signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def isUpdated ( self ) :
"""Figures out if the file had previously errored and hasn ' t
been fixed since given a numerical time""" | modified_time = self . getmtime ( )
valid = modified_time > self . __stamp
return valid |
def get_uri_name ( url ) :
"""Gets the file name from the end of the URL . Only useful for PyBEL ' s testing though since it looks specifically
if the file is from the weird owncloud resources distributed by Fraunhofer""" | url_parsed = urlparse ( url )
url_parts = url_parsed . path . split ( '/' )
log . info ( 'url parts: %s' , url_parts )
return url_parts [ - 1 ] |
def output ( self ) :
"""Returns the default workflow outputs in an ordered dictionary . At the moment this is just
the collection of outputs of the branch tasks , stored with the key ` ` " collection " ` ` .""" | if self . task . target_collection_cls is not None :
cls = self . task . target_collection_cls
elif self . task . outputs_siblings :
cls = SiblingFileCollection
else :
cls = TargetCollection
targets = luigi . task . getpaths ( self . task . get_branch_tasks ( ) )
collection = cls ( targets , threshold = sel... |
def GameTypeEnum ( ctx ) :
"""Game Type Enumeration .""" | return Enum ( ctx , RM = 0 , Regicide = 1 , DM = 2 , Scenario = 3 , Campaign = 4 , KingOfTheHill = 5 , WonderRace = 6 , DefendTheWonder = 7 , TurboRandom = 8 ) |
def get_mysql_pool ( host = None , user = None , password = None , charset = 'utf8' , db = None , size = None , isSync = True , ioloop = None ) :
"""使用工厂方法返回一个连接池""" | factory = mysql_pool_factory ( isSync )
kwargs = { 'host' : host , 'user' : user , 'password' : password , 'charset' : charset , 'db' : db , 'size' : size , }
return factory ( ** kwargs ) |
def getCmdOpts ( self , text ) :
'''Use the _ cmd _ syntax def to split / parse / normalize the cmd line .
Args :
text ( str ) : Command to process .
Notes :
This is implemented independent of argparse ( et al ) due to the
need for syntax aware argument splitting . Also , allows different
split per comm... | off = 0
_ , off = s_syntax . nom ( text , off , s_syntax . whites )
name , off = s_syntax . meh ( text , off , s_syntax . whites )
_ , off = s_syntax . nom ( text , off , s_syntax . whites )
opts = { }
args = collections . deque ( [ synt for synt in self . _cmd_syntax if not synt [ 0 ] . startswith ( '-' ) ] )
switches... |
def send_reset_password_link ( request ) :
'''Send email with reset password link .''' | if not registration_settings . RESET_PASSWORD_VERIFICATION_ENABLED :
raise Http404 ( )
serializer = SendResetPasswordLinkSerializer ( data = request . data )
serializer . is_valid ( raise_exception = True )
login = serializer . validated_data [ 'login' ]
user = None
for login_field in get_login_fields ( ) :
use... |
def run_numerical_analysis ( table , schema_list , args ) :
"""Find min / max values for the numerical columns and writes a json file .
Args :
table : Reference to FederatedTable ( if bigquery _ table is false ) or a
regular Table ( otherwise )
schema _ list : Bigquery schema json object
args : the comman... | import google . datalab . bigquery as bq
# Get list of numerical columns .
numerical_columns = [ ]
for col_schema in schema_list :
col_type = col_schema [ 'type' ] . lower ( )
if col_type == 'integer' or col_type == 'float' :
numerical_columns . append ( col_schema [ 'name' ] )
# Run the numerical analy... |
def updatePotentialRadius ( sp , newPotentialRadius ) :
"""Change the potential radius for all columns
: return :""" | oldPotentialRadius = sp . _potentialRadius
sp . _potentialRadius = newPotentialRadius
numColumns = np . prod ( sp . getColumnDimensions ( ) )
for columnIndex in xrange ( numColumns ) :
potential = sp . _mapPotential ( columnIndex )
sp . _potentialPools . replace ( columnIndex , potential . nonzero ( ) [ 0 ] )
s... |
def get_field_infos ( code , free_format ) :
"""Gets the list of pic fields information from line | start | to line | end | .
: param code : code to parse
: returns : the list of pic fields info found in the specified text .""" | offset = 0
field_infos = [ ]
lines = _clean_code ( code )
previous_offset = 0
for row in process_cobol ( lines , free_format ) :
fi = PicFieldInfo ( )
fi . name = row [ "name" ]
fi . level = row [ "level" ]
fi . pic = row [ "pic" ]
fi . occurs = row [ "occurs" ]
fi . redefines = row [ "redefines... |
def get_datafeed_stats ( self , datafeed_id = None , params = None ) :
"""` < http : / / www . elastic . co / guide / en / elasticsearch / reference / current / ml - get - datafeed - stats . html > ` _
: arg datafeed _ id : The ID of the datafeeds stats to fetch
: arg allow _ no _ datafeeds : Whether to ignore ... | return self . transport . perform_request ( "GET" , _make_path ( "_ml" , "datafeeds" , datafeed_id , "_stats" ) , params = params ) |
def _validate_names ( self , name = None , names = None , deep = False ) :
"""Handles the quirks of having a singular ' name ' parameter for general
Index and plural ' names ' parameter for MultiIndex .""" | from copy import deepcopy
if names is not None and name is not None :
raise TypeError ( "Can only provide one of `names` and `name`" )
elif names is None and name is None :
return deepcopy ( self . names ) if deep else self . names
elif names is not None :
if not is_list_like ( names ) :
raise TypeE... |
def addAction ( self , action ) :
"""Adds the inputed action to this toolbar .
