signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def weighted ( self ) :
"""This method creates a weighted copy of the internal formula . As a
result , an object of class : class : ` WCNF ` is returned . Every clause
of the CNF formula is * soft * in the new WCNF formula and its weight
is equal to ` ` 1 ` ` . The set of hard clauses of the formula is empty ... | wcnf = WCNF ( )
wcnf . nv = self . nv
wcnf . hard = [ ]
wcnf . soft = copy . deepcopy ( self . clauses )
wcnf . wght = [ 1 for cl in wcnf . soft ]
self . topw = len ( wcnf . wght ) + 1
wcnf . comments = self . comments [ : ]
return wcnf |
def _lsb_release_info ( self ) :
"""Get the information items from the lsb _ release command output .
Returns :
A dictionary containing all information items .""" | if not self . include_lsb :
return { }
with open ( os . devnull , 'w' ) as devnull :
try :
cmd = ( 'lsb_release' , '-a' )
stdout = subprocess . check_output ( cmd , stderr = devnull )
except OSError : # Command not found
return { }
content = stdout . decode ( sys . getfilesystemencod... |
def do_chunked_gzip ( infh , outfh , filename ) :
"""A memory - friendly way of compressing the data .""" | import gzip
gzfh = gzip . GzipFile ( 'rawlogs' , mode = 'wb' , fileobj = outfh )
if infh . closed :
infh = open ( infh . name , 'r' )
else :
infh . seek ( 0 )
readsize = 0
sys . stdout . write ( 'Gzipping {0}: ' . format ( filename ) )
if os . stat ( infh . name ) . st_size :
infh . seek ( 0 )
progressb... |
def no_counterpart_found ( string , options , rc_so_far ) :
"""Takes action determined by options . else _ action . Unless told to
raise an exception , this function returns the errno that is supposed
to be returned in this case .
: param string : The lookup string .
: param options : ArgumentParser or equi... | logger . debug ( "options.else_action: %s" , options . else_action )
if options . else_action == "passthrough" :
format_list = [ string ]
output_fd = sys . stdout
elif options . else_action == "exception" :
raise KeyError ( "No counterpart found for: %s" % ( string ) )
elif options . else_action == "error" ... |
def count_in_date ( x = 'date_time' , filter_dict = None , model = DEFAULT_MODEL , app = DEFAULT_APP , sort = True , limit = 100000 ) :
"""Count the number of records for each discrete ( categorical ) value of a field and return a dict of two lists , the field values and the counts .
> > > from django . db import... | sort = sort_prefix ( sort )
model = get_model ( model , app )
filter_dict = filter_dict or { }
x = fuzzy . extractOne ( str ( x ) , model . _meta . get_all_field_names ( ) ) [ 0 ]
objects = model . objects . filter ( ** filter_dict )
objects = objects . extra ( { 'date_bin_for_counting' : 'date(%s)' % x } )
objects = o... |
def remove_event_handler ( self , handler , event_name ) :
"""Remove event handler ` handler ` from registered handlers of the engine
Args :
handler ( callable ) : the callable event handler that should be removed
event _ name : The event the handler attached to .""" | if event_name not in self . _event_handlers :
raise ValueError ( "Input event name '{}' does not exist" . format ( event_name ) )
new_event_handlers = [ ( h , args , kwargs ) for h , args , kwargs in self . _event_handlers [ event_name ] if h != handler ]
if len ( new_event_handlers ) == len ( self . _event_handler... |
def compile_fund ( workbook , sheet , row , col ) :
"""Compile funding entries . Iter both rows at the same time . Keep adding entries until both cells are empty .
: param obj workbook :
: param str sheet :
: param int row :
: param int col :
: return list of dict : l""" | logger_excel . info ( "enter compile_fund" )
l = [ ]
temp_sheet = workbook . sheet_by_name ( sheet )
while col < temp_sheet . ncols :
col += 1
try : # Make a dictionary for this funding entry .
_curr = { 'agency' : temp_sheet . cell_value ( row , col ) , 'grant' : temp_sheet . cell_value ( row + 1 , col... |
def tar_archive ( context ) :
"""Archive specified path to a tar archive .
Args :
context : dictionary - like . context is mandatory .
context [ ' tar ' ] [ ' archive ' ] must exist . It ' s a dictionary .
keys are the paths to archive .
values are the destination output paths .
Example :
tar :
arch... | logger . debug ( "start" )
mode = get_file_mode_for_writing ( context )
for item in context [ 'tar' ] [ 'archive' ] : # value is the destination tar . Allow string interpolation .
destination = context . get_formatted_string ( item [ 'out' ] )
# key is the source to archive
source = context . get_formatted_... |
def asym ( scatterer , h_pol = True ) :
"""Asymmetry parameter for the current setup , with polarization .
Args :
scatterer : a Scatterer instance .
h _ pol : If True ( default ) , use horizontal polarization .
If False , use vertical polarization .
Returns :
The asymmetry parameter .""" | if scatterer . psd_integrator is not None :
return scatterer . psd_integrator . get_angular_integrated ( scatterer . psd , scatterer . get_geometry ( ) , "asym" )
old_geom = scatterer . get_geometry ( )
cos_t0 = np . cos ( scatterer . thet0 * deg_to_rad )
sin_t0 = np . sin ( scatterer . thet0 * deg_to_rad )
p0 = sc... |
def gmres_prolongation_smoothing ( A , T , B , BtBinv , Sparsity_Pattern , maxiter , tol , weighting = 'local' , Cpt_params = None ) :
"""Use GMRES to smooth T by solving A T = 0 , subject to nullspace and sparsity constraints .
