" | header = image . get_header ( )
ra_deg , dec_deg = header [ 'CRVAL1' ] , header [ 'CRVAL2' ]
data_np = image . get_data ( )
# dtype = data _ np . dtype
dtype = None
self . bg_ref = iqcalc . get_median ( data_np )
# TODO : handle skew ( differing rotation for each axis ) ?
skew_limit = self . settings . get ( 'skew_limi... |
def destroy_server ( server_id ) :
'''Given a UUID id of a div removed or replaced in the Jupyter
notebook , destroy the corresponding server sessions and stop it .''' | server = curstate ( ) . uuid_to_server . get ( server_id , None )
if server is None :
log . debug ( "No server instance found for uuid: %r" % server_id )
return
try :
for session in server . get_sessions ( ) :
session . destroy ( )
server . stop ( )
del curstate ( ) . uuid_to_server [ server... |
def get_header ( uri ) :
"""Pull a FITS header from observation at the given URI
@ param uri : The URI of the image in VOSpace .""" | if uri not in astheaders :
astheaders [ uri ] = get_hdu ( uri , cutout = "[1:1,1:1]" ) [ 0 ] . header
return astheaders [ uri ] |
def to_ip ( self , values , from_unit ) :
"""Return values in IP and the units to which the values have been converted .""" | if from_unit in self . ip_units :
return values , from_unit
elif from_unit == 'tonne' :
return self . to_unit ( values , 'ton' , from_unit ) , 'ton'
else :
return self . to_unit ( values , 'lb' , from_unit ) , 'lb' |
def shift ( self , amount ) :
"""shifts position""" | if self . left is not None :
self . left += amount
if self . left is not None :
self . right += amount |
def com_google_fonts_check_fontdata_namecheck ( ttFont , familyname ) :
"""Familyname must be unique according to namecheck . fontdata . com""" | FB_ISSUE_TRACKER = "https://github.com/googlefonts/fontbakery/issues"
import requests
url = f"http://namecheck.fontdata.com/?q={familyname}"
try :
response = requests . get ( url , timeout = 10 )
data = response . content . decode ( "utf-8" )
if "fonts by that exact name" in data :
yield INFO , ( "T... |
def handle_CR ( self , value ) :
"""Parses cited references .""" | citation = self . entry_class ( )
value = strip_tags ( value )
# First - author name and publication date .
ptn = '([\w\s\W]+),\s([0-9]{4}),\s([\w\s]+)'
ny_match = re . match ( ptn , value , flags = re . U )
nj_match = re . match ( '([\w\s\W]+),\s([\w\s]+)' , value , flags = re . U )
if ny_match is not None :
name_... |
def do_refresh ( self , args ) :
"""Refresh the view of the log group""" | print "stackResource: {}" . format ( self . stackResource )
self . roleDetails = AwsConnectionFactory . getIamClient ( ) . get_role ( RoleName = self . stackResource . physical_resource_id )
print "== role details =="
pprint ( self . roleDetails )
self . rolePolicies = self . loadRolePolicies ( )
print "== attached pol... |
def parse_xml_report ( cls , conf , path ) :
"""Parse the ivy xml report corresponding to the name passed to ivy .
: API : public
: param string conf : the ivy conf name ( e . g . " default " )
: param string path : The path to the ivy report file .
: returns : The info in the xml report .
: rtype : : cla... | if not os . path . exists ( path ) :
raise cls . IvyResolveReportError ( 'Missing expected ivy output file {}' . format ( path ) )
logger . debug ( "Parsing ivy report {}" . format ( path ) )
ret = IvyInfo ( conf )
etree = ET . parse ( path )
doc = etree . getroot ( )
for module in doc . findall ( 'dependencies/mod... |
def _replace_bm ( self ) :
"""Replace ` ` _ block _ matcher ` ` with current values .""" | self . _block_matcher = cv2 . StereoSGBM ( minDisparity = self . _min_disparity , numDisparities = self . _num_disp , SADWindowSize = self . _sad_window_size , uniquenessRatio = self . _uniqueness , speckleWindowSize = self . _speckle_window_size , speckleRange = self . _speckle_range , disp12MaxDiff = self . _max_disp... |
def from_bytes ( cls , bitstream ) :
'''Parse the given packet and update properties accordingly''' | packet = 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 type
type_nr = bitst... |
def calcMz ( self , specfiles = None , guessCharge = True , obsMzKey = 'obsMz' ) :
"""Calculate the exact mass for ` ` Sii ` ` elements from the
` ` Sii . peptide ` ` sequence .
: param specfiles : the name of an ms - run file or a list of names . If None
all specfiles are selected .