: param action | < QAction >""" | super ( XDockToolbar , self ) . addAction ( action )
label = XDockActionLabel ( action , self . minimumPixmapSize ( ) , self )
label . setPosition ( self . position ( ) )
layout = self . layout ( )
layout . insertWidget ( layout . count ( ) - 1 , label ) |
def _correct_qualimap_genome_results ( samples ) :
"""fixing java . lang . Double . parseDouble error on entries like " 6,082.49" """ | for s in samples :
if verify_file ( s . qualimap_genome_results_fpath ) :
correction_is_needed = False
with open ( s . qualimap_genome_results_fpath , 'r' ) as f :
content = f . readlines ( )
metrics_started = False
for line in content :
if ">> Ref... |
def _encode_item ( self , item ) :
'''Encode an item object
@ requires : The object be serializable''' | if self . encoding . __name__ == 'pickle' :
return self . encoding . dumps ( item , protocol = - 1 )
else :
return self . encoding . dumps ( item ) |
def batchsd ( trace , batches = 5 ) :
"""Calculates the simulation standard error , accounting for non - independent
samples . The trace is divided into batches , and the standard deviation of
the batch means is calculated .""" | if len ( np . shape ( trace ) ) > 1 :
dims = np . shape ( trace )
# ttrace = np . transpose ( np . reshape ( trace , ( dims [ 0 ] , sum ( dims [ 1 : ] ) ) ) )
ttrace = np . transpose ( [ t . ravel ( ) for t in trace ] )
return np . reshape ( [ batchsd ( t , batches ) for t in ttrace ] , dims [ 1 : ] )
e... |
def on_directory_button_tool_clicked ( self ) :
"""Autoconnect slot activated when directory button is clicked .""" | # noinspection PyCallByClass , PyTypeChecker
# set up parameter from dialog
input_path = self . layer . currentLayer ( ) . source ( )
input_directory , self . output_filename = os . path . split ( input_path )
file_extension = os . path . splitext ( self . output_filename ) [ 1 ]
self . output_filename = os . path . sp... |
def load_layer_without_provider ( layer_uri , layer_name = 'tmp' ) :
"""Helper to load a layer when don ' t know the driver .
Don ' t use it , it ' s an empiric function to try each provider one per one .
OGR / GDAL is printing a lot of error saying that the layer is not valid .
: param layer _ uri : Layer UR... | # Let ' s try the most common vector driver
layer = QgsVectorLayer ( layer_uri , layer_name , VECTOR_DRIVERS [ 0 ] )
if layer . isValid ( ) :
return layer
# Let ' s try the most common raster driver
layer = QgsRasterLayer ( layer_uri , layer_name , RASTER_DRIVERS [ 0 ] )
if layer . isValid ( ) :
return layer
# ... |
def parse_request ( self , request , parameters = None , fake_method = None ) :
'''Parse WebOb request''' | return ( request . method , request . url , request . headers , request . POST . mixed ( ) ) |
def deinit ( bus = DEFAULT_SPI_BUS , chip_select = DEFAULT_SPI_CHIP_SELECT ) :
"""Stops interrupts on all boards . Only required when using
: func : ` digital _ read ` and : func : ` digital _ write ` .
: param bus : SPI bus / dev / spidev < bus > . < chipselect > ( default : { bus } )
: type bus : int
: pa... | global _pifacedigitals
for pfd in _pifacedigitals :
try :
pfd . deinit_board ( )
except AttributeError :
pass |
def split_marker ( marker , fg_id = 1 , bg_id = 2 ) :
"""Splits an integer marker image into two binary image containing the foreground and
background markers respectively .
All encountered 1 ' s are hereby treated as foreground , all 2 ' s as background , all 0 ' s
as neutral marker and all others are ignore... | img_marker = scipy . asarray ( marker )
img_fgmarker = scipy . zeros ( img_marker . shape , scipy . bool_ )
img_fgmarker [ img_marker == fg_id ] = True
img_bgmarker = scipy . zeros ( img_marker . shape , scipy . bool_ )
img_bgmarker [ img_marker == bg_id ] = True
return img_fgmarker , img_bgmarker |
def Lc ( self , value ) :
"""set col rotation""" | assert value . shape == ( self . P , self . P ) , 'dimension mismatch'
self . _Lc = value
self . clear_cache ( ) |
def has_module_perms ( self , user_obj , app_label ) :
"""Check if user have permission of specified app
Parameters
user _ obj : django user model instance
A django user model instance which be checked
app _ label : string
Django application name
Returns
boolean
Whether the specified user have any p... | cache_name = "_has_module_perms_%s_%s_cache" % ( app_label , user_obj . pk )
if hasattr ( self , cache_name ) :
return getattr ( self , cache_name )
if self . app_label != app_label :
setattr ( self , cache_name , False )
else :
for permission in self . get_supported_permissions ( ) :
if user_obj . ... |
def parse_rules ( data , chain ) :
"""Parse the rules for the specified chain .""" | rules = [ ]
for line in data . splitlines ( True ) :
m = re_rule . match ( line )
if m and m . group ( 3 ) == chain :
rule = parse_rule ( m . group ( 4 ) )
rule . packets = int ( m . group ( 1 ) )
rule . bytes = int ( m . group ( 2 ) )
rules . append ( rule )
return rules |
def _decode_input_tensor_to_features_dict ( feature_map , hparams ) :
"""Convert the interactive input format ( see above ) to a dictionary .