Parameters
A : csr _ matrix , bsr _ matrix
SPD sparse NxN matrix
Should be at l... | # For non - SPD system , apply GMRES with Diagonal Preconditioning
# Preallocate space for new search directions
uones = np . zeros ( Sparsity_Pattern . data . shape , dtype = T . dtype )
AV = sparse . bsr_matrix ( ( uones , Sparsity_Pattern . indices , Sparsity_Pattern . indptr ) , shape = ( Sparsity_Pattern . shape )... |
def push_results ( self , results , scheduler_name ) :
"""Send a HTTP request to the satellite ( POST / put _ results )
Send actions results to the satellite
: param results : Results list to send
: type results : list
: param scheduler _ name : Scheduler name
: type scheduler _ name : uuid
: return : T... | logger . debug ( "Pushing %d results" , len ( results ) )
result = self . con . post ( 'put_results' , { 'results' : results , 'from' : scheduler_name } , wait = True )
return result |
def obfn_g ( self , Y ) :
r"""Compute : math : ` g ( \ mathbf { y } ) = g _ 0 ( \ mathbf { y } _ 0 ) +
g _ 1 ( \ mathbf { y } _ 1 ) ` component of ADMM objective function .""" | return self . obfn_g0 ( self . obfn_g0var ( ) ) + self . obfn_g1 ( self . obfn_g1var ( ) ) |
def ranked_attributes ( self ) :
"""Returns the matrix of ranked attributes from the last run .
: return : the Numpy matrix
: rtype : ndarray""" | matrix = javabridge . call ( self . jobject , "rankedAttributes" , "()[[D" )
if matrix is None :
return None
else :
return typeconv . double_matrix_to_ndarray ( matrix ) |
def read ( self , ** keys ) :
"""read data from this HDU
By default , all data are read .
send columns = and rows = to select subsets of the data .
Table data are read into a recarray ; use read _ column ( ) to get a single
column as an ordinary array . You can alternatively use slice notation
fits = fits... | columns = keys . get ( 'columns' , None )
rows = keys . get ( 'rows' , None )
if columns is not None :
if 'columns' in keys :
del keys [ 'columns' ]
data = self . read_columns ( columns , ** keys )
elif rows is not None :
if 'rows' in keys :
del keys [ 'rows' ]
data = self . read_rows ( ... |
def get ( self , collection_id , content = None , ** kwargs ) :
"""Syntactic sugar around to make it easier to get fine - grained access
to the parts of a file without composing a PhyloSchema object .
Possible invocations include :
w . get ( ' pg _ 10 ' )
w . get ( ' pg _ 10 ' , ' trees ' )
w . get ( ' pg... | assert COLLECTION_ID_PATTERN . match ( collection_id )
r = self . get_collection ( collection_id )
if isinstance ( r , dict ) and ( 'data' in r ) :
return r [ 'data' ]
return r |
def start_user_session ( self , username , domain , resource , ** kwargs ) :
"""Method to add a user session for debugging .
Accepted parameters are the same as to the constructor of : py : class : ` ~ xmpp _ backends . base . UserSession ` .""" | kwargs . setdefault ( 'uptime' , pytz . utc . localize ( datetime . utcnow ( ) ) )
kwargs . setdefault ( 'priority' , 0 )
kwargs . setdefault ( 'status' , 'online' )
kwargs . setdefault ( 'status_text' , '' )
kwargs . setdefault ( 'connection_type' , CONNECTION_XMPP )
kwargs . setdefault ( 'encrypted' , True )
kwargs .... |
def wait ( self , status = None , locked = None , wait_interval = None , wait_time = None ) :
"""Poll the server periodically until the droplet has reached some final
state . If ` ` status ` ` is non - ` None ` , ` ` wait ` ` will wait for the
droplet ' s ` ` status ` ` field to equal the given value . If ` ` l... | return next ( self . doapi_manager . wait_droplets ( [ self ] , status , locked , wait_interval , wait_time ) ) |
def GetPattern ( self ) :
"""Return a tuple of Stop objects , in the order visited""" | stoptimes = self . GetStopTimes ( )
return tuple ( st . stop for st in stoptimes ) |
def strip_required_prefix ( string , prefix ) :
"""> > > strip _ required _ prefix ( ' abcdef ' , ' abc ' )
' def '
> > > strip _ required _ prefix ( ' abcdef ' , ' 123 ' )
Traceback ( most recent call last ) :
AssertionError : String starts with ' abc ' , not ' 123'""" | if string . startswith ( prefix ) :
return string [ len ( prefix ) : ]
raise AssertionError ( 'String starts with %r, not %r' % ( string [ : len ( prefix ) ] , prefix ) ) |
def read_feature ( self , dataset , fid ) :
"""Retrieves ( reads ) a feature in a dataset .
Parameters
dataset : str
The dataset id .
fid : str
The feature id .
Returns
request . Response
The response contains a GeoJSON representation of the feature .""" | uri = URITemplate ( self . baseuri + '/{owner}/{did}/features/{fid}' ) . expand ( owner = self . username , did = dataset , fid = fid )
return self . session . get ( uri ) |
def set_white ( self , brightness , colourtemp ) :
"""Set white coloured theme of an rgb bulb .
Args :
brightness ( int ) : Value for the brightness ( 25-255 ) .
colourtemp ( int ) : Value for the colour temperature ( 0-255 ) .""" | if not 25 <= brightness <= 255 :
raise ValueError ( "The brightness needs to be between 25 and 255." )
if not 0 <= colourtemp <= 255 :
raise ValueError ( "The colour temperature needs to be between 0 and 255." )
payload = self . generate_payload ( SET , { self . DPS_INDEX_MODE : self . DPS_MODE_WHITE , self . D... |
def update_instrument_config ( instrument , measured_center ) -> Tuple [ Point , float ] :
"""Update config and pose tree with instrument ' s x and y offsets
and tip length based on delta between probe center and measured _ center ,
persist updated config and return it""" | from copy import deepcopy
from opentrons . trackers . pose_tracker import update
robot = instrument . robot
config = robot . config
instrument_offset = deepcopy ( config . instrument_offset )
dx , dy , dz = array ( measured_center ) - config . tip_probe . center
log . debug ( "This is measured probe center dx {}" . for... |
def _connect_sudo ( spec ) :
"""Return ContextService arguments for sudo as a become method .""" | return { 'method' : 'sudo' , 'enable_lru' : True , 'kwargs' : { 'username' : spec . become_user ( ) , 'password' : spec . become_pass ( ) , 'python_path' : spec . python_path ( ) , 'sudo_path' : spec . become_exe ( ) , 'connect_timeout' : spec . timeout ( ) , 'sudo_args' : spec . sudo_args ( ) , 'remote_name' : get_rem... |
def hwvtep_activate_hwvtep ( self , ** kwargs ) :
"""Activate the hwvtep
Args :
name ( str ) : overlay _ gateway name
callback ( function ) : A function executed upon completion of the
method .
