signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def remove_child ( self , child ) :
'''Remove child from ` ` Node ` ` object
Args :
` ` child ` ` ( ` ` Node ` ` ) : The child to remove''' | if not isinstance ( child , Node ) :
raise TypeError ( "child must be a Node" )
try :
self . children . remove ( child ) ;
child . parent = None
except :
raise RuntimeError ( "Attempting to remove non-existent child" ) |
def convert_block_dicts_to_string ( self , block_1st2nd , block_1st , block_2nd , block_3rd ) :
"""Takes into account whether we need to output all codon positions .""" | out = ""
# We need 1st and 2nd positions
if self . codon_positions in [ 'ALL' , '1st-2nd' ] :
for gene_code , seqs in block_1st2nd . items ( ) :
out += '>{0}_1st-2nd\n----\n' . format ( gene_code )
for seq in seqs :
out += seq
elif self . codon_positions == '1st' :
for gene_code , se... |
def add ( self , component : Union [ Component , Sequence [ Component ] ] ) -> None :
"""Add a widget to the grid in the next available cell .
Searches over columns then rows for available cells .
Parameters
components : bowtie . _ Component
A Bowtie widget instance .""" | try :
self [ Span ( * self . _available_cell ( ) ) ] = component
except NoUnusedCellsError :
span = list ( self . _spans . keys ( ) ) [ - 1 ]
self . _spans [ span ] += component |
def draw_no_data ( self ) :
"""Write the no data text to the svg""" | no_data = self . node ( self . graph . nodes [ 'text_overlay' ] , 'text' , x = self . graph . view . width / 2 , y = self . graph . view . height / 2 , class_ = 'no_data' )
no_data . text = self . graph . no_data_text |
def itermovieshash ( self ) :
"""Iterate over movies hash stored in the database .""" | cur = self . _db . firstkey ( )
while cur is not None :
yield cur
cur = self . _db . nextkey ( cur ) |
def bsp_traverse_inverted_level_order ( node : tcod . bsp . BSP , callback : Callable [ [ tcod . bsp . BSP , Any ] , None ] , userData : Any = 0 , ) -> None :
"""Traverse this nodes hierarchy with a callback .
. . deprecated : : 2.0
Use : any : ` BSP . inverted _ level _ order ` instead .""" | _bsp_traverse ( node . inverted_level_order ( ) , callback , userData ) |
def predict_topk ( self , dataset , output_type = "probability" , k = 3 , missing_value_action = 'auto' ) :
"""Return top - k predictions for the ` ` dataset ` ` , using the trained model .
Predictions are returned as an SFrame with three columns : ` id ` ,
` class ` , and ` probability ` , ` margin ` , or ` ra... | _check_categorical_option_type ( 'output_type' , output_type , [ 'rank' , 'margin' , 'probability' ] )
if missing_value_action == 'auto' :
missing_value_action = _sl . select_default_missing_value_policy ( self , 'predict' )
# Low latency path
if isinstance ( dataset , list ) :
return self . __proxy__ . fast_pr... |
def execute_locally ( self ) :
"""Runs the equivalent command locally in a blocking way .""" | # Make script file #
self . make_script ( )
# Do it #
with open ( self . kwargs [ 'out_file' ] , 'w' ) as handle :
sh . python ( self . script_path , _out = handle , _err = handle ) |
def get_app_voice ( self , item ) :
"""App voice
Returns the js menu compatible voice dict if the user
can see it , None otherwise""" | if item . get ( 'name' , None ) is None :
raise ImproperlyConfigured ( 'App menu voices must have a name key' )
if self . check_apps_permission ( [ item . get ( 'name' , None ) ] ) :
children = [ ]
if item . get ( 'models' , None ) is None :
for name , model in self . apps_dict [ item . get ( 'name'... |
def on_change ( self , server_description ) :
"""Process a new ServerDescription after an ismaster call completes .""" | # We do no I / O holding the lock .
with self . _lock : # Monitors may continue working on ismaster calls for some time
# after a call to Topology . close , so this method may be called at
# any time . Ensure the topology is open before processing the
# change .
# Any monitored server was definitely in the topology des... |
def escalate_incident ( self , incident , update_mask = None , subscriptions = None , tags = None , roles = None , artifacts = None , retry = google . api_core . gapic_v1 . method . DEFAULT , timeout = google . api_core . gapic_v1 . method . DEFAULT , metadata = None , ) :
"""Escalates an incident .
Example :
>... | # Wrap the transport method to add retry and timeout logic .
if "escalate_incident" not in self . _inner_api_calls :
self . _inner_api_calls [ "escalate_incident" ] = google . api_core . gapic_v1 . method . wrap_method ( self . transport . escalate_incident , default_retry = self . _method_configs [ "EscalateIncide... |
def InitPathInfos ( self , client_id , path_infos ) :
"""Initializes a collection of path info records for a client .
Unlike ` WritePathInfo ` , this method clears stat and hash histories of paths
associated with path info records . This method is intended to be used only
in the data migration scripts .
Arg... | self . ClearPathHistory ( client_id , path_infos )
self . WritePathInfos ( client_id , path_infos ) |
def run ( ) : # pylint : disable = too - many - branches
"""Main thread runner for all Duts .