Args :
feature _ map : dict with inputs .
hparams : model hyperparameters
Returns :
a features dictionary , as expected by the decoder .""" | inputs = tf . convert_to_tensor ( feature_map [ "inputs" ] )
input_is_image = False
x = inputs
p_hparams = hparams . problem_hparams
# Add a third empty dimension
x = tf . expand_dims ( x , axis = [ 2 ] )
x = tf . to_int32 ( x )
input_space_id = tf . constant ( p_hparams . input_space_id )
target_space_id = tf . consta... |
def check_expression ( testing_framework , expression_dict ) :
"""> > > class mock _ framework :
. . . def assertIn ( self , item , list , msg = " Failed asserting item is in list " ) :
. . . if item not in list : raise Exception ( msg )
. . . def assertTrue ( self , value , msg = " Failed asserting true " ) ... | expression_sub = get_expression_sub ( )
for expression_type_name , expression_type in expression_dict . items ( ) :
for name , expression_object in expression_type . items ( ) :
if 'Matches' in expression_object . keys ( ) :
for test in expression_object [ 'Matches' ] . split ( '|' ) : # Substit... |
def Channels ( module ) :
'''Returns the channels contained in the given K2 module .''' | nums = { 2 : 1 , 3 : 5 , 4 : 9 , 6 : 13 , 7 : 17 , 8 : 21 , 9 : 25 , 10 : 29 , 11 : 33 , 12 : 37 , 13 : 41 , 14 : 45 , 15 : 49 , 16 : 53 , 17 : 57 , 18 : 61 , 19 : 65 , 20 : 69 , 22 : 73 , 23 : 77 , 24 : 81 }
if module in nums :
return [ nums [ module ] , nums [ module ] + 1 , nums [ module ] + 2 , nums [ module ] ... |
def _send ( self , messagetype , packet ) :
"""Send the GNTP Packet""" | packet . validate ( )
data = packet . encode ( )
logger . debug ( 'To : %s:%s <%s>\n%s' , self . hostname , self . port , packet . __class__ , data )
s = socket . socket ( socket . AF_INET , socket . SOCK_STREAM )
s . settimeout ( self . socketTimeout )
try :
s . connect ( ( self . hostname , self . port ) )
s ... |
def verify_message ( data_to_verify , signature , verify_cert ) :
"""Function parses an ASN . 1 encrypted message and extracts / decrypts
the original message .
: param data _ to _ verify :
A byte string of the data to be verified against the signature .
: param signature : A CMS ASN . 1 byte string contain... | cms_content = cms . ContentInfo . load ( signature )
digest_alg = None
if cms_content [ 'content_type' ] . native == 'signed_data' :
for signer in cms_content [ 'content' ] [ 'signer_infos' ] :
signed_attributes = signer [ 'signed_attrs' ] . copy ( )
digest_alg = signer [ 'digest_algorithm' ] [ 'alg... |
def dir ( base_dir : str , rr_id : str ) -> str :
"""Return correct subdirectory of input base dir for artifacts corresponding to input rev reg id .
: param base _ dir : base directory for tails files , thereafter split by cred def id
: param rr _ id : rev reg id""" | LOGGER . debug ( 'Tails.dir >>> base_dir: %s, rr_id: %s' , base_dir , rr_id )
if not ok_rev_reg_id ( rr_id ) :
LOGGER . debug ( 'Tails.dir <!< Bad rev reg id %s' , rr_id )
raise BadIdentifier ( 'Bad rev reg id {}' . format ( rr_id ) )
rv = join ( base_dir , rev_reg_id2cred_def_id ( rr_id ) )
LOGGER . debug ( 'T... |
async def _make_qr ( self , qr : QuickRepliesList . BaseOption , request : Request ) :
"""Generate a single quick reply ' s content .""" | if isinstance ( qr , QuickRepliesList . TextOption ) :
return { 'content_type' : 'text' , 'title' : await render ( qr . text , request ) , 'payload' : qr . slug , }
elif isinstance ( qr , QuickRepliesList . LocationOption ) :
return { 'content_type' : 'location' , } |
def create_embedded_class ( self , method ) :
"""Build the estimator class .
Returns
: return : string
The built class as string .""" | temp_class = self . temp ( 'embedded.class' )
return temp_class . format ( class_name = self . class_name , method_name = self . method_name , method = method , n_features = self . n_features ) |
def describe ( df , dtype = None ) :
"""Print a description of a Pandas dataframe .
Parameters
df : Pandas . DataFrame
dtype : dict
Maps column names to types""" | if dtype is None :
dtype = { }
print ( 'Number of datapoints: {datapoints}' . format ( datapoints = len ( df ) ) )
column_info , column_info_meta = _get_column_info ( df , dtype )
if len ( column_info [ 'int' ] ) > 0 :
_describe_int ( df , column_info )
if len ( column_info [ 'float' ] ) > 0 :
_describe_flo... |
def get_reservations_for_booking_ids ( self , booking_ids ) :
"""Gets booking information for a given list of booking ids .
: param booking _ ids : a booking id or a list of room ids ( comma separated ) .
: type booking _ ids : string""" | try :
resp = self . _request ( "GET" , "/1.1/space/booking/{}" . format ( booking_ids ) )
except resp . exceptions . HTTPError as error :
raise APIError ( "Server Error: {}" . format ( error ) )
return resp . json ( ) |
def get_lldp_neighbor_detail_output_lldp_neighbor_detail_local_interface_name ( self , ** kwargs ) :
"""Auto Generated Code""" | config = ET . Element ( "config" )
get_lldp_neighbor_detail = ET . Element ( "get_lldp_neighbor_detail" )
config = get_lldp_neighbor_detail
output = ET . SubElement ( get_lldp_neighbor_detail , "output" )
lldp_neighbor_detail = ET . SubElement ( output , "lldp-neighbor-detail" )
remote_interface_name_key = ET . SubElem... |
def compute_route_time_series ( feed : "Feed" , trip_stats_subset : DataFrame , dates : List [ str ] , freq : str = "5Min" , * , split_directions : bool = False , ) -> DataFrame :
"""Compute route stats in time series form for the trips that lie in
the trip stats subset and that start on the given dates .
Param... | dates = feed . restrict_dates ( dates )
if not dates :
return pd . DataFrame ( )
activity = feed . compute_trip_activity ( dates )
ts = trip_stats_subset . copy ( )
# Collect stats for each date , memoizing stats by trip ID sequence
# to avoid unnecessary re - computations .
# Store in dictionary of the form
# trip... |
def _encode_var ( cls , var ) :
"""Encodes a variable to the appropriate string format for ini files .