Returns :
Return value of ` callback ` .
Raises :
None""" | name = kwargs . pop ( 'name' )
name_args = dict ( name = name )
method_name = 'overlay_gateway_activate'
method_class = self . _brocade_tunnels
gw_attr = getattr ( method_class , method_name )
config = gw_attr ( ** name_args )
output = self . _callback ( config )
return output |
def revoke ( self , auth , codetype , code , defer = False ) :
"""Given an activation code , the associated entity is revoked after which the activation
code can no longer be used .
Args :
auth : Takes the owner ' s cik
codetype : The type of code to revoke ( client | share )
code : Code specified by < co... | return self . _call ( 'revoke' , auth , [ codetype , code ] , defer ) |
def register ( self , func , singleton = False , threadlocal = False , name = None ) :
"""Register a dependency function""" | func . _giveme_singleton = singleton
func . _giveme_threadlocal = threadlocal
if name is None :
name = func . __name__
self . _registered [ name ] = func
return func |
def rsa_base64_sign_str ( self , plain , b64 = True ) :
"""对 msg rsa 签名 , 然后使用 base64 encode 编码数据""" | with open ( self . key_file ) as fp :
key_ = RSA . importKey ( fp . read ( ) )
# h = SHA . new ( plain if sys . version _ info < ( 3 , 0 ) else plain . encode ( ' utf - 8 ' ) )
plain = helper . to_bytes ( plain )
# if hasattr ( plain , ' encode ' ) :
# plain = plain . encode ( )
h = SHA . new ( ... |
def _compute_anom_data_using_window ( self ) :
"""Compute anomaly scores using a lagging window .""" | anom_scores = { }
values = self . time_series . values
stdev = numpy . std ( values )
for i , ( timestamp , value ) in enumerate ( self . time_series_items ) :
if i < self . lag_window_size :
anom_score = self . _compute_anom_score ( values [ : i + 1 ] , value )
else :
anom_score = self . _compu... |
def relpath ( path , start = None ) :
"""Return a relative file path to path either from the
current directory or from an optional start directory .
For storage objects , " path " and " start " are relative to
storage root .
" / " are not stripped on storage objects path . The ending slash is required
on ... | relative = get_instance ( path ) . relpath ( path )
if start : # Storage relative path
# Replaces " \ " by " / " for Windows .
return os_path_relpath ( relative , start = start ) . replace ( '\\' , '/' )
return relative |
def is_compliant ( self , path ) :
"""Checks if the directory is compliant .
Used to determine if the path specified and all of its children
directories are in compliance with the check itself .
: param path : the directory path to check
: returns : True if the directory tree is compliant , otherwise False ... | if not os . path . isdir ( path ) :
log ( 'Path specified %s is not a directory.' % path , level = ERROR )
raise ValueError ( "%s is not a directory." % path )
if not self . recursive :
return super ( DirectoryPermissionAudit , self ) . is_compliant ( path )
compliant = True
for root , dirs , _ in os . walk... |
def update_object ( self , form , obj ) :
"""Saves the new value to the target object .""" | field_name = form . cleaned_data [ 'name' ]
value = form . cleaned_data [ 'value' ]
setattr ( obj , field_name , value )
save_kwargs = { }
if CAN_UPDATE_FIELDS :
save_kwargs [ 'update_fields' ] = [ field_name ]
obj . save ( ** save_kwargs )
data = json . dumps ( { 'status' : 'success' , } )
return HttpResponse ( da... |
def getMemoryStats ( self ) :
"""Return JVM Memory Stats for Apache Tomcat Server .
@ return : Dictionary of memory utilization stats .""" | if self . _statusxml is None :
self . initStats ( )
node = self . _statusxml . find ( 'jvm/memory' )
memstats = { }
if node is not None :
for ( key , val ) in node . items ( ) :
memstats [ key ] = util . parse_value ( val )
return memstats |
def recurseforumcontents ( parser , token ) :
"""Iterates over the content nodes and renders the contained forum block for each node .""" | bits = token . contents . split ( )
forums_contents_var = template . Variable ( bits [ 1 ] )
template_nodes = parser . parse ( ( 'endrecurseforumcontents' , ) )
parser . delete_first_token ( )
return RecurseTreeForumVisibilityContentNode ( template_nodes , forums_contents_var ) |
def attitude_target_send ( self , time_boot_ms , type_mask , q , body_roll_rate , body_pitch_rate , body_yaw_rate , thrust , force_mavlink1 = False ) :
'''Reports the current commanded attitude of the vehicle as specified by
the autopilot . This should match the commands sent in
a SET _ ATTITUDE _ TARGET messag... | return self . send ( self . attitude_target_encode ( time_boot_ms , type_mask , q , body_roll_rate , body_pitch_rate , body_yaw_rate , thrust ) , force_mavlink1 = force_mavlink1 ) |
def get_last ( self , table = None ) :
"""Just the last entry .""" | if table is None :
table = self . main_table
query = 'SELECT * FROM "%s" ORDER BY ROWID DESC LIMIT 1;' % table
return self . own_cursor . execute ( query ) . fetchone ( ) |
def as_boxes ( self , solid = False ) :
"""A rough Trimesh representation of the voxels with a box
for each filled voxel .
Parameters
solid : bool , if True return boxes for sparse _ solid
Returns
mesh : Trimesh object made up of one box per filled cell .""" | if solid :
filled = self . sparse_solid
else :
filled = self . sparse_surface
# center points of voxels
centers = indices_to_points ( indices = filled , pitch = self . pitch , origin = self . origin )
mesh = multibox ( centers = centers , pitch = self . pitch )
return mesh |
def read ( self , payloadType , elsClient ) :
"""Fetches the latest data for this entity from api . elsevier . com .