: return : Nothing""" | Dut . _logger . debug ( "Start DUT communication" , extra = { 'type' : '<->' } )
while Dut . _run :
Dut . _sem . acquire ( )
try :
dut = Dut . _signalled_duts . pop ( )
# Check for pending requests
if dut . waiting_for_response is not None :
item = dut . waiting_for_response
... |
def plot ( self , dimension ) :
"""Plot barcode using matplotlib .""" | import matplotlib . pyplot as plt
life_lines = self . get_life_lines ( dimension )
x , y = zip ( * life_lines )
plt . scatter ( x , y )
plt . xlabel ( "Birth" )
plt . ylabel ( "Death" )
if self . max_life is not None :
plt . xlim ( [ 0 , self . max_life ] )
plt . title ( "Persistence Homology Dimension {}" . format... |
def _make_tempy_tag ( self , tag , attrs , void ) :
"""Searches in tempy . tags for the correct tag to use , if does not exists uses the TempyFactory to
create a custom tag .""" | tempy_tag_cls = getattr ( self . tempy_tags , tag . title ( ) , None )
if not tempy_tag_cls :
unknow_maker = [ self . unknown_tag_maker , self . unknown_tag_maker . Void ] [ void ]
tempy_tag_cls = unknow_maker [ tag ]
attrs = { Tag . _TO_SPECIALS . get ( k , k ) : v or True for k , v in attrs }
tempy_tag = temp... |
def trans_history ( self , from_ = None , count = None , from_id = None , end_id = None , order = None , since = None , end = None ) :
"""Returns the history of transactions .
To use this method you need a privilege of the info key .
: param int or None from _ : transaction ID , from which the display starts ( ... | return self . _trade_api_call ( 'TransHistory' , from_ = from_ , count = count , from_id = from_id , end_id = end_id , order = order , since = since , end = end ) |
def validate ( retval , func , args ) : # type : ( int , Any , Tuple [ Any , Any ] ) - > Optional [ Tuple [ Any , Any ] ]
"""Validate the returned value of a Xlib or XRANDR function .""" | if retval != 0 and not ERROR . details :
return args
err = "{}() failed" . format ( func . __name__ )
details = { "retval" : retval , "args" : args }
raise ScreenShotError ( err , details = details ) |
def qdii ( self , min_volume = 0 ) :
"""以字典形式返回QDII数据
: param min _ volume : 最小交易量 , 单位万元""" | # 添加当前的ctime
self . __qdii_url = self . __qdii_url . format ( ctime = int ( time . time ( ) ) )
# 请求数据
rep = requests . get ( self . __qdii_url )
# 获取返回的json字符串
fundjson = json . loads ( rep . text )
# 格式化返回的json字符串
data = self . formatjisilujson ( fundjson )
data = { x : y for x , y in data . items ( ) if y [ "notes" ... |
def split_conditional ( property ) :
"""If ' property ' is conditional property , returns
condition and the property , e . g
< variant > debug , < toolset > gcc : < inlining > full will become
< variant > debug , < toolset > gcc < inlining > full .
Otherwise , returns empty string .""" | assert isinstance ( property , basestring )
m = __re_split_conditional . match ( property )
if m :
return ( m . group ( 1 ) , '<' + m . group ( 2 ) )
return None |
def allowed_values ( self ) :
"""Return a list of allowed values .""" | if self . _allowed_values is None :
self . _allowed_values = ValueList ( )
for val in self . scraper . _fetch_allowed_values ( self ) :
if isinstance ( val , DimensionValue ) :
self . _allowed_values . append ( val )
else :
self . _allowed_values . append ( DimensionValue... |
def _build_option_description ( k ) :
"""Builds a formatted description of a registered option and prints it .""" | o = _get_registered_option ( k )
d = _get_deprecated_option ( k )
buf = [ '{} ' . format ( k ) ]
if o . doc :
doc = '\n' . join ( o . doc . strip ( ) . splitlines ( ) )
else :
doc = 'No description available.'
buf . append ( doc )
if o :
buf . append ( '\n [default: {}] [currently: {}]' . format ( o . de... |
def _validate_unarmor ( self , certs , var_name ) :
"""Takes a list of byte strings or asn1crypto . x509 . Certificates objects ,
validates and loads them while unarmoring any PEM - encoded contents
: param certs :
A list of byte strings or asn1crypto . x509 . Certificate objects
: param var _ name :
A un... | output = [ ]
for cert in certs :
if isinstance ( cert , x509 . Certificate ) :
output . append ( cert )
else :
if not isinstance ( cert , byte_cls ) :
raise TypeError ( pretty_message ( '''
%s must contain only byte strings or
asn1crypt... |
def ceiling_height ( self , value = 99999.0 ) :
"""Corresponds to IDD Field ` ceiling _ height ` This is the value for
ceiling height in m . ( 77777 is unlimited ceiling height . 88888 is
cirroform ceiling . ) It is not currently used in EnergyPlus
calculations .
Args :
value ( float ) : value for IDD Fie... | if value is not None :
try :
value = float ( value )
except ValueError :
raise ValueError ( 'value {} need to be of type float ' 'for field `ceiling_height`' . format ( value ) )
self . _ceiling_height = value |
def is_transition_metal ( self ) :
"""True if element is a transition metal .""" | ns = list ( range ( 21 , 31 ) )
ns . extend ( list ( range ( 39 , 49 ) ) )
ns . append ( 57 )
ns . extend ( list ( range ( 72 , 81 ) ) )
ns . append ( 89 )
ns . extend ( list ( range ( 104 , 113 ) ) )
return self . Z in ns |
def enrich_pubmed_citations ( manager , graph , group_size : Optional [ int ] = None , sleep_time : Optional [ int ] = None , ) -> Set [ str ] :
"""Overwrite all PubMed citations with values from NCBI ' s eUtils lookup service .