: param guessCharge : b... | # TODO : important to test function , since changes were made
_calcMass = maspy . peptidemethods . calcPeptideMass
_calcMzFromMass = maspy . peptidemethods . calcMzFromMass
_massProton = maspy . constants . atomicMassProton
_guessCharge = lambda mass , mz : round ( mass / ( mz - _massProton ) , 0 )
if specfiles is None... |
def read_electrostatic_potential ( self ) :
"""Parses the eletrostatic potential for the last ionic step""" | pattern = { "ngf" : r"\s+dimension x,y,z NGXF=\s+([\.\-\d]+)\sNGYF=\s+([\.\-\d]+)\sNGZF=\s+([\.\-\d]+)" }
self . read_pattern ( pattern , postprocess = int )
self . ngf = self . data . get ( "ngf" , [ [ ] ] ) [ 0 ]
pattern = { "radii" : r"the test charge radii are((?:\s+[\.\-\d]+)+)" }
self . read_pattern ( pattern , r... |
def is_ignored ( resource ) :
'''Check of the resource ' s URL is part of LINKCHECKING _ IGNORE _ DOMAINS''' | ignored_domains = current_app . config [ 'LINKCHECKING_IGNORE_DOMAINS' ]
url = resource . url
if url :
parsed_url = urlparse ( url )
return parsed_url . netloc in ignored_domains
return True |
def delmod_cli ( argv , alter_logger = True ) :
"""Command - line access to ` ` delmod ` ` functionality .
The ` ` delmod ` ` task deletes " on - the - fly " model information from a
Measurement Set . It is so easy to implement that a standalone
function is essentially unnecessary . Just write : :
from pwki... | check_usage ( delmod_doc , argv , usageifnoargs = True )
if alter_logger :
util . logger ( )
cb = util . tools . calibrater ( )
for mspath in argv [ 1 : ] :
cb . open ( b ( mspath ) , addcorr = False , addmodel = False )
cb . delmod ( otf = True , scr = False )
cb . close ( ) |
def show ( context , id ) :
"""show ( context , id )
Show a Feeder .
> > > dcictl feeder - show [ OPTIONS ]
: param string id : ID of the feeder to show [ required ]""" | result = feeder . get ( context , id = id )
utils . format_output ( result , context . format ) |
def _validate_object_can_be_tagged_with_redactor ( self , annotated_object ) :
"""Validates that the object type can be annotated and object does not have
conflicting annotations .""" | data_type = annotated_object . data_type
name = annotated_object . name
loc = annotated_object . _ast_node . lineno , annotated_object . _ast_node . path
curr_data_type = data_type
while isinstance ( curr_data_type , Alias ) or isinstance ( curr_data_type , Nullable ) : # aliases have redactors assocaited with the type... |
def add_directory_digests_for_jars ( self , targets_and_jars ) :
"""For each target , get DirectoryDigests for its jars and return them zipped with the jars .
: param targets _ and _ jars : List of tuples of the form ( Target , [ pants . java . jar . jar _ dependency _ utils . ResolveJar ] )
: return : list [ t... | targets_and_jars = list ( targets_and_jars )
if not targets_and_jars or not self . get_options ( ) . capture_snapshots :
return targets_and_jars
jar_paths = [ ]
for target , jars_to_snapshot in targets_and_jars :
for jar in jars_to_snapshot :
jar_paths . append ( fast_relpath ( jar . pants_path , get_bu... |
def _read_opt_calipso ( self , code , * , desc ) :
"""Read HOPOPT CALIPSO option .
Structure of HOPOPT CALIPSO option [ RFC 5570 ] :
| Next Header | Hdr Ext Len | Option Type | Option Length |
| CALIPSO Domain of Interpretation |
| Cmpt Length | Sens Level | Checksum ( CRC - 16 ) |
| Compartment Bitmap ( ... | _type = self . _read_opt_type ( code )
_size = self . _read_unpack ( 1 )
if _size < 8 and _size % 8 != 0 :
raise ProtocolError ( f'{self.alias}: [Optno {code}] invalid format' )
_cmpt = self . _read_unpack ( 4 )
_clen = self . _read_unpack ( 1 )
if _clen % 2 != 0 :
raise ProtocolError ( f'{self.alias}: [Optno {... |
def insert_line ( self , line ) :
"""Insert a new line""" | if self . current_block is not None :
self . current_block . append ( line )
else :
self . header . append ( line ) |
def fit ( self ) :
r"""Loop over distributions and find best parameter to fit the data for each
When a distribution is fitted onto the data , we populate a set of
dataframes :
- : attr : ` df _ errors ` : sum of the square errors between the data and the fitted
distribution i . e . , : math : ` \ sum _ i \ ... | for distribution in self . distributions :
try : # need a subprocess to check time it takes . If too long , skip it
dist = eval ( "scipy.stats." + distribution )
# TODO here , dist . fit may take a while or just hang forever
# with some distributions . So , I thought to use signal module
... |
def _get_object_parser ( self , json ) :
"""Parses a json document into a pandas object .""" | typ = self . typ
dtype = self . dtype
kwargs = { "orient" : self . orient , "dtype" : self . dtype , "convert_axes" : self . convert_axes , "convert_dates" : self . convert_dates , "keep_default_dates" : self . keep_default_dates , "numpy" : self . numpy , "precise_float" : self . precise_float , "date_unit" : self . d... |
def advance ( self , myDateTime ) :
"""Advances to the next value and returns an appropriate value for the given
time .