Returns True if successful ; else , False .""" | if elsClient :
self . _client = elsClient ;
elif not self . client :
raise ValueError ( '''Entity object not currently bound to elsClient instance. Call .read() with elsClient argument or set .client attribute.''' )
try :
api_response = self . client . exec_request ( self . uri )
if isinstance ( api_res... |
def layout_deck ( self , i ) :
"""Stack the cards , starting at my deck ' s foundation , and proceeding
by ` ` card _ pos _ hint ` `""" | def get_dragidx ( cards ) :
j = 0
for card in cards :
if card . dragging :
return j
j += 1
# Put a None in the card list in place of the card you ' re
# hovering over , if you ' re dragging another card . This will
# result in an empty space where the card will go if you drop
# it no... |
def _set_group ( self , v , load = False ) :
"""Setter method for group , mapped from YANG variable / snmp _ server / group ( list )
If this variable is read - only ( config : false ) in the
source YANG file , then _ set _ group is considered as a private
method . Backends looking to populate this variable sh... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = YANGListType ( "group_name group_version" , group . group , yang_name = "group" , rest_name = "group" , parent = self , is_container = 'list' , user_ordered = False , path_helper = self . _path_helper , yang_keys = 'group-nam... |
def _get_program_dir ( name , config ) :
"""Retrieve directory for a program ( local installs / java jars ) .""" | if config is None :
raise ValueError ( "Could not find directory in config for %s" % name )
elif isinstance ( config , six . string_types ) :
return config
elif "dir" in config :
return expand_path ( config [ "dir" ] )
else :
raise ValueError ( "Could not find directory in config for %s" % name ) |
def _delete_request ( self , url , headers , data = None ) :
"""Issue a DELETE request to the specified endpoint with the data provided .
: param url : str
: pararm headers : dict
: param data : dict""" | return self . _session . delete ( url , headers = headers , data = data ) |
def connect ( self , coro ) :
"""The coroutine ` coro ` is connected to the signal . The coroutine must
return a true value , unless it wants to be disconnected from the
signal .
. . note : :
This is different from the return value convention with
: attr : ` AdHocSignal . STRONG ` and : attr : ` AdHocSign... | self . logger . debug ( "connecting %r" , coro )
return self . _connect ( coro ) |
def generate_random_nhs_number ( ) -> int :
"""Returns a random valid NHS number , as an ` ` int ` ` .""" | check_digit = 10
# NHS numbers with this check digit are all invalid
while check_digit == 10 :
digits = [ random . randint ( 1 , 9 ) ]
# don ' t start with a zero
digits . extend ( [ random . randint ( 0 , 9 ) for _ in range ( 8 ) ] )
# . . . length now 9
check_digit = nhs_check_digit ( digits )
# n... |
def check_undelivered ( to = None ) :
"""Sends a notification email if any undelivered dispatches .
Returns undelivered ( failed ) dispatches count .
: param str | unicode to : Recipient address . If not set Django ADMINS setting is used .
: rtype : int""" | failed_count = Dispatch . objects . filter ( dispatch_status = Dispatch . DISPATCH_STATUS_FAILED ) . count ( )
if failed_count :
from sitemessage . shortcuts import schedule_email
from sitemessage . messages . email import EmailTextMessage
if to is None :
admins = settings . ADMINS
if admins... |
def load_trace ( path , * args , ** kwargs ) :
"""Read a packet trace file , return a : class : ` wltrace . common . WlTrace ` object .
This function first reads the file ' s magic
( first ` ` FILE _ TYPE _ HANDLER ` ` bytes ) , and automatically determine the
file type , and call appropriate handler to proce... | with open ( path , 'rb' ) as f :
magic = f . read ( MAGIC_LEN )
if magic not in FILE_TYPE_HANDLER :
raise Exception ( 'Unknown file magic: %s' % ( binascii . hexlify ( magic ) ) )
return FILE_TYPE_HANDLER [ magic ] ( path , * args , ** kwargs ) |
def to_base64 ( self , skip = ( ) ) :
"""Construct from base64 - encoded JSON .""" | return base64 . b64encode ( ensure_bytes ( self . to_json ( skip = skip ) , encoding = 'utf-8' , ) ) |
def update_history ( self ) -> None :
"""Update messaging history on disk .
: returns : None""" | self . log . debug ( f"Saving history. History is: \n{self.history}" )
jsons = [ ]
for item in self . history :
json_item = item . __dict__
# Convert sub - entries into JSON as well .
json_item [ "output_records" ] = self . _parse_output_records ( item )
jsons . append ( json_item )
if not path . isfile... |
def _kl_divergence ( self , summary_freq , doc_freq ) :
"""Note : Could import scipy . stats and use scipy . stats . entropy ( doc _ freq , summary _ freq )
but this gives equivalent value without the import""" | sum_val = 0
for w in summary_freq :
frequency = doc_freq . get ( w )
if frequency : # missing or zero = no frequency
sum_val += frequency * math . log ( frequency / summary_freq [ w ] )
return sum_val |
def _legislator_objects ( self ) :
'''A cache of dereferenced legislator objects .''' | kwargs = { }
id_getter = operator . itemgetter ( 'leg_id' )
ids = [ ]
for k in ( 'yes' , 'no' , 'other' ) :
ids . extend ( map ( id_getter , self [ k + '_votes' ] ) )
objs = db . legislators . find ( { '_all_ids' : { '$in' : ids } } , ** kwargs )
# Handy to keep a reference to the vote on each legislator .
objs = l... |
def append_data ( self , name , initial_content , size , readonly = False , sort = "unknown" ) : # pylint : disable = unused - argument
"""Append a new data entry into the binary with specific name , content , and size .
: param str name : Name of the data entry . Will be used as the label .