Sets authors as list , so probably a good idea to run : func : ` pybel _ tools . muta... | pmids = get_pubmed_identifiers ( graph )
pmid_data , errors = get_citations_by_pmids ( manager , pmids = pmids , group_size = group_size , sleep_time = sleep_time )
for u , v , k in filter_edges ( graph , has_pubmed ) :
pmid = graph [ u ] [ v ] [ k ] [ CITATION ] [ CITATION_REFERENCE ] . strip ( )
if pmid not i... |
def get_branch_details ( repo : GithubRepository , branch : str ) -> Any :
"""References :
https : / / developer . github . com / v3 / repos / branches / # get - branch""" | url = ( "https://api.github.com/repos/{}/{}/branches/{}" "?access_token={}" . format ( repo . organization , repo . name , branch , repo . access_token ) )
response = requests . get ( url )
if response . status_code != 200 :
raise RuntimeError ( 'Failed to get branch details. Code: {}. Content: {}.' . format ( resp... |
def set_file_path ( self , filePath ) :
"""Set the file path that needs to be locked .
: Parameters :
# . filePath ( None , path ) : The file that needs to be locked . When given and a lock
is acquired , the file will be automatically opened for writing or reading
depending on the given mode . If None is gi... | if filePath is not None :
assert isinstance ( filePath , basestring ) , "filePath must be None or string"
filePath = str ( filePath )
self . __filePath = filePath |
def setProperty ( self , orgresource , protect , dummy = 7046 ) :
"""SetProperty
Args :
orgresource : File path
protect : ' Y ' or ' N ' , 중요 표시
Returns :
Integer number : # of version list
False : Failed to get property""" | url = nurls [ 'setProperty' ]
data = { 'userid' : self . user_id , 'useridx' : self . useridx , 'orgresource' : orgresource , 'protect' : protect , 'dummy' : dummy , }
r = self . session . post ( url = url , data = data )
return resultManager ( r . text ) |
def save ( self , obj ) :
"""save an object
: param obj : the object
: return : the saved object""" | if obj not in self . session :
self . session . add ( obj )
else :
obj = self . session . merge ( obj )
self . session . flush ( )
self . session . refresh ( obj )
return obj |
def frame_from_firmware ( self , firmware ) :
'''extract information from firmware , return pretty string to user''' | # see Tools / scripts / generate - manifest for this map :
frame_to_mavlink_dict = { "quad" : "QUADROTOR" , "hexa" : "HEXAROTOR" , "y6" : "ARDUPILOT_Y6" , "tri" : "TRICOPTER" , "octa" : "OCTOROTOR" , "octa-quad" : "ARDUPILOT_OCTAQUAD" , "heli" : "HELICOPTER" , "Plane" : "FIXED_WING" , "Tracker" : "ANTENNA_TRACKER" , "R... |
def domain_urlize ( value ) :
"""Returns an HTML link to the supplied URL , but only using the domain as the
text . Strips ' www . ' from the start of the domain , if present .
e . g . if ` my _ url ` is ' http : / / www . example . org / foo / ' then :
{ { my _ url | domain _ urlize } }
returns :
< a hre... | parsed_uri = urlparse ( value )
domain = '{uri.netloc}' . format ( uri = parsed_uri )
if domain . startswith ( 'www.' ) :
domain = domain [ 4 : ]
return format_html ( '<a href="{}" rel="nofollow">{}</a>' , value , domain ) |
def mapstr_to_list ( mapstr ) :
"""Convert an ASCII map string with rows to a list of strings , 1 string per row .""" | maplist = [ ]
with StringIO ( mapstr ) as infile :
for row in infile :
maplist . append ( row . strip ( ) )
return maplist |
def _init_humidity ( self ) :
"""Internal . Initialises the humidity sensor via RTIMU""" | if not self . _humidity_init :
self . _humidity_init = self . _humidity . humidityInit ( )
if not self . _humidity_init :
raise OSError ( 'Humidity Init Failed' ) |
def get_precision ( self ) :
""": returns : the ratio part of the dominant label for each unit .
: rtype : 2D : class : ` numpy . ndarray `""" | assert self . classifier is not None , 'not calibrated'
arr = np . zeros ( ( self . _som . nrows , self . _som . ncols ) )
for ij , ( lbl , p ) in self . classifier . items ( ) :
arr [ ij ] = p
return arr |
def get_access_token ( tenant_id , application_id , application_secret ) :
'''get an Azure access token using the adal library .
Args :
tenant _ id ( str ) : Tenant id of the user ' s account .
application _ id ( str ) : Application id of a Service Principal account .
application _ secret ( str ) : Applicat... | context = adal . AuthenticationContext ( get_auth_endpoint ( ) + tenant_id , api_version = None )
token_response = context . acquire_token_with_client_credentials ( get_resource_endpoint ( ) , application_id , application_secret )
return token_response . get ( 'accessToken' ) |
def unescape ( s , quote = False ) :
"""The opposite of the cgi . escape function .
Replace escaped characters ' & amp ; ' , ' & lt ; ' and ' & gt ; ' with the corresponding
regular characters . If the optional flag quote is true , the escaped quotation
mark character ( ' & quot ; ' ) is also translated .""" | s = s . replace ( '<' , '<' )
s = s . replace ( '>' , '>' )
if quote :
s = s . replace ( '"' , '"' )
s = s . replace ( '&' , '&' )
return s |
def remove_empties ( variable ) :
"""Remove empty objects from the * variable * ' s attrs .""" | import h5py
for key , val in variable . attrs . items ( ) :
if isinstance ( val , h5py . _hl . base . Empty ) :
variable . attrs . pop ( key )
return variable |
def InferUserAndSubjectFromUrn ( self ) :
"""Infers user name and subject urn from self . urn .""" | _ , cron_str , cron_job_name , user , _ = self . urn . Split ( 5 )
if cron_str != "cron" :
raise access_control . UnauthorizedAccess ( "Approval object has invalid urn %s." % self . urn , requested_access = self . token . requested_access )
return ( user , aff4 . ROOT_URN . Add ( "cron" ) . Add ( cron_job_name ) ) |
def get_forum ( self ) :
"""Returns the forum to consider .""" | if not hasattr ( self , 'forum' ) :
self . forum = get_object_or_404 ( Forum , pk = self . kwargs [ 'pk' ] )
return self . forum |
def radiance2tb ( self , rad ) :
"""Get the Tb from the radiance using the simple non - linear regression
method .