: param var : The variable to encode
: return : The ini representation of the variable
: rtype : str""" | if isinstance ( var , str ) :
if any ( _ in var for _ in cls . requires_quotes ) : # NOTE : quoted strings should just use ' " ' according to the spec
return '"' + var . replace ( '"' , '\\"' ) + '"'
return var
else :
return str ( var ) |
def command ( self , command ) :
"""Run a command on the currently active container .
: rtype : CommandReply""" | return self . _conn . command ( '[con_id="{}"] {}' . format ( self . id , command ) ) |
def _run_info_from_yaml ( dirs , run_info_yaml , config , sample_names = None , is_cwl = False , integrations = None ) :
"""Read run information from a passed YAML file .""" | validate_yaml ( run_info_yaml , run_info_yaml )
with open ( run_info_yaml ) as in_handle :
loaded = yaml . safe_load ( in_handle )
fc_name , fc_date = None , None
if dirs . get ( "flowcell" ) :
try :
fc_name , fc_date = flowcell . parse_dirname ( dirs . get ( "flowcell" ) )
except ValueError :
... |
def get_port ( self , adapter_number , port_number ) :
"""Return the port for this adapter _ number and port _ number
or returns None if the port is not found""" | for port in self . ports :
if port . adapter_number == adapter_number and port . port_number == port_number :
return port
return None |
def connect_after ( self , detailed_signal , handler , * args ) :
"""connect _ after ( detailed _ signal : str , handler : function , * args ) - > handler _ id : int
The connect _ after ( ) method is similar to the connect ( ) method
except that the handler is added to the signal handler list after
the defaul... | flags = GConnectFlags . CONNECT_AFTER
return self . __connect ( flags , detailed_signal , handler , * args ) |
def is_prime ( n ) :
"""Return True if x is prime , False otherwise .
We use the Miller - Rabin test , as given in Menezes et al . p . 138.
This test is not exact : there are composite values n for which
it returns True .
In testing the odd numbers from 1000001 to 199999,
about 66 composites got past the ... | # ( This is used to study the risk of false positives : )
global miller_rabin_test_count
miller_rabin_test_count = 0
if n <= smallprimes [ - 1 ] :
if n in smallprimes :
return True
else :
return False
if gcd ( n , 2 * 3 * 5 * 7 * 11 ) != 1 :
return False
# Choose a number of iterations suffi... |
def usesTime ( self , fmt = None ) :
'''Check if the format uses the creation time of the record .''' | if fmt is None :
fmt = self . _fmt
if not isinstance ( fmt , basestring ) :
fmt = fmt [ 0 ]
return fmt . find ( '%(asctime)' ) >= 0 |
def init_process ( self ) -> None :
"""GunicornWorker 初始化回调""" | default_loop = asyncio . get_event_loop ( )
if default_loop . is_running ( ) :
default_loop . close ( )
self . loop = asyncio . new_event_loop ( )
asyncio . set_event_loop ( self . loop )
else :
self . loop = default_loop
super ( ) . init_process ( ) |
def list_delete ( self , id ) :
"""Delete a list .""" | id = self . __unpack_id ( id )
self . __api_request ( 'DELETE' , '/api/v1/lists/{0}' . format ( id ) ) |
def modify ( self , ** kwargs ) :
"""We need to implement the custom exclusive parameter check .""" | self . _check_exclusive_parameters ( ** kwargs )
return super ( Rule , self ) . _modify ( ** kwargs ) |
def get_nodes ( self , request ) :
"""This method is used to build the menu tree .""" | nodes = [ ]
for scientist in Scientist . objects . filter ( current = True , visible = True ) :
node = NavigationNode ( scientist . full_name , reverse ( 'lab_members:scientist_detail' , args = ( scientist . slug , ) ) , scientist . slug )
nodes . append ( node )
if Scientist . objects . filter ( current = Fals... |
def api_ebuio_forum_get_topics_by_tag_for_user ( request , key = None , hproPk = None , tag = None , userPk = None ) :
"""Return the list of topics using the tag pk""" | # Check API key ( in order to be sure that we have a valid one and that ' s correspond to the project
if not check_api_key ( request , key , hproPk ) :
return HttpResponseForbidden
if settings . PIAPI_STANDALONE :
return HttpResponse ( json . dumps ( { 'error' : 'no-on-ebuio' } ) , content_type = "application/j... |
def set_options ( self , options ) :
"""options = [ {
' product _ option ' : instance of ProductFinalOption ,
' product _ final ' : instance of ProductFinal ,
' quantity ' : Float""" | with transaction . atomic ( ) :
for option in options :
opt = self . line_basket_option_sales . filter ( product_option = option [ 'product_option' ] ) . first ( )
if opt : # edit
change = False
if opt . quantity != option [ 'quantity' ] :
opt . quantity = opt... |
def _name_messages_complete ( self ) :
"""Check if all name messages have been received""" | for channel in range ( 1 , self . number_of_channels ( ) + 1 ) :
try :
for name_index in range ( 1 , 4 ) :
if not isinstance ( self . _name_data [ channel ] [ name_index ] , str ) :
return False
except Exception :
return False
return True |
def print_context_info ( self ) :
"""Prints moderngl context info .""" | print ( "Context Version:" )
print ( 'ModernGL:' , moderngl . __version__ )
print ( 'vendor:' , self . ctx . info [ 'GL_VENDOR' ] )
print ( 'renderer:' , self . ctx . info [ 'GL_RENDERER' ] )
print ( 'version:' , self . ctx . info [ 'GL_VERSION' ] )
print ( 'python:' , sys . version )
print ( 'platform:' , sys . platfo... |
def close ( self ) :
"""Closes this VPCS VM .""" | if not ( yield from super ( ) . close ( ) ) :
return False
nio = self . _ethernet_adapter . get_nio ( 0 )
if isinstance ( nio , NIOUDP ) :
self . manager . port_manager . release_udp_port ( nio . lport , self . _project )
if self . _local_udp_tunnel :
self . manager . port_manager . release_udp_port ( self ... |
def resolve_json_id ( self , json_id , allow_no_match = False ) :
"""Given an id found in scraped JSON , return a DB id for the object .
params :
json _ id : id from json
allow _ no _ match : just return None if id can ' t be resolved
returns :
database id
raises :
ValueError if id couldn ' t be resol... | if not json_id :
return None
if json_id . startswith ( '~' ) : # keep caches of all the pseudo - ids to avoid doing 1000s of lookups during import
if json_id not in self . pseudo_id_cache :
spec = get_pseudo_id ( json_id )
spec = self . limit_spec ( spec )
if isinstance ( spec , Q ) :
... |
def make_model ( self , grounding_ontology = 'UN' , grounding_threshold = None ) :
"""Return a networkx MultiDiGraph representing a causal analysis graph .