: param bytes initi... | if readonly :
section_name = ".rodata"
else :
section_name = '.data'
if initial_content is None :
initial_content = b""
initial_content = initial_content . ljust ( size , b"\x00" )
data = Data ( self , memory_data = None , section_name = section_name , name = name , initial_content = initial_content , size ... |
def client_details ( self , * args ) :
"""Display known details about a given client""" | self . log ( _ ( 'Client details:' , lang = 'de' ) )
client = self . _clients [ args [ 0 ] ]
self . log ( 'UUID:' , client . uuid , 'IP:' , client . ip , 'Name:' , client . name , 'User:' , self . _users [ client . useruuid ] , pretty = True ) |
def NOAJS_metric ( bpmn_graph ) :
"""Returns the value of the NOAJS metric ( Number of Activities , joins and splits )
for the BPMNDiagramGraph instance .
: param bpmn _ graph : an instance of BpmnDiagramGraph representing BPMN model .""" | activities_count = all_activities_count ( bpmn_graph )
gateways_count = all_gateways_count ( bpmn_graph )
return activities_count + gateways_count |
def upload_part_copy ( Bucket = None , CopySource = None , CopySourceIfMatch = None , CopySourceIfModifiedSince = None , CopySourceIfNoneMatch = None , CopySourceIfUnmodifiedSince = None , CopySourceRange = None , Key = None , PartNumber = None , UploadId = None , SSECustomerAlgorithm = None , SSECustomerKey = None , S... | pass |
def set_location ( self , uri , size , checksum , storage_class = None ) :
"""Set only URI location of for object .
Useful to link files on externally controlled storage . If a file
instance has already been set , this methods raises an
` ` FileInstanceAlreadySetError ` ` exception .
: param uri : Full URI ... | self . file = FileInstance ( )
self . file . set_uri ( uri , size , checksum , storage_class = storage_class )
db . session . add ( self . file )
return self |
def delete ( python_data : LdapObject , database : Optional [ Database ] = None ) -> None :
"""Delete a LdapObject from the database .""" | dn = python_data . get_as_single ( 'dn' )
assert dn is not None
database = get_database ( database )
connection = database . connection
connection . delete ( dn ) |
def listItem ( node ) :
"""An item in a list""" | o = nodes . list_item ( )
for n in MarkDown ( node ) :
o += n
return o |
def get_releasetype ( self , ) :
"""Return the currently selected releasetype
: returns : the selected releasetype
: rtype : str
: raises : None""" | for rt , rb in self . _releasetype_button_mapping . items ( ) :
if rb . isChecked ( ) :
return rt |
def check_hierarchy ( rdf , break_cycles , keep_related , mark_top_concepts , eliminate_redundancy ) :
"""Check for , and optionally fix , problems in the skos : broader hierarchy
using a recursive depth first search algorithm .
: param Graph rdf : An rdflib . graph . Graph object .
: param bool fix _ cycles ... | starttime = time . time ( )
if check . hierarchy_cycles ( rdf , break_cycles ) :
logging . info ( "Some concepts not reached in initial cycle detection. " "Re-checking for loose concepts." )
setup_top_concepts ( rdf , mark_top_concepts )
check . disjoint_relations ( rdf , not keep_related )
check . hierarchical... |
def initialize ( cls ) :
"""Initialize the TLS / SSL platform to prepare it for
making AMQP requests . This only needs to happen once .""" | if cls . initialized :
_logger . debug ( "Platform already initialized." )
else :
_logger . debug ( "Initializing platform." )
c_uamqp . platform_init ( )
cls . initialized = True |
def id_by_index ( index , resources ) :
"""Helper method to fetch the id or address of a resource by its index
Args :
resources ( list of objects ) : The resources to be paginated
index ( integer ) : The index of the target resource
Returns :
str : The address or header _ signature of the resource ,
ret... | if index < 0 or index >= len ( resources ) :
return ''
try :
return resources [ index ] . header_signature
except AttributeError :
return resources [ index ] . address |
def visit_ImportFrom ( self , node ) :
"""Register imported modules and usage symbols .""" | module_path = tuple ( node . module . split ( '.' ) )
self . imports . add ( module_path [ 0 ] )
for alias in node . names :
path = module_path + ( alias . name , )
self . symbols [ alias . asname or alias . name ] = path
self . update = True
return None |
def slice_time ( begin , end = None , duration = datetime . timedelta ( days = 2 ) ) :
""": param begin : datetime
: param end : datetime
: param duration : timedelta
: return : a generator for a set of timeslices of the given duration""" | duration_ms = int ( duration . total_seconds ( ) * 1000 )
previous = int ( unix_time ( begin ) * 1000 )
next = previous + duration_ms
now_ms = unix_time ( datetime . datetime . now ( ) ) * 1000
end_slice = now_ms if not end else min ( now_ms , int ( unix_time ( end ) * 1000 ) )
while next < end_slice :
yield TimeSl... |
def extend ( self , cli_api , command_prefix = "" , sub_command = "" , ** kwargs ) :
"""Extends this CLI api with the commands present in the provided cli _ api object""" | if sub_command and command_prefix :
raise ValueError ( 'It is not currently supported to provide both a command_prefix and sub_command' )
if sub_command :
self . commands [ sub_command ] = cli_api
else :
for name , command in cli_api . commands . items ( ) :
self . commands [ "{}{}" . format ( comma... |
def estimategaps ( args ) :
"""% prog estimategaps input . bed
Estimate sizes of inter - scaffold gaps . The AGP file generated by path ( )
command has unknown gap sizes with a generic number of Ns ( often 100 Ns ) .