rad : Radiance in units = ' mW / m ^ 2 sr ^ - 1 ( cm ^ - 1 ) ^ - 1'""" | # Tb = C2 * νc / { α * log [ C1 * νc * * 3 / L + 1 ] } - β / α
# C1 = 2 * h * c * * 2 and C2 = hc / k
c_1 = 2 * H_PLANCK * C_SPEED ** 2
c_2 = H_PLANCK * C_SPEED / K_BOLTZMANN
vc_ = SEVIRI [ self . bandname ] [ self . platform_name ] [ 0 ]
# Multiply by 100 to get SI units !
vc_ *= 100.0
alpha = SEVIRI [ self . bandname... |
def nvmlDeviceGetBridgeChipInfo ( handle ) :
r"""* Get Bridge Chip Information for all the bridge chips on the board .
* For all fully supported products .
* Only applicable to multi - GPU products .
* @ param device The identifier of the target device
* @ param bridgeHierarchy Reference to the returned bri... | bridgeHierarchy = c_nvmlBridgeChipHierarchy_t ( )
fn = _nvmlGetFunctionPointer ( "nvmlDeviceGetBridgeChipInfo" )
ret = fn ( handle , byref ( bridgeHierarchy ) )
_nvmlCheckReturn ( ret )
return bytes_to_str ( bridgeHierarchy ) |
def cancel ( self ) :
"""Cancel the consumer and clean up resources associated with it .
Consumers that are canceled are allowed to finish processing any
messages before halting .
Returns :
defer . Deferred : A deferred that fires when the consumer has finished
processing any message it was in the middle ... | # Remove it from protocol and factory so it doesn ' t restart later .
try :
del self . _protocol . _consumers [ self . queue ]
except ( KeyError , AttributeError ) :
pass
try :
del self . _protocol . factory . _consumers [ self . queue ]
except ( KeyError , AttributeError ) :
pass
# Signal to the _ read... |
def get_dip ( self ) :
"""Return the fault dip as the average dip over the mesh .
The average dip is defined as the weighted mean inclination
of all the mesh cells . See
: meth : ` openquake . hazardlib . geo . mesh . RectangularMesh . get _ mean _ inclination _ and _ azimuth `
: returns :
The average dip... | # uses the same approach as in simple fault surface
if self . dip is None :
mesh = self . mesh
self . dip , self . strike = mesh . get_mean_inclination_and_azimuth ( )
return self . dip |
def all_pkgs ( self ) :
"""Return a list of all packages .""" | if not self . packages :
self . packages = self . get_pkg_list ( )
return self . packages |
def format ( self , record ) :
'''Format the log record to include exc _ info if the handler is enabled for a specific log level''' | formatted_record = super ( ExcInfoOnLogLevelFormatMixIn , self ) . format ( record )
exc_info_on_loglevel = getattr ( record , 'exc_info_on_loglevel' , None )
exc_info_on_loglevel_formatted = getattr ( record , 'exc_info_on_loglevel_formatted' , None )
if exc_info_on_loglevel is None and exc_info_on_loglevel_formatted ... |
def parse_emails ( self , email_filename , index = 0 ) :
"""Generator function that parse and extract emails from the file
` email _ filename ` starting from the position ` index ` .
Yield : An instance of ` mailbox . mboxMessage ` for each email in the
file .""" | self . log ( "Parsing email dump: %s." % email_filename )
mbox = mailbox . mbox ( email_filename , factory = CustomMessage )
# Get each email from mbox file
# The following implementation was used because the object
# mbox does not support slicing . Converting the object to a
# tuple ( as represented in the code down h... |
def available_backups ( self ) :
"""The backups response contains what backups are available to be restored .""" | if not hasattr ( self , '_avail_backups' ) :
result = self . _client . get ( "{}/backups" . format ( Instance . api_endpoint ) , model = self )
if not 'automatic' in result :
raise UnexpectedResponseError ( 'Unexpected response loading available backups!' , json = result )
automatic = [ ]
for a ... |
def get_shell ( pid = None , max_depth = 6 ) :
"""Get the shell that the supplied pid or os . getpid ( ) is running in .""" | if not pid :
pid = os . getpid ( )
processes = dict ( _iter_process ( ) )
def check_parent ( pid , lvl = 0 ) :
ppid = processes [ pid ] . get ( 'parent_pid' )
shell_name = _get_executable ( processes . get ( ppid ) )
if shell_name in SHELL_NAMES :
return ( shell_name , processes [ ppid ] [ 'exec... |
def get_status_job ( self , id_job , hub = None , group = None , project = None , access_token = None , user_id = None ) :
"""Get the status about a job , by its id""" | if access_token :
self . req . credential . set_token ( access_token )
if user_id :
self . req . credential . set_user_id ( user_id )
if not self . check_credentials ( ) :
respond = { }
respond [ "status" ] = 'Error'
respond [ "error" ] = "Not credentials valid"
return respond
if not id_job :
... |
def stopwatch_now ( ) :
"""Get a timevalue for interval comparisons
When possible it is a monotonic clock to prevent backwards time issues .""" | if six . PY2 :
now = time . time ( )
else :
now = time . monotonic ( )
return now |
def load_plugins ( self ) :
"""Load external plugins .