Parameters
grounding _ ontology : Optional [ str ]
The ontology from which the grounding should be taken
( e . g . UN , FAO )
grounding _ threshold : ... | if grounding_threshold is not None :
self . grounding_threshold = grounding_threshold
self . grounding_ontology = grounding_ontology
# Filter to Influence Statements which are currently supported
statements = [ stmt for stmt in self . statements if isinstance ( stmt , Influence ) ]
# Initialize graph
self . CAG = n... |
def qualname ( self ) -> str :
"""Returns the fully qualified name of the class - under - construction , if possible ,
otherwise just the class name .""" | if self . module :
return self . module + '.' + self . name
return self . name |
def find_codon_mismatches ( sbjct_start , sbjct_seq , qry_seq ) :
"""This function takes two alligned sequence ( subject and query ) , and
the position on the subject where the alignment starts . The sequences
are compared codon by codon . If a mis matches is found it is saved in
' mis _ matches ' . If a gap ... | mis_matches = [ ]
# Find start pos of first codon in frame , i _ start
codon_offset = ( sbjct_start - 1 ) % 3
i_start = 0
if codon_offset != 0 :
i_start = 3 - codon_offset
sbjct_start = sbjct_start + i_start
# Set sequences in frame
sbjct_seq = sbjct_seq [ i_start : ]
qry_seq = qry_seq [ i_start : ]
# Find codon nu... |
def save_profile ( self , userdata , data ) :
"""Save user profile modifications""" | result = userdata
error = False
# Check if updating username .
if not userdata [ "username" ] and "username" in data :
if re . match ( r"^[-_|~0-9A-Z]{4,}$" , data [ "username" ] , re . IGNORECASE ) is None :
error = True
msg = _ ( "Invalid username format." )
elif self . database . users . find... |
def add_attribute ( self , attrkey , attrvalue , append = False , oldvalue = None ) :
"""Add an attribute to this feature .
Feature attributes are stored as nested dictionaries .
Each feature can only have one ID , so ID attribute mapping is ' string '
to ' string ' . All other attributes can have multiple va... | # Handle ID / Parent relationships
if attrkey == 'ID' :
if self . children is not None :
oldid = self . get_attribute ( 'ID' )
for child in self . children :
child . add_attribute ( 'Parent' , attrvalue , oldvalue = oldid )
self . _attrs [ attrkey ] = attrvalue
if self . is_multi... |
def main ( ) :
'''Main routine .''' | # validate command line arguments
argparser = argparse . ArgumentParser ( )
argparser . add_argument ( '--uri' , '-u' , required = True , action = 'store' , help = 'Template URI' )
argparser . add_argument ( '--params' , '-f' , required = True , action = 'store' , help = 'Parameters json file' )
argparser . add_argumen... |
def writeConfig ( self ) :
"""Persists the value of the : attr : ` AbstractJobStore . config ` attribute to the
job store , so that it can be retrieved later by other instances of this class .""" | with self . writeSharedFileStream ( 'config.pickle' , isProtected = False ) as fileHandle :
pickle . dump ( self . __config , fileHandle , pickle . HIGHEST_PROTOCOL ) |
def init_db ( ) :
"""Initialize a new database with the default tables for chill .
Creates the following tables :
Chill
Node
Node _ Node
Route
Query
Template""" | with current_app . app_context ( ) :
for filename in CHILL_CREATE_TABLE_FILES :
db . execute ( text ( fetch_query_string ( filename ) ) ) |
def init_with_keytab ( self ) :
"""Initialize credential cache with keytab""" | creds_opts = { 'usage' : 'initiate' , 'name' : self . _cleaned_options [ 'principal' ] , }
store = { }
if self . _cleaned_options [ 'keytab' ] != DEFAULT_KEYTAB :
store [ 'client_keytab' ] = self . _cleaned_options [ 'keytab' ]
if self . _cleaned_options [ 'ccache' ] != DEFAULT_CCACHE :
store [ 'ccache' ] = sel... |
def write_record ( self , event_str ) :
"""Writes a serialized event to file .""" | header = struct . pack ( 'Q' , len ( event_str ) )
header += struct . pack ( 'I' , masked_crc32c ( header ) )
footer = struct . pack ( 'I' , masked_crc32c ( event_str ) )
self . _writer . write ( header + event_str + footer ) |
def scales ( scale = None ) :
"""Displays a color scale ( HTML )
Parameters :
scale : str
Color scale name
If no scale name is provided then all scales are returned
( max number for each scale )
If scale = ' all ' then all scale combinations available
will be returned
Example :
scales ( ' accent '... | if scale :
if scale == 'all' :
display ( HTML ( cl . to_html ( _scales ) ) )
else :
display ( HTML ( cl . to_html ( get_scales ( scale ) ) ) )
else :
s = ''
keys = list ( _scales_names . keys ( ) )
keys . sort ( )
for k in keys :
scale = get_scales ( k )
s += '<di... |
def _do_anchor ( self , anchor ) :
"""Collects preposition anchors and attachments in a dictionary .