The AGP file ` input . chr . agp ` will be modified in - place .""" | p = OptionParser ( estimategaps . __doc__ )
p . add_option ( "--minsize" , default = 100 , type = "int" , help = "Minimum gap size" )
p . add_option ( "--maxsize" , default = 500000 , type = "int" , help = "Maximum gap size" )
p . add_option ( "--links" , default = 10 , type = "int" , help = "Only use linkage grounds w... |
def plot_confidence ( self , lower = 2.5 , upper = 97.5 , plot_limits = None , fixed_inputs = None , resolution = None , plot_raw = False , apply_link = False , visible_dims = None , which_data_ycols = 'all' , label = 'gp confidence' , predict_kw = None , ** kwargs ) :
"""Plot the confidence interval between the pe... | canvas , kwargs = pl ( ) . new_canvas ( ** kwargs )
ycols = get_which_data_ycols ( self , which_data_ycols )
X = get_x_y_var ( self ) [ 0 ]
helper_data = helper_for_plot_data ( self , X , plot_limits , visible_dims , fixed_inputs , resolution )
helper_prediction = helper_predict_with_model ( self , helper_data [ 2 ] , ... |
def bfd ( items , targets , ** kwargs ) :
"""Best - Fit Decreasing
Complexity O ( n ^ 2)""" | sizes = zip ( items , weight ( items , ** kwargs ) )
sizes = sorted ( sizes , key = operator . itemgetter ( 1 ) , reverse = True )
items = map ( operator . itemgetter ( 0 ) , sizes )
return bf ( items , targets , ** kwargs ) |
def key_diff ( key_bundle , key_defs ) :
"""Creates a difference dictionary with keys that should added and keys that
should be deleted from a Key Bundle to get it updated to a state that
mirrors What is in the key _ defs specification .
: param key _ bundle : The original KeyBundle
: param key _ defs : A s... | keys = key_bundle . get ( )
diff = { }
# My own sorted copy
key_defs = order_key_defs ( key_defs ) [ : ]
used = [ ]
for key in keys :
match = False
for kd in key_defs :
if key . use not in kd [ 'use' ] :
continue
if key . kty != kd [ 'type' ] :
continue
if key . k... |
def _match_cubes ( ccube_clean , ccube_dirty , bexpcube_clean , bexpcube_dirty , hpx_order ) :
"""Match the HEALPIX scheme and order of all the input cubes
return a dictionary of cubes with the same HEALPIX scheme and order""" | if hpx_order == ccube_clean . hpx . order :
ccube_clean_at_order = ccube_clean
else :
ccube_clean_at_order = ccube_clean . ud_grade ( hpx_order , preserve_counts = True )
if hpx_order == ccube_dirty . hpx . order :
ccube_dirty_at_order = ccube_dirty
else :
ccube_dirty_at_order = ccube_dirty . ud_grade (... |
def create_event ( self , register = False ) :
"""Create an asyncio . Event inside the emulation loop .
This method exists as a convenience to create an Event object that is
associated with the correct EventLoop ( ) . If you pass register = True ,
then the event will be registered as an event that must be set... | event = asyncio . Event ( loop = self . _loop )
if register :
self . _events . add ( event )
return event |
def delete ( path , version = - 1 , recursive = False , profile = None , hosts = None , scheme = None , username = None , password = None , default_acl = None ) :
'''Delete znode
path
path to znode
version
only delete if version matches ( Default : - 1 ( always matches ) )
profile
Configured Zookeeper p... | conn = _get_zk_conn ( profile = profile , hosts = hosts , scheme = scheme , username = username , password = password , default_acl = default_acl )
return conn . delete ( path , version , recursive ) |
def unicode ( self , b , encoding = None ) :
"""Convert a byte string to unicode , using string _ encoding and decode _ errors .
Arguments :
b : a byte string .
encoding : the name of an encoding . Defaults to the string _ encoding
attribute for this instance .
Raises :
TypeError : Because this method c... | if encoding is None :
encoding = self . string_encoding
# TODO : Wrap UnicodeDecodeErrors with a message about setting
# the string _ encoding and decode _ errors attributes .
return unicode ( b , encoding , self . decode_errors ) |
def setCheckedRecords ( self , records , column = 0 , parent = None ) :
"""Sets the checked items based on the inputed list of records .
: param records | [ < orb . Table > , . . ]
parent | < QTreeWidgetItem > | | None""" | if parent is None :
for i in range ( self . topLevelItemCount ( ) ) :
item = self . topLevelItem ( i )
try :
has_record = item . record ( ) in records
except AttributeError :
has_record = False
if has_record :
item . setCheckState ( column , Qt . C... |
def get_tree ( ident_hash , baked = False ) :
"""Return a tree structure of the Collection""" | id , version = get_id_n_version ( ident_hash )
stmt = _get_sql ( 'get-tree.sql' )
args = dict ( id = id , version = version , baked = baked )
with db_connect ( ) as db_conn :
with db_conn . cursor ( ) as cursor :
cursor . execute ( stmt , args )
try :
tree = cursor . fetchone ( ) [ 0 ]
... |
def __collapse_stranded ( s , proc_strands , names = False , verbose = False ) :
"""Get the union of a set of genomic intervals .
given a list of genomic intervals with chromosome , start , end and strand
fields , collapse those intervals with strand in the set < proc _ strands >
into a set of non - overlappi... | def get_first_matching_index ( s , proc_strands ) :
for i in range ( 0 , len ( s ) ) :
if s [ i ] . strand in proc_strands :
return i
return None
if proc_strands not in [ set ( "+" ) , set ( "-" ) , set ( [ "+" , "-" ] ) ] :
raise GenomicIntervalError ( "failed collapsing intervals on st... |
def synchronize_switch ( self , switch_ip , expected_acls , expected_bindings ) :
"""Update ACL config on a switch to match expected config
This is done as follows :
1 . Get switch ACL config using show commands
2 . Update expected bindings based on switch LAGs
3 . Get commands to synchronize switch ACLs
... | # Get ACL rules and interface mappings from the switch
switch_acls , switch_bindings = self . _get_dynamic_acl_info ( switch_ip )
# Adjust expected bindings for switch LAG config
expected_bindings = self . adjust_bindings_for_lag ( switch_ip , expected_bindings )
# Get synchronization commands
switch_cmds = list ( )
sw... |
def perform_experiment ( self , engine_list ) :
"""Performs nearest neighbour experiments with custom vector data
for all engines in the specified list .