Custodian is intended to interact with internal and external systems
that are not suitable for embedding into the custodian code base .""" | try :
from pkg_resources import iter_entry_points
except ImportError :
return
for ep in iter_entry_points ( group = "custodian.%s" % self . plugin_type ) :
f = ep . load ( )
f ( ) |
def keys ( self , desc = None ) :
'''numpy asarray does not copy data''' | res = asarray ( self . rc ( 'index' ) )
if desc == True :
return reversed ( res )
else :
return res |
def sexagesimal ( sexathang , latlon , form = 'DDD' ) :
"""Arguments :
sexathang : ( float ) , - 15.560615 ( negative = South ) , - 146.241122 ( negative = West ) # Apataki Carenage
latlon : ( str ) ' lat ' | ' lon '
form : ( str ) , ' DDD ' | ' DMM ' | ' DMS ' , decimal Degrees , decimal Minutes , decimal Se... | cardinal = 'O'
if not isinstance ( sexathang , float ) :
sexathang = 'n/a'
return sexathang
if latlon == 'lon' :
if sexathang > 0.0 :
cardinal = 'E'
if sexathang < 0.0 :
cardinal = 'W'
if latlon == 'lat' :
if sexathang > 0.0 :
cardinal = 'N'
if sexathang < 0.0 :
c... |
def _expand_sources ( sources ) :
'''Expands a user - provided specification of source files into a list of paths .''' | if sources is None :
return [ ]
if isinstance ( sources , six . string_types ) :
sources = [ x . strip ( ) for x in sources . split ( ',' ) ]
elif isinstance ( sources , ( float , six . integer_types ) ) :
sources = [ six . text_type ( sources ) ]
return [ path for source in sources for path in _glob ( sour... |
def export_serving ( model_path ) :
"""Export trained model to use it in TensorFlow Serving or cloudML .""" | pred_config = PredictConfig ( session_init = get_model_loader ( model_path ) , model = InferenceOnlyModel ( ) , input_names = [ 'input_img_bytes' ] , output_names = [ 'prediction_img_bytes' ] )
ModelExporter ( pred_config ) . export_serving ( '/tmp/exported' ) |
def clear_cache ( m , files_processed ) :
"""Remove any files we may have uploaded from the cache .""" | for what , reason , url , path in files_processed :
cp = m . doc . downloader . cache_path ( url )
if m . cache . exists ( cp ) :
m . cache . remove ( cp ) |
def create_from_textgrid ( self , word_list ) :
"""Fills the ParsedResponse object with a list of TextGrid . Word objects originally from a . TextGrid file .
: param list word _ list : List of TextGrid . Word objects corresponding to words / tokens in the subject response .
Modifies :
- self . timing _ includ... | self . timing_included = True
for i , entry in enumerate ( word_list ) :
self . unit_list . append ( Unit ( entry , format = "TextGrid" , type = self . type , index_in_timed_response = i ) )
# combine compound words , remove pluralizations , etc
if self . type == "SEMANTIC" :
self . lemmatize ( )
self . tok... |
def logout ( self , command = 'exit' , note = None , echo = None , timeout = shutit_global . shutit_global_object . default_timeout , nonewline = False , loglevel = logging . DEBUG ) :
"""Logs the user out . Assumes that login has been called .
If login has never been called , throw an error .
@ param command :... | shutit_global . shutit_global_object . yield_to_draw ( )
shutit_pexpect_session = self . get_current_shutit_pexpect_session ( )
return shutit_pexpect_session . logout ( ShutItSendSpec ( shutit_pexpect_session , send = command , note = note , timeout = timeout , nonewline = nonewline , loglevel = loglevel , echo = echo ... |
def _process_qtls_genetic_location ( self , raw , txid , common_name , limit = None ) :
"""This function processes
Triples created :
: param limit :
: return :""" | aql_curie = self . files [ common_name + '_cm' ] [ 'curie' ]
if self . test_mode :
graph = self . testgraph
else :
graph = self . graph
line_counter = 0
geno = Genotype ( graph )
model = Model ( graph )
eco_id = self . globaltt [ 'quantitative trait analysis evidence' ]
taxon_curie = 'NCBITaxon:' + txid
LOG . i... |
def optimize ( self , start = None , n = 2 ) :
"""Run multidimensional scaling on this distance matrix .
Args :
start ( ` None ` or ` array - like ` ) : Starting coordinates . If
` start = None ` , random starting coordinates are used . If
` array - like ` must have shape [ ` m ` * ` n ` , ] .
n ( ` int `... | self . n = n
if start is None :
start = np . random . rand ( self . m * self . n ) * 10
optim = minimize ( fun = self . _error_and_gradient , x0 = start , jac = True , method = 'L-BFGS-B' )
index = self . index if hasattr ( self , "index" ) else None
return Projection . from_optimize_result ( result = optim , n = s... |
def check_filters ( filters ) :
"""Execute range _ check for every element of an iterable .
Parameters
filters : iterable
The collection of filters to check . Each element
must be a two - element tuple of floats or ints .
Returns
The input as - is , or None if it evaluates to False .
Raises
ValueErr... | if not filters :
return None
try :
return [ range_check ( f [ 0 ] , f [ 1 ] ) for f in filters ]
except ValueError as err :
raise ValueError ( "Error in --filter: " + py23_str ( err ) ) |
def _cancel_grpc ( operations_stub , operation_name ) :
"""Cancel an operation using a gRPC client .
Args :
operations _ stub ( google . longrunning . operations _ pb2 . OperationsStub ) :
The gRPC operations stub .
operation _ name ( str ) : The name of the operation .""" | request_pb = operations_pb2 . CancelOperationRequest ( name = operation_name )
operations_stub . CancelOperation ( request_pb ) |
def set_autosession ( self , value = None ) :
"""Turn autosession ( automatic committing after each modification call ) on / off .