Once the dictionary has an entry for both the anchor and the attachment , they are linked .""" | if anchor :
for x in anchor . split ( "-" ) :
A , P = None , None
if x . startswith ( "A" ) and len ( self . chunks ) > 0 : # anchor
A , P = x , x . replace ( "A" , "P" )
self . _anchors [ A ] = self . chunks [ - 1 ]
if x . startswith ( "P" ) and len ( self . pnp ) > ... |
def description_for_number ( numobj , lang , script = None , region = None ) :
"""Return a text description of a PhoneNumber object for the given language .
The description might consist of the name of the country where the phone
number is from and / or the name of the geographical area the phone number
is fr... | ntype = number_type ( numobj )
if ntype == PhoneNumberType . UNKNOWN :
return ""
elif not is_number_type_geographical ( ntype , numobj . country_code ) :
return country_name_for_number ( numobj , lang , script , region )
return description_for_valid_number ( numobj , lang , script , region ) |
def buildFinished ( self , build , wfb ) :
"""This is called when the Build has finished ( either success or
failure ) . Any exceptions during the build are reported with
results = FAILURE , not with an errback .""" | # by the time we get here , the Build has already released the worker ,
# which will trigger a check for any now - possible build requests
# ( maybeStartBuilds )
results = build . build_status . getResults ( )
self . building . remove ( build )
if results == RETRY :
d = self . _resubmit_buildreqs ( build )
d . ... |
def times ( A , b , offset = 0 ) :
"""Times the view of A with b in place ( ! ) .
Returns modified A
Broadcasting is allowed , thus b can be scalar .
if offset is not zero , make sure b is of right shape !
: param ndarray A : 2 dimensional array
: param ndarray - like b : either one dimensional or scalar ... | return _diag_ufunc ( A , b , offset , np . multiply ) |
def generate_sky_catalog ( image , refwcs , ** kwargs ) :
"""Build source catalog from input image using photutils .
This script borrows heavily from build _ source _ catalog .
The catalog returned by this function includes sources found in all chips
of the input image with the positions translated to the coo... | # Extract source catalogs for each chip
source_cats = generate_source_catalog ( image , ** kwargs )
# Build source catalog for entire image
master_cat = None
numSci = countExtn ( image , extname = 'SCI' )
# if no refwcs specified , build one now . . .
if refwcs is None :
refwcs = build_reference_wcs ( [ image ] )
f... |
def whoami ( self ) :
"""Return a Deferred which fires with a 2 - tuple of ( dotted quad ip , port
number ) .""" | def cbWhoAmI ( result ) :
return result [ 'address' ]
return self . callRemote ( WhoAmI ) . addCallback ( cbWhoAmI ) |
def ToScriptHash ( data , unhex = True ) :
"""Get a script hash of the data .
Args :
data ( bytes ) : data to hash .
unhex ( bool ) : ( Default ) True . Set to unhexlify the stream . Use when the bytes are not raw bytes ; i . e . b ' aabb '
Returns :
UInt160 : script hash .""" | if len ( data ) > 1 and unhex :
data = binascii . unhexlify ( data )
return UInt160 ( data = binascii . unhexlify ( bytes ( Crypto . Hash160 ( data ) , encoding = 'utf-8' ) ) ) |
def get_render_data ( self , ** kwargs ) :
"""Adds the model _ name to the context , then calls super .""" | kwargs [ 'model_name' ] = self . model_name
kwargs [ 'model_name_plural' ] = self . model_name_plural
return super ( ModelCMSView , self ) . get_render_data ( ** kwargs ) |
def ts_stream_keys ( self , table , timeout = None ) :
"""Streams keys from a timeseries table , returning an iterator that
yields lists of keys .""" | msg_code = riak . pb . messages . MSG_CODE_TS_LIST_KEYS_REQ
codec = self . _get_codec ( msg_code )
msg = codec . encode_timeseries_listkeysreq ( table , timeout )
self . _send_msg ( msg . msg_code , msg . data )
return PbufTsKeyStream ( self , codec , self . _ts_convert_timestamp ) |
def _start_browsing_some_sites ( self ) :
'''Starts browsing some sites .
Raises :
NoBrowsersAvailable if none available''' | # acquire _ multi ( ) raises NoBrowsersAvailable if none available
browsers = self . _browser_pool . acquire_multi ( ( self . _browser_pool . num_available ( ) + 1 ) // 2 )
try :
sites = self . _frontier . claim_sites ( len ( browsers ) )
except :
self . _browser_pool . release_all ( browsers )
raise
for i ... |
def cues ( self , rename_inhibitors = False ) :
"""Returns stimuli and inhibitors species of this experimental setup
Parameters
rename _ inhibitors : boolean
If True , rename inhibitors with an ending ' i ' as in MIDAS files .
Returns
list
List of species names in order : first stimuli followed by inhib... | if rename_inhibitors :
return self . stimuli + [ i + 'i' for i in self . inhibitors ]
else :
return self . stimuli + self . inhibitors |
def vec_angle ( vec1 , vec2 ) :
"""Angle between two R - dimensional vectors .