Returns self . result contains list of ( distance _ ratio , search _ time )
tuple . All are the averaged values over all request vectors .
search _ time i... | # We will fill this array with measures for all the engines .
result = [ ]
# For each engine , first index vectors and then retrieve neighbours
for engine in engine_list :
print ( 'Engine %d / %d' % ( engine_list . index ( engine ) , len ( engine_list ) ) )
# Clean storage
engine . clean_all_buckets ( )
... |
def get_metric_statistics ( Namespace = None , MetricName = None , Dimensions = None , StartTime = None , EndTime = None , Period = None , Statistics = None , ExtendedStatistics = None , Unit = None ) :
"""Gets statistics for the specified metric .
Amazon CloudWatch retains metric data as follows :
Note that Cl... | pass |
def recv ( self , topic , payload , qos ) :
"""Receive a MQTT message .
Call this method when a message is received from the MQTT broker .""" | data = self . _parse_mqtt_to_message ( topic , payload , qos )
if data is None :
return
_LOGGER . debug ( 'Receiving %s' , data )
self . add_job ( self . logic , data ) |
def make_limited_stream ( stream , limit ) :
"""Makes a stream limited .""" | if not isinstance ( stream , LimitedStream ) :
if limit is None :
raise TypeError ( 'stream not limited and no limit provided.' )
stream = LimitedStream ( stream , limit )
return stream |
def _recv_internal ( self , timeout = None ) :
"""Read a message from kvaser device and return whether filtering has taken place .""" | arb_id = ctypes . c_long ( 0 )
data = ctypes . create_string_buffer ( 64 )
dlc = ctypes . c_uint ( 0 )
flags = ctypes . c_uint ( 0 )
timestamp = ctypes . c_ulong ( 0 )
if timeout is None : # Set infinite timeout
# http : / / www . kvaser . com / canlib - webhelp / group _ _ _ c _ a _ n . html # ga2edd785a87cc16b49ece89... |
def load_gene_exp_to_df ( inst_path ) :
'''Loads gene expression data from 10x in sparse matrix format and returns a
Pandas dataframe''' | import pandas as pd
from scipy import io
from scipy import sparse
from ast import literal_eval as make_tuple
# matrix
Matrix = io . mmread ( inst_path + 'matrix.mtx' )
mat = Matrix . todense ( )
# genes
filename = inst_path + 'genes.tsv'
f = open ( filename , 'r' )
lines = f . readlines ( )
f . close ( )
# # add unique... |
def get_mean_and_stddevs ( self , sites , rup , dists , imt , stddev_types ) :
"""See : meth : ` superclass method
< . base . GroundShakingIntensityModel . get _ mean _ and _ stddevs > `
for spec of input and result values .""" | # extracting dictionary of coefficients specific to required
# intensity measure type .
C = self . COEFFS [ imt ]
# intensity on a reference soil is used for both mean
# and stddev calculations .
ln_y_ref = self . _get_ln_y_ref ( rup , dists , C )
# exp1 and exp2 are parts of eq . 7
exp1 = np . exp ( C [ 'phi3' ] * ( s... |
def delete_workspace_config ( namespace , workspace , cnamespace , config ) :
"""Delete method configuration in workspace .
Args :
namespace ( str ) : project to which workspace belongs
workspace ( str ) : Workspace name
mnamespace ( str ) : Method namespace
method ( str ) : Method name
Swagger :
http... | uri = "workspaces/{0}/{1}/method_configs/{2}/{3}" . format ( namespace , workspace , cnamespace , config )
return __delete ( uri ) |
def read_epw ( self ) :
"""Section 2 - Read EPW file
properties :
self . climateDataPath
self . newPathName
self . _ header # header data
self . epwinput # timestep data for weather
self . lat # latitude
self . lon # longitude
self . GMT # GMT
self . nSoil # Number of soil depths
self . Tsoil # ... | # Make dir path to epw file
self . climateDataPath = os . path . join ( self . epwDir , self . epwFileName )
# Open epw file and feed csv data to climate _ data
try :
climate_data = utilities . read_csv ( self . climateDataPath )
except Exception as e :
raise Exception ( "Failed to read epw file! {}" . format (... |
def traverse_postorder ( self , leaves = True , internal = True ) :
'''Perform a postorder traversal starting at this ` ` Node ` ` object
Args :
` ` leaves ` ` ( ` ` bool ` ` ) : ` ` True ` ` to include leaves , otherwise ` ` False ` `
` ` internal ` ` ( ` ` bool ` ` ) : ` ` True ` ` to include internal nodes... | s1 = deque ( ) ;
s2 = deque ( ) ;
s1 . append ( self )
while len ( s1 ) != 0 :
n = s1 . pop ( ) ;
s2 . append ( n ) ;
s1 . extend ( n . children )
while len ( s2 ) != 0 :
n = s2 . pop ( )
if ( leaves and n . is_leaf ( ) ) or ( internal and not n . is_leaf ( ) ) :
yield n |
def getErrorResponse ( self , errorCode , errorDescr ) :
"""This methods sets error attributes of an external method object .""" | self . errorCode = errorCode
self . errorDescr = errorDescr
self . response = "yes"
return self |
def adjacency_plot_und ( A , coor , tube = False ) :
'''This function in matlab is a visualization helper which translates an
adjacency matrix and an Nx3 matrix of spatial coordinates , and plots a
3D isometric network connecting the undirected unweighted nodes using a
specific plotting format . Including the... | from mayavi import mlab
n = len ( A )
nr_edges = ( n * n - 1 ) // 2
# starts = np . zeros ( ( nr _ edges , 3 ) )
# vecs = np . zeros ( ( nr _ edges , 3 ) )
# adjdat = np . zeros ( ( nr _ edges , ) )
ixes , = np . where ( np . triu ( np . ones ( ( n , n ) ) , 1 ) . flat )
# i = 0
# for r2 in xrange ( n ) :
# for r1 in x... |
def _zscore ( a ) :
"""Calculating z - score of data on the first axis .
If the numbers in any column are all equal , scipy . stats . zscore
will return NaN for this column . We shall correct them all to
be zeros .