If value is None , only query the current value ( don ' t change anything ) .""" | if value is not None :
self . rollback ( )
self . autosession = value
return self . autosession |
def start_capture ( self , * ports ) :
"""Start capture on ports .
: param ports : list of ports to start capture on , if empty start on all ports .""" | IxeCapture . current_object = None
IxeCaptureBuffer . current_object = None
if not ports :
ports = self . ports . values ( )
for port in ports :
port . captureBuffer = None
port_list = self . set_ports_list ( * ports )
self . api . call_rc ( 'ixStartCapture {}' . format ( port_list ) ) |
def _get_parent ( self ) :
""": return : Remote origin as Proxy instance""" | _dir = os . path . dirname ( self . path )
if is_repo ( _dir ) :
return Local ( _dir )
else :
return None |
def run ( self ) :
"""Run formula balance command""" | # Create a set of excluded reactions
exclude = set ( self . _args . exclude )
count = 0
unbalanced = 0
unchecked = 0
for reaction , result in formula_balance ( self . _model ) :
count += 1
if reaction . id in exclude or reaction . equation is None :
continue
if result is None :
unchecked += ... |
def r2deriv ( self , R , z , phi = 0. , t = 0. ) :
"""NAME :
r2deriv
PURPOSE :
evaluate the second spherical radial derivative
INPUT :
R - Cylindrical Galactocentric radius ( can be Quantity )
z - vertical height ( can be Quantity )
phi - azimuth ( optional ; can be Quantity )
t - time ( optional ; ... | r = nu . sqrt ( R ** 2. + z ** 2. )
return ( self . R2deriv ( R , z , phi = phi , t = t , use_physical = False ) * R / r + self . Rzderiv ( R , z , phi = phi , t = t , use_physical = False ) * z / r ) * R / r + ( self . Rzderiv ( R , z , phi = phi , t = t , use_physical = False ) * R / r + self . z2deriv ( R , z , phi ... |
def _encode_binary ( name , value , dummy0 , dummy1 ) :
"""Encode bson . binary . Binary .""" | subtype = value . subtype
if subtype == 2 :
value = _PACK_INT ( len ( value ) ) + value
return b"\x05" + name + _PACK_LENGTH_SUBTYPE ( len ( value ) , subtype ) + value |
def least_squares ( Cui , X , Y , regularization , num_threads = 0 ) :
"""For each user in Cui , calculate factors Xu for them
using least squares on Y .
Note : this is at least 10 times slower than the cython version included
here .""" | users , n_factors = X . shape
YtY = Y . T . dot ( Y )
for u in range ( users ) :
X [ u ] = user_factor ( Y , YtY , Cui , u , regularization , n_factors ) |
def write ( self , originalPrefix , newPrefix = None ) :
"""Write project card to string .
Args :
originalPrefix ( str ) : Original name to give to files that follow the project naming convention
( e . g : prefix . gag ) .
newPrefix ( str , optional ) : If new prefix is desired , pass in this parameter . De... | # Determine number of spaces between card and value for nice alignment
numSpaces = max ( 2 , 25 - len ( self . name ) )
# Handle special case of booleans
if self . value is None :
line = '%s\n' % self . name
else :
if self . name == 'WMS' :
line = '%s %s\n' % ( self . name , self . value )
elif newP... |
def ensure_annotations ( resources , data ) :
"""Prepare any potentially missing annotations for downstream processing in a local directory .""" | transcript_gff = tz . get_in ( [ "rnaseq" , "transcripts" ] , resources )
if transcript_gff and utils . file_exists ( transcript_gff ) :
out_dir = os . path . join ( tz . get_in ( [ "dirs" , "work" ] , data ) , "inputs" , "data" , "annotations" )
resources [ "rnaseq" ] [ "gene_bed" ] = gtf . gtf_to_bed ( transc... |
def _update_ssl_params ( host ) :
"""Update the host ssl params ( port or scheme ) if needed .
: param host :
: return :""" | if host [ HostParsing . HOST ] and EsParser . _is_secure_connection_type ( host ) :
host [ HostParsing . PORT ] = EsParser . SSL_DEFAULT_PORT
host [ HostParsing . USE_SSL ] = True
parsed_url = urlparse ( EsParser . _fix_host_prefix ( host [ HostParsing . HOST ] ) )
host [ HostParsing . HOST ] = parsed_u... |
def section_names ( self , ordkey = "wall_time" ) :
"""Return the names of sections ordered by ordkey .
For the time being , the values are taken from the first timer .""" | section_names = [ ]
# FIXME this is not trivial
for idx , timer in enumerate ( self . timers ( ) ) :
if idx == 0 :
section_names = [ s . name for s in timer . order_sections ( ordkey ) ]
# check = section _ names
# else :
# new _ set = set ( [ s . name for s in timer . order _ sectio... |
def request_finished ( key ) :
"""Remove finished Thread from queue .
: param key : data source key""" | with event_lock :
threads [ key ] = threads [ key ] [ 1 : ]
if threads [ key ] :
threads [ key ] [ 0 ] . run ( ) |
def listFileArray ( self ) :
"""API to list files in DBS . Either non - wildcarded logical _ file _ name , non - wildcarded dataset ,
non - wildcarded block _ name or non - wildcarded lfn list is required .
The combination of a non - wildcarded dataset or block _ name with an wildcarded logical _ file _ name is... | ret = [ ]
try :
body = request . body . read ( )
if body :
data = cjson . decode ( body )
data = validateJSONInputNoCopy ( "files" , data , True )
if 'sumOverLumi' in data and data [ 'sumOverLumi' ] == 1 :
if ( 'logical_file_name' in data and isinstance ( data [ 'logical_file... |
def time_wait ( predicate , timeout_seconds = 120 , sleep_seconds = 1 , ignore_exceptions = True , inverse_predicate = False , noisy = True , required_consecutive_success_count = 1 ) :
"""waits or spins for a predicate and returns the time of the wait .