Angle calculated as :
. . math : :
\\ arccos \\ left [
\\ frac { \\ mathsf { vec1 } \ cdot \\ mathsf { vec2 } }
{ \\ left \\ | \\ mathsf { vec1} \\ right \\ |
\\ left \\ | \\ mathsf { vec2} \\ right \\ | }
\\ right ]
Para... | # Imports
import numpy as np
from scipy import linalg as spla
from . . const import PRM
# Check shape and equal length
if len ( vec1 . shape ) != 1 :
raise ValueError ( "'vec1' is not a vector" )
# # end if
if len ( vec2 . shape ) != 1 :
raise ValueError ( "'vec2' is not a vector" )
# # end if
if vec1 . shape [... |
async def close ( self ) -> None :
"""Explicit exit . Closes pool . For use when keeping pool open across multiple calls .""" | LOGGER . debug ( 'NodePool.close >>>' )
if not self . handle :
LOGGER . warning ( 'Abstaining from closing pool %s: already closed' , self . name )
else :
await pool . close_pool_ledger ( self . handle )
self . _handle = None
LOGGER . debug ( 'NodePool.close <<<' ) |
def ccmod_xstep ( k ) :
"""Do the X step of the ccmod stage . The only parameter is the slice
index ` k ` and there are no return values ; all inputs and outputs are
from and to global variables .""" | YU = mp_D_Y - mp_D_U [ k ]
b = mp_ZSf [ k ] + mp_drho * sl . rfftn ( YU , None , mp_cri . axisN )
Xf = sl . solvedbi_sm ( mp_Zf [ k ] , mp_drho , b , axis = mp_cri . axisM )
mp_D_X [ k ] = sl . irfftn ( Xf , mp_cri . Nv , mp_cri . axisN ) |
def prin ( * args , ** kwargs ) :
r"""Like ` ` print ` ` , but a function . I . e . prints out all arguments as
` ` print ` ` would do . Specify output stream like this : :
print ( ' ERROR ' , ` out = " sys . stderr " ` ` ) .""" | print >> kwargs . get ( 'out' , None ) , " " . join ( [ str ( arg ) for arg in args ] ) |
def ensure_specification_cols_are_in_dataframe ( specification , dataframe ) :
"""Checks whether each column in ` specification ` is in ` dataframe ` . Raises
ValueError if any of the columns are not in the dataframe .
Parameters
specification : OrderedDict .
Keys are a proper subset of the columns in ` dat... | # Make sure specification is an OrderedDict
try :
assert isinstance ( specification , OrderedDict )
except AssertionError :
raise TypeError ( "`specification` must be an OrderedDict." )
# Make sure dataframe is a pandas dataframe
assert isinstance ( dataframe , pd . DataFrame )
problem_cols = [ ]
dataframe_cols... |
def probe_response ( msg , arg ) :
"""Process responses from from the query sent by genl _ ctrl _ probe _ by _ name ( ) .
https : / / github . com / thom311 / libnl / blob / libnl3_2_25 / lib / genl / ctrl . c # L203
Process returned messages , filling out the missing information in the genl _ family structure ... | tb = dict ( ( i , None ) for i in range ( CTRL_ATTR_MAX + 1 ) )
nlh = nlmsg_hdr ( msg )
ret = arg
if genlmsg_parse ( nlh , 0 , tb , CTRL_ATTR_MAX , ctrl_policy ) :
return NL_SKIP
if tb [ CTRL_ATTR_FAMILY_ID ] :
genl_family_set_id ( ret , nla_get_u16 ( tb [ CTRL_ATTR_FAMILY_ID ] ) )
if tb [ CTRL_ATTR_MCAST_GROUP... |
def parse_runway_config ( self ) :
"""Read and parse runway . yml .""" | if not os . path . isfile ( self . runway_config_path ) :
LOGGER . error ( "Runway config file was not found (looking for " "%s)" , self . runway_config_path )
sys . exit ( 1 )
with open ( self . runway_config_path ) as data_file :
return yaml . safe_load ( data_file ) |
def _validate_metadata ( metadata_props ) :
'''Validate metadata properties and possibly show warnings or throw exceptions .
: param metadata _ props : A dictionary of metadata properties , with property names and values ( see : func : ` ~ onnxmltools . utils . metadata _ props . add _ metadata _ props ` for exam... | if len ( CaseInsensitiveDict ( metadata_props ) ) != len ( metadata_props ) :
raise RuntimeError ( 'Duplicate metadata props found' )
for key , value in metadata_props . items ( ) :
valid_values = KNOWN_METADATA_PROPS . get ( key )
if valid_values and value . lower ( ) not in valid_values :
warnings... |
def set_data ( self , data = None , ** kwargs ) :
'''Read data into memory , applying all actions in queue .
Additionally , update queue and history .''' | if data is None :
data = self . get_data ( ** kwargs )
setattr ( self , '_data' , data )
self . history += self . queue
self . queue = [ ] |
def rlmb_tiny_sv2p ( ) :
"""Tiny setting with a tiny sv2p model .""" | hparams = rlmb_ppo_tiny ( )
hparams . generative_model = "next_frame_sv2p"
hparams . generative_model_params = "next_frame_sv2p_tiny"
hparams . grayscale = False
return hparams |
def matrix_mult_opt_order ( M ) :
"""Matrix chain multiplication optimal order
: param M : list of matrices
: returns : matrices opt , arg , such that opt [ i ] [ j ] is the optimal number of
operations to compute M [ i ] * . . . * M [ j ] when done in the order
( M [ i ] * . . . * M [ k ] ) * ( M [ k + 1 ]... | n = len ( M )
r = [ len ( Mi ) for Mi in M ]
c = [ len ( Mi [ 0 ] ) for Mi in M ]
opt = [ [ 0 for j in range ( n ) ] for i in range ( n ) ]
arg = [ [ None for j in range ( n ) ] for i in range ( n ) ]
for j_i in range ( 1 , n ) : # loop on i , j of increasing j - i = j _ i
for i in range ( n - j_i ) :
j = i... |
def read_micromanager_metadata ( fh ) :
"""Read MicroManager non - TIFF settings from open file and return as dict .
The settings can be used to read image data without parsing the TIFF file .
Raise ValueError if the file does not contain valid MicroManager metadata .""" | fh . seek ( 0 )
try :
byteorder = { b'II' : '<' , b'MM' : '>' } [ fh . read ( 2 ) ]
except IndexError :
raise ValueError ( 'not a MicroManager TIFF file' )
result = { }
fh . seek ( 8 )
( index_header , index_offset , display_header , display_offset , comments_header , comments_offset , summary_header , summary_... |
def isPrefixOf ( self , other ) :
"""Indicate if this | ASN . 1 | object is a prefix of other | ASN . 1 | object .
Parameters
other : | ASN . 1 | object
| ASN . 1 | object
Returns
: : class : ` bool `
: class : ` True ` if this | ASN . 1 | object is a parent ( e . g . prefix ) of the other | ASN . 1 | o... | l = len ( self )
if l <= len ( other ) :
if self . _value [ : l ] == other [ : l ] :
return True
return False |
def _must_not_custom_query ( issn ) :
"""Este metodo constroi a lista de filtros por título de periódico que
será aplicada na pesquisa boleana como restrição " must _ not " .