Parameters
a : numpy array
Returns
zscore : numpy array
The z - scores of input " a "... | assert a . ndim > 1 , 'a must have more than one dimensions'
zscore = scipy . stats . zscore ( a , axis = 0 )
zscore [ : , np . logical_not ( np . all ( np . isfinite ( zscore ) , axis = 0 ) ) ] = 0
return zscore |
def _load_sequences_to_strain ( self , strain_id , force_rerun = False ) :
"""Load strain GEMPRO with functional genes defined , load sequences to it , save as new GEMPRO""" | gp_seqs_path = op . join ( self . model_dir , '{}_gp_withseqs.pckl' . format ( strain_id ) )
if ssbio . utils . force_rerun ( flag = force_rerun , outfile = gp_seqs_path ) :
gp_noseqs = ssbio . io . load_pickle ( self . strain_infodict [ strain_id ] [ 'gp_noseqs_path' ] )
strain_sequences = SeqIO . index ( self... |
def analytics ( account = None , * args , ** kwargs ) :
"""Simple Google Analytics integration .
First looks for an ` ` account ` ` parameter . If not supplied , uses
Django ` ` GOOGLE _ ANALYTICS _ ACCOUNT ` ` setting . If account not set ,
raises ` ` TemplateSyntaxError ` ` .
: param account :
Google An... | if not account :
try :
account = settings . GOOGLE_ANALYTICS_ACCOUNT
except :
raise template . TemplateSyntaxError ( "Analytics account could not found either " "in tag parameters or settings" )
return { 'account' : account , 'params' : kwargs } |
def _to_solr ( self , data ) :
'''Sends data to a Solr instance .''' | return self . _dest . index_json ( self . _dest_coll , json . dumps ( data , sort_keys = True ) ) |
def trifurcate_base ( cls , newick ) :
"""Rewrites a newick string so that the base is a trifurcation
( usually means an unrooted tree )""" | t = cls ( newick )
t . _tree . deroot ( )
return t . newick |
def likelihood ( self , outcomes , modelparams , expparams ) :
"""Calculates the likelihood function at the states specified
by modelparams and measurement specified by expparams .
This is given by the Born rule and is the probability of
outcomes given the state and measurement operator .""" | # By calling the superclass implementation , we can consolidate
# call counting there .
super ( MultiQubitStatePauliModel , self ) . likelihood ( outcomes , modelparams , expparams )
# Note that expparams [ ' axis ' ] has shape ( n _ exp , 3 ) .
pr0 = 0.5 * ( 1 + modelparams [ : , expparams [ 'pauli' ] ] )
# Use the fo... |
def create_box ( self , orientation = Gtk . Orientation . HORIZONTAL , spacing = 0 ) :
"""Function creates box . Based on orientation
it can be either HORIZONTAL or VERTICAL""" | h_box = Gtk . Box ( orientation = orientation , spacing = spacing )
h_box . set_homogeneous ( False )
return h_box |
def local ( ) :
"""Load local requirements file .""" | logger . info ( "Loading requirements from local file." )
with open ( REQUIREMENTS_FILE , 'r' ) as f :
requirements = parse ( f )
for r in requirements :
logger . debug ( "Creating new package: %r" , r )
create_package_version ( r ) |
def _data_from_response ( self , resp_body , key = None ) :
"""This works for most API responses , but some don ' t structure their
listing responses the same way , so overriding this method allows
subclasses to handle extraction for those outliers .""" | if key :
data = resp_body . get ( key )
else :
data = resp_body . get ( self . plural_response_key , resp_body )
# NOTE ( ja ) : some services , such as keystone returns values as list as
# { " values " : [ . . . ] } unlike other services which just return the
# list .
if isinstance ( data , dict ) :
try :
... |
def deactivate ( self , plugins = [ ] ) :
"""Deactivates given plugins .
A given plugin must be activated , otherwise it is ignored and no action takes place ( no signals are fired ,
no deactivate functions are called . )
A deactivated plugin is still loaded and initialised and can be reactivated by calling :... | self . _log . debug ( "Plugins Deactivation started" )
if not isinstance ( plugins , list ) :
raise AttributeError ( "plugins must be a list, not %s" % type ( plugins ) )
self . _log . debug ( "Plugins to deactivate: %s" % ", " . join ( plugins ) )
plugins_deactivated = [ ]
for plugin_name in plugins :
if not i... |
def post_event_unpublish ( self , id , ** data ) :
"""POST / events / : id / unpublish /
Unpublishes an event . In order for a free event to be unpublished , it must not have any pending or completed orders ,
even if the event is in the past . In order for a paid event to be unpublished , it must not have any p... | return self . post ( "/events/{0}/unpublish/" . format ( id ) , data = data ) |
def _set_dst_vtep_ip_any ( self , v , load = False ) :
"""Setter method for dst _ vtep _ ip _ any , mapped from YANG variable / overlay / access _ list / type / vxlan / standard / seq / dst _ vtep _ ip _ any ( empty )
If this variable is read - only ( config : false ) in the
source YANG file , then _ set _ dst ... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = YANGBool , is_leaf = True , yang_name = "dst-vtep-ip-any" , rest_name = "dst-vtep-ip-any" , parent = self , choice = ( u'choice-dst-vtep-ip' , u'case-dst-vtep-ip-any' ) , path_helper = self . _path_helper , extmethods = self ... |
def sff ( args ) :
"""% prog sff sffiles
Convert reads formatted as 454 SFF file , and convert to CA frg file .
Turn - - nodedup on if another deduplication mechanism is used ( e . g .
CD - HIT - 454 ) . See assembly . sff . deduplicate ( ) .""" | p = OptionParser ( sff . __doc__ )
p . add_option ( "--prefix" , dest = "prefix" , default = None , help = "Output frg filename prefix" )
p . add_option ( "--nodedup" , default = False , action = "store_true" , help = "Do not remove duplicates [default: %default]" )
p . set_size ( )
opts , args = p . parse_args ( args ... |
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