An exception in the function will be returned .
A timeout ... | start = time_module . time ( )
wait_for ( predicate , timeout_seconds , sleep_seconds , ignore_exceptions , inverse_predicate , noisy , required_consecutive_success_count )
return elapse_time ( start ) |
def _parse_groupwise_input ( group_definitions , group_pairs , MDlogger , mname = '' ) :
r"""For input of group type ( add _ group _ mindist ) , prepare the array of pairs of indices
and groups so that : py : func : ` MinDistanceFeature ` can work
This function will :
- check the input types
- sort the 1D a... | assert isinstance ( group_definitions , list ) , "group_definitions has to be of type list, not %s" % type ( group_definitions )
# Handle the special case of just one group
if len ( group_definitions ) == 1 :
group_pairs = np . array ( [ 0 , 0 ] , ndmin = 2 )
# Sort the elements within each group
parsed_group_defin... |
def find_frametype ( self , gpstime = None , frametype_match = None , host = None , port = None , return_all = False , allow_tape = True ) :
"""Find the containing frametype ( s ) for this ` Channel `
Parameters
gpstime : ` int `
a reference GPS time at which to search for frame files
frametype _ match : ` ... | return datafind . find_frametype ( self , gpstime = gpstime , frametype_match = frametype_match , host = host , port = port , return_all = return_all , allow_tape = allow_tape ) |
def cancel ( self ) :
"""Cancels the current lookup .""" | if self . _running :
self . interrupt ( )
self . _running = False
self . _cancelled = True
self . loadingFinished . emit ( ) |
def derivative ( self , x ) :
"""Derivative of the product space operator .
Parameters
x : ` domain ` element
The point to take the derivative in
Returns
adjoint : linear ` ProductSpaceOperator `
The derivative
Examples
> > > r3 = odl . rn ( 3)
> > > pspace = odl . ProductSpace ( r3 , r3)
> > > ... | # Lazy import to improve ` import odl ` time
import scipy . sparse
# Short circuit optimization
if self . is_linear :
return self
deriv_ops = [ op . derivative ( x [ col ] ) for op , col in zip ( self . ops . data , self . ops . col ) ]
data = np . empty ( len ( deriv_ops ) , dtype = object )
data [ : ] = deriv_ops... |
def typechecked ( call_ : typing . Callable [ ... , T ] ) -> T :
"""A decorator to make a callable object checks its types
. . code - block : : python
from typing import Callable
@ typechecked
def foobar ( x : str ) - > bool :
return x = = ' hello world '
@ typechecked
def hello _ world ( foo : str , ... | @ functools . wraps ( call_ )
def decorator ( * args , ** kwargs ) :
hints = typing . get_type_hints ( call_ )
check_arguments ( call_ , hints , * args , ** kwargs )
result = call_ ( * args , ** kwargs )
check_return ( call_ . __name__ , result , hints )
return result
return decorator |
def print_difftext ( text , other = None ) :
"""Args :
text ( str ) :
CommandLine :
# python - m utool . util _ print - - test - print _ difftext
# autopep8 ingest _ data . py - - diff | python - m utool . util _ print - - test - print _ difftext""" | if other is not None : # hack
text = util_str . difftext ( text , other )
colortext = util_str . color_diff_text ( text )
try :
print ( colortext )
except UnicodeEncodeError as ex : # NOQA
import unicodedata
colortext = unicodedata . normalize ( 'NFKD' , colortext ) . encode ( 'ascii' , 'ignore' )
p... |
def _notify ( self , title , message , expected_action = None ) :
"""Notify user from external event""" | if self . editor is None :
return
inital_value = self . editor . save_on_focus_out
self . editor . save_on_focus_out = False
self . _flg_notify = True
dlg_type = ( QtWidgets . QMessageBox . Yes | QtWidgets . QMessageBox . No )
expected_action = ( lambda * x : None ) if not expected_action else expected_action
if ( ... |
def complete_set ( self , cmd_param_text , full_cmd , * rest ) :
"""TODO : suggest the old value & the current version""" | complete_value = partial ( complete_values , [ "updated-value" ] )
complete_version = partial ( complete_values , [ str ( i ) for i in range ( 1 , 11 ) ] )
completers = [ self . _complete_path , complete_value , complete_version ]
return complete ( completers , cmd_param_text , full_cmd , * rest ) |
def sync ( self , videoQuality , limit = None , unwatched = False , ** kwargs ) :
"""Add current Movie library section as sync item for specified device .
See description of : func : ` plexapi . library . LibrarySection . search ( ) ` for details about filtering / sorting and
: func : ` plexapi . library . Libr... | from plexapi . sync import Policy , MediaSettings
kwargs [ 'mediaSettings' ] = MediaSettings . createVideo ( videoQuality )
kwargs [ 'policy' ] = Policy . create ( limit , unwatched )
return super ( MovieSection , self ) . sync ( ** kwargs ) |
def inverse ( self , z ) :
"""Inverse of the power transform link function
Parameters
` z ` : array - like
Value of the transformed mean parameters at ` p `
Returns
` p ` : array
Mean parameters
Notes
g ^ ( - 1 ) ( z ` ) = ` z ` * * ( 1 / ` power ` )""" | p = np . power ( z , 1. / self . power )
return p |
def update ( self , values , ** context ) :
"""Updates the model with the given dictionary of values .