: param myDateTime : ( datetime ) when to fetch the value for
: return : ( float | int ) value for given time""" | if self . getTime ( ) == myDateTime :
out = self . next ( )
# Sometimes , the stream has no value for this field and returns None , in
# this case we ' ll use the last value as well .
if out is None :
out = self . last ( )
else :
out = self . last ( )
# If there ' s no more data , we must fe... |
def receive ( self , sequence , args ) :
"""Receive one packet
If the sequence number is one we ' ve already seen before , it is dropped .
If it is not the next expected sequence number , it is put into the
_ out _ of _ order queue to be processed once the holes in sequence number
are filled in .
Args :
... | # If we are told to ignore sequence numbers , just pass the packet on
if not self . _reorder :
self . _callback ( * args )
return
# If this packet is in the past , drop it
if self . _next_expected is not None and sequence < self . _next_expected :
print ( "Dropping out of order packet, seq=%d" % sequence )
... |
def downsampled_mesh ( self , step ) :
"""Returns a downsampled copy of this mesh .
Args :
step : the step size for the sampling
Returns :
a new , downsampled Mesh object .
Raises :
ValueError if this Mesh has faces .""" | from lace . mesh import Mesh
if self . f is not None :
raise ValueError ( 'Function `downsampled_mesh` does not support faces.' )
low = Mesh ( )
if self . v is not None :
low . v = self . v [ : : step ]
if self . vc is not None :
low . vc = self . vc [ : : step ]
return low |
def edit ( self , physicalPath , cleanupMode , maxFileAge , description ) :
"""The server directory ' s edit operation allows you to change the path
and clean up properties of the directory . This operation updates
the GIS service configurations ( and points them to the new path )
that are using this director... | url = self . _url + "/edit"
params = { "f" : "json" , "physicalPath" : physicalPath , "cleanupMode" : cleanupMode , "maxFileAge" : maxFileAge , "description" : description }
return self . _post ( url = url , param_dict = params , securityHandler = self . _securityHandler , proxy_url = self . _proxy_url , proxy_port = s... |
def versions ( self ) :
"""Announce Versions of CLI and Server
Args : None
Returns :
The running versions of both the CLI and the Workbench Server""" | print '%s<<< Workbench CLI Version %s >>>%s' % ( color . LightBlue , self . version , color . Normal )
print self . workbench . help ( 'version' ) |
def commit ( self ) :
"""Commit dirty records to the server . This method is automatically
called when the ` auto _ commit ` option is set to ` True ` ( default ) .
It can be useful to set the former option to ` False ` to get better
performance by reducing the number of RPC requests generated .
With ` auto... | # Iterate on a new set , as we remove record during iteration from the
# original one
for record in set ( self . dirty ) :
values = { }
for field in record . _values_to_write :
if record . id in record . _values_to_write [ field ] :
value = record . _values_to_write [ field ] . pop ( record ... |
def cropped ( self , T0 , T1 ) :
"""returns a cropped copy of the path .""" | assert 0 <= T0 <= 1 and 0 <= T1 <= 1
assert T0 != T1
assert not ( T0 == 1 and T1 == 0 )
if T0 == 1 and 0 < T1 < 1 and self . isclosed ( ) :
return self . cropped ( 0 , T1 )
if T1 == 1 :
seg1 = self [ - 1 ]
t_seg1 = 1
i1 = len ( self ) - 1
else :
seg1_idx , t_seg1 = self . T2t ( T1 )
seg1 = self ... |
def _uninstall ( cls ) :
"""uninstall the hook if installed""" | if cls . _hook :
sys . meta_path . remove ( cls . _hook )
cls . _hook = None |
def set_window_geometry ( geometry ) :
"""Set window geometry .
Parameters
geometry : tuple ( 4 integers ) or None
x , y , dx , dy values employed to set the Qt backend geometry .""" | if geometry is not None :
x_geom , y_geom , dx_geom , dy_geom = geometry
mngr = plt . get_current_fig_manager ( )
if 'window' in dir ( mngr ) :
try :
mngr . window . setGeometry ( x_geom , y_geom , dx_geom , dy_geom )
except AttributeError :
pass
else :
... |
async def restart ( request : web . Request ) -> web . Response :
"""Restart the robot .
Blocks while the restart lock is held .""" | async with request . app [ RESTART_LOCK_NAME ] :
asyncio . get_event_loop ( ) . call_later ( 1 , _do_restart )
return web . json_response ( { 'message' : 'Restarting in 1s' } , status = 200 ) |
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