A lista de filtros é coletada do template de pesquisa customizada
do periódico , quanto este template existir .""" | custom_queries = set ( [ utils . cleanup_string ( i ) for i in journal_titles . load ( issn ) . get ( 'must_not' , [ ] ) ] )
for item in custom_queries :
query = { "match" : { "reference_source_cleaned" : item } }
yield query |
def generate_plaintext_random ( plain_vocab , distribution , train_samples , length ) :
"""Generates samples of text from the provided vocabulary .
Args :
plain _ vocab : vocabulary .
distribution : distribution .
train _ samples : samples for training .
length : length .
Returns :
train _ indices ( n... | if distribution is not None :
assert len ( distribution ) == len ( plain_vocab )
train_indices = np . random . choice ( range ( len ( plain_vocab ) ) , ( train_samples , length ) , p = distribution )
return train_indices |
def importcmd ( self , image_path , input_source ) :
'''import will import ( stdin ) to the image
Parameters
image _ path : path to image to import to .
input _ source : input source or file
import _ type : if not specified , imports whatever function is given''' | from spython . utils import check_install
check_install ( )
cmd = [ 'singularity' , 'image.import' , image_path , input_source ]
output = self . run_command ( cmd , sudo = False )
self . println ( output )
return image_path |
def register_forward_hook ( self , hook ) :
r"""Registers a forward hook on the block .
The hook function is called immediately after : func : ` forward ` .
It should not modify the input or output .
Parameters
hook : callable
The forward hook function of form ` hook ( block , input , output ) - > None ` ... | handle = HookHandle ( )
handle . attach ( self . _forward_hooks , hook )
return handle |
def _is_surrounded ( self , b ) :
"""Perform a wrapped LTE comparison only considering the SI bounds
: param a : The first operand
: param b : The second operand
: return : True if a < = b , False otherwise""" | a = self
if a . is_empty :
return True
if a . is_top and b . is_top :
return True
elif a . is_top :
return False
elif b . is_top :
return True
if b . _surrounds_member ( a . lower_bound ) and b . _surrounds_member ( a . upper_bound ) :
if ( ( b . lower_bound == a . lower_bound and b . upper_bound ==... |
def module_function ( string ) :
"""Load a function from a python module using a file name , function name
specification of format :
/ path / to / x . py : function _ name [ : parameter ]""" | parts = string . split ( ':' , 2 )
if len ( parts ) < 2 :
raise ValueError ( "Illegal specification. Should be module:function[:parameter]" )
module_path , function_name = parts [ : 2 ]
# Import the module
module_vars = { }
exec ( compile ( open ( module_path ) . read ( ) , module_path , 'exec' ) , module_vars )
tr... |
def returner ( ret ) :
'''Return data to a influxdb data store''' | serv = _get_serv ( ret )
# strip the ' return ' key to avoid data duplication in the database
json_return = salt . utils . json . dumps ( ret [ 'return' ] )
del ret [ 'return' ]
json_full_ret = salt . utils . json . dumps ( ret )
# create legacy request in case an InfluxDB 0.8 . x version is used
if "influxdb08" in ser... |
def filter_seq ( seq ) :
'''Examines unreserved sequences to see if they are prone to mutation . This
currently ignores solely - power - of - 2 guides with b > 3''' | if seq . res :
return None
n = nt . Factors ( seq . factors )
guide , s , t = aq . canonical_form ( n )
seq . guide = guide
# The target _ tau for the composite is at most the class minus extant prime factor count
cls = aq . get_class ( guide = guide )
num_larges = seq . factors . count ( 'P' )
upper_bound_tau = cl... |
def dict_merge ( dct , merge_dct ) :
"""Recursive dict merge . Inspired by : meth : ` ` dict . update ( ) ` ` , instead of
updating only top - level keys , dict _ merge recurses down into dicts nested
to an arbitrary depth , updating keys . The ` ` merge _ dct ` ` is merged into
` ` dct ` ` .
: param dct : ... | for key in merge_dct . keys ( ) :
if ( key in dct and isinstance ( dct [ key ] , dict ) and isinstance ( merge_dct [ key ] , collections . Mapping ) ) :
dict_merge ( dct [ key ] , merge_dct [ key ] )
else :
dct [ key ] = merge_dct [ key ] |
def terminate ( self ) :
"""Delete all files created by this index , invalidating ` self ` . Use with care .""" | try :
self . id2sims . terminate ( )
except :
pass
import glob
for fname in glob . glob ( self . fname + '*' ) :
try :
os . remove ( fname )
logger . info ( "deleted %s" % fname )
except Exception , e :
logger . warning ( "failed to delete %s: %s" % ( fname , e ) )
for val in sel... |
def create_token_review ( self , body , ** kwargs ) :
"""create a TokenReview
This method makes a synchronous HTTP request by default . To make an
asynchronous HTTP request , please pass async _ req = True
> > > thread = api . create _ token _ review ( body , async _ req = True )
> > > result = thread . get... | kwargs [ '_return_http_data_only' ] = True
if kwargs . get ( 'async_req' ) :
return self . create_token_review_with_http_info ( body , ** kwargs )
else :
( data ) = self . create_token_review_with_http_info ( body , ** kwargs )
return data |
def render_region_tools ( context , feincms_object , region , request = None ) :
"""{ % render _ region _ tools feincms _ page " main " request % }
skip rendering in standalone mode""" | if context . get ( 'standalone' , False ) or not feincms_object :
return { }
edit = False
if getattr ( settings , 'LEONARDO_USE_PAGE_ADMIN' , False ) :
request = context . get ( 'request' , None )
frontend_edit = request . COOKIES . get ( 'frontend_editing' , False )
if frontend_edit :
edit = Tr... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.