: param values : < dict >
: param context : < orb . Context >
: return : < int >""" | schema = self . schema ( )
column_updates = { }
other_updates = { }
for key , value in values . items ( ) :
try :
column_updates [ schema . column ( key ) ] = value
except orb . errors . ColumnNotFound :
other_updates [ key ] = value
# update the columns in order
for col in sorted ( column_updat... |
def get_file_by_id ( self , file_id ) :
"""Gets the PBXFileReference to the given id
: param file _ id : Identifier of the PBXFileReference to be retrieved .
: return : A PBXFileReference if the id is found , None otherwise .""" | file_ref = self . objects [ file_id ]
if not isinstance ( file_ref , PBXFileReference ) :
return None
return file_ref |
def list_to_instance_list ( _self , _list , _Class ) :
"""Takes a list of resource dicts and returns a list
of resource instances , defined by the _ Class param .
: param _ self : Original resource calling the method
: type _ self : core . MarvelObject
: param _ list : List of dicts describing a Resource . ... | items = [ ]
for item in _list :
items . append ( _Class ( _self . marvel , item ) )
return items |
async def on_raw_topic ( self , message ) :
"""TOPIC command .""" | setter , settermeta = self . _parse_user ( message . source )
target , topic = message . params
self . _sync_user ( setter , settermeta )
# Update topic in our own channel list .
if self . in_channel ( target ) :
self . channels [ target ] [ 'topic' ] = topic
self . channels [ target ] [ 'topic_by' ] = setter
... |
def flag ( self , diagnostic , thresh = None ) :
'''Returns indices of diagnostic that satisfy ( return True from ) the
threshold predicate . Will use class - level default threshold if
None provided .
Args :
diagnostic ( str ) : name of the diagnostic
thresh ( func ) : threshold function ( boolean predic... | if thresh is None :
thresh = self . defaults [ diagnostic ]
result = self . results [ diagnostic ]
if isinstance ( result , pd . DataFrame ) :
if diagnostic == 'CorrelationMatrix' :
result = result . copy ( )
np . fill_diagonal ( result . values , 0 )
return result . applymap ( thresh ) . su... |
def swarm ( workingDir ) :
"""Runs a swarm in the giving working directory , assuming it was created by
Menorah .
: param workingDir : absolute or relative path to working directory created by
Menorah""" | name = os . path . splitext ( os . path . basename ( workingDir ) ) [ 0 ]
swarmDescriptionFile = os . path . join ( workingDir , "swarm_description.json" )
with open ( swarmDescriptionFile ) as swarmDesc :
swarmDescription = json . loads ( swarmDesc . read ( ) )
print "==============================================... |
def get_language_data ( self , qid , lang , lang_data_type ) :
"""get language data for specified qid
: param qid :
: param lang : language code
: param lang _ data _ type : ' label ' , ' description ' or ' aliases '
: return : list of strings
If nothing is found :
If lang _ data _ type = = label : retu... | self . init_language_data ( lang , lang_data_type )
current_lang_data = self . loaded_langs [ lang ] [ lang_data_type ]
all_lang_strings = current_lang_data . get ( qid , [ ] )
if not all_lang_strings and lang_data_type in { 'label' , 'description' } :
all_lang_strings = [ '' ]
return all_lang_strings |
def delete_repo ( name , config_path = _DEFAULT_CONFIG_PATH , force = False ) :
'''Remove a local package repository .
: param str name : The name of the local repository .
: param str config _ path : The path to the configuration file for the aptly instance .
: param bool force : Whether to remove the reposi... | _validate_config ( config_path )
force = six . text_type ( bool ( force ) ) . lower ( )
current_repo = __salt__ [ 'aptly.get_repo' ] ( name = name , config_path = config_path )
if not current_repo :
log . debug ( 'Repository already absent: %s' , name )
return True
cmd = [ 'repo' , 'drop' , '-config={}' . forma... |
def _get_fb_device ( self ) :
"""Internal . Finds the correct frame buffer device for the sense HAT
and returns its / dev name .""" | device = None
for fb in glob . glob ( '/sys/class/graphics/fb*' ) :
name_file = os . path . join ( fb , 'name' )
if os . path . isfile ( name_file ) :
with open ( name_file , 'r' ) as f :
name = f . read ( )
if name . strip ( ) == self . SENSE_HAT_FB_NAME :
fb_device = fb... |
def _fit_transform_column ( self , table , metadata , transformer_name , table_name ) :
"""Transform a column from table using transformer and given parameters .
Args :
table ( pandas . DataFrame ) : Dataframe containing column to transform .
metadata ( dict ) : Metadata for given column .
transformer _ nam... | column_name = metadata [ 'name' ]
content = { }
columns = [ ]
if self . missing and table [ column_name ] . isnull ( ) . any ( ) :
null_transformer = transformers . NullTransformer ( metadata )
clean_column = null_transformer . fit_transform ( table [ column_name ] )
null_name = '?' + column_name
column... |
def get ( columns = None ) :
"""Get or create MetaData singleton .""" | if columns is None :
columns = _DEFAULT_COLUMNS
global _METADATA
if not _METADATA :
_METADATA = MetaData ( columns )
return _METADATA |
def seen_tasks ( self , request , context ) :
"""Returns all seen task types .""" | _log_request ( request , context )
result = clearly_pb2 . SeenTasksMessage ( )
result . task_types . extend ( self . listener . memory . task_types ( ) )
return result |
def siphash24 ( message , key = b'' , encoder = nacl . encoding . HexEncoder ) :
"""Computes a keyed MAC of ` ` message ` ` using the short - input - optimized
siphash - 2-4 construction .
: param message : The message to hash .
: type message : bytes
: param key : the message authentication key for the sip... | digest = _sip_hash ( message , key )
return encoder . encode ( digest ) |
def _get_offset ( self ) :
"""Subclasses may override this method .""" | sx , sxy , syx , sy , ox , oy = self . transformation
return ( ox , oy ) |
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